I: pbuilder: network access will be disabled during build
I: Current time: Tue Jun  3 15:04:27 +14 2025
I: pbuilder-time-stamp: 1748912667
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [htsjdk_4.1.0+dfsg-1.dsc]
I: copying [./htsjdk_4.1.0+dfsg.orig.tar.xz]
I: copying [./htsjdk_4.1.0+dfsg-1.debian.tar.xz]
I: Extracting source
gpgv: Signature made Sun Feb 11 21:45:33 2024 
gpgv:                using RSA key 33CB284313E90BD27DCB4523600316A6DC277476
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./htsjdk_4.1.0+dfsg-1.dsc: no acceptable signature found
dpkg-source: info: extracting htsjdk in htsjdk-4.1.0+dfsg
dpkg-source: info: unpacking htsjdk_4.1.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking htsjdk_4.1.0+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 10-build.xml.patch
dpkg-source: info: applying 13-skip_network_tests
dpkg-source: info: applying 20-fix-version.patch
dpkg-source: info: applying 30-disable-scalatest.patch
dpkg-source: info: applying 60-enable-tests
dpkg-source: info: applying 70-removesometests-testng.patch
dpkg-source: info: applying 90-disable-testftp.patch
dpkg-source: info: applying 92-disable-testhttp.patch
dpkg-source: info: applying 100-fix-java11
dpkg-source: info: applying 140-skip-testFlushNotSpammed.patch
dpkg-source: info: applying 150-use-rhino-as-JS-engine.patch
dpkg-source: info: applying 160-mkdirs-before-creating-tempPaths.patch
dpkg-source: info: applying 170-use-mjson.patch
dpkg-source: info: applying 180-ambiguous-assertions.patch
dpkg-source: info: applying 190-newest-vcf.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/787020/tmp/hooks/D01_modify_environment starting
debug: Running on infom02-amd64.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Jun  3 01:04 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/787020/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/787020/tmp/hooks/D02_print_environment starting
I: set
  BASH=/bin/sh
  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
  BASH_ALIASES=()
  BASH_ARGC=()
  BASH_ARGV=()
  BASH_CMDS=()
  BASH_LINENO=([0]="12" [1]="0")
  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
  BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
  BASH_VERSION='5.2.21(1)-release'
  BUILDDIR=/build/reproducible-path
  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
  BUILDUSERNAME=pbuilder2
  BUILD_ARCH=amd64
  DEBIAN_FRONTEND=noninteractive
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
  DIRSTACK=()
  DISTRIBUTION=trixie
  EUID=0
  FUNCNAME=([0]="Echo" [1]="main")
  GROUPS=()
  HOME=/root
  HOSTNAME=i-capture-the-hostname
  HOSTTYPE=x86_64
  HOST_ARCH=amd64
  IFS=' 	
  '
  INVOCATION_ID=24b7b0bedffa460b8a6c756ed49b22e6
  LANG=C
  LANGUAGE=et_EE:et
  LC_ALL=C
  MACHTYPE=x86_64-pc-linux-gnu
  MAIL=/var/mail/root
  OPTERR=1
  OPTIND=1
  OSTYPE=linux-gnu
  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
  PBCURRENTCOMMANDLINEOPERATION=build
  PBUILDER_OPERATION=build
  PBUILDER_PKGDATADIR=/usr/share/pbuilder
  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
  PBUILDER_SYSCONFDIR=/etc
  PIPESTATUS=([0]="0")
  POSIXLY_CORRECT=y
  PPID=787020
  PS4='+ '
  PWD=/
  SHELL=/bin/bash
  SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
  SHLVL=3
  SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.D63VSAQ0/pbuilderrc_gd9A --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.D63VSAQ0/b2 --logfile b2/build.log htsjdk_4.1.0+dfsg-1.dsc'
  SUDO_GID=109
  SUDO_UID=104
  SUDO_USER=jenkins
  TERM=unknown
  TZ=/usr/share/zoneinfo/Etc/GMT-14
  UID=0
  USER=root
  _='I: set'
I: uname -a
  Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 May 24 13:34 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/787020/tmp/hooks/D02_print_environment finished
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: default-jdk, javahelper, gradle-debian-helper, maven-repo-helper, debhelper-compat (= 13), libcommons-jexl2-java, libcommons-logging-java, libjaxb-api-java, libjaxb-java, libmjson-java, librhino-java, libsnappy-java, libcommons-compress-java, libngs-java, default-jdk-doc, junit4, libcommons-lang3-java, libjimfs-java, scala-library
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19901 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
 pbuilder-satisfydepends-dummy depends on default-jdk; however:
  Package default-jdk is not installed.
 pbuilder-satisfydepends-dummy depends on javahelper; however:
  Package javahelper is not installed.
 pbuilder-satisfydepends-dummy depends on gradle-debian-helper; however:
  Package gradle-debian-helper is not installed.
 pbuilder-satisfydepends-dummy depends on maven-repo-helper; however:
  Package maven-repo-helper is not installed.
 pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
  Package debhelper-compat is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-jexl2-java; however:
  Package libcommons-jexl2-java is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-logging-java; however:
  Package libcommons-logging-java is not installed.
 pbuilder-satisfydepends-dummy depends on libjaxb-api-java; however:
  Package libjaxb-api-java is not installed.
 pbuilder-satisfydepends-dummy depends on libjaxb-java; however:
  Package libjaxb-java is not installed.
 pbuilder-satisfydepends-dummy depends on libmjson-java; however:
  Package libmjson-java is not installed.
 pbuilder-satisfydepends-dummy depends on librhino-java; however:
  Package librhino-java is not installed.
 pbuilder-satisfydepends-dummy depends on libsnappy-java; however:
  Package libsnappy-java is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-compress-java; however:
  Package libcommons-compress-java is not installed.
 pbuilder-satisfydepends-dummy depends on libngs-java; however:
  Package libngs-java is not installed.
 pbuilder-satisfydepends-dummy depends on default-jdk-doc; however:
  Package default-jdk-doc is not installed.
 pbuilder-satisfydepends-dummy depends on junit4; however:
  Package junit4 is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-lang3-java; however:
  Package libcommons-lang3-java is not installed.
 pbuilder-satisfydepends-dummy depends on libjimfs-java; however:
  Package libjimfs-java is not installed.
 pbuilder-satisfydepends-dummy depends on scala-library; however:
  Package scala-library is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
  autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} default-jdk-doc{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} file{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{a} gpgconf{a} gpgsm{a} groff-base{a} intltool-debian{a} libactivation-java{a} libapache-pom-java{a} libarchive-zip-perl{a} libassuan0{a} libcommons-compress-java{a} libcommons-jexl2-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-parent-java{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libjaxb-api-java{a} libjimfs-java{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-jquery-ui-theme-base{a} libksba8{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libmjson-java{a} libncbi-ngs3{a} libncbi-vdb3{a} libngs-java{a} libngs-jni{a} libnpth0t64{a} libpipeline1{a} libreadline8t64{a} librhino-java{a} libsasl2-2{a} libsasl2-modules-db{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} ncbi-vdb-data{a} openjdk-17-doc{a} pinentry-curses{a} po-debconf{a} readline-common{a} scala-library{a} sensible-utils{a} 
The following packages are RECOMMENDED but will NOT be installed:
  curl javascript-common libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx wget 
0 packages upgraded, 77 newly installed, 0 to remove and 0 not upgraded.
Need to get 56.0 MB of archives. After unpacking 397 MB will be used.
The following packages have unmet dependencies:
 pbuilder-satisfydepends-dummy : Depends: default-jdk but it is not installable
                                 Depends: javahelper but it is not installable
                                 Depends: gradle-debian-helper but it is not installable
                                 Depends: maven-repo-helper but it is not installable
                                 Depends: libjaxb-java but it is not installable
                                 Depends: junit4 but it is not installable
The following actions will resolve these dependencies:

       Remove the following packages:                                    
1)       libdb5.3 [5.3.28+dfsg2-4+b1 (now)]                              
2)       libssl3 [3.1.5-1 (now)]                                         

       Install the following packages:                                   
3)       adwaita-icon-theme [46.0-1 (testing)]                           
4)       ant [1.10.14-1 (testing)]                                       
5)       ant-optional [1.10.14-1 (testing)]                              
6)       antlr [2.7.7+dfsg-13 (testing)]                                 
7)       at-spi2-common [2.52.0-1 (testing)]                             
8)       binfmt-support [2.2.2-7 (testing)]                              
9)       bnd [5.0.1-5 (testing)]                                         
10)      ca-certificates [20240203 (testing)]                            
11)      ca-certificates-java [20240118 (testing)]                       
12)      dbus-broker [36-1 (testing)]                                    
13)      dbus-session-bus-common [1.14.10-4 (testing)]                   
14)      dbus-system-bus-common [1.14.10-4 (testing)]                    
15)      dbus-user-session [1.14.10-4+b1 (testing)]                      
16)      dconf-gsettings-backend [0.40.0-4+b2 (testing)]                 
17)      dconf-service [0.40.0-4+b2 (testing)]                           
18)      dctrl-tools [2.24-3+b1 (testing)]                               
19)      default-jdk [2:1.17-75 (testing)]                               
20)      default-jdk-headless [2:1.17-75 (testing)]                      
21)      default-jre [2:1.17-75 (testing)]                               
22)      default-jre-headless [2:1.17-75 (testing)]                      
23)      devscripts [2.23.7 (testing)]                                   
24)      dmsetup [2:1.02.196-1+b1 (testing)]                             
25)      fastjar [2:0.98-7 (testing)]                                    
26)      fontconfig [2.15.0-1.1 (testing)]                               
27)      fontconfig-config [2.15.0-1.1 (testing)]                        
28)      fonts-urw-base35 [20200910-8 (testing)]                         
29)      gradle [4.4.1-20 (testing)]                                     
30)      gradle-debian-helper [2.4 (testing)]                            
31)      groovy [2.4.21-10 (testing)]                                    
32)      gtk-update-icon-cache [3.24.41-4 (testing)]                     
33)      hicolor-icon-theme [0.17-2 (testing)]                           
34)      ivy [2.5.2-1 (testing)]                                         
35)      jarwrapper [0.79 (testing)]                                     
36)      java-common [0.75 (testing)]                                    
37)      java-wrappers [0.4 (testing)]                                   
38)      javahelper [0.79 (testing)]                                     
39)      junit4 [4.13.2-4 (testing)]                                     
40)      libantlr-java [2.7.7+dfsg-13 (testing)]                         
41)      libaopalliance-java [20070526-7 (testing)]                      
42)      libapparmor1 [3.0.13-2 (testing)]                               
43)      libargon2-1 [0~20190702+dfsg-4+b1 (testing)]                    
44)      libargs4j-java [2.33-2 (testing)]                               
45)      libasm-java [9.7-1 (testing)]                                   
46)      libasound2-data [1.2.11-1 (testing)]                            
47)      libasound2t64 [1.2.11-1+b1 (testing)]                           
48)      libatinject-jsr330-api-java [1.0+ds1-5 (testing)]               
49)      libatk-bridge2.0-0t64 [2.52.0-1 (testing)]                      
50)      libatk1.0-0t64 [2.52.0-1 (testing)]                             
51)      libatspi2.0-0t64 [2.52.0-1 (testing)]                           
52)      libavahi-client3 [0.8-13+b2 (testing)]                          
53)      libavahi-common-data [0.8-13+b2 (testing)]                      
54)      libavahi-common3 [0.8-13+b2 (testing)]                          
55)      libb-hooks-op-check-perl [0.22-2+b2 (testing)]                  
56)      libbcel-java [6.5.0-2 (testing)]                                
57)      libbcpg-java [1.77-1 (testing)]                                 
58)      libbcprov-java [1.77-1 (testing)]                               
59)      libbrotli1 [1.1.0-2+b3 (testing)]                               
60)      libbsd0 [0.12.2-1 (testing)]                                    
61)      libbsf-java [1:2.4.0-8 (testing)]                               
62)      libbsh-java [2.0b4-20 (testing)]                                
63)      libcairo-gobject2 [1.18.0-1+b1 (testing)]                       
64)      libcairo2 [1.18.0-1+b1 (testing)]                               
65)      libcdi-api-java [1.2-3 (testing)]                               
66)      libclass-method-modifiers-perl [2.15-1 (testing)]               
67)      libclass-xsaccessor-perl [1.19-4+b2 (testing)]                  
68)      libclone-perl [0.46-1+b1 (testing)]                             
69)      libcloudproviders0 [0.3.5-1 (testing)]                          
70)      libcodemodel-java [2.6+jaxb2.3.0.1-10.1 (testing)]              
71)      libcolord2 [1.4.7-1+b1 (testing)]                               
72)      libcommons-cli-java [1.6.0-1 (testing)]                         
73)      libcommons-codec-java [1.16.0-1 (testing)]                      
74)      libcommons-collections3-java [3.2.2-3 (testing)]                
75)      libcommons-io-java [2.16.0-1 (testing)]                         
76)      libcommons-lang-java [2.6-10 (testing)]                         
77)      libcryptsetup12 [2:2.6.1-6+b1 (testing)]                        
78)      libcups2t64 [2.4.7-1.2+b1 (testing)]                            
79)      libdatrie1 [0.2.13-3 (testing)]                                 
80)      libdb5.3t64 [5.3.28+dfsg2-7 (testing)]                          
81)      libdbus-1-3 [1.14.10-4+b1 (testing)]                            
82)      libdconf1 [0.40.0-4+b2 (testing)]                               
83)      libdd-plist-java [1.20-1.1 (testing)]                           
84)      libdeflate0 [1.20-1 (testing)]                                  
85)      libdevel-callchecker-perl [0.008-2+b1 (testing)]                
86)      libdevmapper1.02.1 [2:1.02.196-1+b1 (testing)]                  
87)      libdom4j-java [2.1.4-1 (testing)]                               
88)      libdrm-amdgpu1 [2.4.120-2 (testing)]                            
89)      libdrm-common [2.4.120-2 (testing)]                             
90)      libdrm-intel1 [2.4.120-2 (testing)]                             
91)      libdrm-nouveau2 [2.4.120-2 (testing)]                           
92)      libdrm-radeon1 [2.4.120-2 (testing)]                            
93)      libdrm2 [2.4.120-2 (testing)]                                   
94)      libdtd-parser-java [1.2-1 (testing)]                            
95)      libdynaloader-functions-perl [0.003-3 (testing)]                
96)      libeclipse-jdt-annotation-java [2.2.700+eclipse4.26-2 (testing)]
97)      libedit2 [3.1-20230828-1+b1 (testing)]                          
98)      libel-api-java [3.0.0-3 (testing)]                              
99)      libencode-locale-perl [1.05-3 (testing)]                        
100)     libepoxy0 [1.5.10-1+b2 (testing)]                               
101)     liberror-prone-java [2.18.0-1 (testing)]                        
102)     libexpat1 [2.6.2-1 (testing)]                                   
103)     libfastinfoset-java [1.2.12-3 (testing)]                        
104)     libfdisk1 [2.39.3-6 (testing)]                                  
105)     libfelix-framework-java [4.6.1-2.1 (testing)]                   
106)     libfelix-gogo-runtime-java [0.16.2-1.1 (testing)]               
107)     libfelix-resolver-java [1.16.0-1 (testing)]                     
108)     libfile-dirlist-perl [0.05-3 (testing)]                         
109)     libfile-homedir-perl [1.006-2 (testing)]                        
110)     libfile-listing-perl [6.16-1 (testing)]                         
111)     libfile-touch-perl [0.12-2 (testing)]                           
112)     libfile-which-perl [1.27-2 (testing)]                           
113)     libfindbugs-java [3.1.0~preview2-3 (testing)]                   
114)     libfontconfig1 [2.15.0-1.1 (testing)]                           
115)     libfontenc1 [1:1.1.8-1 (testing)]                               
116)     libfreetype6 [2.13.2+dfsg-1+b4 (testing)]                       
117)     libfribidi0 [1.0.13-3+b1 (testing)]                             
118)     libgdk-pixbuf-2.0-0 [2.42.10+dfsg-3+b3 (testing)]               
119)     libgdk-pixbuf2.0-common [2.42.10+dfsg-3 (testing)]              
120)     libgeronimo-annotation-1.3-spec-java [1.3-1 (testing)]          
121)     libgeronimo-interceptor-3.0-spec-java [1.0.1-4 (testing)]       
122)     libgif7 [5.2.2-1 (testing)]                                     
123)     libgl1 [1.7.0-1+b1 (testing)]                                   
124)     libgl1-mesa-dri [23.3.5-1 (testing)]                            
125)     libglapi-mesa [23.3.5-1 (testing)]                              
126)     libglib2.0-0t64 [2.78.4-7 (testing)]                            
127)     libglvnd0 [1.7.0-1+b1 (testing)]                                
128)     libglx-mesa0 [23.3.5-1 (testing)]                               
129)     libglx0 [1.7.0-1+b1 (testing)]                                  
130)     libgoogle-gson-java [2.10.1-1 (testing)]                        
131)     libgradle-core-java [4.4.1-20 (testing)]                        
132)     libgradle-plugins-java [4.4.1-20 (testing)]                     
133)     libgraphite2-3 [1.3.14-2 (testing)]                             
134)     libgtk-3-0t64 [3.24.41-4 (testing)]                             
135)     libgtk-3-common [3.24.41-4 (testing)]                           
136)     libguava-java [32.0.1-1 (testing)]                              
137)     libguice-java [4.2.3-2 (testing)]                               
138)     libhamcrest-java [2.2-2 (testing)]                              
139)     libharfbuzz0b [8.3.0-2+b1 (testing)]                            
140)     libhawtjni-runtime-java [1.18-1 (testing)]                      
141)     libhtml-parser-perl [3.81-1+b1 (testing)]                       
142)     libhtml-tagset-perl [3.24-1 (testing)]                          
143)     libhtml-tree-perl [5.07-3 (testing)]                            
144)     libhttp-cookies-perl [6.11-1 (testing)]                         
145)     libhttp-date-perl [6.06-1 (testing)]                            
146)     libhttp-message-perl [6.45-1 (testing)]                         
147)     libhttp-negotiate-perl [6.01-2 (testing)]                       
148)     libhttpclient-java [4.5.14-1 (testing)]                         
149)     libhttpcore-java [4.4.16-1 (testing)]                           
150)     libimport-into-perl [1.002005-2 (testing)]                      
151)     libio-html-perl [1.004-3 (testing)]                             
152)     libio-pty-perl [1:1.20-1 (testing)]                             
153)     libio-socket-ssl-perl [2.085-1 (testing)]                       
154)     libipc-run-perl [20231003.0-2 (testing)]                        
155)     libistack-commons-java [3.0.6-5 (testing)]                      
156)     libjansi-java [2.4.1-2 (testing)]                               
157)     libjansi-native-java [1.8-2 (testing)]                          
158)     libjansi1-java [1.18-3 (testing)]                               
159)     libjarjar-java [1.4+svn142-12 (testing)]                        
160)     libjatl-java [0.2.3-1.1 (testing)]                              
161)     libjavaewah-java [1.2.3-1 (testing)]                            
162)     libjaxb-java [2.3.0.1-10.1 (testing)]                           
163)     libjaxen-java [1.1.6-4 (testing)]                               
164)     libjbig0 [2.1-6.1+b1 (testing)]                                 
165)     libjcifs-java [1.3.19-2 (testing)]                              
166)     libjcip-annotations-java [20060626-6 (testing)]                 
167)     libjcommander-java [1.71-4 (testing)]                           
168)     libjetty9-java [9.4.54-1 (testing)]                             
169)     libjformatstring-java [0.10~20131207-2.1 (testing)]             
170)     libjgit-java [4.11.9-2 (testing)]                               
171)     libjline2-java [2.14.6-5 (testing)]                             
172)     libjna-java [5.14.0-1 (testing)]                                
173)     libjna-jni [5.14.0-1 (testing)]                                 
174)     libjpeg62-turbo [1:2.1.5-2+b2 (testing)]                        
175)     libjsch-java [0.1.55-1 (testing)]                               
176)     libjson-c5 [0.17-1+b1 (testing)]                                
177)     libjsoup-java [1.15.3-1 (testing)]                              
178)     libjsp-api-java [2.3.4-3 (testing)]                             
179)     libjsr305-java [0.1~+svn49-11 (testing)]                        
180)     libjzlib-java [1.1.3-3 (testing)]                               
181)     libkmod2 [31+20240202-2 (testing)]                              
182)     libkryo-java [2.20-7 (testing)]                                 
183)     liblcms2-2 [2.14-2+b1 (testing)]                                
184)     liblerc4 [4.0.0+ds-4+b1 (testing)]                              
185)     libllvm17t64 [1:17.0.6-11 (testing)]                            
186)     liblogback-java [1:1.2.11-5 (testing)]                          
187)     liblwp-mediatypes-perl [6.04-2 (testing)]                       
188)     liblwp-protocol-https-perl [6.14-1 (testing)]                   
189)     libmaven-file-management-java [3.0.0-1 (testing)]               
190)     libmaven-parent-java [35-1 (testing)]                           
191)     libmaven-resolver-java [1.6.3-1 (testing)]                      
192)     libmaven-shared-io-java [3.0.0-4 (testing)]                     
193)     libmaven-shared-utils-java [3.3.4-1 (testing)]                  
194)     libmaven3-core-java [3.8.7-2 (testing)]                         
195)     libminlog-java [1.3.0-1.1 (testing)]                            
196)     libmodule-runtime-perl [0.016-2 (testing)]                      
197)     libmoo-perl [2.005005-1 (testing)]                              
198)     libnative-platform-java [0.14-6 (testing)]                      
199)     libnative-platform-jni [0.14-6 (testing)]                       
200)     libnekohtml-java [1.9.22.noko2-0.1 (testing)]                   
201)     libnet-http-perl [6.23-1 (testing)]                             
202)     libnet-ssleay-perl [1.94-1 (testing)]                           
203)     libnspr4 [2:4.35-1.1+b1 (testing)]                              
204)     libnss3 [2:3.99-1 (testing)]                                    
205)     libobjenesis-java [3.3-3 (testing)]                             
206)     libosgi-annotation-java [8.1.0-1 (testing)]                     
207)     libosgi-compendium-java [7.0.0-1 (testing)]                     
208)     libosgi-core-java [8.0.0-2 (testing)]                           
209)     libpam-systemd [255.4-1 (testing)]                              
210)     libpango-1.0-0 [1.52.1+ds-1 (testing)]                          
211)     libpangocairo-1.0-0 [1.52.1+ds-1 (testing)]                     
212)     libpangoft2-1.0-0 [1.52.1+ds-1 (testing)]                       
213)     libparams-classify-perl [0.015-2+b2 (testing)]                  
214)     libpciaccess0 [0.17-3+b1 (testing)]                             
215)     libpcsclite1 [2.0.1-1+b1 (testing)]                             
216)     libpixman-1-0 [0.42.2-1+b1 (testing)]                           
217)     libplexus-archiver-java [4.6.1-1 (testing)]                     
218)     libplexus-cipher-java [2.0-1 (testing)]                         
219)     libplexus-classworlds-java [2.7.0-1 (testing)]                  
220)     libplexus-component-annotations-java [2.1.1-1 (testing)]        
221)     libplexus-container-default-java [2.1.1-1 (testing)]            
222)     libplexus-interpolation-java [1.26-1 (testing)]                 
223)     libplexus-io-java [3.3.1-2 (testing)]                           
224)     libplexus-sec-dispatcher-java [2.0-3 (testing)]                 
225)     libplexus-utils2-java [3.4.2-1 (testing)]                       
226)     libpng16-16t64 [1.6.43-5 (testing)]                             
227)     libpolyglot-maven-java [0.8~tobrien+git20120905-10 (testing)]   
228)     libproc2-0 [2:4.0.4-4 (testing)]                                
229)     libpython3-stdlib [3.11.8-1 (testing)]                          
230)     libpython3.11-minimal [3.11.9-1 (testing)]                      
231)     libpython3.11-stdlib [3.11.9-1 (testing)]                       
232)     libqdox-java [1.12.1-3 (testing)]                               
233)     libreflectasm-java [1.11.9+dfsg-4 (testing)]                    
234)     librelaxng-datatype-java [1.0+ds1-3.1 (testing)]                
235)     librngom-java [2.3.0.1-10.1 (testing)]                          
236)     librole-tiny-perl [2.002004-1 (testing)]                        
237)     libsensors-config [1:3.6.0-9 (testing)]                         
238)     libsensors5 [1:3.6.0-9 (testing)]                               
239)     libservlet-api-java [4.0.1-2 (testing)]                         
240)     libsharpyuv0 [1.3.2-0.4+b1 (testing)]                           
241)     libsimple-http-java [4.1.21-1.1 (testing)]                      
242)     libsisu-inject-java [0.3.4-2 (testing)]                         
243)     libsisu-plexus-java [0.3.4-3 (testing)]                         
244)     libslf4j-java [1.7.32-1 (testing)]                              
245)     libssl3t64 [3.2.1-3 (testing)]                                  
246)     libstax-ex-java [1.7.8-3 (testing)]                             
247)     libstreambuffer-java [1.5.4-1.1 (testing)]                      
248)     libsub-quote-perl [2.006008-1 (testing)]                        
249)     libsystemd-shared [255.4-1 (testing)]                           
250)     libthai-data [0.1.29-2 (testing)]                               
251)     libthai0 [0.1.29-2 (testing)]                                   
252)     libtiff6 [4.5.1+git230720-4 (testing)]                          
253)     libtimedate-perl [2.3300-2 (testing)]                           
254)     libtry-tiny-perl [0.31-2 (testing)]                             
255)     libtxw2-java [2.3.0.1-10.1 (testing)]                           
256)     liburi-perl [5.28-1 (testing)]                                  
257)     libvulkan1 [1.3.280.0-1 (testing)]                              
258)     libwagon-file-java [3.5.3-1 (testing)]                          
259)     libwagon-http-java [3.5.3-1 (testing)]                          
260)     libwagon-provider-api-java [3.5.3-1 (testing)]                  
261)     libwayland-client0 [1.22.0-2.1+b1 (testing)]                    
262)     libwayland-cursor0 [1.22.0-2.1+b1 (testing)]                    
263)     libwayland-egl1 [1.22.0-2.1+b1 (testing)]                       
264)     libwebp7 [1.3.2-0.4+b1 (testing)]                               
265)     libwebsocket-api-java [1.1-2 (testing)]                         
266)     libwww-perl [6.77-1 (testing)]                                  
267)     libwww-robotrules-perl [6.02-1 (testing)]                       
268)     libx11-6 [2:1.8.7-1+b1 (testing)]                               
269)     libx11-data [2:1.8.7-1 (testing)]                               
270)     libx11-xcb1 [2:1.8.7-1+b1 (testing)]                            
271)     libxau6 [1:1.0.9-1+b1 (testing)]                                
272)     libxbean-reflect-java [4.5-8 (testing)]                         
273)     libxcb-dri2-0 [1.15-1 (testing)]                                
274)     libxcb-dri3-0 [1.15-1 (testing)]                                
275)     libxcb-glx0 [1.15-1 (testing)]                                  
276)     libxcb-present0 [1.15-1 (testing)]                              
277)     libxcb-randr0 [1.15-1 (testing)]                                
278)     libxcb-render0 [1.15-1 (testing)]                               
279)     libxcb-shm0 [1.15-1 (testing)]                                  
280)     libxcb-sync1 [1.15-1 (testing)]                                 
281)     libxcb-xfixes0 [1.15-1 (testing)]                               
282)     libxcb1 [1.15-1 (testing)]                                      
283)     libxcomposite1 [1:0.4.5-1+b1 (testing)]                         
284)     libxcursor1 [1:1.2.1-1+b1 (testing)]                            
285)     libxdamage1 [1:1.1.6-1+b1 (testing)]                            
286)     libxdmcp6 [1:1.1.2-3+b1 (testing)]                              
287)     libxerces2-java [2.12.2-1 (testing)]                            
288)     libxext6 [2:1.3.4-1+b1 (testing)]                               
289)     libxfixes3 [1:6.0.0-2+b1 (testing)]                             
290)     libxi6 [2:1.8.1-1 (testing)]                                    
291)     libxinerama1 [2:1.1.4-3+b1 (testing)]                           
292)     libxkbcommon0 [1.6.0-1+b1 (testing)]                            
293)     libxml-commons-external-java [1.4.01-6 (testing)]               
294)     libxml-commons-resolver1.1-java [1.2-11 (testing)]              
295)     libxpp3-java [1.1.4c-3 (testing)]                               
296)     libxrandr2 [2:1.5.4-1 (testing)]                                
297)     libxrender1 [1:0.9.10-1.1+b1 (testing)]                         
298)     libxshmfence1 [1.3-1+b1 (testing)]                              
299)     libxsom-java [2.3.0.1-10.1 (testing)]                           
300)     libxstream-java [1.4.20-1 (testing)]                            
301)     libxtst6 [2:1.2.3-1.1+b1 (testing)]                             
302)     libxxf86vm1 [1:1.1.4-1+b2 (testing)]                            
303)     libxz-java [1.9-1 (testing)]                                    
304)     libyaml-snake-java [1.33-2 (testing)]                           
305)     libz3-4 [4.8.12-3.1+b2 (testing)]                               
306)     maven-repo-helper [1.11 (testing)]                              
307)     media-types [10.1.0 (testing)]                                  
308)     netbase [6.4 (testing)]                                         
309)     openjdk-17-jdk [17.0.11+9-1 (testing)]                          
310)     openjdk-17-jdk-headless [17.0.11+9-1 (testing)]                 
311)     openjdk-17-jre [17.0.11+9-1 (testing)]                          
312)     openjdk-17-jre-headless [17.0.11+9-1 (testing)]                 
313)     openssl [3.2.1-3 (testing)]                                     
314)     patchutils [0.4.2-1 (testing)]                                  
315)     perl-openssl-defaults [7+b2 (testing)]                          
316)     procps [2:4.0.4-4 (testing)]                                    
317)     python3 [3.11.8-1 (testing)]                                    
318)     python3-minimal [3.11.8-1 (testing)]                            
319)     python3.11 [3.11.9-1 (testing)]                                 
320)     python3.11-minimal [3.11.9-1 (testing)]                         
321)     shared-mime-info [2.4-1 (testing)]                              
322)     systemd [255.4-1 (testing)]                                     
323)     systemd-dev [255.4-1 (testing)]                                 
324)     systemd-sysv [255.4-1 (testing)]                                
325)     testng [6.9.12-4 (testing)]                                     
326)     tzdata [2024a-3 (testing)]                                      
327)     unzip [6.0-28 (testing)]                                        
328)     wdiff [1.2.2-6 (testing)]                                       
329)     x11-common [1:7.7+23 (testing)]                                 
330)     xfonts-encodings [1:1.0.4-2.2 (testing)]                        
331)     xfonts-utils [1:7.7+6 (testing)]                                
332)     xkb-data [2.41-2 (testing)]                                     



The following NEW packages will be installed:
  adwaita-icon-theme{a} ant{a} ant-optional{a} antlr{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} binfmt-support{a} bnd{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} dbus-broker{a} dbus-session-bus-common{a} dbus-system-bus-common{a} dbus-user-session{a} dconf-gsettings-backend{a} dconf-service{a} dctrl-tools{a} debhelper{a} default-jdk{a} default-jdk-doc{a} default-jdk-headless{a} default-jre{a} default-jre-headless{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dmsetup{a} dwz{a} fastjar{a} file{a} fontconfig{a} fontconfig-config{a} fonts-urw-base35{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{a} gpgconf{a} gpgsm{a} gradle{a} gradle-debian-helper{a} groff-base{a} groovy{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} intltool-debian{a} ivy{a} jarwrapper{a} java-common{a} java-wrappers{a} javahelper{a} junit4{a} libactivation-java{a} libantlr-java{a} libaopalliance-java{a} libapache-pom-java{a} libapparmor1{a} libarchive-zip-perl{a} libargon2-1{a} libargs4j-java{a} libasm-java{a} libasound2-data{a} libasound2t64{a} libassuan0{a} libatinject-jsr330-api-java{a} libatk-bridge2.0-0t64{a} libatk1.0-0t64{a} libatspi2.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbcel-java{a} libbcpg-java{a} libbcprov-java{a} libbrotli1{a} libbsd0{a} libbsf-java{a} libbsh-java{a} libcairo-gobject2{a} libcairo2{a} libcdi-api-java{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcloudproviders0{a} libcodemodel-java{a} libcolord2{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-compress-java{a} libcommons-io-java{a} libcommons-jexl2-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-parent-java{a} libcryptsetup12{a} libcups2t64{a} libdatrie1{a} libdb5.3t64{a} libdbus-1-3{a} libdconf1{a} libdd-plist-java{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevmapper1.02.1{a} libdom4j-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libdtd-parser-java{a} libdynaloader-functions-perl{a} libeclipse-jdt-annotation-java{a} libedit2{a} libel-api-java{a} libelf1t64{a} libencode-locale-perl{a} libepoxy0{a} liberror-prone-java{a} libexpat1{a} libfastinfoset-java{a} libfdisk1{a} libfelix-framework-java{a} libfelix-gogo-runtime-java{a} libfelix-resolver-java{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libfindbugs-java{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgoogle-gson-java{a} libgradle-core-java{a} libgradle-plugins-java{a} libgraphite2-3{a} libgtk-3-0t64{a} libgtk-3-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhawtjni-runtime-java{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhttpclient-java{a} libhttpcore-java{a} libicu72{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libistack-commons-java{a} libjansi-java{a} libjansi-native-java{a} libjansi1-java{a} libjarjar-java{a} libjatl-java{a} libjavaewah-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{a} libjbig0{a} libjcifs-java{a} libjcip-annotations-java{a} libjcommander-java{a} libjetty9-java{a} libjformatstring-java{a} libjgit-java{a} libjimfs-java{a} libjline2-java{a} libjna-java{a} libjna-jni{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-jquery-ui-theme-base{a} libjsch-java{a} libjson-c5{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjzlib-java{a} libkmod2{a} libkryo-java{a} libksba8{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm17t64{a} liblogback-java{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmaven-file-management-java{a} libmaven-parent-java{a} libmaven-resolver-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven3-core-java{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libminlog-java{a} libmjson-java{a} libmodule-runtime-perl{a} libmoo-perl{a} libnative-platform-java{a} libnative-platform-jni{a} libncbi-ngs3{a} libncbi-vdb3{a} libnekohtml-java{a} libnet-http-perl{a} libnet-ssleay-perl{a} libngs-java{a} libngs-jni{a} libnpth0t64{a} libnspr4{a} libnss3{a} libobjenesis-java{a} libosgi-annotation-java{a} libosgi-compendium-java{a} libosgi-core-java{a} libpam-systemd{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libparams-classify-perl{a} libpciaccess0{a} libpcsclite1{a} libpipeline1{a} libpixman-1-0{a} libplexus-archiver-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libpng16-16t64{a} libpolyglot-maven-java{a} libproc2-0{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqdox-java{a} libreadline8t64{a} libreflectasm-java{a} librelaxng-datatype-java{a} librhino-java{a} librngom-java{a} librole-tiny-perl{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libservlet-api-java{a} libsharpyuv0{a} libsimple-http-java{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libssl3t64{a} libstax-ex-java{a} libstreambuffer-java{a} libsub-override-perl{a} libsub-quote-perl{a} libsystemd-shared{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libtxw2-java{a} libuchardet0{a} liburi-perl{a} libvulkan1{a} libwagon-file-java{a} libwagon-http-java{a} libwagon-provider-api-java{a} libwayland-client0{a} libwayland-cursor0{a} libwayland-egl1{a} libwebp7{a} libwebsocket-api-java{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxbean-reflect-java{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxi6{a} libxinerama1{a} libxkbcommon0{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxpp3-java{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxsom-java{a} libxstream-java{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libyaml-snake-java{a} libz3-4{a} m4{a} man-db{a} maven-repo-helper{a} media-types{a} ncbi-vdb-data{a} netbase{a} openjdk-17-doc{a} openjdk-17-jdk{a} openjdk-17-jdk-headless{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} scala-library{a} sensible-utils{a} shared-mime-info{a} systemd{a} systemd-dev{a} systemd-sysv{a} testng{a} tzdata{a} unzip{a} wdiff{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xkb-data{a} 
The following packages will be REMOVED:
  libdb5.3{a} libssl3{a} 
The following packages are RECOMMENDED but will NOT be installed:
  alsa-topology-conf alsa-ucm-conf at-spi2-core chrony curl dbus dbus-bin debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra javascript-common libarchive-cpio-perl libatk-wrapper-java-jni libbindex-java libdata-dump-perl libdistro-info-perl libgdk-pixbuf2.0-bin libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libgpars-groovy-java libgtk-3-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjson-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libnss-systemd libreflectasm-java-doc librsvg2-common libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libxstring-perl libxt-dev licensecheck lintian lynx mesa-vulkan-drivers ntpsec openntpd pristine-tar psmisc python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg strace systemd-timesyncd wget xdg-user-dirs 
0 packages upgraded, 407 newly installed, 2 to remove and 0 not upgraded.
Need to get 351 MB of archives. After unpacking 1162 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-7 [697 kB]
Get: 2 http://deb.debian.org/debian trixie/main amd64 libssl3t64 amd64 3.2.1-3 [2244 kB]
Get: 3 http://deb.debian.org/debian trixie/main amd64 libapparmor1 amd64 3.0.13-2 [41.6 kB]
Get: 4 http://deb.debian.org/debian trixie/main amd64 libargon2-1 amd64 0~20190702+dfsg-4+b1 [21.1 kB]
Get: 5 http://deb.debian.org/debian trixie/main amd64 dmsetup amd64 2:1.02.196-1+b1 [82.6 kB]
Get: 6 http://deb.debian.org/debian trixie/main amd64 libdevmapper1.02.1 amd64 2:1.02.196-1+b1 [134 kB]
Get: 7 http://deb.debian.org/debian trixie/main amd64 libjson-c5 amd64 0.17-1+b1 [44.2 kB]
Get: 8 http://deb.debian.org/debian trixie/main amd64 libcryptsetup12 amd64 2:2.6.1-6+b1 [224 kB]
Get: 9 http://deb.debian.org/debian trixie/main amd64 libfdisk1 amd64 2.39.3-6 [202 kB]
Get: 10 http://deb.debian.org/debian trixie/main amd64 libkmod2 amd64 31+20240202-2 [59.6 kB]
Get: 11 http://deb.debian.org/debian trixie/main amd64 libsystemd-shared amd64 255.4-1 [1936 kB]
Get: 12 http://deb.debian.org/debian trixie/main amd64 systemd-dev all 255.4-1 [59.7 kB]
Get: 13 http://deb.debian.org/debian trixie/main amd64 systemd amd64 255.4-1 [3528 kB]
Get: 14 http://deb.debian.org/debian trixie/main amd64 systemd-sysv amd64 255.4-1 [50.4 kB]
Get: 15 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB]
Get: 16 http://deb.debian.org/debian trixie/main amd64 binfmt-support amd64 2.2.2-7 [64.3 kB]
Get: 17 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB]
Get: 18 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB]
Get: 19 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB]
Get: 20 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB]
Get: 21 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB]
Get: 22 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB]
Get: 23 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-3 [255 kB]
Get: 24 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB]
Get: 25 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB]
Get: 26 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB]
Get: 27 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB]
Get: 28 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B]
Get: 29 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB]
Get: 30 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB]
Get: 31 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-4 [880 kB]
Get: 32 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB]
Get: 33 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.2.1-3 [1360 kB]
Get: 34 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB]
Get: 35 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB]
Get: 36 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB]
Get: 37 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB]
Get: 38 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB]
Get: 39 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB]
Get: 40 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-3+b1 [1180 kB]
Get: 41 http://deb.debian.org/debian trixie/main amd64 dbus-system-bus-common all 1.14.10-4 [80.1 kB]
Get: 42 http://deb.debian.org/debian trixie/main amd64 dbus-broker amd64 36-1 [159 kB]
Get: 43 http://deb.debian.org/debian trixie/main amd64 libpam-systemd amd64 255.4-1 [260 kB]
Get: 44 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.39.3-6 [89.4 kB]
Get: 45 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.0-3 [1401 kB]
Get: 46 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [307 kB]
Get: 47 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.78.4-7 [1455 kB]
Get: 48 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB]
Get: 49 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB]
Get: 50 http://deb.debian.org/debian trixie/main amd64 shared-mime-info amd64 2.4-1 [751 kB]
Get: 51 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB]
Get: 52 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB]
Get: 53 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB]
Get: 54 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB]
Get: 55 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB]
Get: 56 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.3.2-0.4+b1 [108 kB]
Get: 57 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.3.2-0.4+b1 [308 kB]
Get: 58 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB]
Get: 59 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-3+b3 [138 kB]
Get: 60 http://deb.debian.org/debian trixie/main amd64 gtk-update-icon-cache amd64 3.24.41-4 [46.6 kB]
Get: 61 http://deb.debian.org/debian trixie/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB]
Get: 62 http://deb.debian.org/debian trixie/main amd64 adwaita-icon-theme all 46.0-1 [614 kB]
Get: 63 http://deb.debian.org/debian trixie/main amd64 ca-certificates-java all 20240118 [11.6 kB]
Get: 64 http://deb.debian.org/debian trixie/main amd64 java-common all 0.75 [6640 B]
Get: 65 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB]
Get: 66 http://deb.debian.org/debian trixie/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB]
Get: 67 http://deb.debian.org/debian trixie/main amd64 libnss3 amd64 2:3.99-1 [1408 kB]
Get: 68 http://deb.debian.org/debian trixie/main amd64 libpcsclite1 amd64 2.0.1-1+b1 [51.1 kB]
Get: 69 http://deb.debian.org/debian trixie/main amd64 openjdk-17-jre-headless amd64 17.0.11+9-1 [43.8 MB]
Get: 70 http://deb.debian.org/debian trixie/main amd64 default-jre-headless amd64 2:1.17-75 [3068 B]
Get: 71 http://deb.debian.org/debian trixie/main amd64 ant all 1.10.14-1 [2162 kB]
Get: 72 http://deb.debian.org/debian trixie/main amd64 ant-optional all 1.10.14-1 [455 kB]
Get: 73 http://deb.debian.org/debian trixie/main amd64 libantlr-java all 2.7.7+dfsg-13 [458 kB]
Get: 74 http://deb.debian.org/debian trixie/main amd64 antlr all 2.7.7+dfsg-13 [8272 B]
Get: 75 http://deb.debian.org/debian trixie/main amd64 at-spi2-common all 2.52.0-1 [166 kB]
Get: 76 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB]
Get: 77 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB]
Get: 78 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 79 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get: 80 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB]
Get: 81 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB]
Get: 82 http://deb.debian.org/debian trixie/main amd64 java-wrappers all 0.4 [8916 B]
Get: 83 http://deb.debian.org/debian trixie/main amd64 libhamcrest-java all 2.2-2 [121 kB]
Get: 84 http://deb.debian.org/debian trixie/main amd64 junit4 all 4.13.2-4 [349 kB]
Get: 85 http://deb.debian.org/debian trixie/main amd64 libfelix-framework-java all 4.6.1-2.1 [569 kB]
Get: 86 http://deb.debian.org/debian trixie/main amd64 libfelix-gogo-runtime-java all 0.16.2-1.1 [114 kB]
Get: 87 http://deb.debian.org/debian trixie/main amd64 libosgi-annotation-java all 8.1.0-1 [9436 B]
Get: 88 http://deb.debian.org/debian trixie/main amd64 libosgi-core-java all 8.0.0-2 [182 kB]
Get: 89 http://deb.debian.org/debian trixie/main amd64 libfelix-resolver-java all 1.16.0-1 [180 kB]
Get: 90 http://deb.debian.org/debian trixie/main amd64 libhawtjni-runtime-java all 1.18-1 [36.3 kB]
Get: 91 http://deb.debian.org/debian trixie/main amd64 libjansi-native-java all 1.8-2 [26.0 kB]
Get: 92 http://deb.debian.org/debian trixie/main amd64 libjansi1-java all 1.18-3 [66.5 kB]
Get: 93 http://deb.debian.org/debian trixie/main amd64 libjline2-java all 2.14.6-5 [151 kB]
Get: 94 http://deb.debian.org/debian trixie/main amd64 libosgi-compendium-java all 7.0.0-1 [477 kB]
Get: 95 http://deb.debian.org/debian trixie/main amd64 libslf4j-java all 1.7.32-1 [144 kB]
Get: 96 http://deb.debian.org/debian trixie/main amd64 libxz-java all 1.9-1 [143 kB]
Get: 97 http://deb.debian.org/debian trixie/main amd64 libyaml-snake-java all 1.33-2 [321 kB]
Get: 98 http://deb.debian.org/debian trixie/main amd64 bnd all 5.0.1-5 [10.1 MB]
Get: 99 http://deb.debian.org/debian trixie/main amd64 dbus-session-bus-common all 1.14.10-4 [79.0 kB]
Get: 100 http://deb.debian.org/debian trixie/main amd64 dbus-user-session amd64 1.14.10-4+b1 [79.1 kB]
Get: 101 http://deb.debian.org/debian trixie/main amd64 libdconf1 amd64 0.40.0-4+b2 [41.9 kB]
Get: 102 http://deb.debian.org/debian trixie/main amd64 dconf-service amd64 0.40.0-4+b2 [32.4 kB]
Get: 103 http://deb.debian.org/debian trixie/main amd64 dconf-gsettings-backend amd64 0.40.0-4+b2 [28.7 kB]
Get: 104 http://deb.debian.org/debian trixie/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB]
Get: 105 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB]
Get: 106 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB]
Get: 107 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 108 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 109 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB]
Get: 110 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 111 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 112 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB]
Get: 113 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 114 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB]
Get: 115 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 116 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 117 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB]
Get: 118 http://deb.debian.org/debian trixie/main amd64 libatk1.0-0t64 amd64 2.52.0-1 [50.8 kB]
Get: 119 http://deb.debian.org/debian trixie/main amd64 libdbus-1-3 amd64 1.14.10-4+b1 [203 kB]
Get: 120 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB]
Get: 121 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-1 [131 kB]
Get: 122 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB]
Get: 123 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.15-1 [144 kB]
Get: 124 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB]
Get: 125 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB]
Get: 126 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB]
Get: 127 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB]
Get: 128 http://deb.debian.org/debian trixie/main amd64 libatspi2.0-0t64 amd64 2.52.0-1 [75.9 kB]
Get: 129 http://deb.debian.org/debian trixie/main amd64 libatk-bridge2.0-0t64 amd64 2.52.0-1 [67.0 kB]
Get: 130 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB]
Get: 131 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB]
Get: 132 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1 [23.0 kB]
Get: 133 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23 [252 kB]
Get: 134 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB]
Get: 135 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB]
Get: 136 http://deb.debian.org/debian trixie/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB]
Get: 137 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB]
Get: 138 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB]
Get: 139 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB]
Get: 140 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.15-1 [115 kB]
Get: 141 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB]
Get: 142 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB]
Get: 143 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.0-1+b1 [531 kB]
Get: 144 http://deb.debian.org/debian trixie/main amd64 libcairo-gobject2 amd64 1.18.0-1+b1 [129 kB]
Get: 145 http://deb.debian.org/debian trixie/main amd64 libcloudproviders0 amd64 0.3.5-1 [28.7 kB]
Get: 146 http://deb.debian.org/debian trixie/main amd64 libcolord2 amd64 1.4.7-1+b1 [139 kB]
Get: 147 http://deb.debian.org/debian trixie/main amd64 libavahi-common-data amd64 0.8-13+b2 [112 kB]
Get: 148 http://deb.debian.org/debian trixie/main amd64 libavahi-common3 amd64 0.8-13+b2 [43.3 kB]
Get: 149 http://deb.debian.org/debian trixie/main amd64 libavahi-client3 amd64 0.8-13+b2 [47.0 kB]
Get: 150 http://deb.debian.org/debian trixie/main amd64 libcups2t64 amd64 2.4.7-1.2+b1 [247 kB]
Get: 151 http://deb.debian.org/debian trixie/main amd64 libepoxy0 amd64 1.5.10-1+b2 [191 kB]
Get: 152 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB]
Get: 153 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB]
Get: 154 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB]
Get: 155 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB]
Get: 156 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB]
Get: 157 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB]
Get: 158 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB]
Get: 159 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.52.1+ds-1 [216 kB]
Get: 160 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.52.1+ds-1 [48.3 kB]
Get: 161 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.52.1+ds-1 [35.1 kB]
Get: 162 http://deb.debian.org/debian trixie/main amd64 libwayland-client0 amd64 1.22.0-2.1+b1 [25.7 kB]
Get: 163 http://deb.debian.org/debian trixie/main amd64 libwayland-cursor0 amd64 1.22.0-2.1+b1 [11.3 kB]
Get: 164 http://deb.debian.org/debian trixie/main amd64 libwayland-egl1 amd64 1.22.0-2.1+b1 [5640 B]
Get: 165 http://deb.debian.org/debian trixie/main amd64 libxcomposite1 amd64 1:0.4.5-1+b1 [14.9 kB]
Get: 166 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b1 [20.3 kB]
Get: 167 http://deb.debian.org/debian trixie/main amd64 libxcursor1 amd64 1:1.2.1-1+b1 [36.2 kB]
Get: 168 http://deb.debian.org/debian trixie/main amd64 libxdamage1 amd64 1:1.1.6-1+b1 [15.5 kB]
Get: 169 http://deb.debian.org/debian trixie/main amd64 libxinerama1 amd64 2:1.1.4-3+b1 [16.0 kB]
Get: 170 http://deb.debian.org/debian trixie/main amd64 xkb-data all 2.41-2 [795 kB]
Get: 171 http://deb.debian.org/debian trixie/main amd64 libxkbcommon0 amd64 1.6.0-1+b1 [109 kB]
Get: 172 http://deb.debian.org/debian trixie/main amd64 libxrandr2 amd64 2:1.5.4-1 [36.1 kB]
Get: 173 http://deb.debian.org/debian trixie/main amd64 libgtk-3-common all 3.24.41-4 [4635 kB]
Get: 174 http://deb.debian.org/debian trixie/main amd64 libgtk-3-0t64 amd64 3.24.41-4 [2727 kB]
Get: 175 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b1 [56.3 kB]
Get: 176 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.120-2 [7688 B]
Get: 177 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB]
Get: 178 http://deb.debian.org/debian trixie/main amd64 libglapi-mesa amd64 23.3.5-1 [35.8 kB]
Get: 179 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.7-1+b1 [232 kB]
Get: 180 http://deb.debian.org/debian trixie/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB]
Get: 181 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB]
Get: 182 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB]
Get: 183 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.15-1 [105 kB]
Get: 184 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB]
Get: 185 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB]
Get: 186 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB]
Get: 187 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3-1+b1 [8852 B]
Get: 188 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB]
Get: 189 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.3.280.0-1 [123 kB]
Get: 190 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB]
Get: 191 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB]
Get: 192 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.120-2 [62.7 kB]
Get: 193 http://deb.debian.org/debian trixie/main amd64 libdrm-nouveau2 amd64 2.4.120-2 [19.3 kB]
Get: 194 http://deb.debian.org/debian trixie/main amd64 libdrm-radeon1 amd64 2.4.120-2 [22.2 kB]
Get: 195 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB]
Get: 196 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB]
Get: 197 http://deb.debian.org/debian trixie/main amd64 libllvm17t64 amd64 1:17.0.6-11 [23.7 MB]
Get: 198 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-9 [14.6 kB]
Get: 199 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-9 [34.6 kB]
Get: 200 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 23.3.5-1 [8145 kB]
Get: 201 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 23.3.5-1 [150 kB]
Get: 202 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b1 [35.0 kB]
Get: 203 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b1 [89.8 kB]
Get: 204 http://deb.debian.org/debian trixie/main amd64 libasound2-data all 1.2.11-1 [20.9 kB]
Get: 205 http://deb.debian.org/debian trixie/main amd64 libasound2t64 amd64 1.2.11-1+b1 [369 kB]
Get: 206 http://deb.debian.org/debian trixie/main amd64 libgif7 amd64 5.2.2-1 [43.9 kB]
Get: 207 http://deb.debian.org/debian trixie/main amd64 libxtst6 amd64 2:1.2.3-1.1+b1 [25.9 kB]
Get: 208 http://deb.debian.org/debian trixie/main amd64 openjdk-17-jre amd64 17.0.11+9-1 [185 kB]
Get: 209 http://deb.debian.org/debian trixie/main amd64 default-jre amd64 2:1.17-75 [1056 B]
Get: 210 http://deb.debian.org/debian trixie/main amd64 openjdk-17-jdk-headless amd64 17.0.11+9-1 [71.4 MB]
Get: 211 http://deb.debian.org/debian trixie/main amd64 default-jdk-headless amd64 2:1.17-75 [1108 B]
Get: 212 http://deb.debian.org/debian trixie/main amd64 openjdk-17-jdk amd64 17.0.11+9-1 [10.4 kB]
Get: 213 http://deb.debian.org/debian trixie/main amd64 default-jdk amd64 2:1.17-75 [1068 B]
Get: 214 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 215 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get: 216 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui-theme-base all 1.12.1+dfsg-1.1 [44.3 kB]
Get: 217 http://deb.debian.org/debian trixie/main amd64 openjdk-17-doc all 17.0.11+9-1 [12.8 MB]
Get: 218 http://deb.debian.org/debian trixie/main amd64 default-jdk-doc amd64 2:1.17-75 [3148 B]
Get: 219 http://deb.debian.org/debian trixie/main amd64 libassuan0 amd64 2.5.6-1+b1 [50.4 kB]
Get: 220 http://deb.debian.org/debian trixie/main amd64 gpgconf amd64 2.2.40-1.1+b1 [565 kB]
Get: 221 http://deb.debian.org/debian trixie/main amd64 libksba8 amd64 1.6.6-1 [131 kB]
Get: 222 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-4+b1 [19.7 kB]
Get: 223 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-4+b1 [57.0 kB]
Get: 224 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5+b3 [184 kB]
Get: 225 http://deb.debian.org/debian trixie/main amd64 libnpth0t64 amd64 1.6-3.1 [17.9 kB]
Get: 226 http://deb.debian.org/debian trixie/main amd64 dirmngr amd64 2.2.40-1.1+b1 [793 kB]
Get: 227 http://deb.debian.org/debian trixie/main amd64 gnupg-l10n all 2.2.40-1.1 [1093 kB]
Get: 228 http://deb.debian.org/debian trixie/main amd64 gnupg-utils amd64 2.2.40-1.1+b1 [928 kB]
Get: 229 http://deb.debian.org/debian trixie/main amd64 gpg amd64 2.2.40-1.1+b1 [950 kB]
Get: 230 http://deb.debian.org/debian trixie/main amd64 pinentry-curses amd64 1.2.1-3 [78.1 kB]
Get: 231 http://deb.debian.org/debian trixie/main amd64 gpg-agent amd64 2.2.40-1.1+b1 [695 kB]
Get: 232 http://deb.debian.org/debian trixie/main amd64 gpg-wks-client amd64 2.2.40-1.1+b1 [541 kB]
Get: 233 http://deb.debian.org/debian trixie/main amd64 gpg-wks-server amd64 2.2.40-1.1+b1 [532 kB]
Get: 234 http://deb.debian.org/debian trixie/main amd64 gpgsm amd64 2.2.40-1.1+b1 [671 kB]
Get: 235 http://deb.debian.org/debian trixie/main amd64 gnupg all 2.2.40-1.1 [846 kB]
Get: 236 http://deb.debian.org/debian trixie/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B]
Get: 237 http://deb.debian.org/debian trixie/main amd64 libfile-which-perl all 1.27-2 [15.1 kB]
Get: 238 http://deb.debian.org/debian trixie/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB]
Get: 239 http://deb.debian.org/debian trixie/main amd64 libfile-touch-perl all 0.12-2 [8816 B]
Get: 240 http://deb.debian.org/debian trixie/main amd64 libio-pty-perl amd64 1:1.20-1 [34.1 kB]
Get: 241 http://deb.debian.org/debian trixie/main amd64 libipc-run-perl all 20231003.0-2 [101 kB]
Get: 242 http://deb.debian.org/debian trixie/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB]
Get: 243 http://deb.debian.org/debian trixie/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b2 [36.3 kB]
Get: 244 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b2 [10.7 kB]
Get: 245 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB]
Get: 246 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.008-2+b1 [15.1 kB]
Get: 247 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b2 [22.4 kB]
Get: 248 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB]
Get: 249 http://deb.debian.org/debian trixie/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB]
Get: 250 http://deb.debian.org/debian trixie/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB]
Get: 251 http://deb.debian.org/debian trixie/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB]
Get: 252 http://deb.debian.org/debian trixie/main amd64 libmoo-perl all 2.005005-1 [58.0 kB]
Get: 253 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB]
Get: 254 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB]
Get: 255 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB]
Get: 256 http://deb.debian.org/debian trixie/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB]
Get: 257 http://deb.debian.org/debian trixie/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB]
Get: 258 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.28-1 [98.6 kB]
Get: 259 http://deb.debian.org/debian trixie/main amd64 libhtml-parser-perl amd64 3.81-1+b1 [99.0 kB]
Get: 260 http://deb.debian.org/debian trixie/main amd64 libhtml-tree-perl all 5.07-3 [211 kB]
Get: 261 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.46-1+b1 [13.8 kB]
Get: 262 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB]
Get: 263 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB]
Get: 264 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB]
Get: 265 http://deb.debian.org/debian trixie/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB]
Get: 266 http://deb.debian.org/debian trixie/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB]
Get: 267 http://deb.debian.org/debian trixie/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B]
Get: 268 http://deb.debian.org/debian trixie/main amd64 libnet-ssleay-perl amd64 1.94-1 [338 kB]
Get: 269 http://deb.debian.org/debian trixie/main amd64 libio-socket-ssl-perl all 2.085-1 [218 kB]
Get: 270 http://deb.debian.org/debian trixie/main amd64 libnet-http-perl all 6.23-1 [23.9 kB]
Get: 271 http://deb.debian.org/debian trixie/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB]
Get: 272 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB]
Get: 273 http://deb.debian.org/debian trixie/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB]
Get: 274 http://deb.debian.org/debian trixie/main amd64 libwww-perl all 6.77-1 [183 kB]
Get: 275 http://deb.debian.org/debian trixie/main amd64 patchutils amd64 0.4.2-1 [77.5 kB]
Get: 276 http://deb.debian.org/debian trixie/main amd64 wdiff amd64 1.2.2-6 [119 kB]
Get: 277 http://deb.debian.org/debian trixie/main amd64 devscripts all 2.23.7 [1068 kB]
Get: 278 http://deb.debian.org/debian trixie/main amd64 fastjar amd64 2:0.98-7 [80.1 kB]
Get: 279 http://deb.debian.org/debian trixie/main amd64 ivy all 2.5.2-1 [1295 kB]
Get: 280 http://deb.debian.org/debian trixie/main amd64 libasm-java all 9.7-1 [394 kB]
Get: 281 http://deb.debian.org/debian trixie/main amd64 libbsf-java all 1:2.4.0-8 [76.3 kB]
Get: 282 http://deb.debian.org/debian trixie/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB]
Get: 283 http://deb.debian.org/debian trixie/main amd64 libapache-pom-java all 29-2 [5276 B]
Get: 284 http://deb.debian.org/debian trixie/main amd64 libcommons-parent-java all 56-1 [10.8 kB]
Get: 285 http://deb.debian.org/debian trixie/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB]
Get: 286 http://deb.debian.org/debian trixie/main amd64 libjansi-java all 2.4.1-2 [100 kB]
Get: 287 http://deb.debian.org/debian trixie/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB]
Get: 288 http://deb.debian.org/debian trixie/main amd64 libqdox-java all 1.12.1-3 [172 kB]
Get: 289 http://deb.debian.org/debian trixie/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB]
Get: 290 http://deb.debian.org/debian trixie/main amd64 libxpp3-java all 1.1.4c-3 [292 kB]
Get: 291 http://deb.debian.org/debian trixie/main amd64 libxstream-java all 1.4.20-1 [565 kB]
Get: 292 http://deb.debian.org/debian trixie/main amd64 groovy all 2.4.21-10 [12.8 MB]
Get: 293 http://deb.debian.org/debian trixie/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B]
Get: 294 http://deb.debian.org/debian trixie/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB]
Get: 295 http://deb.debian.org/debian trixie/main amd64 libcommons-compress-java all 1.25.0-1 [635 kB]
Get: 296 http://deb.debian.org/debian trixie/main amd64 libcommons-io-java all 2.16.0-1 [484 kB]
Get: 297 http://deb.debian.org/debian trixie/main amd64 libcommons-lang-java all 2.6-10 [273 kB]
Get: 298 http://deb.debian.org/debian trixie/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB]
Get: 299 http://deb.debian.org/debian trixie/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB]
Get: 300 http://deb.debian.org/debian trixie/main amd64 libguava-java all 32.0.1-1 [2708 kB]
Get: 301 http://deb.debian.org/debian trixie/main amd64 libcommons-codec-java all 1.16.0-1 [297 kB]
Get: 302 http://deb.debian.org/debian trixie/main amd64 libhttpcore-java all 4.4.16-1 [636 kB]
Get: 303 http://deb.debian.org/debian trixie/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB]
Get: 304 http://deb.debian.org/debian trixie/main amd64 libjarjar-java all 1.4+svn142-12 [205 kB]
Get: 305 http://deb.debian.org/debian trixie/main amd64 libjcip-annotations-java all 20060626-6 [11.8 kB]
Get: 306 http://deb.debian.org/debian trixie/main amd64 libjna-jni amd64 5.14.0-1 [64.0 kB]
Get: 307 http://deb.debian.org/debian trixie/main amd64 libjna-java all 5.14.0-1 [237 kB]
Get: 308 http://deb.debian.org/debian trixie/main amd64 libjzlib-java all 1.1.3-3 [79.4 kB]
Get: 309 http://deb.debian.org/debian trixie/main amd64 libjsch-java all 0.1.55-1 [298 kB]
Get: 310 http://deb.debian.org/debian trixie/main amd64 libminlog-java all 1.3.0-1.1 [7928 B]
Get: 311 http://deb.debian.org/debian trixie/main amd64 libobjenesis-java all 3.3-3 [41.3 kB]
Get: 312 http://deb.debian.org/debian trixie/main amd64 libreflectasm-java all 1.11.9+dfsg-4 [25.0 kB]
Get: 313 http://deb.debian.org/debian trixie/main amd64 libkryo-java all 2.20-7 [158 kB]
Get: 314 http://deb.debian.org/debian trixie/main amd64 liblogback-java all 1:1.2.11-5 [701 kB]
Get: 315 http://deb.debian.org/debian trixie/main amd64 libnative-platform-jni amd64 0.14-6 [11.5 kB]
Get: 316 http://deb.debian.org/debian trixie/main amd64 libnative-platform-java all 0.14-6 [69.8 kB]
Get: 317 http://deb.debian.org/debian trixie/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB]
Get: 318 http://deb.debian.org/debian trixie/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB]
Get: 319 http://deb.debian.org/debian trixie/main amd64 libxerces2-java all 2.12.2-1 [1440 kB]
Get: 320 http://deb.debian.org/debian trixie/main amd64 libnekohtml-java all 1.9.22.noko2-0.1 [125 kB]
Get: 321 http://deb.debian.org/debian trixie/main amd64 libxbean-reflect-java all 4.5-8 [133 kB]
Get: 322 http://deb.debian.org/debian trixie/main amd64 libgradle-core-java all 4.4.1-20 [4293 kB]
Get: 323 http://deb.debian.org/debian trixie/main amd64 libbcprov-java all 1.77-1 [5300 kB]
Get: 324 http://deb.debian.org/debian trixie/main amd64 libbcpg-java all 1.77-1 [428 kB]
Get: 325 http://deb.debian.org/debian trixie/main amd64 libbsh-java all 2.0b4-20 [291 kB]
Get: 326 http://deb.debian.org/debian trixie/main amd64 libdd-plist-java all 1.20-1.1 [72.6 kB]
Get: 327 http://deb.debian.org/debian trixie/main amd64 libjaxen-java all 1.1.6-4 [214 kB]
Get: 328 http://deb.debian.org/debian trixie/main amd64 libdom4j-java all 2.1.4-1 [312 kB]
Get: 329 http://deb.debian.org/debian trixie/main amd64 libbcel-java all 6.5.0-2 [634 kB]
Get: 330 http://deb.debian.org/debian trixie/main amd64 libjformatstring-java all 0.10~20131207-2.1 [34.5 kB]
Get: 331 http://deb.debian.org/debian trixie/main amd64 libfindbugs-java all 3.1.0~preview2-3 [3502 kB]
Get: 332 http://deb.debian.org/debian trixie/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB]
Get: 333 http://deb.debian.org/debian trixie/main amd64 libaopalliance-java all 20070526-7 [8572 B]
Get: 334 http://deb.debian.org/debian trixie/main amd64 libguice-java all 4.2.3-2 [1435 kB]
Get: 335 http://deb.debian.org/debian trixie/main amd64 libjatl-java all 0.2.3-1.1 [29.0 kB]
Get: 336 http://deb.debian.org/debian trixie/main amd64 libjcifs-java all 1.3.19-2 [394 kB]
Get: 337 http://deb.debian.org/debian trixie/main amd64 libeclipse-jdt-annotation-java all 2.2.700+eclipse4.26-2 [25.3 kB]
Get: 338 http://deb.debian.org/debian trixie/main amd64 libjavaewah-java all 1.2.3-1 [159 kB]
Get: 339 http://deb.debian.org/debian trixie/main amd64 libel-api-java all 3.0.0-3 [64.9 kB]
Get: 340 http://deb.debian.org/debian trixie/main amd64 libwebsocket-api-java all 1.1-2 [40.1 kB]
Get: 341 http://deb.debian.org/debian trixie/main amd64 libjetty9-java all 9.4.54-1 [2980 kB]
Get: 342 http://deb.debian.org/debian trixie/main amd64 libjgit-java all 4.11.9-2 [2534 kB]
Get: 343 http://deb.debian.org/debian trixie/main amd64 libcommons-lang3-java all 3.14.0-1 [621 kB]
Get: 344 http://deb.debian.org/debian trixie/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB]
Get: 345 http://deb.debian.org/debian trixie/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB]
Get: 346 http://deb.debian.org/debian trixie/main amd64 libmaven-resolver-java all 1.6.3-1 [548 kB]
Get: 347 http://deb.debian.org/debian trixie/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB]
Get: 348 http://deb.debian.org/debian trixie/main amd64 libmaven-parent-java all 35-1 [6140 B]
Get: 349 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-utils-java all 3.3.4-1 [138 kB]
Get: 350 http://deb.debian.org/debian trixie/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB]
Get: 351 http://deb.debian.org/debian trixie/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB]
Get: 352 http://deb.debian.org/debian trixie/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B]
Get: 353 http://deb.debian.org/debian trixie/main amd64 libplexus-interpolation-java all 1.26-1 [76.8 kB]
Get: 354 http://deb.debian.org/debian trixie/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB]
Get: 355 http://deb.debian.org/debian trixie/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B]
Get: 356 http://deb.debian.org/debian trixie/main amd64 libcdi-api-java all 1.2-3 [54.3 kB]
Get: 357 http://deb.debian.org/debian trixie/main amd64 libsisu-inject-java all 0.3.4-2 [347 kB]
Get: 358 http://deb.debian.org/debian trixie/main amd64 libsisu-plexus-java all 0.3.4-3 [181 kB]
Get: 359 http://deb.debian.org/debian trixie/main amd64 libmaven3-core-java all 3.8.7-2 [1573 kB]
Get: 360 http://deb.debian.org/debian trixie/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB]
Get: 361 http://deb.debian.org/debian trixie/main amd64 libpolyglot-maven-java all 0.8~tobrien+git20120905-10 [74.9 kB]
Get: 362 http://deb.debian.org/debian trixie/main amd64 librhino-java all 1.7.14-2.1 [1357 kB]
Get: 363 http://deb.debian.org/debian trixie/main amd64 libsimple-http-java all 4.1.21-1.1 [211 kB]
Get: 364 http://deb.debian.org/debian trixie/main amd64 libwagon-file-java all 3.5.3-1 [8388 B]
Get: 365 http://deb.debian.org/debian trixie/main amd64 libjsoup-java all 1.15.3-1 [431 kB]
Get: 366 http://deb.debian.org/debian trixie/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB]
Get: 367 http://deb.debian.org/debian trixie/main amd64 libjcommander-java all 1.71-4 [73.0 kB]
Get: 368 http://deb.debian.org/debian trixie/main amd64 testng all 6.9.12-4 [795 kB]
Get: 369 http://deb.debian.org/debian trixie/main amd64 libgradle-plugins-java all 4.4.1-20 [5206 kB]
Get: 370 http://deb.debian.org/debian trixie/main amd64 gradle all 4.4.1-20 [398 kB]
Get: 371 http://deb.debian.org/debian trixie/main amd64 maven-repo-helper all 1.11 [142 kB]
Get: 372 http://deb.debian.org/debian trixie/main amd64 gradle-debian-helper all 2.4 [24.5 kB]
Get: 373 http://deb.debian.org/debian trixie/main amd64 jarwrapper all 0.79 [10.1 kB]
Get: 374 http://deb.debian.org/debian trixie/main amd64 javahelper all 0.79 [84.6 kB]
Get: 375 http://deb.debian.org/debian trixie/main amd64 libactivation-java all 1.2.0-2 [84.7 kB]
Get: 376 http://deb.debian.org/debian trixie/main amd64 libargs4j-java all 2.33-2 [138 kB]
Get: 377 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB]
Get: 378 http://deb.debian.org/debian trixie/main amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB]
Get: 379 http://deb.debian.org/debian trixie/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB]
Get: 380 http://deb.debian.org/debian trixie/main amd64 libsnappy1v5 amd64 1.1.10-1+b1 [27.6 kB]
Get: 381 http://deb.debian.org/debian trixie/main amd64 libsnappy-jni amd64 1.1.10.5-2 [6396 B]
Get: 382 http://deb.debian.org/debian trixie/main amd64 libsnappy-java all 1.1.10.5-2 [87.5 kB]
Get: 383 http://deb.debian.org/debian trixie/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB]
Get: 384 http://deb.debian.org/debian trixie/main amd64 libistack-commons-java all 3.0.6-5 [145 kB]
Get: 385 http://deb.debian.org/debian trixie/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-10.1 [164 kB]
Get: 386 http://deb.debian.org/debian trixie/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB]
Get: 387 http://deb.debian.org/debian trixie/main amd64 libdtd-parser-java all 1.2-1 [64.9 kB]
Get: 388 http://deb.debian.org/debian trixie/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB]
Get: 389 http://deb.debian.org/debian trixie/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB]
Get: 390 http://deb.debian.org/debian trixie/main amd64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB]
Get: 391 http://deb.debian.org/debian trixie/main amd64 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB]
Get: 392 http://deb.debian.org/debian trixie/main amd64 libxsom-java all 2.3.0.1-10.1 [400 kB]
Get: 393 http://deb.debian.org/debian trixie/main amd64 libfastinfoset-java all 1.2.12-3 [343 kB]
Get: 394 http://deb.debian.org/debian trixie/main amd64 librngom-java all 2.3.0.1-10.1 [290 kB]
Get: 395 http://deb.debian.org/debian trixie/main amd64 libtxw2-java all 2.3.0.1-10.1 [134 kB]
Get: 396 http://deb.debian.org/debian trixie/main amd64 libjaxb-java all 2.3.0.1-10.1 [1973 kB]
Get: 397 http://deb.debian.org/debian trixie/main amd64 libjimfs-java all 1.1-6 [191 kB]
Get: 398 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB]
Get: 399 http://deb.debian.org/debian trixie/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB]
Get: 400 http://deb.debian.org/debian trixie/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB]
Get: 401 http://deb.debian.org/debian trixie/main amd64 libmjson-java all 1.4.0-3 [60.4 kB]
Get: 402 http://deb.debian.org/debian trixie/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB]
Get: 403 http://deb.debian.org/debian trixie/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2+b1 [1049 kB]
Get: 404 http://deb.debian.org/debian trixie/main amd64 libncbi-ngs3 amd64 3.0.3+dfsg-6 [154 kB]
Get: 405 http://deb.debian.org/debian trixie/main amd64 libngs-jni amd64 3.0.3+dfsg-6 [23.4 kB]
Get: 406 http://deb.debian.org/debian trixie/main amd64 libngs-java amd64 3.0.3+dfsg-6 [110 kB]
Get: 407 http://deb.debian.org/debian trixie/main amd64 scala-library all 2.11.12-5 [9588 kB]
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debconf: delaying package configuration, since apt-utils is not installed
dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested:
 libperl5.38:amd64 depends on libdb5.3.
 libpam-modules:amd64 depends on libdb5.3.

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dpkg: libssl3:amd64: dependency problems, but removing anyway as you requested:
 libkrb5-3:amd64 depends on libssl3 (>= 3.0.0).
 coreutils depends on libssl3 (>= 3.0.0).

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Setting up libcryptsetup12:amd64 (2:2.6.1-6+b1) ...
Setting up systemd (255.4-1) ...
Created symlink /etc/systemd/system/getty.target.wants/getty@tty1.service -> /usr/lib/systemd/system/getty@.service.

Created symlink /etc/systemd/system/multi-user.target.wants/remote-fs.target -> /usr/lib/systemd/system/remote-fs.target.

Created symlink /etc/systemd/system/sysinit.target.wants/systemd-pstore.service -> /usr/lib/systemd/system/systemd-pstore.service.

Initializing machine ID from random generator.

Creating group 'systemd-journal' with GID 999.

Creating group 'systemd-network' with GID 998.

Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998.

Setting up dmsetup (2:1.02.196-1+b1) ...
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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
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Setting up wdiff (1.2.2-6) ...
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Setting up libpciaccess0:amd64 (0.17-3+b1) ...
Setting up libslf4j-java (1.7.32-1) ...
Setting up libfile-which-perl (1.27-2) ...
Setting up systemd-sysv (255.4-1) ...
Setting up libxau6:amd64 (1:1.0.9-1+b1) ...
Setting up libplexus-utils2-java (3.4.2-1) ...
Setting up libnpth0t64:amd64 (1.6-3.1) ...
Setting up libplexus-classworlds-java (2.7.0-1) ...
Setting up libqdox-java (1.12.1-3) ...
Setting up libicu72:amd64 (72.1-4+b1) ...
Setting up liblerc4:amd64 (4.0.0+ds-4+b1) ...
Setting up libjsr305-java (0.1~+svn49-11) ...
Setting up libsimple-http-java (4.1.21-1.1) ...
Setting up bsdextrautils (2.39.3-6) ...
Setting up hicolor-icon-theme (0.17-2) ...
Setting up libmbedcrypto7t64:amd64 (2.28.8-1) ...
Setting up java-common (0.75) ...
Setting up libdynaloader-functions-perl (0.003-3) ...
Setting up libdatrie1:amd64 (0.2.13-3) ...
Setting up libjcip-annotations-java (20060626-6) ...
Setting up libobjenesis-java (3.3-3) ...
Setting up libclass-method-modifiers-perl (2.15-1) ...
Setting up libaopalliance-java (20070526-7) ...
Setting up libcommons-cli-java (1.6.0-1) ...
Setting up libio-pty-perl (1:1.20-1) ...
Setting up libmagic-mgc (1:5.45-3) ...
Setting up liblogback-java (1:1.2.11-5) ...
Setting up libclone-perl:amd64 (0.46-1+b1) ...
Setting up libminlog-java (1.3.0-1.1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglvnd0:amd64 (1.7.0-1+b1) ...
Setting up libgoogle-gson-java (2.10.1-1) ...
Setting up libmjson-java (1.4.0-3) ...
Setting up libhtml-tagset-perl (3.24-1) ...
Setting up unzip (6.0-28) ...
Setting up libdebhelper-perl (13.15.3) ...
Setting up libbrotli1:amd64 (1.1.0-2+b3) ...
Setting up liblwp-mediatypes-perl (6.04-2) ...
Setting up libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ...
Setting up libmagic1t64:amd64 (1:5.45-3) ...
Setting up libasm-java (9.7-1) ...
Setting up libjs-jquery-ui-theme-base (1.12.1+dfsg-1.1) ...
Setting up x11-common (1:7.7+23) ...
Running in chroot, ignoring request.

Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix.
Setting up libtry-tiny-perl (0.31-2) ...
Setting up libsensors-config (1:3.6.0-9) ...
Setting up libdeflate0:amd64 (1.20-1) ...
Setting up perl-openssl-defaults:amd64 (7+b2) ...
Setting up libdd-plist-java (1.20-1.1) ...
Setting up gettext-base (0.21-14+b1) ...
Setting up m4 (1.4.19-4) ...
Setting up libel-api-java (3.0.0-3) ...
Setting up scala-library (2.11.12-5) ...
Setting up xkb-data (2.41-2) ...
Setting up libencode-locale-perl (1.05-3) ...
Setting up libplexus-component-annotations-java (2.1.1-1) ...
Setting up file (1:5.45-3) ...
Setting up libpolyglot-maven-java (0.8~tobrien+git20120905-10) ...
Setting up libfelix-gogo-runtime-java (0.16.2-1.1) ...
Setting up libassuan0:amd64 (2.5.6-1+b1) ...
Setting up libjzlib-java (1.1.3-3) ...
Setting up libjbig0:amd64 (2.1-6.1+b1) ...
Setting up libelf1t64:amd64 (0.191-1+b1) ...
Setting up libsnappy1v5:amd64 (1.1.10-1+b1) ...
Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-4+b1) ...
Setting up tzdata (2024a-3) ...

Current default time zone: 'Etc/UTC'
Local time is now:      Tue Jun  3 01:06:30 UTC 2025.
Universal Time is now:  Tue Jun  3 01:06:30 UTC 2025.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ...
Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ...
Setting up libcommons-collections3-java (3.2.2-3) ...
Setting up libasound2-data (1.2.11-1) ...
Setting up libjsch-java (0.1.55-1) ...
Setting up libreflectasm-java (1.11.9+dfsg-4) ...
Setting up libfontenc1:amd64 (1:1.1.8-1) ...
Setting up librhino-java (1.7.14-2.1) ...
Setting up autotools-dev (20220109.1) ...
Setting up libz3-4:amd64 (4.8.12-3.1+b2) ...
Setting up libglib2.0-0t64:amd64 (2.78.4-7) ...
Setting up libbsf-java (1:2.4.0-8) ...
Setting up libosgi-annotation-java (8.1.0-1) ...
Setting up libjformatstring-java (0.10~20131207-2.1) ...
Setting up libasound2t64:amd64 (1.2.11-1+b1) ...
Setting up libjavaewah-java (1.2.3-1) ...
Setting up libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ...
Setting up libjaxen-java (1.1.6-4) ...
Setting up libx11-data (2:1.8.7-1) ...
Setting up libepoxy0:amd64 (1.5.10-1+b2) ...
Setting up libnspr4:amd64 (2:4.35-1.1+b1) ...
Setting up gnupg-l10n (2.2.40-1.1) ...
Setting up libeclipse-jdt-annotation-java (2.2.700+eclipse4.26-2) ...
Setting up libjansi-java (2.4.1-2) ...
Setting up libapache-pom-java (29-2) ...
Setting up libavahi-common-data:amd64 (0.8-13+b2) ...
Setting up libxpp3-java (1.1.4c-3) ...
Setting up libatinject-jsr330-api-java (1.0+ds1-5) ...
Setting up libdbus-1-3:amd64 (1.14.10-4+b1) ...
Setting up xfonts-encodings (1:1.0.4-2.2) ...
Setting up libwebsocket-api-java (1.1-2) ...
Setting up libfribidi0:amd64 (1.0.13-3+b1) ...
Setting up libproc2-0:amd64 (2:4.0.4-4) ...
Setting up libplexus-interpolation-java (1.26-1) ...
Setting up libpng16-16t64:amd64 (1.6.43-5) ...
Setting up libxml-commons-resolver1.1-java (1.2-11) ...
Setting up libkryo-java (2.20-7) ...
Setting up libxz-java (1.9-1) ...
Setting up libio-html-perl (1.004-3) ...
Setting up libjna-jni (5.14.0-1) ...
Setting up autopoint (0.21-14) ...
Setting up binfmt-support (2.2.2-7) ...
Running in chroot, ignoring request.

invoke-rc.d: policy-rc.d denied execution of start.
Created symlink /etc/systemd/system/multi-user.target.wants/binfmt-support.service -> /usr/lib/systemd/system/binfmt-support.service.

Setting up libb-hooks-op-check-perl:amd64 (0.22-2+b2) ...
Setting up libfelix-framework-java (4.6.1-2.1) ...
Setting up libipc-run-perl (20231003.0-2) ...
Setting up libpcsclite1:amd64 (2.0.1-1+b1) ...
Setting up libsensors5:amd64 (1:3.6.0-9) ...
Setting up libjimfs-java (1.1-6) ...
Setting up libactivation-java (1.2.0-2) ...
Setting up libhamcrest-java (2.2-2) ...
Setting up libglapi-mesa:amd64 (23.3.5-1) ...
Setting up libbsh-java (2.0b4-20) ...
Setting up libjsp-api-java (2.3.4-3) ...
Setting up libsasl2-2:amd64 (2.1.28+dfsg1-4+b1) ...
Setting up libvulkan1:amd64 (1.3.280.0-1) ...
Setting up autoconf (2.71-3) ...
Setting up libwebp7:amd64 (1.3.2-0.4+b1) ...
Setting up libtimedate-perl (2.3300-2) ...
Setting up libgif7:amd64 (5.2.2-1) ...
Setting up libjarjar-java (1.4+svn142-12) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.22) ...
Setting up libxshmfence1:amd64 (1.3-1+b1) ...
Setting up libjsoup-java (1.15.3-1) ...
Setting up at-spi2-common (2.52.0-1) ...
Setting up libtiff6:amd64 (4.5.1+git230720-4) ...
Setting up dbus-session-bus-common (1.14.10-4) ...
Setting up libuchardet0:amd64 (0.0.8-1+b1) ...
Setting up libxml-commons-external-java (1.4.01-6) ...
Setting up procps (2:4.0.4-4) ...
Setting up libjna-java (5.14.0-1) ...
Setting up libxbean-reflect-java (4.5-8) ...
Setting up libservlet-api-java (4.0.1-2) ...
Setting up librole-tiny-perl (2.002004-1) ...
Setting up libsub-override-perl (0.10-1) ...
Setting up ncbi-vdb-data (3.0.2+dfsg-2) ...
Setting up libthai-data (0.1.29-2) ...
Setting up netbase (6.4) ...
Setting up libsub-quote-perl (2.006008-1) ...
Setting up libnative-platform-jni (0.14-6) ...
Setting up libclass-xsaccessor-perl (1.19-4+b2) ...
Setting up libwayland-egl1:amd64 (1.22.0-2.1+b1) ...
Setting up libhttpcore-java (4.4.16-1) ...
Setting up libbcpg-java (1.77-1) ...
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up libxerces2-java (2.12.2-1) ...
Setting up libfile-dirlist-perl (0.05-3) ...
Setting up dbus-system-bus-common (1.14.10-4) ...
Setting up libfile-homedir-perl (1.006-2) ...
Setting up librelaxng-datatype-java (1.0+ds1-3.1) ...
Setting up libantlr-java (2.7.7+dfsg-13) ...
Setting up libyaml-snake-java (1.33-2) ...
Setting up openssl (3.2.1-3) ...
Setting up libbsd0:amd64 (0.12.2-1) ...
Setting up libdrm-common (2.4.120-2) ...
Setting up libcdi-api-java (1.2-3) ...
Setting up libsnappy-jni (1.1.10.5-2) ...
Setting up readline-common (8.2-4) ...
Setting up libhawtjni-runtime-java (1.18-1) ...
Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ...
Setting up liburi-perl (5.28-1) ...
Setting up libargs4j-java (2.33-2) ...
Setting up libfile-touch-perl (0.12-2) ...
Setting up dctrl-tools (2.24-3+b1) ...
Setting up libjatl-java (0.2.3-1.1) ...
Setting up libxkbcommon0:amd64 (1.6.0-1+b1) ...
Setting up libwayland-client0:amd64 (1.22.0-2.1+b1) ...
Setting up libnet-ssleay-perl:amd64 (1.94-1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up pinentry-curses (1.2.1-3) ...
Setting up libdom4j-java (2.1.4-1) ...
Setting up libjaxb-api-java (2.3.1-1) ...
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up libwagon-provider-api-java (3.5.3-1) ...
Setting up libnative-platform-java (0.14-6) ...
Setting up libosgi-core-java (8.0.0-2) ...
Setting up libhttp-date-perl (6.06-1) ...
Setting up libxstream-java (1.4.20-1) ...
Setting up libnekohtml-java (1.9.22.noko2-0.1) ...
Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ...
Setting up libxcb1:amd64 (1.15-1) ...
Setting up gettext (0.21-14+b1) ...
Setting up libmbedx509-1t64:amd64 (2.28.8-1) ...
Setting up libjetty9-java (9.4.54-1) ...
Setting up libxcb-xfixes0:amd64 (1.15-1) ...
Setting up java-wrappers (0.4) ...
Setting up libatk1.0-0t64:amd64 (2.52.0-1) ...
Setting up libfile-listing-perl (6.16-1) ...
Setting up libosgi-compendium-java (7.0.0-1) ...
Setting up jarwrapper (0.79) ...
Setting up libtool (2.4.7-7) ...
Setting up libxcb-render0:amd64 (1.15-1) ...
Setting up libstax-ex-java (1.7.8-3) ...
Setting up libxcb-glx0:amd64 (1.15-1) ...
Setting up libmaven-parent-java (35-1) ...
Setting up libedit2:amd64 (3.1-20230828-1+b1) ...
Setting up libcommons-parent-java (56-1) ...
Setting up libavahi-common3:amd64 (0.8-13+b2) ...
Setting up libcloudproviders0:amd64 (0.3.5-1) ...
Setting up libcommons-logging-java (1.3.0-1) ...
Setting up libnet-http-perl (6.23-1) ...
Setting up libsisu-inject-java (0.3.4-2) ...
Setting up libnss3:amd64 (2:3.99-1) ...
Setting up libxcb-shm0:amd64 (1.15-1) ...
Setting up libdevel-callchecker-perl:amd64 (0.008-2+b1) ...
Setting up libcommons-lang-java (2.6-10) ...
Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) ...
Setting up libcolord2:amd64 (1.4.7-1+b1) ...
Setting up libplexus-cipher-java (2.0-1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libxcb-present0:amd64 (1.15-1) ...
Setting up libdconf1:amd64 (0.40.0-4+b2) ...
Setting up dh-autoreconf (20) ...
Setting up patchutils (0.4.2-1) ...
Setting up libcommons-jexl2-java (2.1.1-6) ...
Setting up libthai0:amd64 (0.1.29-2) ...
Setting up ca-certificates (20240203) ...
Updating certificates in /etc/ssl/certs...
146 added, 0 removed; done.
Setting up libsisu-plexus-java (0.3.4-3) ...
Setting up libbcel-java (6.5.0-2) ...
Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
Setting up libllvm17t64:amd64 (1:17.0.6-11) ...
Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ...
Setting up libxcb-sync1:amd64 (1.15-1) ...
Setting up testng (6.9.12-4) ...
Setting up shared-mime-info (2.4-1) ...
Setting up libstreambuffer-java (1.5.4-1.1) ...
Setting up libcommons-lang3-java (3.14.0-1) ...
Setting up libreadline8t64:amd64 (8.2-4) ...
Setting up libxcb-dri2-0:amd64 (1.15-1) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up libwww-robotrules-perl (6.02-1) ...
Setting up libfelix-resolver-java (1.16.0-1) ...
Setting up librngom-java (2.3.0.1-10.1) ...
Setting up libdrm2:amd64 (2.4.120-2) ...
Setting up libjansi-native-java (1.8-2) ...
Setting up libmbedtls14t64:amd64 (2.28.8-1) ...
Setting up groff-base (1.23.0-3+b1) ...
Setting up libwayland-cursor0:amd64 (1.22.0-2.1+b1) ...
Setting up libxcb-randr0:amd64 (1.15-1) ...
Setting up libhtml-parser-perl:amd64 (3.81-1+b1) ...
Setting up gpgconf (2.2.40-1.1+b1) ...
Setting up openjdk-17-doc (17.0.11+9-1) ...
Setting up libjansi1-java (1.18-3) ...
Setting up libplexus-sec-dispatcher-java (2.0-3) ...
Setting up libx11-6:amd64 (2:1.8.7-1+b1) ...
Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ...
Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3+b3) ...
Setting up dbus-broker (36-1) ...
Created symlink /etc/systemd/user/dbus.service -> /usr/lib/systemd/user/dbus-broker.service.

Created symlink /etc/systemd/system/dbus.service -> /usr/lib/systemd/system/dbus-broker.service.

Setting up libsnappy-java (1.1.10.5-2) ...
Setting up libxsom-java (2.3.0.1-10.1) ...
Setting up ca-certificates-java (20240118) ...
No JRE found. Skipping Java certificates setup.
Setting up libwagon-file-java (3.5.3-1) ...
Setting up libcommons-codec-java (1.16.0-1) ...
Setting up libjline2-java (2.14.6-5) ...
Setting up libxcomposite1:amd64 (1:0.4.5-1+b1) ...
Setting up libavahi-client3:amd64 (0.8-13+b2) ...
Setting up libio-socket-ssl-perl (2.085-1) ...
Setting up gpg (2.2.40-1.1+b1) ...
Setting up gnupg-utils (2.2.40-1.1+b1) ...
Setting up libhttp-message-perl (6.45-1) ...
Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ...
Setting up libxcb-dri3-0:amd64 (1.15-1) ...
Setting up gtk-update-icon-cache (3.24.41-4) ...
Setting up libx11-xcb1:amd64 (2:1.8.7-1+b1) ...
Setting up libhttp-negotiate-perl (6.01-2) ...
Setting up libdrm-nouveau2:amd64 (2.4.120-2) ...
Setting up libfindbugs-java (3.1.0~preview2-3) ...
Setting up libxdamage1:amd64 (1:1.1.6-1+b1) ...
Setting up gpg-agent (2.2.40-1.1+b1) ...
Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-browser.socket -> /usr/lib/systemd/user/gpg-agent-browser.socket.

Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-extra.socket -> /usr/lib/systemd/user/gpg-agent-extra.socket.

Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-ssh.socket -> /usr/lib/systemd/user/gpg-agent-ssh.socket.

Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent.socket -> /usr/lib/systemd/user/gpg-agent.socket.

Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ...
Setting up libcommons-compress-java (1.25.0-1) ...
Setting up libhttp-cookies-perl (6.11-1) ...
Setting up libcommons-io-java (2.16.0-1) ...
Setting up libdrm-radeon1:amd64 (2.4.120-2) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhtml-tree-perl (5.07-3) ...
Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ...
Setting up libparams-classify-perl:amd64 (0.015-2+b2) ...
Setting up gpgsm (2.2.40-1.1+b1) ...
Setting up libdrm-intel1:amd64 (2.4.120-2) ...
Setting up libgl1-mesa-dri:amd64 (23.3.5-1) ...
Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2+b1) ...
Setting up libxext6:amd64 (2:1.3.4-1+b1) ...
Setting up default-jdk-doc (2:1.17-75) ...
Setting up xfonts-utils (1:7.7+6) ...
Setting up man-db (2.12.0-3) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink /etc/systemd/system/timers.target.wants/man-db.timer -> /usr/lib/systemd/system/man-db.timer.

Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ...
Setting up dirmngr (2.2.40-1.1+b1) ...
Created symlink /etc/systemd/user/sockets.target.wants/dirmngr.socket -> /usr/lib/systemd/user/dirmngr.socket.

Setting up libmaven-resolver-java (1.6.3-1) ...
Setting up adwaita-icon-theme (46.0-1) ...
update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode
Setting up libmodule-runtime-perl (0.016-2) ...
Setting up libxfixes3:amd64 (1:6.0.0-2+b1) ...
Setting up libxinerama1:amd64 (2:1.1.4-3+b1) ...
Setting up libxrandr2:amd64 (2:1.5.4-1) ...
Setting up openjdk-17-jre-headless:amd64 (17.0.11+9-1) ...
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up gpg-wks-server (2.2.40-1.1+b1) ...
Setting up libhttpclient-java (4.5.14-1) ...
Setting up libpam-systemd:amd64 (255.4-1) ...
Setting up libwagon-http-java (3.5.3-1) ...
Setting up libmaven-shared-utils-java (3.3.4-1) ...
Setting up libfastinfoset-java (1.2.12-3) ...
Setting up libcups2t64:amd64 (2.4.7-1.2+b1) ...
Setting up libpython3-stdlib:amd64 (3.11.8-1) ...
Setting up libncbi-ngs3:amd64 (3.0.3+dfsg-6) ...
Setting up python3.11 (3.11.9-1) ...
Setting up libjgit-java (4.11.9-2) ...
Setting up libngs-jni:amd64 (3.0.3+dfsg-6) ...
Setting up libplexus-io-java (3.3.1-2) ...
Setting up libglx-mesa0:amd64 (23.3.5-1) ...
Setting up libxi6:amd64 (2:1.8.1-1) ...
Setting up gpg-wks-client (2.2.40-1.1+b1) ...
Setting up libglx0:amd64 (1.7.0-1+b1) ...
Setting up libimport-into-perl (1.002005-2) ...
Setting up libxtst6:amd64 (2:1.2.3-1.1+b1) ...
Setting up libmoo-perl (2.005005-1) ...
Setting up libxcursor1:amd64 (1:1.2.1-1+b1) ...
Setting up debhelper (13.15.3) ...
Setting up python3 (3.11.8-1) ...
Setting up fonts-urw-base35 (20200910-8) ...
Setting up dbus-user-session (1.14.10-4+b1) ...
Setting up libgl1:amd64 (1.7.0-1+b1) ...
Setting up libatspi2.0-0t64:amd64 (2.52.0-1) ...
Setting up gnupg (2.2.40-1.1) ...
Setting up libplexus-archiver-java (4.6.1-1) ...
Setting up libngs-java:amd64 (3.0.3+dfsg-6) ...
Setting up libatk-bridge2.0-0t64:amd64 (2.52.0-1) ...
Setting up fontconfig-config (2.15.0-1.1) ...
Setting up dconf-service (0.40.0-4+b2) ...
Setting up libfontconfig1:amd64 (2.15.0-1.1) ...
Setting up fontconfig (2.15.0-1.1) ...
Regenerating fonts cache... done.
Setting up dconf-gsettings-backend:amd64 (0.40.0-4+b2) ...
Setting up libpango-1.0-0:amd64 (1.52.1+ds-1) ...
Setting up libcairo2:amd64 (1.18.0-1+b1) ...
Setting up libcairo-gobject2:amd64 (1.18.0-1+b1) ...
Setting up libpangoft2-1.0-0:amd64 (1.52.1+ds-1) ...
Setting up libgtk-3-common (3.24.41-4) ...
Setting up libpangocairo-1.0-0:amd64 (1.52.1+ds-1) ...
Setting up libgtk-3-0t64:amd64 (3.24.41-4) ...
Setting up liberror-prone-java (2.18.0-1) ...
Setting up libwww-perl (6.77-1) ...
Setting up devscripts (2.23.7) ...
Setting up libguava-java (32.0.1-1) ...
Setting up javahelper (0.79) ...
Setting up libplexus-container-default-java (2.1.1-1) ...
Setting up liblwp-protocol-https-perl (6.14-1) ...
Setting up libguice-java (4.2.3-2) ...
Setting up libmaven3-core-java (3.8.7-2) ...
Setting up libmaven-shared-io-java (3.0.0-4) ...
Setting up libmaven-file-management-java (3.0.0-1) ...
Processing triggers for libc-bin (2.37-18) ...
Processing triggers for systemd (255.4-1) ...
Processing triggers for ca-certificates-java (20240118) ...
Adding debian:ACCVRAIZ1.pem
Adding debian:AC_RAIZ_FNMT-RCM.pem
Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
Adding debian:ANF_Secure_Server_Root_CA.pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:AffirmTrust_Commercial.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:AffirmTrust_Premium.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:Amazon_Root_CA_1.pem
Adding debian:Amazon_Root_CA_2.pem
Adding debian:Amazon_Root_CA_3.pem
Adding debian:Amazon_Root_CA_4.pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:BJCA_Global_Root_CA1.pem
Adding debian:BJCA_Global_Root_CA2.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:Certainly_Root_E1.pem
Adding debian:Certainly_Root_R1.pem
Adding debian:Certigna.pem
Adding debian:Certigna_Root_CA.pem
Adding debian:Certum_EC-384_CA.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:Certum_Trusted_Network_CA_2.pem
Adding debian:Certum_Trusted_Root_CA.pem
Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
Adding debian:DigiCert_Assured_ID_Root_CA.pem
Adding debian:DigiCert_Assured_ID_Root_G2.pem
Adding debian:DigiCert_Assured_ID_Root_G3.pem
Adding debian:DigiCert_Global_Root_CA.pem
Adding debian:DigiCert_Global_Root_G2.pem
Adding debian:DigiCert_Global_Root_G3.pem
Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
Adding debian:DigiCert_Trusted_Root_G4.pem
Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
Adding debian:Entrust_Root_Certification_Authority.pem
Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
Adding debian:GLOBALTRUST_2020.pem
Adding debian:GTS_Root_R1.pem
Adding debian:GTS_Root_R2.pem
Adding debian:GTS_Root_R3.pem
Adding debian:GTS_Root_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
Adding debian:GlobalSign_Root_CA.pem
Adding debian:GlobalSign_Root_CA_-_R3.pem
Adding debian:GlobalSign_Root_CA_-_R6.pem
Adding debian:GlobalSign_Root_E46.pem
Adding debian:GlobalSign_Root_R46.pem
Adding debian:Go_Daddy_Class_2_CA.pem
Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
Adding debian:HiPKI_Root_CA_-_G1.pem
Adding debian:Hongkong_Post_Root_CA_3.pem
Adding debian:ISRG_Root_X1.pem
Adding debian:ISRG_Root_X2.pem
Adding debian:IdenTrust_Commercial_Root_CA_1.pem
Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
Adding debian:Izenpe.com.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
Adding debian:NAVER_Global_Root_Certification_Authority.pem
Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
Adding debian:QuoVadis_Root_CA_1_G3.pem
Adding debian:QuoVadis_Root_CA_2.pem
Adding debian:QuoVadis_Root_CA_2_G3.pem
Adding debian:QuoVadis_Root_CA_3.pem
Adding debian:QuoVadis_Root_CA_3_G3.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
Adding debian:SZAFIR_ROOT_CA2.pem
Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
Adding debian:SecureSign_RootCA11.pem
Adding debian:SecureTrust_CA.pem
Adding debian:Secure_Global_CA.pem
Adding debian:Security_Communication_ECC_RootCA1.pem
Adding debian:Security_Communication_RootCA2.pem
Adding debian:Security_Communication_RootCA3.pem
Adding debian:Security_Communication_Root_CA.pem
Adding debian:Starfield_Class_2_CA.pem
Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:TeliaSonera_Root_CA_v1.pem
Adding debian:Telia_Root_CA_v2.pem
Adding debian:TrustAsia_Global_Root_CA_G3.pem
Adding debian:TrustAsia_Global_Root_CA_G4.pem
Adding debian:Trustwave_Global_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
Adding debian:TunTrust_Root_CA.pem
Adding debian:UCA_Extended_Validation_Root.pem
Adding debian:UCA_Global_G2_Root.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:XRamp_Global_CA_Root.pem
Adding debian:certSIGN_ROOT_CA.pem
Adding debian:certSIGN_Root_CA_G2.pem
Adding debian:e-Szigno_Root_CA_2017.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:emSign_ECC_Root_CA_-_C3.pem
Adding debian:emSign_ECC_Root_CA_-_G3.pem
Adding debian:emSign_Root_CA_-_C1.pem
Adding debian:emSign_Root_CA_-_G1.pem
Adding debian:vTrus_ECC_Root_CA.pem
Adding debian:vTrus_Root_CA.pem
done.
Setting up antlr (2.7.7+dfsg-13) ...
Setting up openjdk-17-jdk-headless:amd64 (17.0.11+9-1) ...
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode
Setting up ivy (2.5.2-1) ...
Setting up ant (1.10.14-1) ...
Setting up junit4 (4.13.2-4) ...
Setting up groovy (2.4.21-10) ...
update-alternatives: using /usr/share/groovy/bin/groovy to provide /usr/bin/groovy (groovy) in auto mode
update-alternatives: using /usr/share/groovy/bin/groovyc to provide /usr/bin/groovyc (groovyc) in auto mode
update-alternatives: using /usr/share/groovy/bin/grape to provide /usr/bin/grape (grape) in auto mode
update-alternatives: using /usr/share/groovy/bin/startGroovy to provide /usr/bin/startGroovy (startGroovy) in auto mode
update-alternatives: using /usr/share/groovy/bin/groovysh to provide /usr/bin/groovysh (groovysh) in auto mode
update-alternatives: using /usr/share/groovy/bin/java2groovy to provide /usr/bin/java2groovy (java2groovy) in auto mode
update-alternatives: using /usr/share/groovy/bin/groovyConsole to provide /usr/bin/groovyConsole (groovyConsole) in auto mode
update-alternatives: using /usr/share/groovy/bin/groovydoc to provide /usr/bin/groovydoc (groovydoc) in auto mode
Setting up default-jre-headless (2:1.17-75) ...
Setting up openjdk-17-jre:amd64 (17.0.11+9-1) ...
Setting up maven-repo-helper (1.11) ...
Setting up default-jre (2:1.17-75) ...
Setting up openjdk-17-jdk:amd64 (17.0.11+9-1) ...
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode
Setting up ant-optional (1.10.14-1) ...
Setting up bnd (5.0.1-5) ...
Setting up default-jdk-headless (2:1.17-75) ...
Setting up libgradle-core-java (4.4.1-20) ...
Setting up libgradle-plugins-java (4.4.1-20) ...
Setting up gradle (4.4.1-20) ...
Setting up libistack-commons-java (3.0.6-5) ...
Setting up default-jdk (2:1.17-75) ...
Setting up libcodemodel-java (2.6+jaxb2.3.0.1-10.1) ...
Setting up gradle-debian-helper (2.4) ...
Setting up libtxw2-java (2.3.0.1-10.1) ...
Setting up libjaxb-java (2.3.0.1-10.1) ...
Processing triggers for ca-certificates (20240203) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Processing triggers for ca-certificates-java (20240118) ...
done.
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
 -> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/787020/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for trixie
I: user script /srv/workspace/pbuilder/787020/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/htsjdk-4.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S  > ../htsjdk_4.1.0+dfsg-1_source.changes
dpkg-buildpackage: info: source package htsjdk
dpkg-buildpackage: info: source version 4.1.0+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Pierre Gruet <pgt@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh  clean  --buildsystem=gradle --with javahelper,jh_maven_repo_helper
   dh_auto_clean -O--buildsystem=gradle
	sh -c "find . -wholename .*build/tmp | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf"
	sh -c "find . -wholename .*build/debian | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf"
	rm -Rf /build/reproducible-path/htsjdk-4.1.0\+dfsg/.gradle /build/reproducible-path/htsjdk-4.1.0\+dfsg/buildSrc/.gradle .m2
   dh_autoreconf_clean -O--buildsystem=gradle
   jh_clean -O--buildsystem=gradle
	rm -fr debian/_jh_manifest* debian/_jh_build*
	rm -fr debian/.eclipse-build
	rm -f debian/orbitdeps.debhelper
   dh_clean -O--buildsystem=gradle
	rm -f debian/debhelper-build-stamp
	rm -rf debian/.debhelper/
	rm -f -- debian/libhtsjdk-java.substvars debian/libhtsjdk-java-doc.substvars debian/files
	rm -fr -- debian/libhtsjdk-java/ debian/tmp/ debian/libhtsjdk-java-doc/
	find .  \( \( \
		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
		 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
		 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
		 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
		\) -exec rm -f {} + \) -o \
		\( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
 debian/rules binary
dh  binary  --buildsystem=gradle --with javahelper,jh_maven_repo_helper
   dh_update_autotools_config -O--buildsystem=gradle
   dh_autoreconf -O--buildsystem=gradle
   dh_auto_configure -O--buildsystem=gradle
   jh_linkjars -O--buildsystem=gradle
   debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/htsjdk-4.1.0+dfsg'
dh_auto_build -- jar javadoc
	mkdir -p .gradle/init.d
	cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/
	gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=htsjdk -Dfile.encoding=UTF-8 --parallel --max-workers=12 jar javadoc
openjdk version "17.0.11" 2024-04-16
OpenJDK Runtime Environment (build 17.0.11+9-Debian-1)
OpenJDK 64-Bit Server VM (build 17.0.11+9-Debian-1, mixed mode, sharing)
Initialized native services in: /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/native
To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html.
Starting process 'Gradle build daemon'. Working directory: /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1
Successfully started process 'Gradle build daemon'
An attempt to start the daemon took 0.918 secs.
The client will now receive all logging from the daemon (pid: 821943). The daemon log file: /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/daemon/4.4.1/daemon-821943.out.log
Daemon will be stopped at the end of the build stopping after processing
Closing daemon's stdin at end of input.
The daemon will no longer process any standard input.
Using 12 worker leases.
Creating new cache for fileHashes, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@2e783cc9
Creating new cache for resourceHashesCache, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@2e783cc9
Creating new cache for fileHashes, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@787805f6
Starting Build
Compiling initialization script '/build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer.
Creating new cache for metadata-1.1/results, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@5d96c56b
Compiling initialization script '/build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer.
Compiling settings file '/build/reproducible-path/htsjdk-4.1.0+dfsg/settings.gradle' using SubsetScriptTransformer.
Compiling settings file '/build/reproducible-path/htsjdk-4.1.0+dfsg/settings.gradle' using BuildScriptTransformer.
Settings evaluated using settings file '/build/reproducible-path/htsjdk-4.1.0+dfsg/settings.gradle'.
Projects loaded. Root project using build file '/build/reproducible-path/htsjdk-4.1.0+dfsg/build.gradle'.
Included projects: [root project 'htsjdk']
	Keep-alive timer started
	Adding Debian repository to project 'htsjdk'
Parallel execution is an incubating feature.
Evaluating root project 'htsjdk' using build file '/build/reproducible-path/htsjdk-4.1.0+dfsg/build.gradle'.
Compiling build file '/build/reproducible-path/htsjdk-4.1.0+dfsg/build.gradle' using SubsetScriptTransformer.
Compiling build file '/build/reproducible-path/htsjdk-4.1.0+dfsg/build.gradle' using BuildScriptTransformer.
Starting process 'command 'dpkg-parsechangelog''. Working directory: /build/reproducible-path/htsjdk-4.1.0+dfsg Command: dpkg-parsechangelog -S Version
Successfully started process 'command 'dpkg-parsechangelog''
build for version:4.1.0
	Adding Maven pom generation to project 'htsjdk'
	Linking the generated javadoc to the system JDK API documentation
All projects evaluated.
Selected primary task 'jar' from project :
Creating new cache for annotation-processors, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@25b67184
Selected primary task 'javadoc' from project :
Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar', task ':javadoc']
Creating new cache for resourceHashesCache, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@787805f6
Creating new cache for taskHistory, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@55aee263
Creating new cache for outputFiles, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@7a4c43a1
:compileJava (Thread[Task worker for ':' Thread 2,5,main]) started.
:compileJava
executing task ':compileJava' ...
Putting task artifact state for task ':compileJava' into context took 0.004 secs.
Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@3a087dcb
	Loading the Maven rules...
	Replacing gov.nih.nlm.ncbi:ngs-java:jar:2.9.0  ->  gov.nih.nlm.ncbi:ngs-java:jar:debian
	Passing through javax.xml.bind:jaxb-api:jar:debian
	Passing through javax.xml.bind:jaxb-api-parent:jar:debian
	Passing through org.mozilla:rhino:jar:debian
	Replacing org.apache.commons:commons-jexl:jar:2.1.1  ->  org.apache.commons:commons-jexl:jar:debian
	Passing through org.apache.commons:commons-parent:jar:debian
	Passing through org.apache:apache:jar:debian
	Replacing commons-logging:commons-logging:jar:1.2  ->  commons-logging:commons-logging:jar:debian
	Replacing org.xerial.snappy:snappy-java:jar:1.1.10.5  ->  org.xerial.snappy:snappy-java:jar:debian
	Replacing org.apache.commons:commons-compress:jar:1.24.0  ->  org.apache.commons:commons-compress:jar:debian
	Replacing org.tukaani:xz:jar:1.9  ->  org.tukaani:xz:jar:debian
	Replacing org.json:json:jar:20230618  ->  org.sharegov:mjson:jar:debian
	Ignoring org.openjdk.nashorn:nashorn-core:jar:15.4
	Passing through javax.activation:javax.activation-api:jar:debian
javax.activation:javax.activation-api:debian is relocated to com.sun.activation:javax.activation:debian. Please update your dependencies.
	Passing through junit:junit:jar:4.x
	Passing through com.sun.activation:javax.activation:jar:debian
	Passing through com.sun.activation:all:jar:debian
	Passing through org.hamcrest:hamcrest:jar:debian
Up-to-date check for task ':compileJava' took 1.075 secs. It is not up-to-date because:
  No history is available.
All input files are considered out-of-date for incremental task ':compileJava'.
Compiling with JDK Java compiler API.
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
:compileJava (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 8.842 secs.
:processResources (Thread[Task worker for ':' Thread 11,5,main]) started.
:processResources
executing task ':processResources' ...
Putting task artifact state for task ':processResources' into context took 0.0 secs.
Up-to-date check for task ':processResources' took 0.004 secs. It is not up-to-date because:
  No history is available.
:processResources (Thread[Task worker for ':' Thread 11,5,main]) completed. Took 0.026 secs.
:classes (Thread[Task worker for ':' Thread 11,5,main]) started.
:classes
executing task ':classes' ...
Skipping task ':classes' as it has no actions.
:classes (Thread[Task worker for ':' Thread 11,5,main]) completed. Took 0.0 secs.
:debianMavenPom (Thread[Task worker for ':' Thread 11,5,main]) started.
:debianMavenPom
executing task ':debianMavenPom' ...
Putting task artifact state for task ':debianMavenPom' into context took 0.0 secs.
Up-to-date check for task ':debianMavenPom' took 0.0 secs. It is not up-to-date because:
  No history is available.
	Generating pom file /build/reproducible-path/htsjdk-4.1.0+dfsg/build/debian/htsjdk.pom
:debianMavenPom (Thread[Task worker for ':' Thread 11,5,main]) completed. Took 0.065 secs.
:jar (Thread[Task worker for ':' Thread 11,5,main]) started.
:jar
executing task ':jar' ...
Putting task artifact state for task ':jar' into context took 0.0 secs.
Up-to-date check for task ':jar' took 0.021 secs. It is not up-to-date because:
  No history is available.
:jar (Thread[Task worker for ':' Thread 11,5,main]) completed. Took 0.292 secs.
:javadoc (Thread[Task worker for ':' Thread 11,5,main]) started.
:javadoc
executing task ':javadoc' ...
Putting task artifact state for task ':javadoc' into context took 0.0 secs.
Up-to-date check for task ':javadoc' took 0.137 secs. It is not up-to-date because:
  No history is available.
Starting process 'command '/usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc''. Working directory: /build/reproducible-path/htsjdk-4.1.0+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc @/build/reproducible-path/htsjdk-4.1.0+dfsg/build/tmp/javadoc/javadoc.options
Successfully started process 'command '/usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc''
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java:211: warning: invalid input: '<'
     * Closes inner <code>SamIterator</>.
                                     ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java:211: warning: invalid input: '<'
     * Closes inner <code>SamIterator</>.
                                     ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java:52: warning: invalid input: 'instead'
     * @deprecated Use {@link #setAttribute(String, String) instead
                                                            ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java:52: warning: invalid input: 'instead'
     * @deprecated Use {@link #setAttribute(String, String) instead
                                                            ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/beta/codecs/reads/bam/BAMEncoderOptions.java:123: warning: invalid input: '<'
     * @return the compression level for these options, 1 <= compressionLevel <= 9
                                                          ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/beta/codecs/reads/bam/BAMEncoderOptions.java:123: warning: invalid input: '<'
     * @return the compression level for these options, 1 <= compressionLevel <= 9
                                                                              ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/beta/codecs/reads/bam/BAMEncoderOptions.java:133: warning: invalid input: '<'
     * @param compressionLevel the compression level for these options, 1 <= compressionLevel <= 9
                                                                          ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/beta/codecs/reads/bam/BAMEncoderOptions.java:133: warning: invalid input: '<'
     * @param compressionLevel the compression level for these options, 1 <= compressionLevel <= 9
                                                                                              ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/Bin.java:108: warning: invalid input: '<'
     * @return -1 if this < other, 0 if this == other, 1 if this > other.
                          ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:140: warning: invalid input: '<'
     * @param compressionLevel 1 <= compressionLevel <= 9
                                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:140: warning: invalid input: '<'
     * @param compressionLevel 1 <= compressionLevel <= 9
                                                     ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:148: warning: invalid input: '<'
     * @param compressionLevel 1 <= compressionLevel <= 9
                                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:148: warning: invalid input: '<'
     * @param compressionLevel 1 <= compressionLevel <= 9
                                                     ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:158: warning: invalid input: '<'
     * @param compressionLevel 1 <= compressionLevel <= 9
                                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:158: warning: invalid input: '<'
     * @param compressionLevel 1 <= compressionLevel <= 9
                                                     ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:167: warning: invalid input: '<'
     * @param compressionLevel 1 <= compressionLevel <= 9
                                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:167: warning: invalid input: '<'
     * @param compressionLevel 1 <= compressionLevel <= 9
                                                     ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:64: warning: invalid input: '<'
     * @param compressionLevel 1 <= compressionLevel <= 9
                                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:64: warning: invalid input: '<'
     * @param compressionLevel 1 <= compressionLevel <= 9
                                                     ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/BlockGunzipper.java:104: warning: Parameter "compressedBlock" is documented more than once.
     * @param compressedBlock  the offset into the compressed data.
       ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/CloserUtil.java:57: warning: invalid input: '<'
     * NOTE: This method must take a List<? extends Object>, not List<Object>, otherwise the overload above will be selected
                                         ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/cram/structure/CompressionHeader.java:87: warning: Tag @return cannot be used in constructor documentation.  It can only be used in the following types of documentation: method, inline text.
     * @return a new CompressionHeader
       ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/cram/structure/ContainerHeader.java:131: warning: Tag @return cannot be used in constructor documentation.  It can only be used in the following types of documentation: method, inline text.
     * @return a new {@link ContainerHeader} object with container header values filled out but empty body (no slices and blocks).
       ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/CoordinateSortedPairInfoMap.java:194: warning: invalid input: '<'
     * @return number of elements stored in RAM.  Always <= size()
                                                         ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/cram/structure/CRAMEncodingStrategy.java:90: warning: invalid input: '<'
    * This number must be < the value for {@link #getReadsPerSlice}
                          ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/DuplicateScoringStrategy.java:125: warning: invalid input: '<'
     * We allow different scoring strategies. We return <0 if rec1 has a better strategy than rec2.
                                                        ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/DuplicateScoringStrategy.java:150: warning: invalid input: '<'
     * We allow different scoring strategies. We return <0 if rec1 has a better strategy than rec2.
                                                        ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/reference/FastaReferenceWriter.java:56: warning: invalid input: '<'
 *      for (int i = 0; i < seqNames.length; i++) {
                          ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/FormatUtil.java:97: warning: invalid input: '&'
    /** Formats date & time */
                     ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/FormatUtil.java:97: warning: invalid input: '&'
    /** Formats date & time */
                     ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/GenomicIndexUtil.java:106: warning: invalid input: '&'
     * Described in "The Human Genome Browser at UCSC. Kent & al. doi: 10.1101/gr.229102 "
                                                            ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/GenomicIndexUtil.java:124: warning: invalid input: '&'
     * Described in "The Human Genome Browser at UCSC. Kent & al. doi: 10.1101/gr.229102 "
                                                            ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeLikelihoods.java:443: warning: invalid input: '&lt'
     * @throws IllegalArgumentException if altAlleles or ploidy &lt= 0
                                                                ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeLikelihoods.java:456: warning: invalid input: '<'
     * @throws IllegalStateException if PLindex < 0 or ploidy < 0
                                                ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeLikelihoods.java:456: warning: invalid input: '<'
     * @throws IllegalStateException if PLindex < 0 or ploidy < 0
                                                              ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/Histogram.java:344: warning: invalid input: '<'
     * Returns the cumulative probability of observing a value <= v when sampling the
                                                               ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/Histogram.java:520: warning: invalid input: '<'
     * Trims the histogram so that only bins <= width are kept.
                                             ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/Histogram.java:344: warning: invalid input: '<'
     * Returns the cumulative probability of observing a value <= v when sampling the
                                                               ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/Histogram.java:520: warning: invalid input: '<'
     * Trims the histogram so that only bins <= width are kept.
                                             ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/beta/plugin/HtsCodec.java:79: warning: Tag @link: reference not found: htsjdk.beta.plugin.features
 *     <li> For {@link HtsContentType#FEATURES} codecs, see the {@link htsjdk.beta.plugin.features} package </li>
                                                                ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/beta/plugin/HtsContentType.java:18: warning: Tag @link: reference not found: htsjdk.beta.plugin.features
 *     <li> For {@link HtsContentType#FEATURES} codecs, see the {@link htsjdk.beta.plugin.features} package </li>
                                                                ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/beta/plugin/HtsContentType.java:46: warning: Tag @link: reference not found: htsjdk.beta.plugin.features
     * Features content type (see {@link htsjdk.beta.plugin.features} for related formats)
                                  ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/beta/plugin/HtsContentType.java:46: warning: Tag @link: reference not found: htsjdk.beta.plugin.features
     * Features content type (see {@link htsjdk.beta.plugin.features} for related formats)
                                  ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/io/HtsPath.java:55: warning: invalid input: '<'
 *     <scheme>:<scheme-specific-part>
                ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/io/HtsPath.java:68: warning: invalid input: '&'
 *         uric_no_slash = unreserved | escaped | ";" | "?" | ":" | "@" | "&" | "=" | "+" | "$" | ","
                                                                           ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/io/IOPath.java:48: warning: invalid input: '{@code java.nio File System
     * There are cases where a valid URI with a valid scheme backed by an installed {@code java.nio File System
                                                                                    ^
   still can't be turned into a {@code java.nio.file.Path}, i.e., the following specifies an invalid
   authority "namenode":
  
    hdfs://namenode/to/file
  
   The current implementation returns false for these cases (toPath will fail, getInvalidPathReason
   returns the reason code).'
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/filter/IntervalFilter.java:53: warning: invalid input: '&'
     * @param intervals -- must be locus-ordered & non-overlapping
                                                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:242: warning: invalid usage of tag {@link #uniqued()#getIntervals()
     * @deprecated use {@link #uniqued()#getIntervals()} instead.
                       ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:303: warning: invalid usage of tag {@link #uniqued(boolean)#getIntervals()
     * @deprecated use {@link #uniqued(boolean)#getIntervals()} or {@link #getUniqueIntervals(IntervalList, boolean)} instead.
                       ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:242: warning: invalid usage of tag {@link #uniqued()#getIntervals()
     * @deprecated use {@link #uniqued()#getIntervals()} instead.
                       ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:303: warning: invalid usage of tag {@link #uniqued(boolean)#getIntervals()
     * @deprecated use {@link #uniqued(boolean)#getIntervals()} or {@link #getUniqueIntervals(IntervalList, boolean)} instead.
                       ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/io/IOPath.java:48: warning: invalid input: '{@code java.nio File System
     * There are cases where a valid URI with a valid scheme backed by an installed {@code java.nio File System
                                                                                    ^
   still can't be turned into a {@code java.nio.file.Path}, i.e., the following specifies an invalid
   authority "namenode":
  
    hdfs://namenode/to/file
  
   The current implementation returns false for these cases (toPath will fail, getInvalidPathReason
   returns the reason code).'
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/IOUtil.java:167: warning: invalid input: '<'
     * @param compressionLevel 0 <= compressionLevel <= 9
                                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/IOUtil.java:167: warning: invalid input: '<'
     * @param compressionLevel 0 <= compressionLevel <= 9
                                                     ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/cram/io/ITF8.java:17: warning: invalid input: '<'
 * If highest bit < 8:
                  ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/tribble/index/linear/LinearIndex.java:166: warning: invalid input: '<'
     * <= ((i + 1) * binWidth))
       ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/tribble/readers/LongLineBufferedReader.java:75: warning: invalid input: '<'
     * @throws IllegalArgumentException If sz is <= 0
                                                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/tribble/readers/LongLineBufferedReader.java:453: warning: invalid input: '<'
     * @throws IllegalArgumentException If readAheadLimit is < 0
                                                             ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/QueryInterval.java:18: warning: invalid input: '<'
    /** 1-based, inclusive.  If <= 0, implies that the interval goes to the end of the reference sequence */
                                ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMFileHeader.java:291: warning: invalid input: 'instead'
     * @deprecated Use {@link #setAttribute(String, String) instead
                                                            ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMFileHeader.java:291: warning: invalid input: 'instead'
     * @deprecated Use {@link #setAttribute(String, String) instead
                                                            ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMFileWriterImpl.java:35: warning: invalid input: '&'
 * Mostly this manages accumulation & sorting of SAMRecords when appropriate,
                                    ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMLineParser.java:221: warning: invalid input: '<'
     *                   can be <=0.
                                ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:60: warning: invalid input: '&'
 * Note also that there are a number of getters & setters that are linked, i.e. they present different representations
                                                ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:166: warning: invalid input: '<'
     * abs(insertSize) must be <= this
                               ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:1641: warning: invalid input: ''
     * @return 1-based inclusive leftmost position of the clipped sequence, or 0 if there is no position.
       ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:166: warning: invalid input: '<'
     * abs(insertSize) must be <= this
                               ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:778: warning: invalid input: '&'
     * @return insert size (difference btw 5' end of read & 5' end of mate), if possible, else 0.
                                                          ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:1641: warning: invalid input: ''
     * @return 1-based inclusive leftmost position of the clipped sequence, or 0 if there is no position.
       ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMRecordComparator.java:37: warning: invalid input: '<'
     * @return negative if samRecord1 < samRecord2,  0 if equal, else positive
                                      ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:39: warning: invalid input: '<'
 * if A < B, then B > A
        ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning: invalid input: '<'
 * if A < B && B < C, then A < C
        ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning: invalid input: '&'
 * if A < B && B < C, then A < C
            ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning: invalid input: '&'
 * if A < B && B < C, then A < C
             ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning: invalid input: '<'
 * if A < B && B < C, then A < C
                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning: invalid input: '<'
 * if A < B && B < C, then A < C
                             ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:85: warning: invalid input: '<'
     * @return negative if samRecord1 < samRecord2,  0 if equal, else positive
                                      ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMRecordComparator.java:37: warning: invalid input: '<'
     * @return negative if samRecord1 < samRecord2,  0 if equal, else positive
                                      ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMRecordQueryNameComparator.java:77: warning: invalid input: '<'
     * @return negative if samRecord1 < samRecord2,  0 if equal, else positive
                                      ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMRecordQueryNameComparator.java:77: warning: invalid input: '<'
     * @return negative if samRecord1 < samRecord2,  0 if equal, else positive
                                      ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMSortOrderChecker.java:42: warning: invalid input: '<'
     * @return True if sort order is unsorted, if this is the first record, or if previous <= rec.
                                                                                           ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:646: warning: invalid input: '<'
     * @return negative if mapq1 < mapq2, etc.
                                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:647: warning: invalid input: '<'
     * Note that MAPQ(0) < MAPQ(255) < MAPQ(1)
                         ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:647: warning: invalid input: '<'
     * Note that MAPQ(0) < MAPQ(255) < MAPQ(1)
                                     ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:1139: warning: invalid input: '<'
     * @return true if value is >= 0 and <= {@link BinaryCodec#MAX_UINT}, and false otherwise
                                         ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/cram/structure/Slice.java:171: warning: Tag @return cannot be used in constructor documentation.  It can only be used in the following types of documentation: method, inline text.
     * @return a Slice corresponding to the given records
       ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:778: warning: invalid input: '&'
     * @return insert size (difference btw 5' end of read & 5' end of mate), if possible, else 0.
                                                          ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/StringUtil.java:201: warning: invalid input: '<'
     * have length <= maxLineLength.  if a word is too long, it is simply broken
                   ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/StringUtil.java:201: warning: invalid input: '<'
     * have length <= maxLineLength.  if a word is too long, it is simply broken
                   ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.java:381: warning: @return tag cannot be used in method with void return type.
    public static void unsetDefaultOption(final Options option) {
                       ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/variant/vcf/VCFEncoder.java:103: warning: @return tag cannot be used in method with void return type.
    public void write(final Appendable vcfOutput, final VariantContext context) throws IOException {
                ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/variant/vcf/VCFEncoder.java:388: warning: invalid usage of tag {@link this#buildAlleleStrings(VariantContext)
     * @param alleleMap a mapping of Allele -> GT allele value (from {@link this#buildAlleleStrings(VariantContext)}
                                                                     ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/variant/vcf/VCFEncoder.java:432: warning: invalid usage of tag {@link this#writeGtField(Map, Appendable, Genotype)
     * {@link this#writeGtField(Map, Appendable, Genotype)} because of redundant Map initializations
       ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java:52: warning: invalid input: 'instead'
     * @deprecated Use {@link #setAttribute(String, String) instead
                                                            ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/SAMFileHeader.java:291: warning: invalid input: 'instead'
     * @deprecated Use {@link #setAttribute(String, String) instead
                                                            ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:242: warning: invalid usage of tag {@link #uniqued()#getIntervals()
     * @deprecated use {@link #uniqued()#getIntervals()} instead.
                       ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:303: warning: invalid usage of tag {@link #uniqued(boolean)#getIntervals()
     * @deprecated use {@link #uniqued(boolean)#getIntervals()} or {@link #getUniqueIntervals(IntervalList, boolean)} instead.
                       ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java:211: warning: invalid input: '<'
     * Closes inner <code>SamIterator</>.
                                     ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/beta/plugin/HtsContentType.java:46: warning: Tag @link: reference not found: htsjdk.beta.plugin.features
     * Features content type (see {@link htsjdk.beta.plugin.features} for related formats)
                                  ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/FormatUtil.java:97: warning: invalid input: '&'
    /** Formats date & time */
                     ^
100 warnings
:javadoc (Thread[Task worker for ':' Thread 11,5,main]) completed. Took 8.397 secs.

BUILD SUCCESSFUL in 22s
5 actionable tasks: 5 executed
make[1]: Leaving directory '/build/reproducible-path/htsjdk-4.1.0+dfsg'
   jh_build -O--buildsystem=gradle
	rm -f debian/libhtsjdk-java-doc.debhelper.log debian/libhtsjdk-java.debhelper.log
   debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/htsjdk-4.1.0+dfsg'
# testng bug 895886: testng: jcommander classes not found
dh_auto_build -- test
	mkdir -p .gradle/init.d
	cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/
	gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=htsjdk -Dfile.encoding=UTF-8 --parallel --max-workers=12 test
openjdk version "17.0.11" 2024-04-16
OpenJDK Runtime Environment (build 17.0.11+9-Debian-1)
OpenJDK 64-Bit Server VM (build 17.0.11+9-Debian-1, mixed mode, sharing)
Initialized native services in: /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/native
To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html.
Starting process 'Gradle build daemon'. Working directory: /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1
Successfully started process 'Gradle build daemon'
An attempt to start the daemon took 0.783 secs.
The client will now receive all logging from the daemon (pid: 822748). The daemon log file: /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/daemon/4.4.1/daemon-822748.out.log
Daemon will be stopped at the end of the build stopping after processing
Closing daemon's stdin at end of input.
The daemon will no longer process any standard input.
Using 12 worker leases.
Creating new cache for fileHashes, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@51d297b9
Creating new cache for resourceHashesCache, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@51d297b9
Creating new cache for fileHashes, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@67456c59
Starting Build
Creating new cache for metadata-1.1/results, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@2d7a8cda
Settings evaluated using settings file '/build/reproducible-path/htsjdk-4.1.0+dfsg/settings.gradle'.
Projects loaded. Root project using build file '/build/reproducible-path/htsjdk-4.1.0+dfsg/build.gradle'.
Included projects: [root project 'htsjdk']
	Keep-alive timer started
	Adding Debian repository to project 'htsjdk'
Parallel execution is an incubating feature.
Evaluating root project 'htsjdk' using build file '/build/reproducible-path/htsjdk-4.1.0+dfsg/build.gradle'.
Starting process 'command 'dpkg-parsechangelog''. Working directory: /build/reproducible-path/htsjdk-4.1.0+dfsg Command: dpkg-parsechangelog -S Version
Successfully started process 'command 'dpkg-parsechangelog''
build for version:4.1.0
	Adding Maven pom generation to project 'htsjdk'
	Linking the generated javadoc to the system JDK API documentation
All projects evaluated.
Selected primary task 'test' from project :
Creating new cache for annotation-processors, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@182c488e
Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':compileTestJava', task ':processTestResources', task ':testClasses', task ':testWithDefaultReference', task ':testWithOptimisticVCF4_4', task ':test']
Creating new cache for resourceHashesCache, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@67456c59
Creating new cache for taskHistory, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@1500db0a
Creating new cache for outputFiles, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@42287545
:compileJava (Thread[Task worker for ':' Thread 3,5,main]) started.
:compileJava
executing task ':compileJava' ...
Putting task artifact state for task ':compileJava' into context took 0.003 secs.
Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@47c95edc
	Loading the Maven rules...
	Replacing gov.nih.nlm.ncbi:ngs-java:jar:2.9.0  ->  gov.nih.nlm.ncbi:ngs-java:jar:debian
	Passing through javax.xml.bind:jaxb-api:jar:debian
	Passing through javax.xml.bind:jaxb-api-parent:jar:debian
	Passing through org.mozilla:rhino:jar:debian
	Replacing org.apache.commons:commons-jexl:jar:2.1.1  ->  org.apache.commons:commons-jexl:jar:debian
	Passing through org.apache.commons:commons-parent:jar:debian
	Passing through org.apache:apache:jar:debian
	Replacing commons-logging:commons-logging:jar:1.2  ->  commons-logging:commons-logging:jar:debian
	Replacing org.xerial.snappy:snappy-java:jar:1.1.10.5  ->  org.xerial.snappy:snappy-java:jar:debian
	Replacing org.apache.commons:commons-compress:jar:1.24.0  ->  org.apache.commons:commons-compress:jar:debian
	Replacing org.tukaani:xz:jar:1.9  ->  org.tukaani:xz:jar:debian
	Replacing org.json:json:jar:20230618  ->  org.sharegov:mjson:jar:debian
	Ignoring org.openjdk.nashorn:nashorn-core:jar:15.4
	Passing through javax.activation:javax.activation-api:jar:debian
javax.activation:javax.activation-api:debian is relocated to com.sun.activation:javax.activation:debian. Please update your dependencies.
	Passing through junit:junit:jar:4.x
	Passing through com.sun.activation:javax.activation:jar:debian
	Passing through com.sun.activation:all:jar:debian
	Passing through org.hamcrest:hamcrest:jar:debian
Skipping task ':compileJava' as it is up-to-date (took 0.701 secs).
:compileJava UP-TO-DATE
:compileJava (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.745 secs.
:processResources (Thread[Task worker for ':' Thread 3,5,main]) started.
:processResources
executing task ':processResources' ...
Putting task artifact state for task ':processResources' into context took 0.0 secs.
Skipping task ':processResources' as it is up-to-date (took 0.003 secs).
:processResources UP-TO-DATE
:processResources (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.006 secs.
:classes (Thread[Task worker for ':' Thread 3,5,main]) started.
:classes
executing task ':classes' ...
Skipping task ':classes' as it has no actions.
:classes UP-TO-DATE
:classes (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.0 secs.
:compileTestJava (Thread[Task worker for ':' Thread 3,5,main]) started.
:compileTestJava
executing task ':compileTestJava' ...
Putting task artifact state for task ':compileTestJava' into context took 0.0 secs.
Malformed class file [BCF2Type.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath.
	at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60)
	at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44)
	at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47)
	at org.gradle.api.internal.changedetection.state.ClasspathEntrySnapshotBuilder.visitFileSnapshot(ClasspathEntrySnapshotBuilder.java:62)
	at org.gradle.api.internal.changedetection.state.FileTree.visit(FileTree.java:36)
	at org.gradle.api.internal.changedetection.state.AbstractClasspathSnapshotBuilder.visitFileTreeSnapshot(AbstractClasspathSnapshotBuilder.java:66)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitDirectoryTree(AbstractFileCollectionSnapshotter.java:100)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitCollection(AbstractFileCollectionSnapshotter.java:82)
	at org.gradle.api.internal.file.AbstractFileCollection.visitRootElements(AbstractFileCollection.java:234)
	at org.gradle.api.internal.file.CompositeFileCollection.visitRootElements(CompositeFileCollection.java:185)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter.snapshot(AbstractFileCollectionSnapshotter.java:53)
	at org.gradle.api.internal.changedetection.state.DefaultCompileClasspathSnapshotter.snapshot(DefaultCompileClasspathSnapshotter.java:38)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.snapshotTaskFiles(CacheBackedTaskHistoryRepository.java:331)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.createExecution(CacheBackedTaskHistoryRepository.java:154)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.access$100(CacheBackedTaskHistoryRepository.java:61)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository$1.getCurrentExecution(CacheBackedTaskHistoryRepository.java:114)
	at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.getStates(DefaultTaskArtifactStateRepository.java:201)
	at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.isUpToDate(DefaultTaskArtifactStateRepository.java:86)
	at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:53)
	at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:60)
	at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:97)
	at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:87)
	at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
	at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
	at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
	at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:123)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:79)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:104)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:98)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:626)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:581)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:98)
	at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
	at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
	at java.base/java.lang.Thread.run(Thread.java:840)
Malformed class file [SAMSequenceDictionaryExtractor$TYPE.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath.
	at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60)
	at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44)
	at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47)
	at org.gradle.api.internal.changedetection.state.ClasspathEntrySnapshotBuilder.visitFileSnapshot(ClasspathEntrySnapshotBuilder.java:62)
	at org.gradle.api.internal.changedetection.state.FileTree.visit(FileTree.java:36)
	at org.gradle.api.internal.changedetection.state.AbstractClasspathSnapshotBuilder.visitFileTreeSnapshot(AbstractClasspathSnapshotBuilder.java:66)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitDirectoryTree(AbstractFileCollectionSnapshotter.java:100)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitCollection(AbstractFileCollectionSnapshotter.java:82)
	at org.gradle.api.internal.file.AbstractFileCollection.visitRootElements(AbstractFileCollection.java:234)
	at org.gradle.api.internal.file.CompositeFileCollection.visitRootElements(CompositeFileCollection.java:185)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter.snapshot(AbstractFileCollectionSnapshotter.java:53)
	at org.gradle.api.internal.changedetection.state.DefaultCompileClasspathSnapshotter.snapshot(DefaultCompileClasspathSnapshotter.java:38)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.snapshotTaskFiles(CacheBackedTaskHistoryRepository.java:331)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.createExecution(CacheBackedTaskHistoryRepository.java:154)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.access$100(CacheBackedTaskHistoryRepository.java:61)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository$1.getCurrentExecution(CacheBackedTaskHistoryRepository.java:114)
	at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.getStates(DefaultTaskArtifactStateRepository.java:201)
	at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.isUpToDate(DefaultTaskArtifactStateRepository.java:86)
	at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:53)
	at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:60)
	at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:97)
	at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:87)
	at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
	at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
	at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
	at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:123)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:79)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:104)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:98)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:626)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:581)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:98)
	at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
	at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
	at java.base/java.lang.Thread.run(Thread.java:840)
Malformed class file [VariantContext$Validation.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath.
	at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60)
	at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44)
	at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47)
	at org.gradle.api.internal.changedetection.state.ClasspathEntrySnapshotBuilder.visitFileSnapshot(ClasspathEntrySnapshotBuilder.java:62)
	at org.gradle.api.internal.changedetection.state.FileTree.visit(FileTree.java:36)
	at org.gradle.api.internal.changedetection.state.AbstractClasspathSnapshotBuilder.visitFileTreeSnapshot(AbstractClasspathSnapshotBuilder.java:66)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitDirectoryTree(AbstractFileCollectionSnapshotter.java:100)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitCollection(AbstractFileCollectionSnapshotter.java:82)
	at org.gradle.api.internal.file.AbstractFileCollection.visitRootElements(AbstractFileCollection.java:234)
	at org.gradle.api.internal.file.CompositeFileCollection.visitRootElements(CompositeFileCollection.java:185)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter.snapshot(AbstractFileCollectionSnapshotter.java:53)
	at org.gradle.api.internal.changedetection.state.DefaultCompileClasspathSnapshotter.snapshot(DefaultCompileClasspathSnapshotter.java:38)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.snapshotTaskFiles(CacheBackedTaskHistoryRepository.java:331)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.createExecution(CacheBackedTaskHistoryRepository.java:154)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.access$100(CacheBackedTaskHistoryRepository.java:61)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository$1.getCurrentExecution(CacheBackedTaskHistoryRepository.java:114)
	at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.getStates(DefaultTaskArtifactStateRepository.java:201)
	at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.isUpToDate(DefaultTaskArtifactStateRepository.java:86)
	at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:53)
	at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:60)
	at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:97)
	at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:87)
	at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
	at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
	at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
	at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:123)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:79)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:104)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:98)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:626)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:581)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:98)
	at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
	at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
	at java.base/java.lang.Thread.run(Thread.java:840)
Malformed class file [Gff3Codec$Gff3Directive.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath.
	at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60)
	at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44)
	at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47)
	at org.gradle.api.internal.changedetection.state.ClasspathEntrySnapshotBuilder.visitFileSnapshot(ClasspathEntrySnapshotBuilder.java:62)
	at org.gradle.api.internal.changedetection.state.FileTree.visit(FileTree.java:36)
	at org.gradle.api.internal.changedetection.state.AbstractClasspathSnapshotBuilder.visitFileTreeSnapshot(AbstractClasspathSnapshotBuilder.java:66)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitDirectoryTree(AbstractFileCollectionSnapshotter.java:100)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitCollection(AbstractFileCollectionSnapshotter.java:82)
	at org.gradle.api.internal.file.AbstractFileCollection.visitRootElements(AbstractFileCollection.java:234)
	at org.gradle.api.internal.file.CompositeFileCollection.visitRootElements(CompositeFileCollection.java:185)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter.snapshot(AbstractFileCollectionSnapshotter.java:53)
	at org.gradle.api.internal.changedetection.state.DefaultCompileClasspathSnapshotter.snapshot(DefaultCompileClasspathSnapshotter.java:38)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.snapshotTaskFiles(CacheBackedTaskHistoryRepository.java:331)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.createExecution(CacheBackedTaskHistoryRepository.java:154)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.access$100(CacheBackedTaskHistoryRepository.java:61)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository$1.getCurrentExecution(CacheBackedTaskHistoryRepository.java:114)
	at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.getStates(DefaultTaskArtifactStateRepository.java:201)
	at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.isUpToDate(DefaultTaskArtifactStateRepository.java:86)
	at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:53)
	at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:60)
	at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:97)
	at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:87)
	at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
	at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
	at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
	at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:123)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:79)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:104)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:98)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:626)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:581)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:98)
	at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
	at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
	at java.base/java.lang.Thread.run(Thread.java:840)
Malformed class file [SERIES.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath.
	at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60)
	at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44)
	at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47)
	at org.gradle.api.internal.changedetection.state.ClasspathEntrySnapshotBuilder.visitFileSnapshot(ClasspathEntrySnapshotBuilder.java:62)
	at org.gradle.api.internal.changedetection.state.FileTree.visit(FileTree.java:36)
	at org.gradle.api.internal.changedetection.state.AbstractClasspathSnapshotBuilder.visitFileTreeSnapshot(AbstractClasspathSnapshotBuilder.java:66)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitDirectoryTree(AbstractFileCollectionSnapshotter.java:100)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitCollection(AbstractFileCollectionSnapshotter.java:82)
	at org.gradle.api.internal.file.AbstractFileCollection.visitRootElements(AbstractFileCollection.java:234)
	at org.gradle.api.internal.file.CompositeFileCollection.visitRootElements(CompositeFileCollection.java:185)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter.snapshot(AbstractFileCollectionSnapshotter.java:53)
	at org.gradle.api.internal.changedetection.state.DefaultCompileClasspathSnapshotter.snapshot(DefaultCompileClasspathSnapshotter.java:38)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.snapshotTaskFiles(CacheBackedTaskHistoryRepository.java:331)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.createExecution(CacheBackedTaskHistoryRepository.java:154)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.access$100(CacheBackedTaskHistoryRepository.java:61)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository$1.getCurrentExecution(CacheBackedTaskHistoryRepository.java:114)
	at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.getStates(DefaultTaskArtifactStateRepository.java:201)
	at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.isUpToDate(DefaultTaskArtifactStateRepository.java:86)
	at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:53)
	at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:60)
	at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:97)
	at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:87)
	at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
	at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
	at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
	at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:123)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:79)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:104)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:98)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:626)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:581)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:98)
	at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
	at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
	at java.base/java.lang.Thread.run(Thread.java:840)
Malformed class file [ContentDigests$KNOWN_DIGESTS.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath.
	at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60)
	at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44)
	at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47)
	at org.gradle.api.internal.changedetection.state.ClasspathEntrySnapshotBuilder.visitFileSnapshot(ClasspathEntrySnapshotBuilder.java:62)
	at org.gradle.api.internal.changedetection.state.FileTree.visit(FileTree.java:36)
	at org.gradle.api.internal.changedetection.state.AbstractClasspathSnapshotBuilder.visitFileTreeSnapshot(AbstractClasspathSnapshotBuilder.java:66)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitDirectoryTree(AbstractFileCollectionSnapshotter.java:100)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitCollection(AbstractFileCollectionSnapshotter.java:82)
	at org.gradle.api.internal.file.AbstractFileCollection.visitRootElements(AbstractFileCollection.java:234)
	at org.gradle.api.internal.file.CompositeFileCollection.visitRootElements(CompositeFileCollection.java:185)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter.snapshot(AbstractFileCollectionSnapshotter.java:53)
	at org.gradle.api.internal.changedetection.state.DefaultCompileClasspathSnapshotter.snapshot(DefaultCompileClasspathSnapshotter.java:38)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.snapshotTaskFiles(CacheBackedTaskHistoryRepository.java:331)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.createExecution(CacheBackedTaskHistoryRepository.java:154)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.access$100(CacheBackedTaskHistoryRepository.java:61)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository$1.getCurrentExecution(CacheBackedTaskHistoryRepository.java:114)
	at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.getStates(DefaultTaskArtifactStateRepository.java:201)
	at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.isUpToDate(DefaultTaskArtifactStateRepository.java:86)
	at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:53)
	at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:60)
	at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:97)
	at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:87)
	at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
	at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
	at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
	at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:123)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:79)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:104)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:98)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:626)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:581)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:98)
	at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
	at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
	at java.base/java.lang.Thread.run(Thread.java:840)
Malformed class file [SRALazyRecord$LazyField.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath.
	at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60)
	at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44)
	at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47)
	at org.gradle.api.internal.changedetection.state.ClasspathEntrySnapshotBuilder.visitFileSnapshot(ClasspathEntrySnapshotBuilder.java:62)
	at org.gradle.api.internal.changedetection.state.FileTree.visit(FileTree.java:36)
	at org.gradle.api.internal.changedetection.state.AbstractClasspathSnapshotBuilder.visitFileTreeSnapshot(AbstractClasspathSnapshotBuilder.java:66)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitDirectoryTree(AbstractFileCollectionSnapshotter.java:100)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitCollection(AbstractFileCollectionSnapshotter.java:82)
	at org.gradle.api.internal.file.AbstractFileCollection.visitRootElements(AbstractFileCollection.java:234)
	at org.gradle.api.internal.file.CompositeFileCollection.visitRootElements(CompositeFileCollection.java:185)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter.snapshot(AbstractFileCollectionSnapshotter.java:53)
	at org.gradle.api.internal.changedetection.state.DefaultCompileClasspathSnapshotter.snapshot(DefaultCompileClasspathSnapshotter.java:38)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.snapshotTaskFiles(CacheBackedTaskHistoryRepository.java:331)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.createExecution(CacheBackedTaskHistoryRepository.java:154)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.access$100(CacheBackedTaskHistoryRepository.java:61)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository$1.getCurrentExecution(CacheBackedTaskHistoryRepository.java:114)
	at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.getStates(DefaultTaskArtifactStateRepository.java:201)
	at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.isUpToDate(DefaultTaskArtifactStateRepository.java:86)
	at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:53)
	at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:60)
	at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:97)
	at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:87)
	at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
	at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
	at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
	at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:123)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:79)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:104)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:98)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:626)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:581)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:98)
	at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
	at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
	at java.base/java.lang.Thread.run(Thread.java:840)
Malformed class file [SRALazyRecord$LazyAttribute.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath.
	at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60)
	at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44)
	at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47)
	at org.gradle.api.internal.changedetection.state.ClasspathEntrySnapshotBuilder.visitFileSnapshot(ClasspathEntrySnapshotBuilder.java:62)
	at org.gradle.api.internal.changedetection.state.FileTree.visit(FileTree.java:36)
	at org.gradle.api.internal.changedetection.state.AbstractClasspathSnapshotBuilder.visitFileTreeSnapshot(AbstractClasspathSnapshotBuilder.java:66)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitDirectoryTree(AbstractFileCollectionSnapshotter.java:100)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitCollection(AbstractFileCollectionSnapshotter.java:82)
	at org.gradle.api.internal.file.AbstractFileCollection.visitRootElements(AbstractFileCollection.java:234)
	at org.gradle.api.internal.file.CompositeFileCollection.visitRootElements(CompositeFileCollection.java:185)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter.snapshot(AbstractFileCollectionSnapshotter.java:53)
	at org.gradle.api.internal.changedetection.state.DefaultCompileClasspathSnapshotter.snapshot(DefaultCompileClasspathSnapshotter.java:38)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.snapshotTaskFiles(CacheBackedTaskHistoryRepository.java:331)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.createExecution(CacheBackedTaskHistoryRepository.java:154)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.access$100(CacheBackedTaskHistoryRepository.java:61)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository$1.getCurrentExecution(CacheBackedTaskHistoryRepository.java:114)
	at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.getStates(DefaultTaskArtifactStateRepository.java:201)
	at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.isUpToDate(DefaultTaskArtifactStateRepository.java:86)
	at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:53)
	at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:60)
	at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:97)
	at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:87)
	at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
	at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
	at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
	at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:123)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:79)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:104)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:98)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:626)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:581)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:98)
	at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
	at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
	at java.base/java.lang.Thread.run(Thread.java:840)
Malformed class file [SRALazyRecord$LazyFlag.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath.
	at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60)
	at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44)
	at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47)
	at org.gradle.api.internal.changedetection.state.ClasspathEntrySnapshotBuilder.visitFileSnapshot(ClasspathEntrySnapshotBuilder.java:62)
	at org.gradle.api.internal.changedetection.state.FileTree.visit(FileTree.java:36)
	at org.gradle.api.internal.changedetection.state.AbstractClasspathSnapshotBuilder.visitFileTreeSnapshot(AbstractClasspathSnapshotBuilder.java:66)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitDirectoryTree(AbstractFileCollectionSnapshotter.java:100)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitCollection(AbstractFileCollectionSnapshotter.java:82)
	at org.gradle.api.internal.file.AbstractFileCollection.visitRootElements(AbstractFileCollection.java:234)
	at org.gradle.api.internal.file.CompositeFileCollection.visitRootElements(CompositeFileCollection.java:185)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter.snapshot(AbstractFileCollectionSnapshotter.java:53)
	at org.gradle.api.internal.changedetection.state.DefaultCompileClasspathSnapshotter.snapshot(DefaultCompileClasspathSnapshotter.java:38)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.snapshotTaskFiles(CacheBackedTaskHistoryRepository.java:331)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.createExecution(CacheBackedTaskHistoryRepository.java:154)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.access$100(CacheBackedTaskHistoryRepository.java:61)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository$1.getCurrentExecution(CacheBackedTaskHistoryRepository.java:114)
	at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.getStates(DefaultTaskArtifactStateRepository.java:201)
	at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.isUpToDate(DefaultTaskArtifactStateRepository.java:86)
	at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:53)
	at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:60)
	at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:97)
	at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:87)
	at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
	at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
	at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
	at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:123)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:79)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:104)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:98)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:626)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:581)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:98)
	at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
	at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
	at java.base/java.lang.Thread.run(Thread.java:840)
Malformed class file [SamReaderFactory$Option.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath.
	at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60)
	at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44)
	at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47)
	at org.gradle.api.internal.changedetection.state.ClasspathEntrySnapshotBuilder.visitFileSnapshot(ClasspathEntrySnapshotBuilder.java:62)
	at org.gradle.api.internal.changedetection.state.FileTree.visit(FileTree.java:36)
	at org.gradle.api.internal.changedetection.state.AbstractClasspathSnapshotBuilder.visitFileTreeSnapshot(AbstractClasspathSnapshotBuilder.java:66)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitDirectoryTree(AbstractFileCollectionSnapshotter.java:100)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitCollection(AbstractFileCollectionSnapshotter.java:82)
	at org.gradle.api.internal.file.AbstractFileCollection.visitRootElements(AbstractFileCollection.java:234)
	at org.gradle.api.internal.file.CompositeFileCollection.visitRootElements(CompositeFileCollection.java:185)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter.snapshot(AbstractFileCollectionSnapshotter.java:53)
	at org.gradle.api.internal.changedetection.state.DefaultCompileClasspathSnapshotter.snapshot(DefaultCompileClasspathSnapshotter.java:38)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.snapshotTaskFiles(CacheBackedTaskHistoryRepository.java:331)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.createExecution(CacheBackedTaskHistoryRepository.java:154)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.access$100(CacheBackedTaskHistoryRepository.java:61)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository$1.getCurrentExecution(CacheBackedTaskHistoryRepository.java:114)
	at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.getStates(DefaultTaskArtifactStateRepository.java:201)
	at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.isUpToDate(DefaultTaskArtifactStateRepository.java:86)
	at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:53)
	at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:60)
	at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:97)
	at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:87)
	at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
	at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
	at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
	at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:123)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:79)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:104)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:98)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:626)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:581)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:98)
	at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
	at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
	at java.base/java.lang.Thread.run(Thread.java:840)
Malformed class file [SamFlagField.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath.
	at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60)
	at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44)
	at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47)
	at org.gradle.api.internal.changedetection.state.ClasspathEntrySnapshotBuilder.visitFileSnapshot(ClasspathEntrySnapshotBuilder.java:62)
	at org.gradle.api.internal.changedetection.state.FileTree.visit(FileTree.java:36)
	at org.gradle.api.internal.changedetection.state.AbstractClasspathSnapshotBuilder.visitFileTreeSnapshot(AbstractClasspathSnapshotBuilder.java:66)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitDirectoryTree(AbstractFileCollectionSnapshotter.java:100)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitCollection(AbstractFileCollectionSnapshotter.java:82)
	at org.gradle.api.internal.file.AbstractFileCollection.visitRootElements(AbstractFileCollection.java:234)
	at org.gradle.api.internal.file.CompositeFileCollection.visitRootElements(CompositeFileCollection.java:185)
	at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter.snapshot(AbstractFileCollectionSnapshotter.java:53)
	at org.gradle.api.internal.changedetection.state.DefaultCompileClasspathSnapshotter.snapshot(DefaultCompileClasspathSnapshotter.java:38)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.snapshotTaskFiles(CacheBackedTaskHistoryRepository.java:331)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.createExecution(CacheBackedTaskHistoryRepository.java:154)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.access$100(CacheBackedTaskHistoryRepository.java:61)
	at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository$1.getCurrentExecution(CacheBackedTaskHistoryRepository.java:114)
	at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.getStates(DefaultTaskArtifactStateRepository.java:201)
	at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.isUpToDate(DefaultTaskArtifactStateRepository.java:86)
	at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:53)
	at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:60)
	at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:97)
	at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:87)
	at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
	at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
	at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
	at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:123)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:79)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:104)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:98)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:626)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:581)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:98)
	at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
	at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
	at java.base/java.lang.Thread.run(Thread.java:840)
	Replacing org.testng:testng:jar:7.7.0  ->  org.testng:testng:jar:debian
	Replacing com.google.jimfs:jimfs:jar:1.2  ->  com.google.jimfs:jimfs:jar:debian
	Passing through com.google.jimfs:jimfs-parent:jar:debian
	Replacing com.google.guava:guava:jar:31.1-jre  ->  com.google.guava:guava:jar:debian
	Passing through com.google.guava:guava-parent:jar:debian
	Replacing org.apache.commons:commons-lang3:jar:3.12.0  ->  org.apache.commons:commons-lang3:jar:debian
	Passing through org.beanshell:bsh:jar:debian
	Passing through com.beust:jcommander:jar:debian
	Passing through org.jsr-305:jsr305:jar:0.x
	Passing through com.google.errorprone:error_prone_annotations:jar:debian
	Passing through com.google.errorprone:error_prone_parent:jar:debian
Up-to-date check for task ':compileTestJava' took 1.104 secs. It is not up-to-date because:
  No history is available.
All input files are considered out-of-date for incremental task ':compileTestJava'.
Compiling with JDK Java compiler API.
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:15: warning: [removal] Byte(byte) in Byte has been deprecated and marked for removal
                {new Byte((byte) 7)},
                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:16: warning: [removal] Short(short) in Short has been deprecated and marked for removal
                {new Short((short) 8)},
                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:17: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
                {new Integer(0)},
                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:18: warning: [removal] Character(char) in Character has been deprecated and marked for removal
                {new Character('C')},
                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:19: warning: [removal] Float(float) in Float has been deprecated and marked for removal
                {new Float(0.1F)},
                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:21: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new Long(0)},
                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:22: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new Long(BinaryCodec.MAX_UINT)},
                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:24: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new Long(-1L)},
                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:25: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new Long(Integer.MAX_VALUE)},
                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:26: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new Long(Integer.MIN_VALUE)},
                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:48: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new Long(BinaryCodec.MAX_UINT + 1L)},
                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new Long(Integer.MIN_VALUE - 1L)},
                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:50: warning: [removal] Double(double) in Double has been deprecated and marked for removal
                {new Double(0.3F)},
                 ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:103: warning: [removal] Byte(byte) in Byte has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Byte((byte) 0)), new SAMBinaryTagAndValue(tag, new Byte((byte) 0)), true, true},
                                               ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:103: warning: [removal] Byte(byte) in Byte has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Byte((byte) 0)), new SAMBinaryTagAndValue(tag, new Byte((byte) 0)), true, true},
                                                                                                  ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:104: warning: [removal] Byte(byte) in Byte has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Byte((byte) 0)), new SAMBinaryTagAndValue(tag, new Byte((byte) 1)), false, false},
                                               ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:104: warning: [removal] Byte(byte) in Byte has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Byte((byte) 0)), new SAMBinaryTagAndValue(tag, new Byte((byte) 1)), false, false},
                                                                                                  ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:106: warning: [removal] Short(short) in Short has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Short((short) 0)), new SAMBinaryTagAndValue(tag, new Short((short) 0)), true, true},
                                               ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:106: warning: [removal] Short(short) in Short has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Short((short) 0)), new SAMBinaryTagAndValue(tag, new Short((short) 0)), true, true},
                                                                                                    ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:107: warning: [removal] Short(short) in Short has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Short((short) 0)), new SAMBinaryTagAndValue(tag, new Short((short) 1)), false, false},
                                               ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:107: warning: [removal] Short(short) in Short has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Short((short) 0)), new SAMBinaryTagAndValue(tag, new Short((short) 1)), false, false},
                                                                                                    ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:109: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Integer(0)), new SAMBinaryTagAndValue(tag, new Integer(0)), true, true},
                                               ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:109: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Integer(0)), new SAMBinaryTagAndValue(tag, new Integer(0)), true, true},
                                                                                              ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:110: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Integer(0)), new SAMBinaryTagAndValue(tag, new Integer(0)), true, true},
                                               ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:110: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Integer(0)), new SAMBinaryTagAndValue(tag, new Integer(0)), true, true},
                                                                                              ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:112: warning: [removal] Character(char) in Character has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Character('C')), new SAMBinaryTagAndValue(tag, new Character('C')), true, true},
                                               ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:112: warning: [removal] Character(char) in Character has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Character('C')), new SAMBinaryTagAndValue(tag, new Character('C')), true, true},
                                                                                                  ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:113: warning: [removal] Character(char) in Character has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Character('C')), new SAMBinaryTagAndValue(tag, new Character('D')), false, false},
                                               ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:113: warning: [removal] Character(char) in Character has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Character('C')), new SAMBinaryTagAndValue(tag, new Character('D')), false, false},
                                                                                                  ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:115: warning: [removal] Float(float) in Float has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag,new Float(0.1F)), new SAMBinaryTagAndValue(tag, new Float(0.1F)), true, true},
                                              ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:115: warning: [removal] Float(float) in Float has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag,new Float(0.1F)), new SAMBinaryTagAndValue(tag, new Float(0.1F)), true, true},
                                                                                              ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:116: warning: [removal] Float(float) in Float has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Float(0.1F)), new SAMBinaryTagAndValue(tag, new Float(0.2F)), false, false},
                                               ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:116: warning: [removal] Float(float) in Float has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Float(0.1F)), new SAMBinaryTagAndValue(tag, new Float(0.2F)), false, false},
                                                                                               ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:118: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag,new Long(37L)), new SAMBinaryTagAndValue(tag, new Long(37L)), true, true},
                                              ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:118: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag,new Long(37L)), new SAMBinaryTagAndValue(tag, new Long(37L)), true, true},
                                                                                            ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:119: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Long(37L)), new SAMBinaryTagAndValue(tag, new Long(38L)), false, false},
                                               ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:119: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Long(37L)), new SAMBinaryTagAndValue(tag, new Long(38L)), false, false},
                                                                                             ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:121: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag,new Long(BinaryCodec.MAX_UINT)), new SAMBinaryTagAndValue(tag, new Long(BinaryCodec.MAX_UINT)), true, true},
                                              ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:121: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag,new Long(BinaryCodec.MAX_UINT)), new SAMBinaryTagAndValue(tag, new Long(BinaryCodec.MAX_UINT)), true, true},
                                                                                                             ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:122: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Long(BinaryCodec.MAX_UINT)), new SAMBinaryTagAndValue(tag, new Long(BinaryCodec.MAX_UINT-1)), false, false},
                                               ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:122: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Long(BinaryCodec.MAX_UINT)), new SAMBinaryTagAndValue(tag, new Long(BinaryCodec.MAX_UINT-1)), false, false},
                                                                                                              ^
/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMTextWriterTest.java:88: warning: [removal] Character(char) in Character has been deprecated and marked for removal
        tagMap.put("XC", new Character('q'));
                         ^
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
42 warnings
:compileTestJava (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 7.523 secs.
:processTestResources (Thread[Task worker for ':' Thread 3,5,main]) started.
:processTestResources
executing task ':processTestResources' ...
Putting task artifact state for task ':processTestResources' into context took 0.0 secs.
Up-to-date check for task ':processTestResources' took 0.309 secs. It is not up-to-date because:
  No history is available.
:processTestResources (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.885 secs.
:testClasses (Thread[Task worker for ':' Thread 3,5,main]) started.
:testClasses
executing task ':testClasses' ...
Skipping task ':testClasses' as it has no actions.
:testClasses (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.0 secs.
:testWithDefaultReference (Thread[Task worker for ':' Thread 3,5,main]) started.
:testWithDefaultReference
executing task ':testWithDefaultReference' ...
Putting task artifact state for task ':testWithDefaultReference' into context took 0.0 secs.
Up-to-date check for task ':testWithDefaultReference' took 0.193 secs. It is not up-to-date because:
  Task.upToDateWhen is false.
Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/htsjdk-4.1.0+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false -Dsamjdk.reference_fasta=src/test/resources/htsjdk/samtools/cram/ce.fa @/tmp/gradle-worker-classpath18004479675575439867txt -Xms1G -Xmx2G -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 1'
Successfully started process 'Gradle Test Executor 1'
Gradle Test Executor 1 started executing tests.

Gradle Test Executor 1 STANDARD_ERROR
    INFO	2025-06-03 15:07:46	Defaults	Found file for property samjdk.reference_fasta: /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa 

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[5](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[6](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[7](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[8](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstElementOfIterator runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstElementOfIterator runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstElementOfIterator runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstElementOfIterator runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstElementOfIterator runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[5](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstElementOfIterator runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[6](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstElementOfIterator runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[7](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstElementOfIterator runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[8](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstElementOfIterator runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstSequence runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testFirstSequence runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstSequence runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testFirstSequence runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstSequence runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstSequenceExtended runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testFirstSequenceExtended runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstSequenceExtended runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testFirstSequenceExtended runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstSequenceExtended runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testLastCompleteContigRead runtime: 6ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testLastCompleteContigRead runtime: 3ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testLastCompleteContigRead runtime: 2ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testLastCompleteContigRead runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testLastCompleteContigRead runtime: 10ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[5](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testLastCompleteContigRead runtime: 8ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[6](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testLastCompleteContigRead runtime: 13ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[7](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testLastCompleteContigRead runtime: 8ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[8](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testLastCompleteContigRead runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstOfChr1 runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testFirstOfChr1 runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstOfChr1 runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testFirstOfChr1 runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstOfChr1 runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testNextElementOfIterator runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testNextElementOfIterator runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testNextElementOfIterator runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testNextElementOfIterator runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testNextElementOfIterator runtime: 7ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[5](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testNextElementOfIterator runtime: 8ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[6](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testNextElementOfIterator runtime: 8ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[7](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testNextElementOfIterator runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[8](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testNextElementOfIterator runtime: 2ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testOpenFile runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testOpenFile runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testOpenFile runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testOpenFile runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testOpenFile runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadPastEndOfContig[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadPastEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadPastEndOfContig[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadPastEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadPastEndOfContig[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadPastEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadPastEndOfContig[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadPastEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadPastEndOfContig[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testReadPastEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadStartingInCenterOfFirstLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadStartingInCenterOfFirstLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadStartingInCenterOfFirstLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadStartingInCenterOfFirstLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testReadStartingInCenterOfFirstLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadStartingInCenterOfMiddleLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadStartingInCenterOfMiddleLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadStartingInCenterOfMiddleLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadStartingInCenterOfMiddleLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testReadStartingInCenterOfMiddleLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadThroughEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadThroughEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadThroughEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadThroughEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testReadThroughEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReset runtime: 2ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReset runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReset runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReset runtime: 2ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testReset runtime: 10ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[5](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testReset runtime: 10ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[6](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testReset runtime: 10ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[7](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReset runtime: 2ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[8](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReset runtime: 2ms

Gradle suite > Gradle test > htsjdk.tribble.AsciiFeatureCodecTest.testMakeIndexableSourceFromUnknownStream STANDARD_ERROR
    WARNING	2025-06-03 15:07:52	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testFromStream[2](java.io.ByteArrayInputStream@1a3dcfb8, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR
    WARNING	2025-06-03 15:07:52	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testReadLines STANDARD_ERROR
    WARNING	2025-06-03 15:07:52	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
Finished 200 tests

Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLength STANDARD_ERROR
    WARNING	2025-06-03 15:07:52	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLengthAtEof STANDARD_ERROR
    WARNING	2025-06-03 15:07:52	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.samtools.BAMFileIndexTest.testQueryUnmapped STANDARD_OUT
    Found start of unmapped reads.  Num mapped reads: 9721
    Time so far: 0
    Linear scan total time: 0
    queryUnmapped time: 0
    Number of unmapped reads:279

Gradle suite > Gradle test > htsjdk.samtools.BAMFileIndexTest.testRandomQueries STANDARD_OUT
    Testing query chr11_random:7211102-7392752 ...
    Testing query chrX_random:2969904-3087323 ...
    Testing query chr5:9255377-9796767 ...
    Testing query chr16_random:9067406-9976989 ...
    Testing query chr6:2164417-9572211 ...
    Testing query chr8_random:5688357-6576007 ...
    Testing query chr4_random:4241203-6327831 ...
    Testing query chr2_random:411082-4462819 ...
    Testing query chr13_random:145947-4307287 ...
    Testing query chr15_random:3298214-6356603 ...
    Testing query chr21:472385-8291032 ...
    Testing query chr2:4177649-9835176 ...
    Testing query chr22_random:1490587-8781106 ...
    Testing query chr14:2167927-6299701 ...
    Testing query chr7:4700515-5593851 ...
    Testing query chr22:5016764-7470151 ...
    Testing query chr22_random:7524398-8627117 ...
    Testing query chr8:3764754-6977071 ...
    Testing query chr1_random:1725504-3204042 ...
    Testing query chr21:2025794-4625889 ...
    Testing query chr14:1426554-6327490 ...
    Testing query chrX_random:1992622-9650667 ...
    Testing query chr4:2669418-7183639 ...
    Testing query chr10:2967472-3641376 ...
    Testing query chr10_random:3273594-3427480 ...
    Testing query chr19_random:4582311-5090524 ...
    Testing query chr9_random:7218100-8812477 ...
    Testing query chrX:257134-4337775 ...
    Testing query chr9_random:713930-3536575 ...
    Testing query chrX:2523687-4774316 ...
    Testing query chr21:513221-829881 ...
    Testing query chr14:6924617-9048044 ...
    Testing query chr6:4945372-7173211 ...
    Testing query chr6_random:7501139-9077397 ...
    Testing query chr19:2934833-5141776 ...
    Testing query chr9:863231-7545153 ...
    Testing query chr2:4308042-6742767 ...
    Testing query chr12:293858-324418 ...
    Testing query chr6_random:3308674-4557713 ...
    Testing query chr2_random:6755655-7330097 ...
    Testing query chr9_random:1234763-6135261 ...
    Testing query chr17:7042296-7582149 ...
    Testing query chr18:6749235-8476299 ...
    Testing query chr22:1198031-6226173 ...
    Testing query chr22:9446557-9458998 ...
    Testing query chr15:473293-1136600 ...
    Testing query chr13:8001267-8034858 ...
    Testing query chr7_random:12779-8349897 ...
    Testing query chrX:6476995-9046675 ...
    Testing query chr22:455684-9901546 ...
    Testing query chr20:2540726-9004820 ...
    Testing query chr1:5290124-7772462 ...
    Testing query chr2_random:4562177-7629291 ...
    Testing query chr4:5992612-7734912 ...
    Testing query chr5:1027938-6017856 ...
    Testing query chr5:3945452-4558863 ...
    Testing query chr7_random:1434224-8766265 ...
    Testing query chr13_random:2806926-8471270 ...
    Testing query chr21:5896937-6230120 ...
    Testing query chr10_random:2325170-6773979 ...
    Testing query chr4:768115-9242973 ...
    Testing query chr9:204376-1523700 ...
    Testing query chr15:6918456-9920136 ...
    Testing query chr8:195836-2912231 ...
    Testing query chr4_random:8569316-9601747 ...
    Testing query chr14:7539676-8479802 ...
    Testing query chr17_random:6016149-9676582 ...
    Testing query chr3:2401075-5926977 ...
    Testing query chr7:6825835-8610049 ...
    Testing query chr4:8589977-9226779 ...
    Testing query chr22_random:881883-9900377 ...
    Testing query chr19:2282185-2974234 ...
    Testing query chr2_random:530137-7997036 ...
    Testing query chr11_random:1524078-8571487 ...
    Testing query chrX:3561537-3812547 ...
    Testing query chr7_random:5345040-8399303 ...
    Testing query chr22:1586323-6546266 ...
    Testing query chr13:356087-8263221 ...
    Testing query chr9:6308509-8761532 ...
    Testing query chr8:3702301-5705153 ...
    Testing query chr13_random:1656308-4034137 ...
    Testing query chr3:4684965-7862719 ...
    Testing query chr19_random:5585589-7312648 ...
    Testing query chr18:8395777-9280098 ...
    Testing query chr6_random:738052-6252176 ...
    Testing query chr5_random:6874632-8838246 ...
    Testing query chr7_random:4576401-9601286 ...
    Testing query chr6_random:1277796-9240909 ...
    Testing query chr22:2128956-7451924 ...
    Testing query chr9:5866041-7641214 ...
    Testing query chr6_random:2900603-6324004 ...
    Testing query chr5:3340073-3878152 ...
    Testing query chr7_random:6065731-8117472 ...
    Testing query chr22:6980282-9420307 ...
    Testing query chr3_random:7896234-9902729 ...
    Testing query chr4:5226514-9465698 ...
    Testing query chr11_random:2710966-7297413 ...
    Testing query chr4:5814391-6477874 ...
    Testing query chr17:3411447-7945931 ...
    Testing query chr19_random:1563833-8954930 ...
    Testing query chr4:2666458-5577064 ...
    Testing query chrM:2495375-2785830 ...
    Testing query chr22_random:2741863-7160257 ...
    Testing query chr20:3030962-4839827 ...
    Testing query chrX_random:1999206-3290596 ...
    Testing query chr1_random:7581574-9491516 ...
    Testing query chr5:8544911-9905206 ...
    Testing query chr17_random:5247411-8818598 ...
    Testing query chr18:2206748-2542618 ...
    Testing query chr6:5560095-6841213 ...
    Testing query chrX:5584638-8069137 ...
    Testing query chr2_random:893746-4019636 ...
    Testing query chr4_random:7220619-8625179 ...
    Testing query chr17_random:7487783-7745825 ...
    Testing query chr13_random:140415-4339843 ...
    Testing query chr22:3465880-9918684 ...
    Testing query chr16_random:2228554-5218116 ...
    Testing query chr6:3812651-9020894 ...
    Testing query chr19:4897072-8152584 ...
    Testing query chr15_random:2493596-3303830 ...
    Testing query chr17:7330256-9331563 ...
    Testing query chr7_random:2372609-7660988 ...
    Testing query chr21:16468-1408282 ...
    Testing query chrM:946718-7866529 ...
    Testing query chr6:636772-5261193 ...
    Testing query chr4:4081985-5160778 ...
    Testing query chr4_random:3992937-8001782 ...
    Testing query chr3_random:4269902-7314671 ...
    Testing query chr8_random:5398008-9100867 ...
    Testing query chr11_random:4717946-5886722 ...
    Testing query chr14:3324888-9762784 ...
    Testing query chr3_random:447076-2904415 ...
    Testing query chr18_random:4656587-8830031 ...
    Testing query chr15_random:2677992-8013872 ...
    Testing query chr8:8741342-9773821 ...
    Testing query chrM:638643-3884353 ...
    Testing query chr6:1102480-2996219 ...
    Testing query chr13:27071-9001996 ...
    Testing query chr8_random:133575-8239847 ...
    Testing query chr4:5119076-7497751 ...
    Testing query chr6_random:8932876-9157638 ...
    Testing query chr2:8039126-9556281 ...
    Testing query chr18:2759483-4424919 ...
    Testing query chr7_random:2162721-7693312 ...
    Testing query chr17_random:3212242-7079443 ...
    Testing query chrX_random:9441944-9675063 ...
    Testing query chrX:1483850-9503277 ...
    Testing query chrY:708618-2939362 ...
    Testing query chr1:1457571-8460228 ...
    Testing query chrM:5153488-6390263 ...
    Testing query chr8:2469944-5489240 ...
    Testing query chr4:2270560-9937550 ...
    Testing query chr10:1924284-4282155 ...
    Testing query chrY:5044757-9726553 ...
    Testing query chr21_random:8138434-8862076 ...
    Testing query chr17_random:8064209-8585636 ...
    Testing query chr22:7325448-9656485 ...
    Testing query chr11:6475178-6915306 ...
    Testing query chrM:1569370-6357214 ...
    Testing query chr8_random:1676954-7528262 ...
    Testing query chr8:3436473-9972209 ...
    Testing query chr19_random:8309162-8766514 ...
    Testing query chr7_random:6416981-6735864 ...
    Testing query chr19:3484685-3801122 ...
    Testing query chr1:1868925-6151268 ...
    Testing query chr1:536419-4044558 ...
    Testing query chr1:2522877-4924643 ...
    Testing query chr11_random:676633-9128847 ...
    Testing query chr6_random:3598124-6981657 ...
    Testing query chr5_random:7166103-8219161 ...
    Testing query chr19:1684800-5872548 ...
    Testing query chr1_random:3315026-8441262 ...
    Testing query chr18_random:2290355-8594736 ...
    Testing query chr20:3121858-8750525 ...
    Testing query chr5:1854779-7785465 ...
    Testing query chr3:2844488-8229201 ...
    Testing query chr9:98994-6937193 ...
    Testing query chr7_random:566405-4329525 ...
    Testing query chrM:3349123-8858299 ...
    Testing query chr18_random:2476805-3333909 ...
    Testing query chr5_random:2947230-5023103 ...
    Testing query chrY:858711-3764404 ...
    Testing query chrM:3202756-4087290 ...
    Testing query chr3:2241212-3744434 ...
    Testing query chr2:294299-2791063 ...
    Testing query chr16:5636813-7725712 ...
    Testing query chrY:190457-4183568 ...
    Testing query chr15_random:1757556-6243468 ...
    Testing query chr21_random:2404640-9698959 ...
    Testing query chrY:2899895-8525822 ...
    Testing query chr14:5316023-9325638 ...
    Testing query chr5_random:3836137-6496666 ...
    Testing query chr10_random:1992029-2390509 ...
    Testing query chr15:2008393-5397033 ...
    Testing query chr6:3033491-5689013 ...
    Testing query chr13:4802709-6651494 ...
    Testing query chr11_random:1126435-2590416 ...
    Testing query chr14:674415-1741256 ...
    Testing query chr2:5945864-7917088 ...
    Testing query chr4:2984861-4376484 ...
    Testing query chr1_random:5661261-9348854 ...
    Testing query chr18:2892586-9538492 ...
    Testing query chr19_random:2666788-6214501 ...
    Testing query chr5_random:2892340-8892790 ...
    Testing query chr3:8321138-9156829 ...
    Testing query chr20:1010051-2675065 ...
    Testing query chr12:2016127-9734230 ...
    Testing query chr17:6565364-9842724 ...
    Testing query chr2_random:1534009-9935421 ...
    Testing query chr22_random:1798866-3566302 ...
    Testing query chr9_random:2863862-4098636 ...
    Testing query chr7_random:6695702-7166373 ...
    Testing query chr19_random:7774915-8904502 ...
    Testing query chr4_random:1354793-3060860 ...
    Testing query chr16_random:680783-7967813 ...
    Testing query chr22_random:1679274-1962853 ...
    Testing query chr5:1405068-3861785 ...
    Testing query chr8_random:6642950-9011653 ...
    Testing query chr16:1873173-7921837 ...
    Testing query chr7_random:2750681-9520458 ...
    Testing query chr16_random:885218-3713066 ...
    Testing query chr10_random:4952036-9328892 ...
    Testing query chr1_random:1556041-9207413 ...
    Testing query chrX:3509058-4668683 ...
    Testing query chr22_random:5775297-9086853 ...
    Testing query chr1:1171026-6903635 ...
    Testing query chr17_random:706069-7256916 ...
    Testing query chr1:7825983-8559769 ...
    Testing query chr7_random:7709758-9250068 ...
    Testing query chr6:4475592-7218806 ...
    Testing query chr5_random:7263397-7305993 ...
    Testing query chr16_random:5376132-9863064 ...
    Testing query chr5:4383593-4921390 ...
    Testing query chr12:5541381-6329888 ...
    Testing query chr7_random:297473-6191920 ...
    Testing query chr7_random:5797186-6007720 ...
    Testing query chr14:6288978-7147625 ...
    Testing query chrY:3280527-6071425 ...
    Testing query chr2_random:341241-9849655 ...
    Testing query chr18_random:2756400-5124352 ...
    Testing query chr18_random:3245587-6421468 ...
    Testing query chr7_random:1108885-7011416 ...
    Testing query chr19:55506-8032351 ...
    Testing query chr9_random:507759-1925801 ...
    Testing query chr21_random:5641470-6291456 ...
    Testing query chr16_random:2647045-6473932 ...
    Testing query chr3:8883638-9872842 ...
    Testing query chr17:2328196-3652679 ...
    Testing query chr22_random:2297511-5498425 ...
    Testing query chrX_random:3773240-4693054 ...
    Testing query chr13:1575245-9070298 ...
    Testing query chr8_random:5301468-7005527 ...
    Testing query chr4:6535020-9656212 ...
    Testing query chr18:5782944-8199590 ...
    Testing query chr5_random:1102579-7463246 ...
    Testing query chr5:2779653-6802521 ...
    Testing query chr10:99615-2172940 ...
    Testing query chr7:2762506-2870870 ...
    Testing query chr15_random:981768-8907527 ...
    Testing query chr16:436530-5189740 ...
    Testing query chr15:9551545-9569163 ...
    Testing query chr17_random:432471-8074112 ...
    Testing query chr8:4845184-5039976 ...
    Testing query chr7:3531770-6086719 ...
    Testing query chr17:2693356-7185572 ...
    Testing query chr6:6650063-9646384 ...
    Testing query chrY:121317-4718433 ...
    Testing query chr1_random:1003027-1831870 ...
    Testing query chr21:8788645-9420609 ...
    Testing query chr13_random:987064-4341370 ...
    Testing query chr13_random:842466-5111480 ...
    Testing query chrM:7654248-8310027 ...
    Testing query chr2:1532378-3980671 ...
    Testing query chr16_random:2308350-8259941 ...
    Testing query chr18_random:7619793-8200073 ...
    Testing query chr16:908998-6962421 ...
    Testing query chr1_random:4760134-7897692 ...
    Testing query chr4_random:351969-2613223 ...
    Testing query chr16:3482498-9633584 ...
    Testing query chr22:7907949-9933800 ...
    Testing query chr15:5854248-7275283 ...
    Testing query chr14:3664791-8748133 ...
    Testing query chrX:896137-9572469 ...
    Testing query chrX:1865390-3062428 ...
    Testing query chr6:595893-8247348 ...
    Testing query chr9_random:1425130-4402172 ...
    Testing query chr7_random:463001-1378501 ...
    Testing query chr10:5465621-8140677 ...
    Testing query chr22:4007755-6030817 ...
    Testing query chr19:2152758-4285738 ...
    Testing query chrX_random:6197638-7278734 ...
    Testing query chr8_random:2506286-3132074 ...
    Testing query chr3:5088917-6346018 ...
    Testing query chr21_random:709245-2447062 ...
    Testing query chr7_random:2297450-2733491 ...
    Testing query chrX_random:75616-6715390 ...
    Testing query chr14:1451557-9217186 ...
    Testing query chr22:4216648-4273083 ...
    Testing query chr22_random:2900019-9495009 ...
    Testing query chr4:6062237-9450155 ...
    Testing query chr3_random:2205998-8038523 ...
    Testing query chr19:4006735-8497976 ...
    Testing query chrM:4367909-8743630 ...
    Testing query chr1:3235237-5886681 ...
    Testing query chr18:2455071-8918070 ...
    Testing query chr3:715763-7415212 ...
    Testing query chr2_random:3698070-6718252 ...
    Testing query chr10:4035923-8780337 ...
    Testing query chr1_random:4369783-9221375 ...
    Testing query chr11:3488452-9565235 ...
    Testing query chrX:3524615-7110878 ...
    Testing query chr19_random:7779323-8424172 ...
    Testing query chr15_random:910898-4876910 ...
    Testing query chr15_random:1015024-3678499 ...
    Testing query chr9:3393986-9417756 ...
    Testing query chr18_random:857279-9200045 ...
    Testing query chr18:1396324-2772435 ...
    Testing query chr12:5614369-9031405 ...
    Testing query chr5:3780359-4070909 ...
    Testing query chr17:4508678-5389778 ...
    Testing query chr21_random:6972726-7854603 ...
    Testing query chr12:3182535-8039198 ...
    Testing query chr10:3951103-7166395 ...
    Testing query chr5_random:6532707-9837900 ...
    Testing query chr13_random:7985015-9743703 ...
    Testing query chr20:6134113-9969678 ...
    Testing query chrY:1542908-4899134 ...
    Testing query chr19_random:324180-7673324 ...
    Testing query chr22_random:4465119-8807791 ...
    Testing query chr14:4342424-6275354 ...
    Testing query chr21:3393386-7099240 ...
    Testing query chr3_random:2130566-2642809 ...
    Testing query chr1_random:2534189-6047752 ...
    Testing query chrM:3319509-8627744 ...
    Testing query chr4_random:7027413-8546790 ...
    Testing query chr18:5213087-7307044 ...
    Testing query chrX_random:5138706-7179617 ...
    Testing query chr21:1746459-3369825 ...
    Testing query chr17_random:4364489-9952653 ...
    Testing query chr21_random:2852383-6343308 ...
    Testing query chr16:1718072-7027200 ...
    Testing query chr7:2836942-5941970 ...
    Testing query chr21_random:6013526-6739121 ...
    Testing query chr6:2041720-8080188 ...
    Testing query chr20:5614189-8320637 ...
    Testing query chr18:7510033-9259036 ...
    Testing query chr7_random:5464431-5858425 ...
    Testing query chrX_random:2642097-9170108 ...
    Testing query chr21_random:2372613-7228145 ...
    Testing query chr7:7643929-8629915 ...
    Testing query chrM:1496669-3662785 ...
    Testing query chrM:5816559-7988640 ...
    Testing query chr4_random:3216837-5344216 ...
    Testing query chr8_random:7939352-9193364 ...
    Testing query chr11_random:4477474-7119222 ...
    Testing query chr22:1795085-7018163 ...
    Testing query chr2:489045-5507534 ...
    Testing query chr20:228222-2645827 ...
    Testing query chr2_random:6696262-7193942 ...
    Testing query chrX:624678-2022130 ...
    Testing query chr11_random:7420609-7476969 ...
    Testing query chr7_random:35741-8947140 ...
    Testing query chr9:2887670-8574309 ...
    Testing query chr9_random:5022666-8213630 ...
    Testing query chr16_random:2811399-8122673 ...
    Testing query chr19:2563169-2938289 ...
    Testing query chr15_random:3165794-8354108 ...
    Testing query chr1_random:4114915-9235471 ...
    Testing query chr10_random:983161-9480146 ...
    Testing query chr2:5984445-9861542 ...
    Testing query chr21:2955353-3709382 ...
    Testing query chr18:4220403-7713605 ...
    Testing query chr9:5837376-6191557 ...
    Testing query chr18:3760903-6211242 ...
    Testing query chr4:2604919-6869284 ...
    Testing query chr14:8243966-8657979 ...
    Testing query chrX:8572226-9566286 ...
    Testing query chr15_random:1776922-9379642 ...
    Testing query chr11:6484864-9835462 ...
    Testing query chr13_random:2265643-8434104 ...
    Testing query chr18_random:2936640-6667223 ...
    Testing query chr21_random:6212251-8673018 ...
    Testing query chr1_random:1062720-2585432 ...
    Testing query chr21_random:5965453-7655829 ...
    Testing query chrX_random:2147524-2773583 ...
    Testing query chr13_random:368974-2821747 ...
    Testing query chr5_random:1943780-5626512 ...
    Testing query chr20:30472-8431478 ...
    Testing query chr10_random:1574710-2300026 ...
    Testing query chr16_random:5290469-9294719 ...
    Testing query chr22:2213818-3185623 ...
    Testing query chr18:2186838-5554932 ...
    Testing query chr1_random:4416515-6829118 ...
    Testing query chr17_random:4168349-9033195 ...
    Testing query chr4_random:7231065-9006087 ...
    Testing query chr3:6627861-7098084 ...
    Testing query chr21:4791386-7462661 ...
    Testing query chr6:5486440-6497547 ...
    Testing query chr7:7583780-8490132 ...
    Testing query chr15:4167629-9516050 ...
    Testing query chr13:412129-3106131 ...
    Testing query chr6:2242528-3392002 ...
    Testing query chr13:4573366-8565166 ...
    Testing query chr14:1012727-4265512 ...
    Testing query chrX:8331093-8914945 ...
    Testing query chr19:3587675-9174187 ...
    Testing query chr7:296443-1800051 ...
    Testing query chr3:5277077-9767087 ...
    Testing query chr21:7692109-7739057 ...
    Testing query chr11:3448455-8411453 ...
    Testing query chr1_random:2275881-3676442 ...
    Testing query chr4_random:6322956-7587151 ...
    Testing query chr22_random:4609088-7067795 ...
    Testing query chr11:1103974-5115622 ...
    Testing query chr17:8733322-9618772 ...
    Testing query chr5_random:1779768-6935553 ...
    Testing query chr8_random:2538535-9879832 ...
    Testing query chr22:768294-3209930 ...
    Testing query chr22:943981-2330158 ...
    Testing query chr12:4987241-7314877 ...
    Testing query chr2:3120747-6311500 ...
    Testing query chrX:1829150-5592634 ...
    Testing query chr7:795351-9692074 ...
    Testing query chr9:5469158-7108447 ...
    Testing query chr18:1967306-6204810 ...
    Testing query chr4_random:8969152-9598463 ...
    Testing query chr4_random:1579186-2839628 ...
    Testing query chr15:5974419-7281533 ...
    Testing query chr8_random:3609626-6631230 ...
    Testing query chr17:3094989-6618173 ...
    Testing query chr15:1799279-6576530 ...
    Testing query chr3:5157964-8423765 ...
    Testing query chr22_random:2813926-5797993 ...
    Testing query chr2:2248206-3931961 ...
    Testing query chr7:3205910-9801772 ...
    Testing query chr21_random:623490-6775587 ...
    Testing query chrM:8166786-8509161 ...
    Testing query chr17:1804940-2950404 ...
    Testing query chr10_random:2511464-6816559 ...
    Testing query chr21_random:153036-5827934 ...
    Testing query chr2_random:8263243-9685626 ...
    Testing query chr21:1111482-5812333 ...
    Testing query chr8:4290604-9166817 ...
    Testing query chr13:3398929-7913910 ...
    Testing query chr10:4553797-9072246 ...
    Testing query chr20:7207944-7471721 ...
    Testing query chrY:1982521-2897985 ...
    Testing query chr10_random:5100074-7818426 ...
    Testing query chr15:4365944-8388476 ...
    Testing query chr13:50044-8373169 ...
    Testing query chr12:5115399-7648840 ...
    Testing query chr4:2962742-8829366 ...
    Testing query chr6_random:1322565-9235978 ...
    Testing query chr12:6057343-7930326 ...
    Testing query chr3:1612029-2982153 ...
    Testing query chr15:6582900-8591795 ...
    Testing query chr21:5009971-6424414 ...
    Testing query chr6:706279-8162934 ...
    Testing query chr16:3267535-9670332 ...
    Testing query chr16:2694606-3346697 ...
    Testing query chrY:9108749-9339860 ...
    Testing query chr18:1265164-5476362 ...
    Testing query chr8_random:1135765-3131623 ...
    Testing query chr1_random:4068577-5850392 ...
    Testing query chr10_random:8086436-9515610 ...
    Testing query chr12:786080-9272524 ...
    Testing query chr2_random:3529918-9107547 ...
    Testing query chrX:33039-720704 ...
    Testing query chrY:7759964-8753893 ...
    Testing query chr18_random:9023306-9399435 ...
    Testing query chr6:5281117-9258674 ...
    Testing query chr2_random:3737881-7335740 ...
    Testing query chr18_random:486302-3415910 ...
    Testing query chr9_random:4036001-4224366 ...
    Testing query chr1_random:676459-981484 ...
    Testing query chr21:213055-9194219 ...
    Testing query chr3:5273397-7935759 ...
    Testing query chr7:5844019-5928029 ...
    Testing query chr22:4400032-4947008 ...
    Testing query chr1_random:6368632-9050986 ...
    Testing query chr6_random:3521181-8577335 ...
    Testing query chr11_random:4864475-5742060 ...
    Testing query chr9:691952-3618418 ...
    Testing query chr16:5899296-6778697 ...
    Testing query chr16:865613-6607475 ...
    Testing query chr17_random:4739682-6923211 ...
    Testing query chrY:2356621-4914419 ...
    Testing query chr3_random:1842297-6259766 ...
    Testing query chr3_random:5126637-7321281 ...
    Testing query chrX:4209013-9761426 ...
    Testing query chr5_random:4596157-5675945 ...
    Testing query chr21_random:3696079-6024271 ...
    Testing query chr3_random:5067064-8876286 ...
    Testing query chr21_random:5565110-6689301 ...
    Testing query chr21_random:15781-4584722 ...
    Testing query chr1:3346110-7059075 ...
    Testing query chrX:5966696-6933232 ...
    Testing query chr17:5021510-8070334 ...
    Testing query chr6:1149206-6788407 ...
    Testing query chr3_random:3744515-8291994 ...
    Testing query chr2:22996-4588290 ...
    Testing query chr17_random:5326761-6699939 ...
    Testing query chr11_random:2696057-3080563 ...
    Testing query chr9:6885746-7594235 ...
    Testing query chr2:4534733-7295296 ...
    Testing query chr13_random:3998213-9469962 ...
    Testing query chr1_random:5426791-6149949 ...
    Testing query chr9_random:530950-725978 ...
    Testing query chr11:4184033-9403368 ...
    Testing query chr15_random:1456012-6938955 ...
    Testing query chr4:527074-2332486 ...
    Testing query chr15:6231961-6744661 ...
    Testing query chr4_random:1429017-4799661 ...
    Testing query chrX_random:1288951-8906564 ...
    Testing query chr5:203973-5396390 ...
    Testing query chr22_random:6924137-9556382 ...
    Testing query chr13:3692768-5792536 ...
    Testing query chr7_random:4736121-7190035 ...
    Testing query chr19_random:1067060-5424230 ...
    Testing query chr5:4645403-9655346 ...
    Testing query chr21:6194788-9692460 ...
    Testing query chr3_random:6249249-8849610 ...
    Testing query chr1_random:116005-4931104 ...
    Testing query chr9_random:2264542-9177908 ...
    Testing query chr5:1920701-3940100 ...
    Testing query chr19:3510626-6120416 ...
    Testing query chr8_random:1385330-9139475 ...
    Testing query chr5_random:4560385-9932819 ...
    Testing query chr10_random:1546770-4255829 ...
    Testing query chrY:1634712-6195051 ...
    Testing query chr21:1934284-3805640 ...
    Testing query chr10:1098075-1222293 ...
    Testing query chrX:3147440-5915627 ...
    Testing query chr12:644340-9578661 ...
    Testing query chr7:3815107-7552297 ...
    Testing query chr7_random:979254-6592345 ...
    Testing query chr15_random:4031375-9529529 ...
    Testing query chr20:809453-6417655 ...
    Testing query chr3_random:1311668-6592135 ...
    Testing query chr16_random:4796848-9917504 ...
    Testing query chr2:2316239-8809758 ...
    Testing query chr22_random:3700813-7193581 ...
    Testing query chr2_random:5629881-8301170 ...
    Testing query chr2:4292815-5793077 ...
    Testing query chr16:4963697-5732378 ...
    Testing query chr20:1818167-2602981 ...
    Testing query chr13_random:857910-3186701 ...
    Testing query chr8:7828099-7863231 ...
    Testing query chr2:3039751-5869790 ...
    Testing query chr7_random:948462-2258714 ...
    Testing query chr12:2176474-8835346 ...
    Testing query chr4_random:4818082-9335116 ...
    Testing query chr9_random:949590-4937462 ...
    Testing query chr3_random:139177-2147902 ...
    Testing query chr15_random:4086655-7110200 ...
    Testing query chr7:1707937-7031178 ...
    Testing query chr15:6704897-7523233 ...
    Testing query chr8_random:3261310-3388805 ...
    Testing query chr11:4627964-9758513 ...
    Testing query chr3_random:1269243-5807226 ...
    Testing query chr9_random:564250-7036410 ...
    Testing query chr8_random:5129373-5437488 ...
    Testing query chr18:2171501-3304941 ...
    Testing query chr17_random:5747642-6505556 ...
    Testing query chrY:3819311-5517038 ...
    Testing query chr11_random:4980823-9419145 ...
    Testing query chrX:3246258-6297440 ...
    Testing query chr1_random:810216-9835846 ...
    Testing query chr9_random:227030-6294798 ...
    Testing query chr1_random:301295-1576363 ...
    Testing query chr21:4560202-9527465 ...
    Testing query chr11:3926303-4702504 ...
    Testing query chr13_random:4053954-7799426 ...
    Testing query chr8_random:1615788-4228091 ...
    Testing query chrX:5354321-7998054 ...
    Testing query chr5:428791-7222158 ...
    Testing query chrY:5600982-5656729 ...
    Testing query chr4_random:3857931-8313241 ...
    Testing query chr15:1925774-5199208 ...
    Testing query chr11_random:1107850-6997032 ...
    Testing query chr14:2769511-5526141 ...
    Testing query chr22:1129798-7717631 ...
    Testing query chr22_random:2940332-5279177 ...
    Testing query chr9:1067427-1150594 ...
    Testing query chr8:5146545-9541542 ...
    Testing query chr15:7089597-8473958 ...
    Testing query chr12:5527737-5802706 ...
    Testing query chr7:1551097-6396733 ...
    Testing query chr2_random:3022570-3558123 ...
    Testing query chr5_random:385945-6563916 ...
    Testing query chr19_random:3546106-9160937 ...
    Testing query chr15_random:3701260-8137083 ...
    Testing query chr5:1805515-5128679 ...
    Testing query chr10_random:748486-5680503 ...
    Testing query chr18:1342370-7881611 ...
    Testing query chr18_random:770908-6308398 ...
    Testing query chr19:7484581-8473209 ...
    Testing query chr7:4518548-7588072 ...
    Testing query chr9_random:7255308-8443827 ...
    Testing query chrX:5799987-8117438 ...
    Testing query chr14:7540848-8413963 ...
    Testing query chr19_random:2328053-2556284 ...
    Testing query chr16_random:7230921-7518347 ...
    Testing query chr19_random:276347-1547597 ...
    Testing query chr13:765679-7048818 ...
    Testing query chrM:2605992-5897739 ...
    Testing query chrX:7913839-8348655 ...
    Testing query chr2_random:7115229-7577760 ...
    Testing query chr21:7618516-8976664 ...
    Testing query chr10_random:5113402-9511617 ...
    Testing query chr3_random:2749825-6235208 ...
    Testing query chr7_random:4542464-5736534 ...
    Testing query chr22:3287391-8684233 ...
    Testing query chr1:6551268-8138439 ...
    Testing query chr18_random:7072081-7642659 ...
    Testing query chr1_random:375703-2560467 ...
    Testing query chr21:5140483-9431223 ...
    Testing query chr19:320517-7295855 ...
    Testing query chr12:585392-5511186 ...
    Testing query chr18_random:8083366-8235379 ...
    Testing query chr10:126713-1547118 ...
    Testing query chr10:5632955-8746379 ...
    Testing query chr10_random:3676138-6848091 ...
    Testing query chr9:4589897-9207905 ...
    Testing query chr6_random:7846883-9764185 ...
    Testing query chr18_random:4290690-8214747 ...
    Testing query chr13_random:2540819-4559633 ...
    Testing query chr11_random:3861379-5778337 ...
    Testing query chr16_random:1701866-3678380 ...
    Testing query chr15:6359944-8126244 ...
    Testing query chr9_random:3748170-8007098 ...
    Testing query chr9:7943740-9455802 ...
    Testing query chr19_random:1042691-5523628 ...
    Testing query chr1_random:1492517-5228447 ...
    Testing query chr6:5705000-6113711 ...
    Testing query chr20:323999-8013692 ...
    Testing query chr10_random:2403788-4666817 ...
    Testing query chr12:809220-4859122 ...
    Testing query chr7:4626441-6767688 ...
    Testing query chr9:1227373-9861818 ...
    Testing query chr9_random:1646320-4830906 ...
    Testing query chr5:1816686-8010796 ...
    Testing query chr18_random:2978620-4099625 ...
    Testing query chr2:2092284-6363784 ...
    Testing query chr11:6697928-8978854 ...
    Testing query chr15:4328362-7736553 ...
    Testing query chr19:2684370-4694361 ...
    Testing query chr8_random:1549783-2052889 ...
    Testing query chr10_random:343773-5114298 ...
    Testing query chr22:239978-7311092 ...
    Testing query chr10:59830-4498628 ...
    Testing query chr6_random:4394006-8726576 ...
    Testing query chr2:2521493-6006376 ...
    Testing query chrY:174190-248602 ...
    Testing query chr5_random:3175374-3810594 ...
    Testing query chr21:458207-4328406 ...
    Testing query chr7:746735-8755260 ...
    Testing query chr1:8376346-9926832 ...
    Testing query chrX:1558302-6671795 ...
    Testing query chr3:90115-6523026 ...
    Testing query chr17_random:1954593-2055586 ...
    Testing query chr9:2137572-9471850 ...
    Testing query chr18_random:7412031-7927783 ...
    Testing query chr7:2153207-4745373 ...
    Testing query chrX:4532293-8914932 ...
    Testing query chr11:2910609-3421044 ...
    Testing query chr9:6096367-7279687 ...
    Testing query chr3:2070513-7395995 ...
    Testing query chr8_random:835918-1827839 ...
    Testing query chr18:248820-4981110 ...
    Testing query chr11_random:4573607-7438971 ...
    Testing query chrX:4061785-7455437 ...
    Testing query chr3:5179852-5811856 ...
    Testing query chr7_random:3320586-3880101 ...
    Testing query chr22:1201575-8615117 ...
    Testing query chr4:6832003-9027563 ...
    Testing query chr5_random:2075108-2231968 ...
    Testing query chrX_random:59800-714902 ...
    Testing query chrX_random:2828941-5491980 ...
    Testing query chr8:1038109-7255118 ...
    Testing query chr19:564478-5162536 ...
    Testing query chr21:6696589-7247970 ...
    Testing query chr6:918960-1474816 ...
    Testing query chrM:5636321-9968137 ...
    Testing query chr7_random:5485027-5682623 ...
    Testing query chrY:4149126-7271874 ...
    Testing query chrX_random:2119447-7981903 ...
    Testing query chr8:392266-4278110 ...
    Testing query chr15:126791-8741531 ...
    Testing query chrY:1970354-3699838 ...
    Testing query chr16:4070891-8181737 ...
    Testing query chr18_random:1308317-5408953 ...
    Testing query chr9:1486842-2579174 ...
    Testing query chr9_random:3614823-8021197 ...
    Testing query chr19_random:4100590-7401362 ...
    Testing query chr13:9198949-9562213 ...
    Testing query chr13_random:3477250-5979150 ...
    Testing query chr8:702816-7724269 ...
    Testing query chrX:1173848-9916277 ...
    Testing query chr19_random:1528939-7213477 ...
    Testing query chrY:4055178-8006125 ...
    Testing query chr21_random:5600720-8897721 ...
    Testing query chr13:5754292-7802376 ...
    Testing query chr6_random:2337681-6172508 ...
    Testing query chr2:5799739-7134812 ...
    Testing query chrX_random:3353632-6262401 ...
    Testing query chr21:945894-5132876 ...
    Testing query chr18_random:2350673-9531784 ...
    Testing query chr22_random:5048930-8474866 ...
    Testing query chr19:6352226-8501858 ...
    Testing query chr20:3392059-9830746 ...
    Testing query chr16_random:4090981-7752074 ...
    Testing query chr11_random:5905570-6251642 ...
    Testing query chr13:360298-9358487 ...
    Testing query chr6_random:882947-4758560 ...
    Testing query chr11:2340078-2932391 ...
    Testing query chr22_random:2213551-2534609 ...
    Testing query chr21:5841676-5846763 ...
    Testing query chr11_random:4038782-7000307 ...
    Testing query chr6_random:25409-5762752 ...
    Testing query chr16:5928354-8501435 ...
    Testing query chrY:694230-6280406 ...
    Testing query chr11:7243231-8376959 ...
    Testing query chr16_random:7306380-8046651 ...
    Testing query chr16:1271045-7843225 ...
    Testing query chr15:3261152-4143715 ...
    Testing query chr16:3643483-7977448 ...
    Testing query chrM:2682115-4251696 ...
    Testing query chrM:8447185-9660353 ...
    Testing query chr17_random:4662108-9040099 ...
    Testing query chr15:2717869-3422290 ...
    Testing query chr9_random:2276674-4258729 ...
    Testing query chrX_random:975097-5521164 ...
    Testing query chr11:2146529-8617542 ...
    Testing query chr10_random:1180053-8007684 ...
    Testing query chr3_random:3693000-4565796 ...
    Testing query chr11:145445-2682401 ...
    Testing query chr8_random:6750591-7945127 ...
    Testing query chr1:8320362-9511438 ...
    Testing query chr8:7013549-9472948 ...
    Testing query chr13_random:3536637-5003209 ...
    Testing query chr9:6558793-7284938 ...
    Testing query chr21_random:2580219-9412760 ...
    Testing query chr10:406321-2977770 ...
    Testing query chr21:492284-7994828 ...
    Testing query chr8:2657319-7983432 ...
    Testing query chrX:4732048-8043746 ...
    Testing query chr20:3307597-9305376 ...
    Testing query chr2_random:755380-8957174 ...
    Testing query chrY:2933069-9880634 ...
    Testing query chr6:774738-5674081 ...
    Testing query chr22_random:715809-9050909 ...
    Testing query chr4:1349527-3344979 ...
    Testing query chr6:8028105-9684178 ...
    Testing query chr5_random:4787471-8881473 ...
    Testing query chr10_random:2634703-3696440 ...
    Testing query chr11_random:829085-1727870 ...
    Testing query chr15_random:592933-9165180 ...
    Testing query chr4_random:4418610-8898086 ...
    Testing query chrX_random:2431444-6884713 ...
    Testing query chr8_random:6475456-8480814 ...
    Testing query chr7:3815530-7026545 ...
    Testing query chr19:7331585-7602899 ...
    Testing query chr1_random:874465-3320587 ...
    Testing query chr13_random:733794-6825035 ...
    Testing query chr15_random:9014536-9668872 ...
    Testing query chr17_random:6591609-9129777 ...
    Testing query chrM:656068-4356620 ...
    Testing query chr8:405654-9125605 ...
    Testing query chrX:2091850-6675177 ...
    Testing query chr17_random:7703315-8296743 ...
    Testing query chr5:6509082-7915180 ...
    Testing query chr22:2553656-7681295 ...
    Testing query chr14:3268086-7514168 ...
    Testing query chr8:4422671-6192314 ...
    Testing query chr1:65591-912831 ...
    Testing query chr3_random:5754696-6365576 ...
    Testing query chr19:3761804-6226235 ...
    Testing query chr15_random:437782-2343429 ...
    Testing query chr21_random:6464723-8352688 ...
    Testing query chr2:2429164-5768260 ...
    Testing query chr4:470318-7002218 ...
    Testing query chr4:3690943-5461445 ...
    Testing query chr22_random:5183905-6703677 ...
    Testing query chr6:956010-4837181 ...
    Testing query chr22_random:4644999-6726863 ...
    Testing query chr3:461910-2847795 ...
    Testing query chrM:1898841-4804510 ...
    Testing query chr17_random:4508018-9521979 ...
    Testing query chr5_random:324986-2917264 ...
    Testing query chr21_random:5399136-5748620 ...
    Testing query chr22:2778077-4812793 ...
    Testing query chr10:4969555-6126688 ...
    Testing query chr18:1713300-5060476 ...
    Testing query chr13_random:3333348-5290509 ...
    Testing query chr11_random:4081564-5917103 ...
    Testing query chr4_random:5054748-8642850 ...
    Testing query chr1:2326146-4227874 ...
    Testing query chr18:1537257-7925976 ...
    Testing query chr22_random:8252153-8805544 ...
    Testing query chr3_random:1198809-9011283 ...
    Testing query chr17_random:6967406-8885184 ...
    Testing query chr13:1386877-2947412 ...
    Testing query chrM:6757870-7928951 ...
    Testing query chr21:4074861-7649457 ...
    Testing query chrX_random:1019101-6500619 ...
    Testing query chrX:1825987-5504513 ...
    Testing query chr21_random:3186073-5713305 ...
    Testing query chr4:6259611-8028235 ...
    Testing query chr4:1743818-8599191 ...
    Testing query chr17:1858282-6524491 ...
    Testing query chr15_random:4438074-7157093 ...
    Testing query chr3_random:397131-735889 ...
    Testing query chr8:6928096-9944821 ...
    Testing query chr4_random:1300717-4919221 ...
    Testing query chr5_random:338852-4544685 ...
    Testing query chr7_random:9056136-9688355 ...
    Testing query chr13:2503131-3346435 ...
    Testing query chr15_random:4163332-8152391 ...
    Testing query chr11_random:3309623-7440495 ...
    Testing query chr5_random:9256148-9879716 ...
    Testing query chr17_random:1285404-9731324 ...
    Testing query chr11:8839451-9081378 ...
    Testing query chr13:8871343-9845159 ...
    Testing query chr22:4961912-7272246 ...
    Testing query chr7_random:1546612-1704922 ...
    Testing query chr4_random:3988885-5892099 ...
    Testing query chr16:3240803-6856154 ...
    Testing query chr16:217614-7256181 ...
    Testing query chr8_random:9247976-9386452 ...
    Testing query chr3_random:6627763-9791298 ...
    Testing query chr2:2529288-4212123 ...
    Testing query chrX_random:2988973-8007994 ...
    Testing query chr15:7917609-9330719 ...
    Testing query chr11_random:3494062-5554433 ...
    Testing query chr10_random:550231-9169795 ...
    Testing query chrM:2348914-4789264 ...
    Testing query chr10_random:1774094-2022615 ...
    Testing query chrY:1233622-1787356 ...
    Testing query chr16:1423379-2759956 ...
    Testing query chr15_random:2179216-5955676 ...
    Testing query chr13_random:4485355-8258869 ...
    Testing query chr16:1540718-7599890 ...
    Testing query chr16:3470124-5210468 ...
    Testing query chr5_random:2480219-3389498 ...
    Testing query chrX_random:2150354-9183393 ...
    Testing query chr4_random:7326066-8687796 ...
    Testing query chr9_random:778644-7335950 ...
    Testing query chr3_random:117405-711777 ...
    Testing query chr3_random:1627027-5946622 ...
    Testing query chr14:1896619-3058485 ...
    Testing query chr4:361451-8469991 ...
    Testing query chr13:8016007-9409673 ...
    Testing query chr15_random:4902505-9345392 ...
    Testing query chr11_random:7321862-9499733 ...
    Testing query chr4:1033220-5712150 ...
    Testing query chr8:3549734-9090035 ...
    Testing query chrM:5081509-5962772 ...
    Testing query chrX_random:97240-6137606 ...
    Testing query chr8_random:4271059-4291635 ...
    Testing query chrX_random:530035-1682825 ...
    Testing query chr15:2788773-5483281 ...
    Testing query chrX_random:4759178-9377757 ...
    Testing query chrM:3245025-4297984 ...
    Testing query chr19_random:3021529-4576251 ...
    Testing query chr4_random:1397040-5761345 ...
    Testing query chrM:561371-7187972 ...
    Testing query chr22:5413646-8736775 ...
    Testing query chr17_random:1425366-7019792 ...
    Testing query chr3_random:572179-7205526 ...
    Testing query chr5:4328737-9239750 ...
    Testing query chr22:5069432-6659616 ...
    Testing query chr13:48249-7303858 ...
    Testing query chr3:305799-6869287 ...
    Testing query chr21:3873459-5093561 ...
    Testing query chr19:5939843-9027189 ...
    Testing query chr2:5873453-6683127 ...
    Testing query chr22_random:3713598-5598641 ...
    Testing query chr20:179927-8450235 ...
    Testing query chr13_random:8308459-9668938 ...
    Testing query chr11:1199780-7649669 ...
    Testing query chr19:4137076-6447341 ...
    Testing query chrM:78280-8559488 ...
    Testing query chr4:623887-7069138 ...
    Testing query chr16:3039657-4345359 ...
    Testing query chr17:3391405-4744719 ...
    Testing query chr20:2910861-7899348 ...
    Testing query chr19_random:913985-2128081 ...
    Testing query chr22:1426695-8605324 ...
    Testing query chr12:1887213-4358077 ...
    Testing query chrX:5563613-8375913 ...
    Testing query chr7_random:136737-595720 ...
    Testing query chr22:3649338-3715557 ...
    Testing query chr22_random:1857324-2876705 ...
    Testing query chr3_random:1299041-9034999 ...
    Testing query chr15:978485-8350193 ...
    Testing query chr19_random:4068601-6523086 ...
    Testing query chr2:201488-4273604 ...
    Testing query chr19_random:5966187-9871009 ...
    Testing query chrM:1330413-9761840 ...
    Testing query chr7:4263424-8956444 ...
    Testing query chr5:710131-1481160 ...
    Testing query chr22_random:3228001-4696776 ...
    Testing query chr3:64585-1673488 ...
    Testing query chr16:8045346-8459636 ...
    Testing query chr13_random:1741393-4393228 ...
    Testing query chr22_random:2624571-7878001 ...
    Testing query chr20:4312366-7263897 ...
    Testing query chr2_random:792986-9926045 ...
    Testing query chr4:876557-8032416 ...
    Testing query chr7_random:9474728-9775529 ...
    Testing query chrY:196281-2297210 ...
    Testing query chr11_random:1815604-1988691 ...
    Testing query chr17:327462-9941596 ...
    Testing query chr4:1225057-5716342 ...
    Testing query chrX_random:5518830-9291836 ...
    Testing query chr19_random:8850582-9837888 ...
    Testing query chr10_random:906079-4133872 ...
    Testing query chrX:1487717-2363048 ...
    Testing query chrX:315413-7567516 ...
    Testing query chr8_random:6478215-9426080 ...
    Testing query chr20:2999407-4776774 ...
    Testing query chr5_random:1309090-5902755 ...
    Testing query chr4_random:4737388-7952008 ...
    Testing query chr21_random:3092337-5111212 ...
    Testing query chr12:4888197-9051400 ...
    Testing query chr13_random:4483564-5744770 ...
    Testing query chr22_random:54755-6638497 ...
    Testing query chr13_random:5891419-7679795 ...
    Testing query chr12:1730038-8775120 ...
    Testing query chr10:3971454-8725046 ...
    Testing query chr13_random:2420218-3946730 ...
    Testing query chr16_random:6268326-9602951 ...
    Testing query chr15_random:6201359-7624324 ...
    Testing query chr8_random:1897294-5156982 ...
    Testing query chr1:2597385-4514890 ...
    Testing query chrX_random:338730-7953560 ...
    Testing query chr7:5484367-7925032 ...
    Testing query chr5_random:6298235-7470139 ...
    Testing query chr21_random:3834366-4459713 ...
    Testing query chr5:2361767-8905807 ...
    Testing query chrM:3162105-9086123 ...
    Testing query chrX_random:4940689-6482079 ...
    Testing query chr4:4948264-5128137 ...
    Testing query chr3:4207686-7342748 ...
    Testing query chr19_random:2021389-9994958 ...
    Testing query chr18:3680011-9706840 ...
    Testing query chr17_random:5951397-8238603 ...
    Testing query chr15_random:4175461-7481270 ...
    Testing query chr4:498362-9165782 ...
    Testing query chr21:4179687-5159563 ...
    Testing query chr1:5178637-7992880 ...
    Testing query chr15_random:6053128-8149868 ...
    Testing query chr5:4008322-7971530 ...
    Testing query chr19_random:1097409-1939223 ...
    Testing query chr15:7469377-8821183 ...
    Testing query chr11_random:1627957-5387469 ...
    Testing query chr9:5855393-7238773 ...
    Testing query chr22:3055704-4751301 ...
    Testing query chr18_random:2752026-7569770 ...
    Testing query chr6:2659325-3383321 ...
    Testing query chr19_random:6031799-9193165 ...
    Testing query chr10:2867928-7456748 ...
    Testing query chr17:803521-2016747 ...
    Testing query chr11_random:2756837-9309974 ...
    Testing query chr9_random:4932323-6215308 ...
    Testing query chr19_random:1738738-9429398 ...
    Testing query chr4_random:162435-8328176 ...
    Testing query chr17:138893-2694455 ...
    Testing query chrX_random:4137996-9339319 ...
    Testing query chr19:2497402-8914940 ...
    Testing query chr13_random:3513964-5910759 ...
    Testing query chrX:1099583-2639169 ...
    Testing query chr11_random:6266637-8387131 ...
    Testing query chr8_random:3059827-5229064 ...
    Testing query chr6:380960-2560436 ...
    Testing query chr15_random:5618328-6876961 ...
    Testing query chr2_random:3878460-5680854 ...
    Testing query chr8_random:2477614-4148075 ...
    Testing query chr18_random:5415785-8338387 ...
    Testing query chr10_random:8209397-8355863 ...
    Testing query chr11_random:4475489-6604223 ...
    Testing query chr1_random:754948-7226484 ...
    Testing query chr9:2946100-8357028 ...
    Testing query chr15:7199317-8245905 ...
    Testing query chr7_random:7269507-8820498 ...
    Testing query chr16:1621267-2368637 ...
    Testing query chr7_random:2996833-9854987 ...
    Testing query chrM:6484003-6911983 ...
    Testing query chr13:1771424-4738191 ...
    Testing query chr13_random:1828228-4302873 ...
    Testing query chrM:2962858-5957962 ...
    Testing query chr6_random:4242794-9824359 ...
    Testing query chr13:415874-9331256 ...
    Testing query chr8:7417568-9299672 ...
    Testing query chr5_random:6880184-8188312 ...
    Testing query chr10_random:1892176-5188920 ...
    Testing query chr21_random:4076206-6101050 ...
    Testing query chr20:5126731-9990106 ...
    Testing query chr4:3133535-3261569 ...

Gradle suite > Gradle test > htsjdk.samtools.BAMFileReaderTest.testGetIndexTypeOK STANDARD_OUT
    chrM length=	16571	Aligned= 23	Unaligned= 0
    chr1 length=	247249719	Aligned= 885	Unaligned= 0
    chr2 length=	242951149	Aligned= 837	Unaligned= 0
    chr3 length=	199501827	Aligned= 683	Unaligned= 0
    chr4 length=	191273063	Aligned= 633	Unaligned= 0
    chr5 length=	180857866	Aligned= 611	Unaligned= 0
    chr6 length=	170899992	Aligned= 585	Unaligned= 0
    chr7 length=	158821424	Aligned= 521	Unaligned= 0
    chr8 length=	146274826	Aligned= 507	Unaligned= 0
    chr9 length=	140273252	Aligned= 388	Unaligned= 0
    chr10 length=	135374737	Aligned= 477	Unaligned= 0
    chr11 length=	134452384	Aligned= 467	Unaligned= 0
    chr12 length=	132349534	Aligned= 459	Unaligned= 0
    chr13 length=	114142980	Aligned= 327	Unaligned= 0
    chr14 length=	106368585	Aligned= 310	Unaligned= 0
    chr15 length=	100338915	Aligned= 280	Unaligned= 0
    chr16 length=	88827254	Aligned= 278	Unaligned= 0
    chr17 length=	78774742	Aligned= 269	Unaligned= 0
    chr18 length=	76117153	Aligned= 265	Unaligned= 0
    chr19 length=	63811651	Aligned= 178	Unaligned= 0
    chr20 length=	62435964	Aligned= 228	Unaligned= 0
    chr21 length=	46944323	Aligned= 123	Unaligned= 0
    chr22 length=	49691432	Aligned= 121	Unaligned= 0
    chrX length=	154913754	Aligned= 237	Unaligned= 0
    chrY length=	57772954	Aligned= 29	Unaligned= 0
    chr1_random length=	1663265	Aligned= 0	Unaligned= 0
    chr2_random length=	185571	Aligned= 0	Unaligned= 0
    chr3_random length=	749256	Aligned= 0	Unaligned= 0
    chr4_random length=	842648	Aligned= 0	Unaligned= 0
    chr5_random length=	143687	Aligned= 0	Unaligned= 0
    chr6_random length=	1875562	Aligned= 0	Unaligned= 0
    chr7_random length=	549659	Aligned= 0	Unaligned= 0
    chr8_random length=	943810	Aligned= 0	Unaligned= 0
    chr9_random length=	1146434	Aligned= 0	Unaligned= 0
    chr10_random length=	113275	Aligned= 0	Unaligned= 0
    chr11_random length=	215294	Aligned= 0	Unaligned= 0
    chr13_random length=	186858	Aligned= 0	Unaligned= 0
    chr15_random length=	784346	Aligned= 0	Unaligned= 0
    chr16_random length=	105485	Aligned= 0	Unaligned= 0
    chr17_random length=	2617613	Aligned= 0	Unaligned= 0
    chr18_random length=	4262	Aligned= 0	Unaligned= 0
    chr19_random length=	301858	Aligned= 0	Unaligned= 0
    chr21_random length=	1679693	Aligned= 0	Unaligned= 0
    chr22_random length=	257318	Aligned= 0	Unaligned= 0
    chrX_random length=	1719168	Aligned= 0	Unaligned= 0
    NoCoordinateCount= 279
Finished 400 tests

Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteBinary STANDARD_OUT
    #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.2750161010191483551.bai
    #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.15830538535078931576.bai
    #BAMIndexWriterTest diff /tmp/javaBai.2750161010191483551.bai /tmp/cBai.15830538535078931576.bai

Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteText STANDARD_OUT
    #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.17387163724022175056.bai.txt
    #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.613650840951684057java.bai
    #BAMIndexWriterTest diff /tmp/javaBai.613650840951684057java.bai.txt /tmp/cBai.17387163724022175056.bai.txt
Finished 600 tests

Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.readPastEndOfFile STANDARD_OUT
    4ms to write

Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.timeTest STANDARD_OUT
    3ms to write

Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedInputStreamTest.testCustomInflater SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testBasic STANDARD_OUT
    Creating file /tmp/BCOST.1766175562148577771.gz

Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testCustomDeflater STANDARD_OUT
    Creating file /tmp/testCustomDeflater.14881755396101322987.gz

Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testOverflow STANDARD_OUT
    Creating file /tmp/BCOST.9768897646454591960.gz
Finished 800 tests

Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromContainer STANDARD_ERROR
    WARNING	2025-06-03 15:08:45	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:08:45	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromStream STANDARD_ERROR
    WARNING	2025-06-03 15:08:45	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:08:45	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.fullVerificationTest[0](c1#bounds) STANDARD_ERROR
    WARNING	2025-06-03 15:08:46	CRAMReferenceRegion	The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12
    WARNING	2025-06-03 15:08:46	Slice	Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0.
    WARNING	2025-06-03 15:08:46	CRAMReferenceRegion	The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12
    WARNING	2025-06-03 15:08:46	Slice	Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0.

Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testCRAMThroughBAMRoundTrip[4](src/test/resources/htsjdk/samtools/cram/test.cram, src/test/resources/htsjdk/samtools/cram/auxf.fa) STANDARD_ERROR
    WARNING	2025-06-03 15:08:48	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:08:48	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testCRAMThroughBAMRoundTrip[5](src/test/resources/htsjdk/samtools/cram/test2.cram, src/test/resources/htsjdk/samtools/cram/auxf.fa) STANDARD_ERROR
    WARNING	2025-06-03 15:08:48	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:08:48	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testObsoleteDataSeriesNotWritten STANDARD_ERROR
    WARNING	2025-06-03 15:08:48	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:08:48	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testContigNotFoundInRef STANDARD_ERROR
    WARNING	2025-06-03 15:08:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:08:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testNullsAndBeyondRef STANDARD_ERROR
    WARNING	2025-06-03 15:08:49	CRAMReferenceRegion	The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3
    WARNING	2025-06-03 15:08:49	Slice	Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0.
    WARNING	2025-06-03 15:08:49	CRAMReferenceRegion	The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3
    WARNING	2025-06-03 15:08:49	Slice	Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0.

Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testUnsorted STANDARD_ERROR
    WARNING	2025-06-03 15:08:49	CRAMReferenceRegion	The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37
    WARNING	2025-06-03 15:08:49	Slice	Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0.
    WARNING	2025-06-03 15:08:49	CRAMReferenceRegion	The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37
    WARNING	2025-06-03 15:08:49	Slice	Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0.

Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCRAMReader1_ReferenceRequired STANDARD_ERROR
    INFO	2025-06-03 15:12:50	ReferenceSource	Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that.
    WARNING	2025-06-03 15:12:50	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:12:50	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCramIteratorWithoutCallingHasNextFirst STANDARD_ERROR
    WARNING	2025-06-03 15:12:50	CRAMReferenceRegion	The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37
    WARNING	2025-06-03 15:12:50	Slice	Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0.
    WARNING	2025-06-03 15:12:50	CRAMReferenceRegion	The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37
    WARNING	2025-06-03 15:12:50	Slice	Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0.
Finished 1000 tests

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[1](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@26b34cc7, [Ljava.lang.String;@158a4b46) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@abe8545, [Ljava.lang.String;@6d5f1b6c) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryAlignmentStart[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, 2) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryAlignmentStart[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, 24) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@2fd0a849, [Ljava.lang.String;@2ab252c2) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2e72cd4f, [Ljava.lang.String;@642b5dd0) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7016df9e, [Ljava.lang.String;@674d8ebc) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5f7c7d9a, [Ljava.lang.String;@656f10ff) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4b1f64f2, [Ljava.lang.String;@5a8d090c) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6422ca55, [Ljava.lang.String;@23059242) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5ea22955, [Ljava.lang.String;@7882246a) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@521cdd00, [Ljava.lang.String;@49732172) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1772dc30, [Ljava.lang.String;@5181959e) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@40ba5199, [Ljava.lang.String;@18e0b741) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7ea611, [Ljava.lang.String;@343df691) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1d98e885, [Ljava.lang.String;@1a5fd792) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@8170ccc, [Ljava.lang.String;@308f92dc) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@f459574, [Ljava.lang.String;@3b887553) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3c95814a, [Ljava.lang.String;@731c5da7) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6e5d1a9d, [Ljava.lang.String;@77d2b510) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@441cc7ae, [Ljava.lang.String;@8f97330) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@ba10461) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@2f6d26ea) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@27c26f57) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@6f0b8922) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@622a4ff0) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@7b49e6cf) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@f13bcfe) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@45483a7) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryMate[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryMate[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@58841f6d, [Ljava.lang.String;@760bbafa) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5bd6b6c0, [Ljava.lang.String;@27f93e66) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@aaf93a2, [Ljava.lang.String;@3336a055) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@41a566cb, [Ljava.lang.String;@3ee66948) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@68ed98b2, [Ljava.lang.String;@1328696d) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@256c4496, [Ljava.lang.String;@34ecff3d) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@38c313b4, [Ljava.lang.String;@4fdbaca0) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
Finished 1200 tests

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@49d373cf, [Ljava.lang.String;@5dab0100) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@105c44d2, [Ljava.lang.String;@7040589b) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6ab6779d, [Ljava.lang.String;@706ccdcb) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6fb540c2, [Ljava.lang.String;@ba94394) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@59f7539e, [Ljava.lang.String;@17603971) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1feb8755, [Ljava.lang.String;@290772c8) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@21154d26, [Ljava.lang.String;@5f4f9958) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@393f9d, [Ljava.lang.String;@35d84281) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@50dd8534, [Ljava.lang.String;@f882bc6) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4bff85c, [Ljava.lang.String;@60704931) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@7da29b32) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@345a7459) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@5c3c5bc1) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@25b4f001) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@4d6c3078) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@77febc08) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@5fc0fddf) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@646b446c) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@1244c5e3) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@32f65fff) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@9187ee5) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@1d545f24) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@439484ae) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@4a95e2c5) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@639aacad) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@302909a0) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@a73803e) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@5dc604e) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@4ca6a516) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@7a8e4c25) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@549dc7c9) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@10425cf0) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@1147d181) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@66fa8f23) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@7e8b34a9) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@349e6caf) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@13708843) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@68331fc1) STANDARD_ERROR
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@1b758296) STANDARD_ERROR
    WARNING	2025-06-03 15:15:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@3b1247f3) STANDARD_ERROR
    WARNING	2025-06-03 15:15:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@717f8253) STANDARD_ERROR
    WARNING	2025-06-03 15:15:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@17bf13e0, 5) STANDARD_ERROR
    WARNING	2025-06-03 15:15:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMMergerTest.test STANDARD_ERROR
    WARNING	2025-06-03 15:15:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.cram.ref.CRAMReferenceRegionTest.testGetReferenceBasesByRegionExceedsContigLength STANDARD_ERROR
    WARNING	2025-06-03 15:15:35	CRAMReferenceRegion	The bases of length 5000 returned by the reference source do not satisfy the requested fragment length 15000

Gradle suite > Gradle test > htsjdk.samtools.CRAMReferencelessTest.testForNPE STANDARD_ERROR
    INFO	2025-06-03 15:15:35	ReferenceSource	Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that.

Gradle suite > Gradle test > htsjdk.samtools.CRAMReferencelessTest.testReadCRAMNoReferenceRequired STANDARD_ERROR
    INFO	2025-06-03 15:15:35	ReferenceSource	Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that.

Gradle suite > Gradle test > htsjdk.samtools.CRAMReferencelessTest.testReadCRAMWithEmbeddedReference STANDARD_ERROR
    INFO	2025-06-03 15:15:36	ReferenceSource	Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that.
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Read name 20FUKAAXX100202:2:1:20271:61529, Mate Alignment start (9999748) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Read name 20FUKAAXX100202:2:1:20271:61529, Mate Alignment start (9999748) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 1, Read name 20FUKAAXX100202:3:27:11237:128368, Mate Alignment start (9999703) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 1, Read name 20FUKAAXX100202:3:27:11237:128368, Mate Alignment start (9999703) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 2, Read name 20FUKAAXX100202:3:27:11250:128353, Mate Alignment start (9999703) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 2, Read name 20FUKAAXX100202:3:27:11250:128353, Mate Alignment start (9999703) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 3, Read name 20GAVAAXX100126:4:23:2251:22957, Mate Alignment start (9999692) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 3, Read name 20GAVAAXX100126:4:23:2251:22957, Mate Alignment start (9999692) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 4, Read name 20FUKAAXX100202:2:41:20497:197885, Mate Alignment start (10000344) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 4, Read name 20FUKAAXX100202:2:41:20497:197885, Mate Alignment start (10000344) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 5, Read name 20FUKAAXX100202:7:67:1995:131468, Mate Alignment start (9999746) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 5, Read name 20FUKAAXX100202:7:67:1995:131468, Mate Alignment start (9999746) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 6, Read name 20GAVAAXX100126:2:64:13726:30107, Mate Alignment start (10000306) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 6, Read name 20GAVAAXX100126:2:64:13726:30107, Mate Alignment start (10000306) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 7, Read name 20FUKAAXX100202:4:43:20796:59238, Mate Alignment start (9999709) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 7, Read name 20FUKAAXX100202:4:43:20796:59238, Mate Alignment start (9999709) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 8, Read name 20GAVAAXX100126:1:23:7794:118351, Mate Alignment start (10000299) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 8, Read name 20GAVAAXX100126:1:23:7794:118351, Mate Alignment start (10000299) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 9, Read name 20GAVAAXX100126:4:68:6400:174077, Mate Alignment start (10000335) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 9, Read name 20GAVAAXX100126:4:68:6400:174077, Mate Alignment start (10000335) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 10, Read name 20GAVAAXX100126:5:27:13558:117863, Mate Alignment start (9999715) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 10, Read name 20GAVAAXX100126:5:27:13558:117863, Mate Alignment start (9999715) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 11, Read name 20FUKAAXX100202:1:64:5977:190591, Mate Alignment start (10000296) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 11, Read name 20FUKAAXX100202:1:64:5977:190591, Mate Alignment start (10000296) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 12, Read name 20FUKAAXX100202:8:68:8163:66511, Mate Alignment start (10000285) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 12, Read name 20FUKAAXX100202:8:68:8163:66511, Mate Alignment start (10000285) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 13, Read name 20GAVAAXX100126:2:65:15310:41789, Mate Alignment start (9999670) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 13, Read name 20GAVAAXX100126:2:65:15310:41789, Mate Alignment start (9999670) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 14, Read name 20GAVAAXX100126:7:66:12507:22293, Mate Alignment start (10000236) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 14, Read name 20GAVAAXX100126:7:66:12507:22293, Mate Alignment start (10000236) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 15, Read name 20FUKAAXX100202:4:28:1593:6464, Mate Alignment start (9999607) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 15, Read name 20FUKAAXX100202:4:28:1593:6464, Mate Alignment start (9999607) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 16, Read name 20FUKAAXX100202:3:43:19691:103757, Mate Alignment start (10000257) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 16, Read name 20FUKAAXX100202:3:43:19691:103757, Mate Alignment start (10000257) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 17, Read name 20FUKAAXX100202:5:24:20426:8780, Mate Alignment start (10000318) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 17, Read name 20FUKAAXX100202:5:24:20426:8780, Mate Alignment start (10000318) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 18, Read name 20GAVAAXX100126:3:43:6705:167739, Mate Alignment start (10000257) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 18, Read name 20GAVAAXX100126:3:43:6705:167739, Mate Alignment start (10000257) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 19, Read name 20GAVAAXX100126:3:66:17154:191764, Mate Alignment start (9999760) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 19, Read name 20GAVAAXX100126:3:66:17154:191764, Mate Alignment start (9999760) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 20, Read name 20GAVAAXX100126:6:66:18327:134560, Mate Alignment start (9999694) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 20, Read name 20GAVAAXX100126:6:66:18327:134560, Mate Alignment start (9999694) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 23, Read name 20FUKAAXX100202:5:64:19991:74214, Mate Alignment start (10000274) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 23, Read name 20FUKAAXX100202:5:64:19991:74214, Mate Alignment start (10000274) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 24, Read name 20FUKAAXX100202:2:41:7948:31113, Mate Alignment start (9999705) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 24, Read name 20FUKAAXX100202:2:41:7948:31113, Mate Alignment start (9999705) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 25, Read name 20GAVAAXX100126:8:67:6825:84706, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 25, Read name 20GAVAAXX100126:8:67:6825:84706, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 26, Read name 20FUKAAXX100202:5:46:8200:95675, Mate Alignment start (10000307) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 26, Read name 20FUKAAXX100202:5:46:8200:95675, Mate Alignment start (10000307) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 27, Read name 20FUKAAXX100202:5:46:8201:95696, Mate Alignment start (10000307) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 27, Read name 20FUKAAXX100202:5:46:8201:95696, Mate Alignment start (10000307) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 28, Read name 20FUKAAXX100202:6:5:15635:154535, Mate Alignment start (10000315) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 28, Read name 20FUKAAXX100202:6:5:15635:154535, Mate Alignment start (10000315) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 29, Read name 20FUKAAXX100202:7:41:10752:140666, Mate Alignment start (9999753) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 29, Read name 20FUKAAXX100202:7:41:10752:140666, Mate Alignment start (9999753) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 30, Read name 20GAVAAXX100126:2:23:4627:33063, Mate Alignment start (10000346) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 30, Read name 20GAVAAXX100126:2:23:4627:33063, Mate Alignment start (10000346) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 31, Read name 20GAVAAXX100126:2:23:4640:33082, Mate Alignment start (10000346) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 31, Read name 20GAVAAXX100126:2:23:4640:33082, Mate Alignment start (10000346) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 32, Read name 20GAVAAXX100126:3:25:2015:120007, Mate Alignment start (9999741) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 32, Read name 20GAVAAXX100126:3:25:2015:120007, Mate Alignment start (9999741) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 33, Read name 20GAVAAXX100126:3:25:2028:120028, Mate Alignment start (9999741) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 33, Read name 20GAVAAXX100126:3:25:2028:120028, Mate Alignment start (9999741) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 34, Read name 20FUKAAXX100202:5:41:14163:52829, Mate Alignment start (10000260) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 34, Read name 20FUKAAXX100202:5:41:14163:52829, Mate Alignment start (10000260) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 35, Read name 20GAVAAXX100126:7:46:18099:135243, Mate Alignment start (9999721) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 35, Read name 20GAVAAXX100126:7:46:18099:135243, Mate Alignment start (9999721) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 36, Read name 20GAVAAXX100126:2:47:15498:55100, Mate Alignment start (9999706) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 36, Read name 20GAVAAXX100126:2:47:15498:55100, Mate Alignment start (9999706) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 37, Read name 20FUKAAXX100202:8:21:4919:132430, Mate Alignment start (10000321) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 37, Read name 20FUKAAXX100202:8:21:4919:132430, Mate Alignment start (10000321) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 38, Read name 20FUKAAXX100202:3:67:3748:19953, Mate Alignment start (10000279) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 38, Read name 20FUKAAXX100202:3:67:3748:19953, Mate Alignment start (10000279) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 39, Read name 20FUKAAXX100202:2:2:3418:95829, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 39, Read name 20FUKAAXX100202:2:2:3418:95829, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 40, Read name 20FUKAAXX100202:6:5:5332:102974, Mate Alignment start (10000361) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 40, Read name 20FUKAAXX100202:6:5:5332:102974, Mate Alignment start (10000361) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 41, Read name 20FUKAAXX100202:2:8:7024:145363, Mate Alignment start (10000353) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 41, Read name 20FUKAAXX100202:2:8:7024:145363, Mate Alignment start (10000353) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 42, Read name 20GAVAAXX100126:3:25:20036:5188, Mate Alignment start (9999721) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 42, Read name 20GAVAAXX100126:3:25:20036:5188, Mate Alignment start (9999721) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 43, Read name 20FUKAAXX100202:5:2:4432:167162, Mate Alignment start (9999749) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 43, Read name 20FUKAAXX100202:5:2:4432:167162, Mate Alignment start (9999749) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 44, Read name 20GAVAAXX100126:3:63:6482:2143, Mate Alignment start (10000263) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 44, Read name 20GAVAAXX100126:3:63:6482:2143, Mate Alignment start (10000263) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 45, Read name 20GAVAAXX100126:3:63:6488:2160, Mate Alignment start (10000263) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 45, Read name 20GAVAAXX100126:3:63:6488:2160, Mate Alignment start (10000263) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 48, Read name 20FUKAAXX100202:1:21:2273:66026, Mate Alignment start (10000322) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 48, Read name 20FUKAAXX100202:1:21:2273:66026, Mate Alignment start (10000322) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 49, Read name 20FUKAAXX100202:1:21:2285:66012, Mate Alignment start (10000322) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 49, Read name 20FUKAAXX100202:1:21:2285:66012, Mate Alignment start (10000322) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 50, Read name 20FUKAAXX100202:4:8:13315:108160, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 50, Read name 20FUKAAXX100202:4:8:13315:108160, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 51, Read name 20FUKAAXX100202:2:21:15808:57403, Mate Alignment start (10000379) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 51, Read name 20FUKAAXX100202:2:21:15808:57403, Mate Alignment start (10000379) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 52, Read name 20FUKAAXX100202:8:41:10876:123643, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 52, Read name 20FUKAAXX100202:8:41:10876:123643, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 53, Read name 20FUKAAXX100202:8:41:10891:123658, Mate Alignment start (10000357) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 53, Read name 20FUKAAXX100202:8:41:10891:123658, Mate Alignment start (10000357) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 54, Read name 20FUKAAXX100202:1:8:10582:193735, Mate Alignment start (9999814) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 54, Read name 20FUKAAXX100202:1:8:10582:193735, Mate Alignment start (9999814) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 55, Read name 20FUKAAXX100202:4:23:20668:198863, Mate Alignment start (10000391) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 55, Read name 20FUKAAXX100202:4:23:20668:198863, Mate Alignment start (10000391) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 56, Read name 20FUKAAXX100202:3:27:18714:174324, Mate Alignment start (10000329) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 56, Read name 20FUKAAXX100202:3:27:18714:174324, Mate Alignment start (10000329) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 57, Read name 20GAVAAXX100126:3:3:7922:39057, Mate Alignment start (9999758) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 57, Read name 20GAVAAXX100126:3:3:7922:39057, Mate Alignment start (9999758) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 58, Read name 20GAVAAXX100126:3:26:15712:87893, Mate Alignment start (10000309) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 58, Read name 20GAVAAXX100126:3:26:15712:87893, Mate Alignment start (10000309) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 59, Read name 20GAVAAXX100126:4:23:3530:147535, Mate Alignment start (9999796) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 59, Read name 20GAVAAXX100126:4:23:3530:147535, Mate Alignment start (9999796) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 60, Read name 20GAVAAXX100126:5:24:17054:156839, Mate Alignment start (10000359) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 60, Read name 20GAVAAXX100126:5:24:17054:156839, Mate Alignment start (10000359) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 61, Read name 20GAVAAXX100126:5:24:17070:156829, Mate Alignment start (10000359) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 61, Read name 20GAVAAXX100126:5:24:17070:156829, Mate Alignment start (10000359) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 62, Read name 20GAVAAXX100126:5:28:14493:46327, Mate Alignment start (10000381) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 62, Read name 20GAVAAXX100126:5:28:14493:46327, Mate Alignment start (10000381) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 63, Read name 20GAVAAXX100126:5:28:14509:46338, Mate Alignment start (10000381) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 63, Read name 20GAVAAXX100126:5:28:14509:46338, Mate Alignment start (10000381) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 64, Read name 20FUKAAXX100202:3:3:19592:17448, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 64, Read name 20FUKAAXX100202:3:3:19592:17448, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 65, Read name 20FUKAAXX100202:5:61:14815:105709, Mate Alignment start (9999813) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 65, Read name 20FUKAAXX100202:5:61:14815:105709, Mate Alignment start (9999813) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 66, Read name 20GAVAAXX100126:2:1:17704:50462, Mate Alignment start (9999830) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 66, Read name 20GAVAAXX100126:2:1:17704:50462, Mate Alignment start (9999830) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 67, Read name 20GAVAAXX100126:2:5:19558:132530, Mate Alignment start (10000310) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 67, Read name 20GAVAAXX100126:2:5:19558:132530, Mate Alignment start (10000310) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 68, Read name 20FUKAAXX100202:2:42:6225:11993, Mate Alignment start (10000403) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 68, Read name 20FUKAAXX100202:2:42:6225:11993, Mate Alignment start (10000403) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 69, Read name 20FUKAAXX100202:1:6:12511:73800, Mate Alignment start (10000338) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 69, Read name 20FUKAAXX100202:1:6:12511:73800, Mate Alignment start (10000338) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 70, Read name 20FUKAAXX100202:3:3:7237:174227, Mate Alignment start (9999772) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 70, Read name 20FUKAAXX100202:3:3:7237:174227, Mate Alignment start (9999772) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 71, Read name 20GAVAAXX100126:2:44:2924:108763, Mate Alignment start (9999762) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 71, Read name 20GAVAAXX100126:2:44:2924:108763, Mate Alignment start (9999762) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 72, Read name 20FUKAAXX100202:5:46:18326:99323, Mate Alignment start (9999771) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 72, Read name 20FUKAAXX100202:5:46:18326:99323, Mate Alignment start (9999771) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 73, Read name 20FUKAAXX100202:1:41:13026:43433, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 73, Read name 20FUKAAXX100202:1:41:13026:43433, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 74, Read name 20FUKAAXX100202:7:41:10475:81635, Mate Alignment start (10000316) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 74, Read name 20FUKAAXX100202:7:41:10475:81635, Mate Alignment start (10000316) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 75, Read name 20FUKAAXX100202:6:7:6837:63100, Mate Alignment start (10000335) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 75, Read name 20FUKAAXX100202:6:7:6837:63100, Mate Alignment start (10000335) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 76, Read name 20FUKAAXX100202:8:41:15613:40512, Mate Alignment start (10000400) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 76, Read name 20FUKAAXX100202:8:41:15613:40512, Mate Alignment start (10000400) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 77, Read name 20GAVAAXX100126:4:66:5628:46560, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 77, Read name 20GAVAAXX100126:4:66:5628:46560, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 78, Read name 20GAVAAXX100126:2:43:11751:59743, Mate Alignment start (9999772) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 78, Read name 20GAVAAXX100126:2:43:11751:59743, Mate Alignment start (9999772) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 79, Read name 20GAVAAXX100126:4:6:17284:168594, Mate Alignment start (9999791) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 79, Read name 20GAVAAXX100126:4:6:17284:168594, Mate Alignment start (9999791) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 80, Read name 20FUKAAXX100202:8:41:1273:146353, Mate Alignment start (10000404) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 80, Read name 20FUKAAXX100202:8:41:1273:146353, Mate Alignment start (10000404) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 81, Read name 20FUKAAXX100202:5:43:11657:127515, Mate Alignment start (9999834) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 81, Read name 20FUKAAXX100202:5:43:11657:127515, Mate Alignment start (9999834) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 82, Read name 20FUKAAXX100202:5:43:11665:127498, Mate Alignment start (9999834) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 82, Read name 20FUKAAXX100202:5:43:11665:127498, Mate Alignment start (9999834) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 83, Read name 20FUKAAXX100202:1:48:13750:136932, Mate Alignment start (10000350) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 83, Read name 20FUKAAXX100202:1:48:13750:136932, Mate Alignment start (10000350) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 84, Read name 20FUKAAXX100202:1:2:3754:138352, Mate Alignment start (10000379) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 84, Read name 20FUKAAXX100202:1:2:3754:138352, Mate Alignment start (10000379) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 85, Read name 20GAVAAXX100126:7:46:18080:135229, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 85, Read name 20GAVAAXX100126:7:46:18080:135229, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 86, Read name 20FUKAAXX100202:7:22:18885:27661, Mate Alignment start (9999857) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 86, Read name 20FUKAAXX100202:7:22:18885:27661, Mate Alignment start (9999857) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 87, Read name 20GAVAAXX100126:2:68:19001:156273, Mate Alignment start (9999800) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 87, Read name 20GAVAAXX100126:2:68:19001:156273, Mate Alignment start (9999800) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 88, Read name 20GAVAAXX100126:7:23:12948:100075, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 88, Read name 20GAVAAXX100126:7:23:12948:100075, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 89, Read name 20GAVAAXX100126:3:44:17022:23968, Mate Alignment start (9999797) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 89, Read name 20GAVAAXX100126:3:44:17022:23968, Mate Alignment start (9999797) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 90, Read name 20FUKAAXX100202:1:21:6910:153058, Mate Alignment start (10000324) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 90, Read name 20FUKAAXX100202:1:21:6910:153058, Mate Alignment start (10000324) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 91, Read name 20GAVAAXX100126:4:43:14464:8329, Mate Alignment start (10000409) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 91, Read name 20GAVAAXX100126:4:43:14464:8329, Mate Alignment start (10000409) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 92, Read name 20GAVAAXX100126:4:43:14480:8346, Mate Alignment start (10000408) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 92, Read name 20GAVAAXX100126:4:43:14480:8346, Mate Alignment start (10000408) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 93, Read name 20FUKAAXX100202:6:27:18144:27680, Mate Alignment start (10000498) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 93, Read name 20FUKAAXX100202:6:27:18144:27680, Mate Alignment start (10000498) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 94, Read name 20GAVAAXX100126:8:44:5555:179202, Mate Alignment start (9999834) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 94, Read name 20GAVAAXX100126:8:44:5555:179202, Mate Alignment start (9999834) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 95, Read name 20GAVAAXX100126:5:63:15490:26472, Mate Alignment start (10000395) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 95, Read name 20GAVAAXX100126:5:63:15490:26472, Mate Alignment start (10000395) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 96, Read name 20FUKAAXX100202:6:24:17640:150063, Mate Alignment start (9999667) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 96, Read name 20FUKAAXX100202:6:24:17640:150063, Mate Alignment start (9999667) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 97, Read name 20FUKAAXX100202:2:46:7154:171464, Mate Alignment start (10000326) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 97, Read name 20FUKAAXX100202:2:46:7154:171464, Mate Alignment start (10000326) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 98, Read name 20FUKAAXX100202:2:46:7154:171487, Mate Alignment start (10000326) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 98, Read name 20FUKAAXX100202:2:46:7154:171487, Mate Alignment start (10000326) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 99, Read name 20FUKAAXX100202:3:4:1882:78979, Mate Alignment start (10000344) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 99, Read name 20FUKAAXX100202:3:4:1882:78979, Mate Alignment start (10000344) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 100, Read name 20FUKAAXX100202:4:5:13072:190773, Mate Alignment start (9999748) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 100, Read name 20FUKAAXX100202:4:5:13072:190773, Mate Alignment start (9999748) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 101, Read name 20FUKAAXX100202:8:63:5291:16081, Mate Alignment start (9999671) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 101, Read name 20FUKAAXX100202:8:63:5291:16081, Mate Alignment start (9999671) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 102, Read name 20GAVAAXX100126:5:48:11843:159383, Mate Alignment start (9999699) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 102, Read name 20GAVAAXX100126:5:48:11843:159383, Mate Alignment start (9999699) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 103, Read name 20GAVAAXX100126:6:21:4070:89543, Mate Alignment start (9999671) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 103, Read name 20GAVAAXX100126:6:21:4070:89543, Mate Alignment start (9999671) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 104, Read name 20GAVAAXX100126:7:44:7446:1891, Mate Alignment start (9999669) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 104, Read name 20GAVAAXX100126:7:44:7446:1891, Mate Alignment start (9999669) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 105, Read name 20FUKAAXX100202:6:67:17100:172461, Mate Alignment start (9999764) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 105, Read name 20FUKAAXX100202:6:67:17100:172461, Mate Alignment start (9999764) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 106, Read name 20GAVAAXX100126:6:64:2441:17495, Mate Alignment start (9999764) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 106, Read name 20GAVAAXX100126:6:64:2441:17495, Mate Alignment start (9999764) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 107, Read name 20FUKAAXX100202:1:5:14642:152032, Mate Alignment start (10000246) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 107, Read name 20FUKAAXX100202:1:5:14642:152032, Mate Alignment start (10000246) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 108, Read name 20FUKAAXX100202:4:6:12695:123335, Mate Alignment start (10000333) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 108, Read name 20FUKAAXX100202:4:6:12695:123335, Mate Alignment start (10000333) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 109, Read name 20FUKAAXX100202:1:61:11336:198565, Mate Alignment start (9999704) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 109, Read name 20FUKAAXX100202:1:61:11336:198565, Mate Alignment start (9999704) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 110, Read name 20GAVAAXX100126:7:48:10601:51282, Mate Alignment start (9999727) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 110, Read name 20GAVAAXX100126:7:48:10601:51282, Mate Alignment start (9999727) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 111, Read name 20GAVAAXX100126:8:62:18437:38607, Mate Alignment start (9999701) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 111, Read name 20GAVAAXX100126:8:62:18437:38607, Mate Alignment start (9999701) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 112, Read name 20GAVAAXX100126:4:7:20111:148814, Mate Alignment start (10000281) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 112, Read name 20GAVAAXX100126:4:7:20111:148814, Mate Alignment start (10000281) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 113, Read name 20FUKAAXX100202:8:43:12077:86650, Mate Alignment start (9999682) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 113, Read name 20FUKAAXX100202:8:43:12077:86650, Mate Alignment start (9999682) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 114, Read name 20GAVAAXX100126:5:25:17399:72164, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 114, Read name 20GAVAAXX100126:5:25:17399:72164, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 117, Read name 20FUKAAXX100202:3:48:16538:10482, Mate Alignment start (10000457) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 117, Read name 20FUKAAXX100202:3:48:16538:10482, Mate Alignment start (10000457) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 118, Read name 20GAVAAXX100126:7:46:11904:195602, Mate Alignment start (10000293) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 118, Read name 20GAVAAXX100126:7:46:11904:195602, Mate Alignment start (10000293) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 121, Read name 20GAVAAXX100126:4:21:14134:132604, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 121, Read name 20GAVAAXX100126:4:21:14134:132604, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 122, Read name 20FUKAAXX100202:5:47:2763:24217, Mate Alignment start (9999701) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 122, Read name 20FUKAAXX100202:5:47:2763:24217, Mate Alignment start (9999701) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 123, Read name 20GAVAAXX100126:8:21:2096:123816, Mate Alignment start (9999768) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 123, Read name 20GAVAAXX100126:8:21:2096:123816, Mate Alignment start (9999768) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 126, Read name 20FUKAAXX100202:4:23:7470:195860, Mate Alignment start (10000353) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 126, Read name 20FUKAAXX100202:4:23:7470:195860, Mate Alignment start (10000353) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 127, Read name 20GAVAAXX100126:5:5:9475:54882, Mate Alignment start (10000264) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 127, Read name 20GAVAAXX100126:5:5:9475:54882, Mate Alignment start (10000264) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 128, Read name 20GAVAAXX100126:6:68:9971:99340, Mate Alignment start (10000372) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 128, Read name 20GAVAAXX100126:6:68:9971:99340, Mate Alignment start (10000372) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 129, Read name 20GAVAAXX100126:8:4:2514:172766, Mate Alignment start (9999751) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 129, Read name 20GAVAAXX100126:8:4:2514:172766, Mate Alignment start (9999751) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 130, Read name 20FUKAAXX100202:8:45:1989:15113, Mate Alignment start (10000303) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 130, Read name 20FUKAAXX100202:8:45:1989:15113, Mate Alignment start (10000303) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 131, Read name 20FUKAAXX100202:5:43:9081:11499, Mate Alignment start (9999706) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 131, Read name 20FUKAAXX100202:5:43:9081:11499, Mate Alignment start (9999706) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 132, Read name 20GAVAAXX100126:6:2:3042:60022, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 132, Read name 20GAVAAXX100126:6:2:3042:60022, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 133, Read name 20FUKAAXX100202:1:25:16659:142466, Mate Alignment start (9999713) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 133, Read name 20FUKAAXX100202:1:25:16659:142466, Mate Alignment start (9999713) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 134, Read name 20GAVAAXX100126:7:47:6583:18921, Mate Alignment start (9999712) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 134, Read name 20GAVAAXX100126:7:47:6583:18921, Mate Alignment start (9999712) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 135, Read name 20FUKAAXX100202:8:25:6061:158813, Mate Alignment start (9999688) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 135, Read name 20FUKAAXX100202:8:25:6061:158813, Mate Alignment start (9999688) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 136, Read name 20GAVAAXX100126:8:65:19600:82097, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 136, Read name 20GAVAAXX100126:8:65:19600:82097, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 137, Read name 20GAVAAXX100126:8:65:19610:82077, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 137, Read name 20GAVAAXX100126:8:65:19610:82077, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 138, Read name 20FUKAAXX100202:2:22:8993:175344, Mate Alignment start (9999717) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 138, Read name 20FUKAAXX100202:2:22:8993:175344, Mate Alignment start (9999717) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 139, Read name 20GAVAAXX100126:1:21:7801:54762, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 139, Read name 20GAVAAXX100126:1:21:7801:54762, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 140, Read name 20GAVAAXX100126:4:1:13342:97110, Mate Alignment start (9999743) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 140, Read name 20GAVAAXX100126:4:1:13342:97110, Mate Alignment start (9999743) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 141, Read name 20FUKAAXX100202:3:2:9552:27284, Mate Alignment start (9999718) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 141, Read name 20FUKAAXX100202:3:2:9552:27284, Mate Alignment start (9999718) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 142, Read name 20FUKAAXX100202:4:3:6934:181831, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 142, Read name 20FUKAAXX100202:4:3:6934:181831, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 143, Read name 20GAVAAXX100126:8:7:2115:102977, Mate Alignment start (9999745) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 143, Read name 20GAVAAXX100126:8:7:2115:102977, Mate Alignment start (9999745) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 144, Read name 20FUKAAXX100202:5:45:17899:193943, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 144, Read name 20FUKAAXX100202:5:45:17899:193943, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 145, Read name 20FUKAAXX100202:7:24:21385:130712, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 145, Read name 20FUKAAXX100202:7:24:21385:130712, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 146, Read name 20FUKAAXX100202:7:2:15287:105342, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 146, Read name 20FUKAAXX100202:7:2:15287:105342, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 147, Read name 20FUKAAXX100202:2:61:15800:106937, Mate Alignment start (9999698) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 147, Read name 20FUKAAXX100202:2:61:15800:106937, Mate Alignment start (9999698) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 148, Read name 20GAVAAXX100126:8:41:3599:9555, Mate Alignment start (9999698) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 148, Read name 20GAVAAXX100126:8:41:3599:9555, Mate Alignment start (9999698) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 149, Read name 20FUKAAXX100202:1:44:3588:13144, Mate Alignment start (10000326) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 149, Read name 20FUKAAXX100202:1:44:3588:13144, Mate Alignment start (10000326) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 150, Read name 20GAVAAXX100126:2:8:6126:168407, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 150, Read name 20GAVAAXX100126:2:8:6126:168407, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 151, Read name 20GAVAAXX100126:2:8:6143:168418, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 151, Read name 20GAVAAXX100126:2:8:6143:168418, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 152, Read name 20FUKAAXX100202:3:28:12160:117165, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 152, Read name 20FUKAAXX100202:3:28:12160:117165, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 153, Read name 20GAVAAXX100126:4:45:8053:140082, Mate Alignment start (9999604) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 153, Read name 20GAVAAXX100126:4:45:8053:140082, Mate Alignment start (9999604) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 154, Read name 20GAVAAXX100126:6:28:11134:174564, Mate Alignment start (9999697) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 154, Read name 20GAVAAXX100126:6:28:11134:174564, Mate Alignment start (9999697) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 155, Read name 20GAVAAXX100126:6:28:11146:174578, Mate Alignment start (9999697) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 155, Read name 20GAVAAXX100126:6:28:11146:174578, Mate Alignment start (9999697) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 156, Read name 20FUKAAXX100202:8:2:10382:194128, Mate Alignment start (10000347) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 156, Read name 20FUKAAXX100202:8:2:10382:194128, Mate Alignment start (10000347) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 157, Read name 20FUKAAXX100202:3:61:14021:185070, Mate Alignment start (9999731) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 157, Read name 20FUKAAXX100202:3:61:14021:185070, Mate Alignment start (9999731) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 158, Read name 20FUKAAXX100202:5:62:19690:9570, Mate Alignment start (9999729) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 158, Read name 20FUKAAXX100202:5:62:19690:9570, Mate Alignment start (9999729) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 159, Read name 20GAVAAXX100126:1:63:20142:132241, Mate Alignment start (9999715) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 159, Read name 20GAVAAXX100126:1:63:20142:132241, Mate Alignment start (9999715) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 160, Read name 20GAVAAXX100126:5:5:16399:184379, Mate Alignment start (9999725) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 160, Read name 20GAVAAXX100126:5:5:16399:184379, Mate Alignment start (9999725) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 161, Read name 20GAVAAXX100126:2:8:11075:186130, Mate Alignment start (10000336) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 161, Read name 20GAVAAXX100126:2:8:11075:186130, Mate Alignment start (10000336) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 162, Read name 20FUKAAXX100202:3:64:18891:180836, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 162, Read name 20FUKAAXX100202:3:64:18891:180836, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 163, Read name 20GAVAAXX100126:6:41:1651:77368, Mate Alignment start (9999762) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 163, Read name 20GAVAAXX100126:6:41:1651:77368, Mate Alignment start (9999762) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 164, Read name 20FUKAAXX100202:4:24:12641:3924, Mate Alignment start (9999704) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 164, Read name 20FUKAAXX100202:4:24:12641:3924, Mate Alignment start (9999704) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 165, Read name 20GAVAAXX100126:1:67:21027:67363, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 165, Read name 20GAVAAXX100126:1:67:21027:67363, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 166, Read name 20GAVAAXX100126:6:23:2944:66430, Mate Alignment start (9999718) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 166, Read name 20GAVAAXX100126:6:23:2944:66430, Mate Alignment start (9999718) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 167, Read name 20FUKAAXX100202:5:27:9785:178062, Mate Alignment start (10000338) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 167, Read name 20FUKAAXX100202:5:27:9785:178062, Mate Alignment start (10000338) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 168, Read name 20FUKAAXX100202:7:25:3261:114933, Mate Alignment start (9999772) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 168, Read name 20FUKAAXX100202:7:25:3261:114933, Mate Alignment start (9999772) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 169, Read name 20FUKAAXX100202:7:68:14596:106064, Mate Alignment start (9999731) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 169, Read name 20FUKAAXX100202:7:68:14596:106064, Mate Alignment start (9999731) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 170, Read name 20GAVAAXX100126:3:27:20408:42852, Mate Alignment start (9999751) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 170, Read name 20GAVAAXX100126:3:27:20408:42852, Mate Alignment start (9999751) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 171, Read name 20GAVAAXX100126:5:27:19872:165078, Mate Alignment start (9999729) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 171, Read name 20GAVAAXX100126:5:27:19872:165078, Mate Alignment start (9999729) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 172, Read name 20GAVAAXX100126:8:46:5544:82405, Mate Alignment start (9999696) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 172, Read name 20GAVAAXX100126:8:46:5544:82405, Mate Alignment start (9999696) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 173, Read name 20FUKAAXX100202:6:5:13733:127380, Mate Alignment start (10000378) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 173, Read name 20FUKAAXX100202:6:5:13733:127380, Mate Alignment start (10000378) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 174, Read name 20FUKAAXX100202:6:61:9436:123634, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 174, Read name 20FUKAAXX100202:6:61:9436:123634, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 175, Read name 20FUKAAXX100202:1:4:6802:198636, Mate Alignment start (9999734) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 175, Read name 20FUKAAXX100202:1:4:6802:198636, Mate Alignment start (9999734) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 176, Read name 20FUKAAXX100202:3:61:2345:190213, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 176, Read name 20FUKAAXX100202:3:61:2345:190213, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 177, Read name 20FUKAAXX100202:7:66:18422:38530, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 177, Read name 20FUKAAXX100202:7:66:18422:38530, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 178, Read name 20FUKAAXX100202:1:1:11716:63554, Mate Alignment start (10000217) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 178, Read name 20FUKAAXX100202:1:1:11716:63554, Mate Alignment start (10000217) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 179, Read name 20FUKAAXX100202:7:2:20791:62084, Mate Alignment start (10000415) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 179, Read name 20FUKAAXX100202:7:2:20791:62084, Mate Alignment start (10000415) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 180, Read name 20FUKAAXX100202:8:7:11983:56692, Mate Alignment start (10000329) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 180, Read name 20FUKAAXX100202:8:7:11983:56692, Mate Alignment start (10000329) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 181, Read name 20GAVAAXX100126:4:62:3221:106888, Mate Alignment start (9999712) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 181, Read name 20GAVAAXX100126:4:62:3221:106888, Mate Alignment start (9999712) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 182, Read name 20GAVAAXX100126:4:8:17348:119983, Mate Alignment start (9999711) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 182, Read name 20GAVAAXX100126:4:8:17348:119983, Mate Alignment start (9999711) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 183, Read name 20FUKAAXX100202:4:5:8921:109860, Mate Alignment start (10000352) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 183, Read name 20FUKAAXX100202:4:5:8921:109860, Mate Alignment start (10000352) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 184, Read name 20FUKAAXX100202:3:61:5334:12201, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 184, Read name 20FUKAAXX100202:3:61:5334:12201, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 185, Read name 20FUKAAXX100202:6:25:20343:31574, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 185, Read name 20FUKAAXX100202:6:25:20343:31574, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 186, Read name 20FUKAAXX100202:6:25:20360:31581, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 186, Read name 20FUKAAXX100202:6:25:20360:31581, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 187, Read name 20GAVAAXX100126:3:7:12571:28928, Mate Alignment start (9999729) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 187, Read name 20GAVAAXX100126:3:7:12571:28928, Mate Alignment start (9999729) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 188, Read name 20GAVAAXX100126:7:45:8702:45252, Mate Alignment start (10000303) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 188, Read name 20GAVAAXX100126:7:45:8702:45252, Mate Alignment start (10000303) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 189, Read name 20FUKAAXX100202:4:26:8462:86912, Mate Alignment start (10000373) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 189, Read name 20FUKAAXX100202:4:26:8462:86912, Mate Alignment start (10000373) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 190, Read name 20GAVAAXX100126:8:45:6375:103133, Mate Alignment start (10000350) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 190, Read name 20GAVAAXX100126:8:45:6375:103133, Mate Alignment start (10000350) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 191, Read name 20FUKAAXX100202:4:23:21082:72960, Mate Alignment start (9999741) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 191, Read name 20FUKAAXX100202:4:23:21082:72960, Mate Alignment start (9999741) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 192, Read name 20FUKAAXX100202:4:5:5992:35455, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 192, Read name 20FUKAAXX100202:4:5:5992:35455, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 193, Read name 20GAVAAXX100126:6:4:12978:135278, Mate Alignment start (10000348) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 193, Read name 20GAVAAXX100126:6:4:12978:135278, Mate Alignment start (10000348) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 194, Read name 20GAVAAXX100126:2:5:1838:180237, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 194, Read name 20GAVAAXX100126:2:5:1838:180237, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 195, Read name 20GAVAAXX100126:7:63:11003:164288, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 195, Read name 20GAVAAXX100126:7:63:11003:164288, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 196, Read name 20FUKAAXX100202:3:48:15406:75661, Mate Alignment start (10000347) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 196, Read name 20FUKAAXX100202:3:48:15406:75661, Mate Alignment start (10000347) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 197, Read name 20GAVAAXX100126:8:65:18514:117061, Mate Alignment start (9999703) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 197, Read name 20GAVAAXX100126:8:65:18514:117061, Mate Alignment start (9999703) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 200, Read name 20FUKAAXX100202:4:46:4678:167193, Mate Alignment start (9999725) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 200, Read name 20FUKAAXX100202:4:46:4678:167193, Mate Alignment start (9999725) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 201, Read name 20GAVAAXX100126:4:27:15355:60703, Mate Alignment start (9999746) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 201, Read name 20GAVAAXX100126:4:27:15355:60703, Mate Alignment start (9999746) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 202, Read name 20FUKAAXX100202:4:63:3107:142967, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 202, Read name 20FUKAAXX100202:4:63:3107:142967, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 203, Read name 20GAVAAXX100126:1:46:17524:10808, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 203, Read name 20GAVAAXX100126:1:46:17524:10808, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 204, Read name 20GAVAAXX100126:2:45:9532:172440, Mate Alignment start (10000366) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 204, Read name 20GAVAAXX100126:2:45:9532:172440, Mate Alignment start (10000366) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 205, Read name 20FUKAAXX100202:4:43:4771:2441, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 205, Read name 20FUKAAXX100202:4:43:4771:2441, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 206, Read name 20FUKAAXX100202:1:23:16512:3262, Mate Alignment start (9999728) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 206, Read name 20FUKAAXX100202:1:23:16512:3262, Mate Alignment start (9999728) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 207, Read name 20GAVAAXX100126:6:66:6108:99558, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 207, Read name 20GAVAAXX100126:6:66:6108:99558, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 208, Read name 20FUKAAXX100202:3:23:19248:42689, Mate Alignment start (10000341) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 208, Read name 20FUKAAXX100202:3:23:19248:42689, Mate Alignment start (10000341) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 209, Read name 20FUKAAXX100202:4:67:19946:84115, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 209, Read name 20FUKAAXX100202:4:67:19946:84115, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 210, Read name 20FUKAAXX100202:4:67:19957:84130, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 210, Read name 20FUKAAXX100202:4:67:19957:84130, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 211, Read name 20GAVAAXX100126:8:46:6721:107141, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 211, Read name 20GAVAAXX100126:8:46:6721:107141, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 212, Read name 20FUKAAXX100202:2:44:11476:56122, Mate Alignment start (10000402) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 212, Read name 20FUKAAXX100202:2:44:11476:56122, Mate Alignment start (10000402) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 213, Read name 20FUKAAXX100202:2:62:3370:172539, Mate Alignment start (10000406) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 213, Read name 20FUKAAXX100202:2:62:3370:172539, Mate Alignment start (10000406) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 214, Read name 20FUKAAXX100202:5:27:20510:84577, Mate Alignment start (9999762) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 214, Read name 20FUKAAXX100202:5:27:20510:84577, Mate Alignment start (9999762) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 215, Read name 20FUKAAXX100202:5:43:10418:69609, Mate Alignment start (10000351) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 215, Read name 20FUKAAXX100202:5:43:10418:69609, Mate Alignment start (10000351) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 216, Read name 20FUKAAXX100202:8:22:10804:10935, Mate Alignment start (10000400) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 216, Read name 20FUKAAXX100202:8:22:10804:10935, Mate Alignment start (10000400) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 217, Read name 20FUKAAXX100202:8:28:12970:89358, Mate Alignment start (10000394) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 217, Read name 20FUKAAXX100202:8:28:12970:89358, Mate Alignment start (10000394) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 218, Read name 20GAVAAXX100126:1:3:9885:16197, Mate Alignment start (10000221) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 218, Read name 20GAVAAXX100126:1:3:9885:16197, Mate Alignment start (10000221) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 219, Read name 20GAVAAXX100126:5:41:2927:129979, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 219, Read name 20GAVAAXX100126:5:41:2927:129979, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 220, Read name 20FUKAAXX100202:6:3:13871:76745, Mate Alignment start (9999759) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 220, Read name 20FUKAAXX100202:6:3:13871:76745, Mate Alignment start (9999759) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 221, Read name 20GAVAAXX100126:8:8:9677:53860, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 221, Read name 20GAVAAXX100126:8:8:9677:53860, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 222, Read name 20GAVAAXX100126:2:7:6406:190923, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 222, Read name 20GAVAAXX100126:2:7:6406:190923, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 225, Read name 20GAVAAXX100126:5:45:7084:89817, Mate Alignment start (9999773) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 225, Read name 20GAVAAXX100126:5:45:7084:89817, Mate Alignment start (9999773) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 226, Read name 20FUKAAXX100202:2:8:8921:13714, Mate Alignment start (9999637) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 226, Read name 20FUKAAXX100202:2:8:8921:13714, Mate Alignment start (9999637) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 227, Read name 20FUKAAXX100202:3:25:5393:174013, Mate Alignment start (9999699) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 227, Read name 20FUKAAXX100202:3:25:5393:174013, Mate Alignment start (9999699) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 228, Read name 20GAVAAXX100126:4:61:19483:178175, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 228, Read name 20GAVAAXX100126:4:61:19483:178175, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 229, Read name 20FUKAAXX100202:6:61:13597:167016, Mate Alignment start (9999733) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 229, Read name 20FUKAAXX100202:6:61:13597:167016, Mate Alignment start (9999733) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 230, Read name 20GAVAAXX100126:2:46:9819:189801, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 230, Read name 20GAVAAXX100126:2:46:9819:189801, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 231, Read name 20GAVAAXX100126:1:47:11960:43085, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 231, Read name 20GAVAAXX100126:1:47:11960:43085, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 232, Read name 20FUKAAXX100202:8:61:8547:37887, Mate Alignment start (10000431) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 232, Read name 20FUKAAXX100202:8:61:8547:37887, Mate Alignment start (10000431) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 233, Read name 20GAVAAXX100126:1:64:13278:136055, Mate Alignment start (10000387) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 233, Read name 20GAVAAXX100126:1:64:13278:136055, Mate Alignment start (10000387) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 234, Read name 20GAVAAXX100126:8:8:10069:1815, Mate Alignment start (10000360) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 234, Read name 20GAVAAXX100126:8:8:10069:1815, Mate Alignment start (10000360) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 235, Read name 20FUKAAXX100202:6:43:12464:95867, Mate Alignment start (9999715) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 235, Read name 20FUKAAXX100202:6:43:12464:95867, Mate Alignment start (9999715) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 236, Read name 20GAVAAXX100126:8:4:3360:104730, Mate Alignment start (9999724) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 236, Read name 20GAVAAXX100126:8:4:3360:104730, Mate Alignment start (9999724) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 237, Read name 20GAVAAXX100126:7:23:5527:173596, Mate Alignment start (10000333) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 237, Read name 20GAVAAXX100126:7:23:5527:173596, Mate Alignment start (10000333) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 238, Read name 20FUKAAXX100202:3:63:15601:87681, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 238, Read name 20FUKAAXX100202:3:63:15601:87681, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 239, Read name 20GAVAAXX100126:8:7:19780:99577, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 239, Read name 20GAVAAXX100126:8:7:19780:99577, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 240, Read name 20FUKAAXX100202:7:64:11274:28663, Mate Alignment start (10000350) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 240, Read name 20FUKAAXX100202:7:64:11274:28663, Mate Alignment start (10000350) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 241, Read name 20FUKAAXX100202:5:46:7034:130269, Mate Alignment start (9999775) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 241, Read name 20FUKAAXX100202:5:46:7034:130269, Mate Alignment start (9999775) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 242, Read name 20FUKAAXX100202:6:42:13864:97949, Mate Alignment start (9999770) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 242, Read name 20FUKAAXX100202:6:42:13864:97949, Mate Alignment start (9999770) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 243, Read name 20FUKAAXX100202:7:63:12812:59167, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 243, Read name 20FUKAAXX100202:7:63:12812:59167, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 244, Read name 20FUKAAXX100202:3:42:10889:9286, Mate Alignment start (9999781) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 244, Read name 20FUKAAXX100202:3:42:10889:9286, Mate Alignment start (9999781) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 245, Read name 20FUKAAXX100202:7:44:10464:154941, Mate Alignment start (9999777) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 245, Read name 20FUKAAXX100202:7:44:10464:154941, Mate Alignment start (9999777) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 246, Read name 20GAVAAXX100126:2:62:9149:111864, Mate Alignment start (10000382) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 246, Read name 20GAVAAXX100126:2:62:9149:111864, Mate Alignment start (10000382) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 247, Read name 20GAVAAXX100126:3:6:21157:147419, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 247, Read name 20GAVAAXX100126:3:6:21157:147419, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 248, Read name 20FUKAAXX100202:2:6:7367:104244, Mate Alignment start (10000408) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 248, Read name 20FUKAAXX100202:2:6:7367:104244, Mate Alignment start (10000408) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 249, Read name 20GAVAAXX100126:8:23:12150:79883, Mate Alignment start (10000363) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 249, Read name 20GAVAAXX100126:8:23:12150:79883, Mate Alignment start (10000363) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 250, Read name 20GAVAAXX100126:2:66:8843:33721, Mate Alignment start (10000388) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 250, Read name 20GAVAAXX100126:2:66:8843:33721, Mate Alignment start (10000388) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 251, Read name 20GAVAAXX100126:2:66:8848:33740, Mate Alignment start (10000388) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 251, Read name 20GAVAAXX100126:2:66:8848:33740, Mate Alignment start (10000388) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 252, Read name 20GAVAAXX100126:2:66:8861:33717, Mate Alignment start (10000388) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 252, Read name 20GAVAAXX100126:2:66:8861:33717, Mate Alignment start (10000388) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 253, Read name 20FUKAAXX100202:6:24:9789:119768, Mate Alignment start (9999745) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 253, Read name 20FUKAAXX100202:6:24:9789:119768, Mate Alignment start (9999745) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 254, Read name 20GAVAAXX100126:4:48:13006:180541, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 254, Read name 20GAVAAXX100126:4:48:13006:180541, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 255, Read name 20FUKAAXX100202:4:61:14645:192554, Mate Alignment start (10000352) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 255, Read name 20FUKAAXX100202:4:61:14645:192554, Mate Alignment start (10000352) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 256, Read name 20GAVAAXX100126:2:27:18806:87123, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 256, Read name 20GAVAAXX100126:2:27:18806:87123, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 257, Read name 20GAVAAXX100126:2:66:8554:80197, Mate Alignment start (9999742) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 257, Read name 20GAVAAXX100126:2:66:8554:80197, Mate Alignment start (9999742) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 258, Read name 20FUKAAXX100202:5:44:18607:97922, Mate Alignment start (10000375) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 258, Read name 20FUKAAXX100202:5:44:18607:97922, Mate Alignment start (10000375) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 259, Read name 20FUKAAXX100202:6:7:20029:86575, Mate Alignment start (9999724) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 259, Read name 20FUKAAXX100202:6:7:20029:86575, Mate Alignment start (9999724) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 262, Read name 20GAVAAXX100126:7:28:19343:119692, Mate Alignment start (10000324) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 262, Read name 20GAVAAXX100126:7:28:19343:119692, Mate Alignment start (10000324) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 263, Read name 20GAVAAXX100126:8:3:19154:172785, Mate Alignment start (10000444) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 263, Read name 20GAVAAXX100126:8:3:19154:172785, Mate Alignment start (10000444) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 264, Read name 20FUKAAXX100202:4:2:11323:157919, Mate Alignment start (9999727) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 264, Read name 20FUKAAXX100202:4:2:11323:157919, Mate Alignment start (9999727) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 265, Read name 20FUKAAXX100202:4:24:20755:63383, Mate Alignment start (10000420) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 265, Read name 20FUKAAXX100202:4:24:20755:63383, Mate Alignment start (10000420) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 266, Read name 20GAVAAXX100126:6:41:12737:140458, Mate Alignment start (10000391) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 266, Read name 20GAVAAXX100126:6:41:12737:140458, Mate Alignment start (10000391) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 267, Read name 20FUKAAXX100202:1:41:8855:77865, Mate Alignment start (10000406) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 267, Read name 20FUKAAXX100202:1:41:8855:77865, Mate Alignment start (10000406) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 268, Read name 20FUKAAXX100202:2:7:20289:162172, Mate Alignment start (10000401) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 268, Read name 20FUKAAXX100202:2:7:20289:162172, Mate Alignment start (10000401) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 269, Read name 20FUKAAXX100202:3:5:15184:151247, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 269, Read name 20FUKAAXX100202:3:5:15184:151247, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 270, Read name 20GAVAAXX100126:5:8:18245:6953, Mate Alignment start (10000327) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 270, Read name 20GAVAAXX100126:5:8:18245:6953, Mate Alignment start (10000327) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 271, Read name 20FUKAAXX100202:3:24:9989:45675, Mate Alignment start (9999781) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 271, Read name 20FUKAAXX100202:3:24:9989:45675, Mate Alignment start (9999781) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 272, Read name 20FUKAAXX100202:3:25:21206:43648, Mate Alignment start (9999754) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 272, Read name 20FUKAAXX100202:3:25:21206:43648, Mate Alignment start (9999754) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 273, Read name 20GAVAAXX100126:8:7:10416:22501, Mate Alignment start (9999744) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 273, Read name 20GAVAAXX100126:8:7:10416:22501, Mate Alignment start (9999744) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 274, Read name 20GAVAAXX100126:8:7:10417:22480, Mate Alignment start (9999744) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 274, Read name 20GAVAAXX100126:8:7:10417:22480, Mate Alignment start (9999744) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 275, Read name 20FUKAAXX100202:2:23:12195:137492, Mate Alignment start (10000417) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 275, Read name 20FUKAAXX100202:2:23:12195:137492, Mate Alignment start (10000417) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 276, Read name 20FUKAAXX100202:2:68:14803:9019, Mate Alignment start (10000435) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 276, Read name 20FUKAAXX100202:2:68:14803:9019, Mate Alignment start (10000435) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 277, Read name 20FUKAAXX100202:2:68:1649:5921, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 277, Read name 20FUKAAXX100202:2:68:1649:5921, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 278, Read name 20GAVAAXX100126:6:67:14138:53447, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 278, Read name 20GAVAAXX100126:6:67:14138:53447, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 279, Read name 20GAVAAXX100126:6:27:17917:125886, Mate Alignment start (10000392) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 279, Read name 20GAVAAXX100126:6:27:17917:125886, Mate Alignment start (10000392) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 280, Read name 20GAVAAXX100126:6:27:17919:125864, Mate Alignment start (10000392) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 280, Read name 20GAVAAXX100126:6:27:17919:125864, Mate Alignment start (10000392) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 281, Read name 20GAVAAXX100126:4:23:11820:142520, Mate Alignment start (9999792) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 281, Read name 20GAVAAXX100126:4:23:11820:142520, Mate Alignment start (9999792) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 282, Read name 20FUKAAXX100202:3:22:1789:82621, Mate Alignment start (10000372) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 282, Read name 20FUKAAXX100202:3:22:1789:82621, Mate Alignment start (10000372) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 283, Read name 20GAVAAXX100126:6:21:6652:178712, Mate Alignment start (10000425) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 283, Read name 20GAVAAXX100126:6:21:6652:178712, Mate Alignment start (10000425) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 284, Read name 20FUKAAXX100202:4:43:6140:91204, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 284, Read name 20FUKAAXX100202:4:43:6140:91204, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 285, Read name 20FUKAAXX100202:4:43:6159:91203, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 285, Read name 20FUKAAXX100202:4:43:6159:91203, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 288, Read name 20GAVAAXX100126:4:28:9009:173490, Mate Alignment start (10000424) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 288, Read name 20GAVAAXX100126:4:28:9009:173490, Mate Alignment start (10000424) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 289, Read name 20FUKAAXX100202:8:45:1884:47673, Mate Alignment start (9999784) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 289, Read name 20FUKAAXX100202:8:45:1884:47673, Mate Alignment start (9999784) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 290, Read name 20FUKAAXX100202:8:45:1902:47680, Mate Alignment start (9999784) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 290, Read name 20FUKAAXX100202:8:45:1902:47680, Mate Alignment start (9999784) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 293, Read name 20FUKAAXX100202:5:26:19959:88445, Mate Alignment start (9999764) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 293, Read name 20FUKAAXX100202:5:26:19959:88445, Mate Alignment start (9999764) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 294, Read name 20FUKAAXX100202:6:26:12485:190127, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 294, Read name 20FUKAAXX100202:6:26:12485:190127, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 295, Read name 20FUKAAXX100202:6:26:12497:190143, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 295, Read name 20FUKAAXX100202:6:26:12497:190143, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 296, Read name 20FUKAAXX100202:7:67:18360:176157, Mate Alignment start (10000361) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 296, Read name 20FUKAAXX100202:7:67:18360:176157, Mate Alignment start (10000361) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 297, Read name 20GAVAAXX100126:3:7:6468:165793, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 297, Read name 20GAVAAXX100126:3:7:6468:165793, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 298, Read name 20FUKAAXX100202:3:63:14607:69414, Mate Alignment start (10000374) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 298, Read name 20FUKAAXX100202:3:63:14607:69414, Mate Alignment start (10000374) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 299, Read name 20FUKAAXX100202:4:66:18078:75058, Mate Alignment start (10000422) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 299, Read name 20FUKAAXX100202:4:66:18078:75058, Mate Alignment start (10000422) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 300, Read name 20FUKAAXX100202:4:66:18086:75040, Mate Alignment start (10000422) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 300, Read name 20FUKAAXX100202:4:66:18086:75040, Mate Alignment start (10000422) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 301, Read name 20GAVAAXX100126:6:62:12722:64586, Mate Alignment start (10000424) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 301, Read name 20GAVAAXX100126:6:62:12722:64586, Mate Alignment start (10000424) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 304, Read name 20FUKAAXX100202:2:65:8299:177086, Mate Alignment start (10000414) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 304, Read name 20FUKAAXX100202:2:65:8299:177086, Mate Alignment start (10000414) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 305, Read name 20FUKAAXX100202:5:1:12372:198214, Mate Alignment start (10000442) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 305, Read name 20FUKAAXX100202:5:1:12372:198214, Mate Alignment start (10000442) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 306, Read name 20GAVAAXX100126:7:44:13710:11047, Mate Alignment start (10000383) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 306, Read name 20GAVAAXX100126:7:44:13710:11047, Mate Alignment start (10000383) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 309, Read name 20FUKAAXX100202:6:27:15343:160627, Mate Alignment start (9999796) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 309, Read name 20FUKAAXX100202:6:27:15343:160627, Mate Alignment start (9999796) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 310, Read name 20FUKAAXX100202:8:21:1790:48091, Mate Alignment start (9999943) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 310, Read name 20FUKAAXX100202:8:21:1790:48091, Mate Alignment start (9999943) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 311, Read name 20GAVAAXX100126:4:67:14214:45473, Mate Alignment start (9999769) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 311, Read name 20GAVAAXX100126:4:67:14214:45473, Mate Alignment start (9999769) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 312, Read name 20GAVAAXX100126:7:45:7524:110161, Mate Alignment start (9999815) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 312, Read name 20GAVAAXX100126:7:45:7524:110161, Mate Alignment start (9999815) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 313, Read name 20GAVAAXX100126:5:27:11481:127142, Mate Alignment start (10000390) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 313, Read name 20GAVAAXX100126:5:27:11481:127142, Mate Alignment start (10000390) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 314, Read name 20GAVAAXX100126:6:41:19998:100609, Mate Alignment start (10000440) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 314, Read name 20GAVAAXX100126:6:41:19998:100609, Mate Alignment start (10000440) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 315, Read name 20GAVAAXX100126:2:41:5807:152808, Mate Alignment start (10000365) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 315, Read name 20GAVAAXX100126:2:41:5807:152808, Mate Alignment start (10000365) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 316, Read name 20GAVAAXX100126:5:67:8769:184399, Mate Alignment start (10000413) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 316, Read name 20GAVAAXX100126:5:67:8769:184399, Mate Alignment start (10000413) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 317, Read name 20GAVAAXX100126:1:1:8996:5944, Mate Alignment start (9999798) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 317, Read name 20GAVAAXX100126:1:1:8996:5944, Mate Alignment start (9999798) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 318, Read name 20GAVAAXX100126:5:42:12694:142155, Mate Alignment start (10000420) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 318, Read name 20GAVAAXX100126:5:42:12694:142155, Mate Alignment start (10000420) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 319, Read name 20GAVAAXX100126:7:44:8840:83089, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 319, Read name 20GAVAAXX100126:7:44:8840:83089, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 320, Read name 20FUKAAXX100202:7:26:12026:80165, Mate Alignment start (10000385) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 320, Read name 20FUKAAXX100202:7:26:12026:80165, Mate Alignment start (10000385) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 321, Read name 20GAVAAXX100126:1:4:21009:20022, Mate Alignment start (10000385) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 321, Read name 20GAVAAXX100126:1:4:21009:20022, Mate Alignment start (10000385) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 322, Read name 20FUKAAXX100202:2:68:3792:94879, Mate Alignment start (10000432) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 322, Read name 20FUKAAXX100202:2:68:3792:94879, Mate Alignment start (10000432) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 323, Read name 20GAVAAXX100126:8:25:12361:154123, Mate Alignment start (9999756) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 323, Read name 20GAVAAXX100126:8:25:12361:154123, Mate Alignment start (9999756) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 324, Read name 20GAVAAXX100126:8:25:12382:154125, Mate Alignment start (9999756) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 324, Read name 20GAVAAXX100126:8:25:12382:154125, Mate Alignment start (9999756) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 325, Read name 20GAVAAXX100126:3:65:18493:115113, Mate Alignment start (10000436) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 325, Read name 20GAVAAXX100126:3:65:18493:115113, Mate Alignment start (10000436) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 326, Read name 20FUKAAXX100202:7:67:21244:6474, Mate Alignment start (10000458) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 326, Read name 20FUKAAXX100202:7:67:21244:6474, Mate Alignment start (10000458) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 327, Read name 20FUKAAXX100202:4:46:2349:67300, Mate Alignment start (9999771) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 327, Read name 20FUKAAXX100202:4:46:2349:67300, Mate Alignment start (9999771) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 328, Read name 20FUKAAXX100202:4:64:17702:39209, Mate Alignment start (9999785) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 328, Read name 20FUKAAXX100202:4:64:17702:39209, Mate Alignment start (9999785) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 329, Read name 20FUKAAXX100202:1:43:15726:132914, Mate Alignment start (10000377) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 329, Read name 20FUKAAXX100202:1:43:15726:132914, Mate Alignment start (10000377) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 330, Read name 20FUKAAXX100202:6:64:3811:167383, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 330, Read name 20FUKAAXX100202:6:64:3811:167383, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 331, Read name 20FUKAAXX100202:8:27:7323:75566, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 331, Read name 20FUKAAXX100202:8:27:7323:75566, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 332, Read name 20GAVAAXX100126:2:28:15360:131557, Mate Alignment start (10000418) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 332, Read name 20GAVAAXX100126:2:28:15360:131557, Mate Alignment start (10000418) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 333, Read name 20GAVAAXX100126:2:66:5383:81213, Mate Alignment start (9999769) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 333, Read name 20GAVAAXX100126:2:66:5383:81213, Mate Alignment start (9999769) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 334, Read name 20GAVAAXX100126:6:22:11440:95696, Mate Alignment start (9999766) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 334, Read name 20GAVAAXX100126:6:22:11440:95696, Mate Alignment start (9999766) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 335, Read name 20GAVAAXX100126:6:67:12425:123302, Mate Alignment start (9999799) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 335, Read name 20GAVAAXX100126:6:67:12425:123302, Mate Alignment start (9999799) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 336, Read name 20FUKAAXX100202:1:41:1662:13912, Mate Alignment start (10000331) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 336, Read name 20FUKAAXX100202:1:41:1662:13912, Mate Alignment start (10000331) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 337, Read name 20FUKAAXX100202:3:21:19677:162487, Mate Alignment start (10000332) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 337, Read name 20FUKAAXX100202:3:21:19677:162487, Mate Alignment start (10000332) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 340, Read name 20FUKAAXX100202:6:46:13213:95672, Mate Alignment start (10000321) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 340, Read name 20FUKAAXX100202:6:46:13213:95672, Mate Alignment start (10000321) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 341, Read name 20GAVAAXX100126:2:67:11830:144272, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 341, Read name 20GAVAAXX100126:2:67:11830:144272, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 342, Read name 20GAVAAXX100126:6:25:11700:156967, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 342, Read name 20GAVAAXX100126:6:25:11700:156967, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 343, Read name 20GAVAAXX100126:8:2:1530:90452, Mate Alignment start (10000415) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 343, Read name 20GAVAAXX100126:8:2:1530:90452, Mate Alignment start (10000415) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 344, Read name 20FUKAAXX100202:1:41:15735:31577, Mate Alignment start (9999745) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 344, Read name 20FUKAAXX100202:1:41:15735:31577, Mate Alignment start (9999745) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 345, Read name 20FUKAAXX100202:7:67:19743:72886, Mate Alignment start (10000397) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 345, Read name 20FUKAAXX100202:7:67:19743:72886, Mate Alignment start (10000397) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 346, Read name 20GAVAAXX100126:2:62:5242:113457, Mate Alignment start (10000452) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 346, Read name 20GAVAAXX100126:2:62:5242:113457, Mate Alignment start (10000452) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 347, Read name 20FUKAAXX100202:7:41:10114:15727, Mate Alignment start (9999528) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 347, Read name 20FUKAAXX100202:7:41:10114:15727, Mate Alignment start (9999528) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 348, Read name 20FUKAAXX100202:5:27:14631:113616, Mate Alignment start (10000394) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 348, Read name 20FUKAAXX100202:5:27:14631:113616, Mate Alignment start (10000394) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 349, Read name 20FUKAAXX100202:8:26:8051:103852, Mate Alignment start (10000399) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 349, Read name 20FUKAAXX100202:8:26:8051:103852, Mate Alignment start (10000399) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 350, Read name 20GAVAAXX100126:4:1:11639:105967, Mate Alignment start (9999769) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 350, Read name 20GAVAAXX100126:4:1:11639:105967, Mate Alignment start (9999769) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 351, Read name 20GAVAAXX100126:8:6:11303:64367, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 351, Read name 20GAVAAXX100126:8:6:11303:64367, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 352, Read name 20GAVAAXX100126:8:6:11319:64357, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 352, Read name 20GAVAAXX100126:8:6:11319:64357, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21
Finished 1400 tests
Finished 1600 tests

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testAllCRAMEncodingsRoundTripThroughStream STANDARD_ERROR
    WARNING	2025-06-03 15:15:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testIgnoreObsoleteDataseriesOnRead STANDARD_ERROR
    WARNING	2025-06-03 15:15:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
Finished 1800 tests

Gradle suite > Gradle test > htsjdk.samtools.util.CoordSpanInputSteamTest.test_3_ranges_byte_single_read STANDARD_ERROR
    Adding chunk: 0 - 100
    Adding chunk: 10 - 20
    Adding chunk: 100 - 200
    Adding chunk: 1048575 - 1048576

Gradle suite > Gradle test > htsjdk.samtools.util.CoordSpanInputSteamTest.test_first_3_bytes STANDARD_ERROR
    Adding chunk: 0 - 1
    Adding chunk: 1 - 2
    Adding chunk: 2 - 3

Gradle suite > Gradle test > htsjdk.samtools.util.CoordSpanInputSteamTest.test_range_read STANDARD_ERROR
    Adding chunk: 0 - 100
    Adding chunk: 10 - 20
    Adding chunk: 100 - 200
    Adding chunk: 1048575 - 1048576
    Adding chunk: 0 - 100
    Adding chunk: 10 - 20
    Adding chunk: 100 - 200
    Adding chunk: 1048575 - 1048576

Gradle suite > Gradle test > htsjdk.samtools.cram.build.CramIOTest.testCheckHeaderAndEOF SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.cram.build.CramIOTest.testRejectUnknownCRAMVersion SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.util.DiskBackedQueueTest STANDARD_ERROR
    Resetting tmpdir

Gradle suite > Gradle test STANDARD_ERROR
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
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    Resetting tmpdir
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    Resetting tmpdir
    Resetting tmpdir

Gradle suite > Gradle test > htsjdk.samtools.DownsamplingIteratorTests.testBasicFunction STANDARD_ERROR
    Could not delete file /tmp/pbuilder2/DiskBackedQueueTest/diskbackedqueue.6442482656622782408.tmp
Finished 2000 tests
Finished 2200 tests
Finished 2400 tests
Finished 2600 tests
Finished 2800 tests
Finished 3000 tests

Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testBuildFromFasta[1](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    WARNING	2025-06-03 15:15:49	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testCreate[1](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    WARNING	2025-06-03 15:15:49	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
Finished 3200 tests
Finished 3400 tests
Finished 3600 tests

Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR
    WARNING	2025-06-03 15:15:50	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200

Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicShallowDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR
    WARNING	2025-06-03 15:15:50	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200

Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.codecFilterOutFieldsTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR
    WARNING	2025-06-03 15:15:51	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200

Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.testGZipped[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3.gz) STANDARD_ERROR
    WARNING	2025-06-03 15:15:51	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200
    WARNING	2025-06-03 15:15:51	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200

Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.testGZippedShallow[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3.gz) STANDARD_ERROR
    WARNING	2025-06-03 15:15:51	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200
    WARNING	2025-06-03 15:15:51	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200

Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3WriterTest.testRoundTrip[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3) STANDARD_ERROR
    WARNING	2025-06-03 15:15:51	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200
    WARNING	2025-06-03 15:15:51	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200
Finished 3800 tests

Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombLongEncodingTest.testToString STANDARD_ERROR
    WARNING	2025-06-03 15:15:51	ExperimentalEncoding	Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding which is untested and scheduled for removal from the CRAM spec

Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombRiceIntegerEncodingTest.testToString STANDARD_ERROR
    WARNING	2025-06-03 15:15:51	ExperimentalEncoding	Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[1](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@29bbfece, [Ljava.lang.String;@2d23d098) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@22077796, [Ljava.lang.String;@4f691d1a) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryAlignmentStart[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, 2) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryAlignmentStart[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, 24) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@3d74dea9) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@1131ac64) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@17cc8e2f) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@7deff0ab) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@609a8352) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@27bcc14) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@7e557ede) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@6fe92f70) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@41dec66f, [Ljava.lang.String;@3b72ac56) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7c4dfaf5, [Ljava.lang.String;@504e82eb) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@475ee7bb, [Ljava.lang.String;@3a59d01a) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@425b1872, [Ljava.lang.String;@708d13ef) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@406dfdf3, [Ljava.lang.String;@42496cd5) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2fe2944, [Ljava.lang.String;@6d6c03de) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4636299d, [Ljava.lang.String;@2ba57293) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1c770d6, [Ljava.lang.String;@5ba3d4e5) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5bec9aa7, [Ljava.lang.String;@5f6cb196) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@37020d3d, [Ljava.lang.String;@711fb110) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5af0ff85, [Ljava.lang.String;@2b80e24f) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3999c154, [Ljava.lang.String;@70be755) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@125f58c4, [Ljava.lang.String;@439a9d80) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@506defe1, [Ljava.lang.String;@4eec9211) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7cb775e0, [Ljava.lang.String;@1b9e86dd) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@55c90623, [Ljava.lang.String;@1a8afbd0) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@187bb9da, [Ljava.lang.String;@3343c44) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMate[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:52	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMate[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMateEnsureInternalIteratorsClosed[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMateEnsureInternalIteratorsClosed[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@37a26b6b) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@68e83d5) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@272a32ae) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@1c9d806a) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@1726a6d6) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@1d8b5585, [Ljava.lang.String;@4cdf6609) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3b67c38d, [Ljava.lang.String;@2b7972f3) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1220329f, [Ljava.lang.String;@f18653a) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5d2ac651, [Ljava.lang.String;@23578e64) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2fdcdbfc, [Ljava.lang.String;@364ee866) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@fc5988f, [Ljava.lang.String;@5ddd6e30) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@154852b1, [Ljava.lang.String;@5ff63552) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@256652a3, [Ljava.lang.String;@6d13cb55) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4187bc56, [Ljava.lang.String;@3f2ee212) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@318d3d59, [Ljava.lang.String;@1ecd8e9) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@77adc72a, [Ljava.lang.String;@69707963) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
Finished 4000 tests

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@21f714a2, [Ljava.lang.String;@55b8beed) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5bd9c9d6, [Ljava.lang.String;@3e15e1b6) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7685448, [Ljava.lang.String;@288f9a18) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4270e3e6, [Ljava.lang.String;@582b4292) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3329f657, [Ljava.lang.String;@31d268d6) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@53f6f1cb, [Ljava.lang.String;@63d8d9ac) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@374e89c3) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@38cf6215) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@37effc3f) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@4462b97f) STANDARD_ERROR
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:53	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@342fdf0b) STANDARD_ERROR
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@2b25cf93) STANDARD_ERROR
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@74e31747) STANDARD_ERROR
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@4ca6bb07) STANDARD_ERROR
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@7df7b45f) STANDARD_ERROR
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@25c182f1) STANDARD_ERROR
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@1890e435) STANDARD_ERROR
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@233b7153) STANDARD_ERROR
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@62aff41) STANDARD_ERROR
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@164ccde5) STANDARD_ERROR
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@45b5616) STANDARD_ERROR
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@1bc1dc48) STANDARD_ERROR
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@b8d567e) STANDARD_ERROR
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueries[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 12, 7) STANDARD_ERROR
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@45dd7bea, 5) STANDARD_ERROR
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:15:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForDecodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@201d5a88, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@5391807a], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR
    WARNING	2025-06-03 15:15:54	HtsCodecResolver	The specified format string (BOGUS_FORMAT) does not correspond to any registered codec for content type (ALIGNED_READS)

Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[1]([], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR
    WARNING	2025-06-03 15:15:54	HtsCodecResolver	The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS)

Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[2]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2343855a, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@150dbd1d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@15777215, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@54cd886, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4db43140], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR
    WARNING	2025-06-03 15:15:54	HtsCodecResolver	The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS)

Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2343855a, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@150dbd1d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@15777215, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@54cd886, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4db43140], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR
    WARNING	2025-06-03 15:15:54	HtsCodecResolver	The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS)

Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[5]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2343855a, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@150dbd1d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@15777215, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@54cd886, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4db43140], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR
    WARNING	2025-06-03 15:15:54	HtsCodecResolver	The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS)
Finished 4200 tests
Finished 4400 tests
some stuffFinished 4600 tests

Gradle suite > Gradle test > htsjdk.samtools.util.IOUtilTest.testDeleteSingleWithDeletePaths STANDARD_ERROR
    Could not delete file tmp
    Could not delete file file12829976832041055813.bad
Finished 4800 tests

Gradle suite > Gradle test > htsjdk.samtools.util.IntervalTreeTest.performanceTest STANDARD_OUT
    Time to construct a tree with 50000 nodes: 29 milliseconds
    Queried for the same 100-length mapping 209851170 times in 10 seconds.

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[0](chr3:50911035-50911051	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95)
Finished 5000 tests
Finished 5200 tests

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[279](chr2:111013693-111013832	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95)
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[280](chr3:14174511-14175398	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[281](chr3:50911035-50911051	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[282](chr6:32071709-32071869	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[283](chr6:32072183-32072358	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[284](chr6:32104446-32104606	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[285](chr6:32104920-32105095	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[286](chr7:101995561-101995739	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[288](chr7:142179850-142180013	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95)
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[292](chr15:19335778-19336302	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[293](chr17:33364376-33364428	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95)
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[294](chr17:33546162-33546214	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95)
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[295](chr17:33706667-33706736	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[0](chr3:50911035-50911051	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95)
Finished 5400 tests

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[279](chr2:111013693-111013832	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95)
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[280](chr3:14174511-14175398	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[281](chr3:50911035-50911051	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[282](chr6:32071709-32071869	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[283](chr6:32072183-32072358	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[284](chr6:32104446-32104606	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[285](chr6:32104920-32105095	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[286](chr7:101995561-101995739	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[288](chr7:142179850-142180013	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95)
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[292](chr15:19335778-19336302	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[293](chr17:33364376-33364428	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95)
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[294](chr17:33546162-33546214	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95)
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[295](chr17:33706667-33706736	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95)
Finished 5600 tests

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[0](chr3:50911035-50911051	+	.) STANDARD_OUT
    Diagnosing chr3:50911035-50911051	+	. (len 17)
    chr3:50911035-50911051	+	null intersection null (len 17)=>chr3:50936014-50936030	+	.(+) using chain 3 ; pct matched 0.9411765

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[1](chr2:111013693-111013832	+	.) STANDARD_OUT
    Diagnosing chr2:111013693-111013832	+	. (len 140)
    chr2:111013693-111013832	+	null intersection null (len 140)=>null using chain 1
    chr2:111013693-111013832	+	null intersection null (len 140)=>chr2:108482693-108482783	-	.(-) using chain 53 ; pct matched 0.65
    chr2:111013693-111013832	+	null intersection null (len 140)=>chr2:113152284-113152332	+	.(+) using chain 310 ; pct matched 0.35

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[2](chr3:14174511-14175398	+	.) STANDARD_OUT
    Diagnosing chr3:14174511-14175398	+	. (len 888)
    chr3:14174511-14175398	+	null intersection null (len 888)=>chr3:14199509-14200394	+	.(+) using chain 3 ; pct matched 0.9166667

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[3](chr3:50911035-50911051	+	.) STANDARD_OUT
    Diagnosing chr3:50911035-50911051	+	. (len 17)
    chr3:50911035-50911051	+	null intersection null (len 17)=>chr3:50936014-50936030	+	.(+) using chain 3 ; pct matched 0.9411765

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[4](chr6:32071709-32071869	+	.) STANDARD_OUT
    Diagnosing chr6:32071709-32071869	+	. (len 161)
    chr6:32071709-32071869	+	null intersection null (len 161)=>chr6:31963730-31963890	+	.(+) using chain 6 ; pct matched 0.89440995

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[5](chr6:32072183-32072358	+	.) STANDARD_OUT
    Diagnosing chr6:32072183-32072358	+	. (len 176)
    chr6:32072183-32072358	+	null intersection null (len 176)=>chr6:31964204-31964379	+	.(+) using chain 6 ; pct matched 0.90909094

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[6](chr6:32104446-32104606	+	.) STANDARD_OUT
    Diagnosing chr6:32104446-32104606	+	. (len 161)
    chr6:32104446-32104606	+	null intersection null (len 161)=>chr6:31996468-31996628	+	.(+) using chain 6 ; pct matched 0.89440995

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[7](chr6:32104920-32105095	+	.) STANDARD_OUT
    Diagnosing chr6:32104920-32105095	+	. (len 176)
    chr6:32104920-32105095	+	null intersection null (len 176)=>chr6:31996942-31997117	+	.(+) using chain 6 ; pct matched 0.90909094

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[8](chr7:101995561-101995739	+	.) STANDARD_OUT
    Diagnosing chr7:101995561-101995739	+	. (len 179)
    chr7:101995561-101995739	+	null intersection null (len 179)=>chr7:102208488-102208633	+	.(+) using chain 7 ; pct matched 0.8156425

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[9](chr7:142178782-142178825	+	.) STANDARD_OUT
    Diagnosing chr7:142178782-142178825	+	. (len 44)
    chr7:142178782-142178825	+	null intersection null (len 44)=>null using chain 7

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[10](chr7:142179850-142180013	+	.) STANDARD_OUT
    Diagnosing chr7:142179850-142180013	+	. (len 164)
    chr7:142179850-142179857	+	null intersection null (len 8)=>chr7:142479907-142479914	+	.(+) using chain 31548103 ; pct matched 0.048780486
    chr7:142179946-142180009	+	null intersection null (len 64)=>chr7:142480003-142480066	+	.(+) using chain 30171758 ; pct matched 0.3902439
    chr7:142179850-142180013	+	null intersection null (len 164)=>null using chain 7

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[11](chr7:142181067-142181324	+	.) STANDARD_OUT
    Diagnosing chr7:142181067-142181324	+	. (len 258)
    chr7:142181067-142181324	+	null intersection null (len 258)=>null using chain 7

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[12](chr7:142181720-142181860	+	.) STANDARD_OUT
    Diagnosing chr7:142181720-142181860	+	. (len 141)
    chr7:142181720-142181860	+	null intersection null (len 141)=>null using chain 7

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[13](chr7:142182157-142182313	+	.) STANDARD_OUT
    Diagnosing chr7:142182157-142182313	+	. (len 157)
    chr7:142182157-142182313	+	null intersection null (len 157)=>null using chain 7

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[14](chr15:19335778-19336302	+	.) STANDARD_OUT
    Diagnosing chr15:19335778-19336302	+	. (len 525)
    chr15:19335778-19336302	+	null intersection null (len 525)=>chr15:21071199-21071612	+	.(+) using chain 16 ; pct matched 0.7885714
    chr15:19335778-19336302	+	null intersection null (len 525)=>null using chain 110

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[15](chr17:33364376-33364428	+	.) STANDARD_OUT
    Diagnosing chr17:33364376-33364428	+	. (len 53)
    chr17:33364376-33364428	+	null intersection null (len 53)=>chr17:36289992-36290044	+	.(+) using chain 18 ; pct matched 0.3207547
    chr17:33364385-33364428	+	null intersection null (len 44)=>chr17:36342590-36342625	-	.(-) using chain 363 ; pct matched 0.6792453

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[16](chr17:33546162-33546214	+	.) STANDARD_OUT
    Diagnosing chr17:33546162-33546214	+	. (len 53)
    chr17:33546162-33546214	+	null intersection null (len 53)=>null using chain 18
    chr17:33546162-33546214	+	null intersection null (len 53)=>null using chain 1564
    chr17:33546162-33546214	+	null intersection null (len 53)=>chr17:36289992-36290044	-	.(-) using chain 363 ; pct matched 0.3207547
    chr17:33546162-33546214	+	null intersection null (len 53)=>chr17:36342590-36342625	+	.(+) using chain 1571 ; pct matched 0.6792453

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[17](chr17:33706667-33706736	+	.) STANDARD_OUT
    Diagnosing chr17:33706667-33706736	+	. (len 70)
    chr17:33706667-33706736	+	null intersection null (len 70)=>chr17:36453148-36453217	+	.(+) using chain 18 ; pct matched 0.75714284

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[18](chr17:59772721-59772781	+	.) STANDARD_OUT
    Diagnosing chr17:59772721-59772781	+	. (len 61)
    chr17:59772721-59772781	+	null intersection null (len 61)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[19](chr17:59779355-59779421	+	.) STANDARD_OUT
    Diagnosing chr17:59779355-59779421	+	. (len 67)
    chr17:59779355-59779421	+	null intersection null (len 67)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[20](chr17:59781483-59781540	+	.) STANDARD_OUT
    Diagnosing chr17:59781483-59781540	+	. (len 58)
    chr17:59781483-59781540	+	null intersection null (len 58)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[21](chr17:59783488-59783565	+	.) STANDARD_OUT
    Diagnosing chr17:59783488-59783565	+	. (len 78)
    chr17:59783488-59783565	+	null intersection null (len 78)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[22](chr17:59784584-59784615	+	.) STANDARD_OUT
    Diagnosing chr17:59784584-59784615	+	. (len 32)
    chr17:59784584-59784615	+	null intersection null (len 32)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[23](chr17:59786025-59786136	+	.) STANDARD_OUT
    Diagnosing chr17:59786025-59786136	+	. (len 112)
    chr17:59786025-59786136	+	null intersection null (len 112)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[24](chr17:59787203-59787494	+	.) STANDARD_OUT
    Diagnosing chr17:59787203-59787494	+	. (len 292)
    chr17:59787203-59787494	+	null intersection null (len 292)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[25](chr17:59791235-59791514	+	.) STANDARD_OUT
    Diagnosing chr17:59791235-59791514	+	. (len 280)
    chr17:59791235-59791514	+	null intersection null (len 280)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[26](chr17:59794247-59794502	+	.) STANDARD_OUT
    Diagnosing chr17:59794247-59794502	+	. (len 256)
    chr17:59794247-59794502	+	null intersection null (len 256)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[27](chr17:59801884-59802193	+	.) STANDARD_OUT
    Diagnosing chr17:59801884-59802193	+	. (len 310)
    chr17:59801884-59802193	+	null intersection null (len 310)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[28](chr17:59804685-59804982	+	.) STANDARD_OUT
    Diagnosing chr17:59804685-59804982	+	. (len 298)
    chr17:59804685-59804982	+	null intersection null (len 298)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[29](chr17:59817352-59817382	+	.) STANDARD_OUT
    Diagnosing chr17:59817352-59817382	+	. (len 31)
    chr17:59817352-59817382	+	null intersection null (len 31)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[30](chr17:59817465-59817532	+	.) STANDARD_OUT
    Diagnosing chr17:59817465-59817532	+	. (len 68)
    chr17:59817465-59817532	+	null intersection null (len 68)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[31](chr17:59875754-59875812	+	.) STANDARD_OUT
    Diagnosing chr17:59875754-59875812	+	. (len 59)
    chr17:59875754-59875812	+	null intersection null (len 59)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[32](chr17:59875899-59875944	+	.) STANDARD_OUT
    Diagnosing chr17:59875899-59875944	+	. (len 46)
    chr17:59875899-59875944	+	null intersection null (len 46)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[33](chr17:59879183-59879456	+	.) STANDARD_OUT
    Diagnosing chr17:59879183-59879456	+	. (len 274)
    chr17:59879183-59879456	+	null intersection null (len 274)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[34](chr17:59883988-59884276	+	.) STANDARD_OUT
    Diagnosing chr17:59883988-59884276	+	. (len 289)
    chr17:59883988-59884276	+	null intersection null (len 289)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[35](chr17:59887398-59887512	+	.) STANDARD_OUT
    Diagnosing chr17:59887398-59887512	+	. (len 115)
    chr17:59887398-59887512	+	null intersection null (len 115)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[36](chrX:48774611-48775058	+	.) STANDARD_OUT
    Diagnosing chrX:48774611-48775058	+	. (len 448)
    chrX:48774611-48775058	+	null intersection null (len 448)=>null using chain 8
Finished 5800 tests

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testLiftoverCounter[0](chr3:50911035-50911051	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:16:08	LiftOver	Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95)
Finished 6000 tests
Finished 6200 tests

Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaCoordinateMultiIterator STANDARD_OUT
    read_28833_29006_6945	0	chr21	28833	255	36M	*	0	0	AAGCTGGAGATTACCATACTTAGGCTCATGTAGCCA	?.QC5:&34LA#;K;A'5L*!.;.LJ?)FO?'?D2<	RG:Z:1

    read_28833_29006_6945	0	chr21	30000	255	36M	*	0	0	AAGCTGGAGATTACCATACTTAGGCTCATGTAGCCA	?.QC5:&34LA#;K;A'5L*!.;.LJ?)FO?'?D2<	RG:Z:1

    read_28701_28881_323b	0	chrX	28834	255	36M	*	0	0	GCCCTATCGCCAGATCAATCGTCGCTGTGGAACTAG	$>8BE+:L!M$K(L*MQ>PO8N*8>;;=5IA>B,*O	RG:Z:1

    read_28701_28881_323b	0	chrX	28835	255	36M	*	0	0	GCCCTATCGCCAGATCAATCGTCGCTGTGGAACTAG	$>8BE+:L!M$K(L*MQ>PO8N*8>;;=5IA>B,*O	RG:Z:1

    read_28701_28881_323c	0	chrX	28835	255	36M	*	0	0	CTCAACGTATTCATACAGGCCCTTTTCGAATAGCTG	%$=LPJ?D6&@R!"KJCOI+05?>>J9CJ)'@-O>K	RG:Z:1


Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaReadOrderMultiIterator STANDARD_OUT
    a
    b
    c
    d
    e

Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaUnsortedMultiIterator STANDARD_OUT
    b
    d
    e
    c
    a
Finished 6400 tests
Finished 6600 tests

Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[0](@HD	VN:1.0	SO:UNSORTED
) STANDARD_ERROR
    WARNING	2025-06-03 15:16:34	SAMTextHeaderCodec	Found non-conforming header SO tag: UNSORTED. Treating as 'unknown'.

Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[1](@HD	VN:1.0	SO:FALSE
) STANDARD_ERROR
    WARNING	2025-06-03 15:16:34	SAMTextHeaderCodec	Found non-conforming header SO tag: FALSE. Treating as 'unknown'.

Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[2](@HD	VN:1.0	SO:COORDINATE
) STANDARD_ERROR
    WARNING	2025-06-03 15:16:34	SAMTextHeaderCodec	Found non-conforming header SO tag: COORDINATE. Treating as 'unknown'.

Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[3](@HD	VN:1.0	SO:uNknOWn
) STANDARD_ERROR
    WARNING	2025-06-03 15:16:34	SAMTextHeaderCodec	Found non-conforming header SO tag: uNknOWn. Treating as 'unknown'.

Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[4](@HD	VN:1.0	SO:cOoRdinate
) STANDARD_ERROR
    WARNING	2025-06-03 15:16:34	SAMTextHeaderCodec	Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'.

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.specialFileWriterTest STANDARD_ERROR
    WARNING	2025-06-03 15:16:34	SAMFileWriterFactory	Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null
    WARNING	2025-06-03 15:16:34	SAMFileWriterFactory	Cannot create index for BAM because output file is not a regular file: file:///dev/null

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeCRAMWriterWithNoReference STANDARD_ERROR
    INFO	2025-06-03 15:16:34	SAMFileWriterFactory	Reference fasta is not provided when writing CRAM file file:///tmp/tmp.1568143910345870867..cram
    INFO	2025-06-03 15:16:34	SAMFileWriterFactory	Will attempt to use a default reference or download as set by defaults:
    INFO	2025-06-03 15:16:34	SAMFileWriterFactory	Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): src/test/resources/htsjdk/samtools/cram/ce.fa
    INFO	2025-06-03 15:16:34	SAMFileWriterFactory	Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false
    INFO	2025-06-03 15:16:34	ReferenceSource	Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that.

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeSamOrBamForCramExtension STANDARD_ERROR
    INFO	2025-06-03 15:16:34	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension12599895228598270492.cram

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriter[0](sam) STANDARD_ERROR
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriter[1](bam) STANDARD_ERROR
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /tmp/tmp.3256785474167497241.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForCramExtensionNoReference STANDARD_ERROR
    INFO	2025-06-03 15:16:34	SAMFileWriterFactory	Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension5602041274548275673.cram
    INFO	2025-06-03 15:16:34	SAMFileWriterFactory	Will attempt to use a default reference or download as set by defaults:
    INFO	2025-06-03 15:16:34	SAMFileWriterFactory	Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): src/test/resources/htsjdk/samtools/cram/ce.fa
    INFO	2025-06-03 15:16:34	SAMFileWriterFactory	Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false
    INFO	2025-06-03 15:16:34	ReferenceSource	Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that.

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForNoExtension STANDARD_ERROR
    INFO	2025-06-03 15:16:34	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension8220755866087596270

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForUnknownFileExtension STANDARD_ERROR
    INFO	2025-06-03 15:16:34	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension3280966596230784115.png

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[0](sam) STANDARD_ERROR
    INFO	2025-06-03 15:16:34	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: jimfs://4a3e844d-ebac-49bd-a9e8-fbcfd7763535/work/testMakeWriterPathsam
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathsam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[1](bam) STANDARD_ERROR
    INFO	2025-06-03 15:16:34	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: jimfs://f0d0b879-c4e6-4547-9b3d-47a6c2cb0317/work/testMakeWriterPathbam
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathbam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[2](cram) STANDARD_ERROR
    INFO	2025-06-03 15:16:34	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: jimfs://8b42eb1b-2189-4374-97c3-54b797340b52/work/testMakeWriterPathcram
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathcram, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPathAndReferencePath[0](sam) STANDARD_ERROR
    INFO	2025-06-03 15:16:34	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: jimfs://c86421eb-158b-4385-91f7-93e69c80d63c/work/testMakeWriterPathsam
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathsam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPathAndReferencePath[1](bam) STANDARD_ERROR
    INFO	2025-06-03 15:16:34	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: jimfs://68c30191-e1a4-49e8-b62f-fb86c71f9743/work/testMakeWriterPathbam
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathbam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPathAndReferencePath[2](cram) STANDARD_ERROR
    INFO	2025-06-03 15:16:34	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: jimfs://8ab1edc9-3d21-4563-9721-829070cb61b3/work/testMakeWriterPathcram
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathcram, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1
Finished 6800 tests
Finished 7000 tests

Gradle suite > Gradle test > htsjdk.samtools.SAMSequenceDictionaryTest.testMergeDictionaries[7](SAMSequenceRecord(name=chr1,length=101,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=0,dict_index=0,assembly=null,alternate_names=[]), false) STANDARD_ERROR
    ERROR	2025-06-03 15:16:46	SAMSequenceDictionary	Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2.

Gradle suite > Gradle test > htsjdk.samtools.sra.SRAAccessionTest STANDARD_ERROR
    ngs-java: DLL download was disabled

Gradle suite > Gradle test > htsjdk.samtools.sra.SRAAccessionTest.testIsValidAcc[0](SRR000123, true) SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.sra.SRAAccessionTest.testIsValidAcc[1](DRR010511, true) SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.sra.SRAAccessionTest.testIsValidAcc[2](src/test/resources/htsjdk/samtools/sra/test_archive.sra, true) SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.sra.SRAAccessionTest.testIsValidAcc[3](src/test/resources/htsjdk/samtools/compressed.bam, false) SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.sra.SRAAccessionTest.testIsValidAcc[4](src/test/resources/htsjdk/samtools/uncompressed.sam, false) SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.sra.SRALazyRecordTest.testCloneAndEquals[0](SRR2096940) SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.sra.SRALazyRecordTest.testSerialization[0](SRR2096940) SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.sra.SRAQueryTest.testQueryCounts[0](SRR2096940, CM000681.1, 0, 59128983, true, 10591, 0) SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.sra.SRAQueryTest.testQueryCounts[1](SRR2096940, CM000681.1, 55627015, 59128983, true, 10591, 0) SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.sra.SRAQueryTest.testQueryCounts[2](SRR2096940, CM000681.1, 55627016, 59128983, true, 0, 0) SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.sra.SRAQueryTest.testQueryCounts[3](SRR2096940, CM000681.1, 55627016, 59128983, false, 10591, -1) SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.sra.SRAQueryTest.testReferenceAlignedCounts[0](SRR2096940, CM000681.1, 0, 10591) SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.sra.SRAQueryTest.testReferenceAlignedCounts[1](SRR2096940, CM000681.1, 55627015, 10591) SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.sra.SRAQueryTest.testReferenceAlignedCounts[2](SRR2096940, CM000681.1, 55627016, 0) SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.sra.SRAReferenceTest.testReference[0](SRR2096940, CM000681.1, 95001, 95050, AGATGATTCAGTCTCACCAAGAACACTGAAAGTCACATGGCTACCAGCAT) SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.sra.SRAReferenceTest.testReferenceMt[0](SRR353866, [AAAB01001871.1:1-50 = TGACGCGCATGAATGGATTAACGAGATTCCCTCTGTCCCTATCTACTATC, AAAB01001871.1:901-950 = ACCAAGCGTACGATTGTTCACCCTTTCAAGGGAACGTGAGCTGGGTTTAG, AAAB01008987.1:1-50 = TTTTGGACGATGTTTTTGGTGAACAGAAAACGAGCTCAATCATCCAGAGC, AAAB01008859.1:1-50 = CAAAACGATGCCACAGATCAGAAGTTAATTAACGCACATTCTCCACCCAC]) SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.SamFilesTest.testIndexSymlinking[2](src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai) STANDARD_ERROR
    WARNING	2025-06-03 15:16:47	SamFiles	The index file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam
    WARNING	2025-06-03 15:16:47	SamFiles	The index file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam
Finished 7200 tests

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.customReaderFactoryTest STANDARD_ERROR
    INFO	2025-06-03 15:16:48	CustomReaderFactory	Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory
    INFO	2025-06-03 15:16:48	CustomReaderFactory	Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory
    INFO	2025-06-03 15:16:48	CustomReaderFactory	Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from  this jar
    INFO	2025-06-03 15:16:48	SamReaderFactoryTest	Opening customr reader for src/test/resources/htsjdk/samtools/uncompressed.sam

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.exhaustInputResourcePermutation SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.openPath STANDARD_ERROR
    INFO	2025-06-03 15:16:48	SamReaderFactoryTest	Reading from src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam ...

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.queryInputResourcePermutation SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.queryStreamingPathBamWithFileIndex STANDARD_ERROR
    INFO	2025-06-03 15:16:48	SamReaderFactoryTest	Query from data=PATH:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam;index=FILE:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai ...
    INFO	2025-06-03 15:16:48	SamReaderFactoryTest	Finished queries in 60ms

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURL STANDARD_ERROR
    WARNING	2025-06-03 15:16:48	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:16:48	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLNoIndexFile STANDARD_ERROR
    WARNING	2025-06-03 15:16:48	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:16:48	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:16:48	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:16:48	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:16:48	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:16:48	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:16:48	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:16:48	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLStream STANDARD_ERROR
    WARNING	2025-06-03 15:16:48	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:16:48	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromMalformedSeekableStream STANDARD_ERROR
    WARNING	2025-06-03 15:16:48	SamReaderFactory	Unable to detect file format from input URL or stream, assuming SAM format.

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromSeekableStream STANDARD_ERROR
    WARNING	2025-06-03 15:16:48	SamReaderFactory	Unable to detect file format from input URL or stream, assuming SAM format.

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromURL STANDARD_ERROR
    WARNING	2025-06-03 15:16:48	SamReaderFactory	Unable to detect file format from input URL or stream, assuming SAM format.

Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[0](cram/test.cram, cram/auxf.fa, 0:12-13, Jim) STANDARD_ERROR
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[1](cram_with_bai_index.cram, hg19mini.fasta, 3:700-0, k) STANDARD_ERROR
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[2](cram_with_crai_index.cram, hg19mini.fasta, 2:350-0, i) STANDARD_ERROR
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testIterateCRAMWithIndex[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testIterateCRAMWithIndex[1](cram_with_crai_index.cram, hg19mini.fasta) STANDARD_ERROR
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testReferenceRequiredForCRAM[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR
    INFO	2025-06-03 15:16:49	ReferenceSource	Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that.
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testReferenceRequiredForCRAM[1](cram_with_crai_index.cram, hg19mini.fasta) STANDARD_ERROR
    INFO	2025-06-03 15:16:49	ReferenceSource	Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that.
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:16:49	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testBamIntegers[1](inttest_large_coordinates.bam) STANDARD_ERROR
    WARNING	2025-06-03 15:16:49	BAMRecordCodec	Reference length is too large for BAM bin field.
    WARNING	2025-06-03 15:16:49	BAMRecordCodec	Reads on references longer than 536870912bp will have bin set to 0.

Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testSamIntegers[1](inttest_large_coordinates.sam) STANDARD_ERROR
    WARNING	2025-06-03 15:16:49	BAMRecordCodec	Reference length is too large for BAM bin field.
    WARNING	2025-06-03 15:16:49	BAMRecordCodec	Reads on references longer than 536870912bp will have bin set to 0.

Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testCRAMConversion SKIPPED

Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testSamtoolsIsAvailable SKIPPED

Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testSamtoolsVersion SKIPPED
Finished 7400 tests
Finished 7600 tests

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlockReadStreamTest.testSliceBlocksReadStreamsRoundTrip SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlocksTest.testSliceBlocksRoundTrip SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests STANDARD_ERROR
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index.

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.sliceStateTest[6]([htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772, htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111, htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0, htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f, htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee, htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d, htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c, htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb, htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a, htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09], true, UNMAPPED_UNPLACED, 0, 0) STANDARD_ERROR
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index.

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.sliceStateTest[7]([htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772, htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111, htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0, htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f, htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee, htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d, htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c, htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb, htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a, htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09], false, UNMAPPED_UNPLACED, 0, 0) STANDARD_ERROR
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:16:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index.

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.testValidateReferenceMD5Fails STANDARD_ERROR
    WARNING	2025-06-03 15:16:49	CRAMReferenceRegion	The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20
    WARNING	2025-06-03 15:16:49	Slice	Slice mapped outside of reference bases length 20: slice reference context=SINGLE_REFERENCE: 0, start=1, span=20, counter=0.
Finished 7800 tests

Gradle suite > Gradle test > htsjdk.samtools.util.SortingCollectionTest STANDARD_ERROR
    Resetting tmpdir

Gradle suite > Gradle test STANDARD_ERROR
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
Finished 8000 tests
Finished 8200 tests
Finished 8400 tests
Finished 8600 tests
Finished 8800 tests
Finished 9000 tests
Finished 9200 tests
Finished 9400 tests
Finished 9600 tests
Finished 9800 tests
Finished 10000 tests
	Gradle is still running, please be patient...
Finished 10200 tests

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[398](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[399](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[400](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[401](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[402](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[403](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[404](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[405](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[406](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[407](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[408](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[414](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:18:03	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:18:03	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:18:03	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:18:03	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:18:03	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:18:03	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:18:03	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:18:03	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:18:03	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:18:03	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:18:03	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:18:03	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:18:03	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:18:03	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:18:03	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:18:03	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:18:03	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:18:03	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:18:03	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index.

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[426](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[427](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[428](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[429](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[430](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[431](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[432](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[433](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[434](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[435](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[436](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:18:03	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
Finished 10400 tests

Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingMultiSampleVCF STANDARD_ERROR
    WARNING	2025-06-03 15:18:04	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSingleSampleVCF STANDARD_ERROR
    WARNING	2025-06-03 15:18:04	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSitesOnlyVCF STANDARD_ERROR
    WARNING	2025-06-03 15:18:04	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
Finished 10600 tests
Finished 10800 tests

Gradle suite > Gradle test > htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.demonstrateTestWriteToPipeDoesNotHang_1 STANDARD_ERROR
    java.lang.RuntimeException: oops
    	at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.lambda$demonstrateTestWriteToPipeDoesNotHang_1$0(VariantContextWriterBuilderUnitTest.java:497)
    	at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.lambda$testWriteToPipe$2(VariantContextWriterBuilderUnitTest.java:522)
    	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
    	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
    	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    	at java.base/java.lang.Thread.run(Thread.java:840)

Gradle suite > Gradle test > htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.demonstrateTestWriteToPipeDoesNotHang_2 STANDARD_ERROR
    java.lang.RuntimeException: oops
    	at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.lambda$demonstrateTestWriteToPipeDoesNotHang_2$1(VariantContextWriterBuilderUnitTest.java:503)
    	at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.lambda$testWriteToPipe$2(VariantContextWriterBuilderUnitTest.java:522)
    	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
    	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
    	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    	at java.base/java.lang.Thread.run(Thread.java:840)
Finished 11000 tests
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Gradle Test Executor 1 finished executing tests.
WARNING: A terminally deprecated method in java.lang.System has been called
WARNING: System::setSecurityManager has been called by org.gradle.api.internal.tasks.testing.worker.TestWorker (file:/usr/share/gradle/lib/plugins/gradle-testing-base-4.4.1.jar)
WARNING: Please consider reporting this to the maintainers of org.gradle.api.internal.tasks.testing.worker.TestWorker
WARNING: System::setSecurityManager will be removed in a future release
Results: SUCCESS (35817 tests, 35791 successes, 0 failures, 26 skipped)
Finished generating test XML results (0.292 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/test-results/testWithDefaultReference
Generating HTML test report...
Finished generating test html results (0.241 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/reports/tests/testWithDefaultReference
:testWithDefaultReference (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 11 mins 55.929 secs.
:testWithOptimisticVCF4_4 (Thread[Task worker for ':' Thread 3,5,main]) started.
:testWithOptimisticVCF4_4
executing task ':testWithOptimisticVCF4_4' ...
Putting task artifact state for task ':testWithOptimisticVCF4_4' into context took 0.0 secs.
Up-to-date check for task ':testWithOptimisticVCF4_4' took 0.045 secs. It is not up-to-date because:
  Task.upToDateWhen is false.
Starting process 'Gradle Test Executor 2'. Working directory: /build/reproducible-path/htsjdk-4.1.0+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false -Dsamjdk.optimistic_vcf_4_4=true @/tmp/gradle-worker-classpath3557541738552212450txt -Xms1G -Xmx2G -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 2'
Successfully started process 'Gradle Test Executor 2'
Gradle Test Executor 2 started executing tests.
Gradle Test Executor 2 finished executing tests.
WARNING: A terminally deprecated method in java.lang.System has been called
WARNING: System::setSecurityManager has been called by org.gradle.api.internal.tasks.testing.worker.TestWorker (file:/usr/share/gradle/lib/plugins/gradle-testing-base-4.4.1.jar)
WARNING: Please consider reporting this to the maintainers of org.gradle.api.internal.tasks.testing.worker.TestWorker
WARNING: System::setSecurityManager will be removed in a future release
Results: SUCCESS (0 tests, 0 successes, 0 failures, 0 skipped)
Finished generating test XML results (0.0 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/test-results/testWithOptimisticVCF4_4
Generating HTML test report...
Finished generating test html results (0.004 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/reports/tests/testWithOptimisticVCF4_4
:testWithOptimisticVCF4_4 (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 1.435 secs.
:test (Thread[Task worker for ':' Thread 3,5,main]) started.
:test
executing task ':test' ...
Putting task artifact state for task ':test' into context took 0.0 secs.
Up-to-date check for task ':test' took 0.04 secs. It is not up-to-date because:
  Task.upToDateWhen is false.
Starting process 'Gradle Test Executor 3'. Working directory: /build/reproducible-path/htsjdk-4.1.0+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false @/tmp/gradle-worker-classpath7145509439580589075txt -Xms1G -Xmx2G -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 3'
Successfully started process 'Gradle Test Executor 3'
Gradle Test Executor 3 started executing tests.

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[5](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[6](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[7](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[8](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstElementOfIterator runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstElementOfIterator runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstElementOfIterator runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstElementOfIterator runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstElementOfIterator runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[5](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstElementOfIterator runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[6](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstElementOfIterator runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[7](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstElementOfIterator runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[8](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstElementOfIterator runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstSequence runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testFirstSequence runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstSequence runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testFirstSequence runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstSequence runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstSequenceExtended runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testFirstSequenceExtended runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstSequenceExtended runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testFirstSequenceExtended runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstSequenceExtended runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testLastCompleteContigRead runtime: 6ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testLastCompleteContigRead runtime: 5ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testLastCompleteContigRead runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testLastCompleteContigRead runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testLastCompleteContigRead runtime: 9ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[5](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testLastCompleteContigRead runtime: 8ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[6](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testLastCompleteContigRead runtime: 8ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[7](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testLastCompleteContigRead runtime: 8ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[8](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testLastCompleteContigRead runtime: 5ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstOfChr1 runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testFirstOfChr1 runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstOfChr1 runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testFirstOfChr1 runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstOfChr1 runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testNextElementOfIterator runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testNextElementOfIterator runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testNextElementOfIterator runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testNextElementOfIterator runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testNextElementOfIterator runtime: 8ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[5](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testNextElementOfIterator runtime: 8ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[6](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testNextElementOfIterator runtime: 8ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[7](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testNextElementOfIterator runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[8](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testNextElementOfIterator runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testOpenFile runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testOpenFile runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testOpenFile runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testOpenFile runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testOpenFile runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadPastEndOfContig[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadPastEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadPastEndOfContig[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadPastEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadPastEndOfContig[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadPastEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadPastEndOfContig[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadPastEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadPastEndOfContig[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testReadPastEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadStartingInCenterOfFirstLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadStartingInCenterOfFirstLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadStartingInCenterOfFirstLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadStartingInCenterOfFirstLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testReadStartingInCenterOfFirstLine runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadStartingInCenterOfMiddleLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadStartingInCenterOfMiddleLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadStartingInCenterOfMiddleLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadStartingInCenterOfMiddleLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testReadStartingInCenterOfMiddleLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadThroughEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadThroughEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadThroughEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadThroughEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testReadThroughEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReset runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReset runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReset runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReset runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testReset runtime: 8ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[5](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testReset runtime: 8ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[6](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testReset runtime: 9ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[7](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReset runtime: 2ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[8](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReset runtime: 2ms

Gradle suite > Gradle test > htsjdk.tribble.AsciiFeatureCodecTest.testMakeIndexableSourceFromUnknownStream STANDARD_ERROR
    WARNING	2025-06-03 15:19:49	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testFromStream[2](java.io.ByteArrayInputStream@169c6e28, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR
    WARNING	2025-06-03 15:19:49	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testReadLines STANDARD_ERROR
    WARNING	2025-06-03 15:19:49	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
Finished 200 tests

Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLength STANDARD_ERROR
    WARNING	2025-06-03 15:19:49	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLengthAtEof STANDARD_ERROR
    WARNING	2025-06-03 15:19:49	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.samtools.BAMFileIndexTest.testQueryUnmapped STANDARD_OUT
    Found start of unmapped reads.  Num mapped reads: 9721
    Time so far: 0
    Linear scan total time: 0
    queryUnmapped time: 0
    Number of unmapped reads:279

Gradle suite > Gradle test > htsjdk.samtools.BAMFileIndexTest.testRandomQueries STANDARD_OUT
    Testing query chr11_random:7211102-7392752 ...
    Testing query chrX_random:2969904-3087323 ...
    Testing query chr5:9255377-9796767 ...
    Testing query chr16_random:9067406-9976989 ...
    Testing query chr6:2164417-9572211 ...
    Testing query chr8_random:5688357-6576007 ...
    Testing query chr4_random:4241203-6327831 ...
    Testing query chr2_random:411082-4462819 ...
    Testing query chr13_random:145947-4307287 ...
    Testing query chr15_random:3298214-6356603 ...
    Testing query chr21:472385-8291032 ...
    Testing query chr2:4177649-9835176 ...
    Testing query chr22_random:1490587-8781106 ...
    Testing query chr14:2167927-6299701 ...
    Testing query chr7:4700515-5593851 ...
    Testing query chr22:5016764-7470151 ...
    Testing query chr22_random:7524398-8627117 ...
    Testing query chr8:3764754-6977071 ...
    Testing query chr1_random:1725504-3204042 ...
    Testing query chr21:2025794-4625889 ...
    Testing query chr14:1426554-6327490 ...
    Testing query chrX_random:1992622-9650667 ...
    Testing query chr4:2669418-7183639 ...
    Testing query chr10:2967472-3641376 ...
    Testing query chr10_random:3273594-3427480 ...
    Testing query chr19_random:4582311-5090524 ...
    Testing query chr9_random:7218100-8812477 ...
    Testing query chrX:257134-4337775 ...
    Testing query chr9_random:713930-3536575 ...
    Testing query chrX:2523687-4774316 ...
    Testing query chr21:513221-829881 ...
    Testing query chr14:6924617-9048044 ...
    Testing query chr6:4945372-7173211 ...
    Testing query chr6_random:7501139-9077397 ...
    Testing query chr19:2934833-5141776 ...
    Testing query chr9:863231-7545153 ...
    Testing query chr2:4308042-6742767 ...
    Testing query chr12:293858-324418 ...
    Testing query chr6_random:3308674-4557713 ...
    Testing query chr2_random:6755655-7330097 ...
    Testing query chr9_random:1234763-6135261 ...
    Testing query chr17:7042296-7582149 ...
    Testing query chr18:6749235-8476299 ...
    Testing query chr22:1198031-6226173 ...
    Testing query chr22:9446557-9458998 ...
    Testing query chr15:473293-1136600 ...
    Testing query chr13:8001267-8034858 ...
    Testing query chr7_random:12779-8349897 ...
    Testing query chrX:6476995-9046675 ...
    Testing query chr22:455684-9901546 ...
    Testing query chr20:2540726-9004820 ...
    Testing query chr1:5290124-7772462 ...
    Testing query chr2_random:4562177-7629291 ...
    Testing query chr4:5992612-7734912 ...
    Testing query chr5:1027938-6017856 ...
    Testing query chr5:3945452-4558863 ...
    Testing query chr7_random:1434224-8766265 ...
    Testing query chr13_random:2806926-8471270 ...
    Testing query chr21:5896937-6230120 ...
    Testing query chr10_random:2325170-6773979 ...
    Testing query chr4:768115-9242973 ...
    Testing query chr9:204376-1523700 ...
    Testing query chr15:6918456-9920136 ...
    Testing query chr8:195836-2912231 ...
    Testing query chr4_random:8569316-9601747 ...
    Testing query chr14:7539676-8479802 ...
    Testing query chr17_random:6016149-9676582 ...
    Testing query chr3:2401075-5926977 ...
    Testing query chr7:6825835-8610049 ...
    Testing query chr4:8589977-9226779 ...
    Testing query chr22_random:881883-9900377 ...
    Testing query chr19:2282185-2974234 ...
    Testing query chr2_random:530137-7997036 ...
    Testing query chr11_random:1524078-8571487 ...
    Testing query chrX:3561537-3812547 ...
    Testing query chr7_random:5345040-8399303 ...
    Testing query chr22:1586323-6546266 ...
    Testing query chr13:356087-8263221 ...
    Testing query chr9:6308509-8761532 ...
    Testing query chr8:3702301-5705153 ...
    Testing query chr13_random:1656308-4034137 ...
    Testing query chr3:4684965-7862719 ...
    Testing query chr19_random:5585589-7312648 ...
    Testing query chr18:8395777-9280098 ...
    Testing query chr6_random:738052-6252176 ...
    Testing query chr5_random:6874632-8838246 ...
    Testing query chr7_random:4576401-9601286 ...
    Testing query chr6_random:1277796-9240909 ...
    Testing query chr22:2128956-7451924 ...
    Testing query chr9:5866041-7641214 ...
    Testing query chr6_random:2900603-6324004 ...
    Testing query chr5:3340073-3878152 ...
    Testing query chr7_random:6065731-8117472 ...
    Testing query chr22:6980282-9420307 ...
    Testing query chr3_random:7896234-9902729 ...
    Testing query chr4:5226514-9465698 ...
    Testing query chr11_random:2710966-7297413 ...
    Testing query chr4:5814391-6477874 ...
    Testing query chr17:3411447-7945931 ...
    Testing query chr19_random:1563833-8954930 ...
    Testing query chr4:2666458-5577064 ...
    Testing query chrM:2495375-2785830 ...
    Testing query chr22_random:2741863-7160257 ...
    Testing query chr20:3030962-4839827 ...
    Testing query chrX_random:1999206-3290596 ...
    Testing query chr1_random:7581574-9491516 ...
    Testing query chr5:8544911-9905206 ...
    Testing query chr17_random:5247411-8818598 ...
    Testing query chr18:2206748-2542618 ...
    Testing query chr6:5560095-6841213 ...
    Testing query chrX:5584638-8069137 ...
    Testing query chr2_random:893746-4019636 ...
    Testing query chr4_random:7220619-8625179 ...
    Testing query chr17_random:7487783-7745825 ...
    Testing query chr13_random:140415-4339843 ...
    Testing query chr22:3465880-9918684 ...
    Testing query chr16_random:2228554-5218116 ...
    Testing query chr6:3812651-9020894 ...
    Testing query chr19:4897072-8152584 ...
    Testing query chr15_random:2493596-3303830 ...
    Testing query chr17:7330256-9331563 ...
    Testing query chr7_random:2372609-7660988 ...
    Testing query chr21:16468-1408282 ...
    Testing query chrM:946718-7866529 ...
    Testing query chr6:636772-5261193 ...
    Testing query chr4:4081985-5160778 ...
    Testing query chr4_random:3992937-8001782 ...
    Testing query chr3_random:4269902-7314671 ...
    Testing query chr8_random:5398008-9100867 ...
    Testing query chr11_random:4717946-5886722 ...
    Testing query chr14:3324888-9762784 ...
    Testing query chr3_random:447076-2904415 ...
    Testing query chr18_random:4656587-8830031 ...
    Testing query chr15_random:2677992-8013872 ...
    Testing query chr8:8741342-9773821 ...
    Testing query chrM:638643-3884353 ...
    Testing query chr6:1102480-2996219 ...
    Testing query chr13:27071-9001996 ...
    Testing query chr8_random:133575-8239847 ...
    Testing query chr4:5119076-7497751 ...
    Testing query chr6_random:8932876-9157638 ...
    Testing query chr2:8039126-9556281 ...
    Testing query chr18:2759483-4424919 ...
    Testing query chr7_random:2162721-7693312 ...
    Testing query chr17_random:3212242-7079443 ...
    Testing query chrX_random:9441944-9675063 ...
    Testing query chrX:1483850-9503277 ...
    Testing query chrY:708618-2939362 ...
    Testing query chr1:1457571-8460228 ...
    Testing query chrM:5153488-6390263 ...
    Testing query chr8:2469944-5489240 ...
    Testing query chr4:2270560-9937550 ...
    Testing query chr10:1924284-4282155 ...
    Testing query chrY:5044757-9726553 ...
    Testing query chr21_random:8138434-8862076 ...
    Testing query chr17_random:8064209-8585636 ...
    Testing query chr22:7325448-9656485 ...
    Testing query chr11:6475178-6915306 ...
    Testing query chrM:1569370-6357214 ...
    Testing query chr8_random:1676954-7528262 ...
    Testing query chr8:3436473-9972209 ...
    Testing query chr19_random:8309162-8766514 ...
    Testing query chr7_random:6416981-6735864 ...
    Testing query chr19:3484685-3801122 ...
    Testing query chr1:1868925-6151268 ...
    Testing query chr1:536419-4044558 ...
    Testing query chr1:2522877-4924643 ...
    Testing query chr11_random:676633-9128847 ...
    Testing query chr6_random:3598124-6981657 ...
    Testing query chr5_random:7166103-8219161 ...
    Testing query chr19:1684800-5872548 ...
    Testing query chr1_random:3315026-8441262 ...
    Testing query chr18_random:2290355-8594736 ...
    Testing query chr20:3121858-8750525 ...
    Testing query chr5:1854779-7785465 ...
    Testing query chr3:2844488-8229201 ...
    Testing query chr9:98994-6937193 ...
    Testing query chr7_random:566405-4329525 ...
    Testing query chrM:3349123-8858299 ...
    Testing query chr18_random:2476805-3333909 ...
    Testing query chr5_random:2947230-5023103 ...
    Testing query chrY:858711-3764404 ...
    Testing query chrM:3202756-4087290 ...
    Testing query chr3:2241212-3744434 ...
    Testing query chr2:294299-2791063 ...
    Testing query chr16:5636813-7725712 ...
    Testing query chrY:190457-4183568 ...
    Testing query chr15_random:1757556-6243468 ...
    Testing query chr21_random:2404640-9698959 ...
    Testing query chrY:2899895-8525822 ...
    Testing query chr14:5316023-9325638 ...
    Testing query chr5_random:3836137-6496666 ...
    Testing query chr10_random:1992029-2390509 ...
    Testing query chr15:2008393-5397033 ...
    Testing query chr6:3033491-5689013 ...
    Testing query chr13:4802709-6651494 ...
    Testing query chr11_random:1126435-2590416 ...
    Testing query chr14:674415-1741256 ...
    Testing query chr2:5945864-7917088 ...
    Testing query chr4:2984861-4376484 ...
    Testing query chr1_random:5661261-9348854 ...
    Testing query chr18:2892586-9538492 ...
    Testing query chr19_random:2666788-6214501 ...
    Testing query chr5_random:2892340-8892790 ...
    Testing query chr3:8321138-9156829 ...
    Testing query chr20:1010051-2675065 ...
    Testing query chr12:2016127-9734230 ...
    Testing query chr17:6565364-9842724 ...
    Testing query chr2_random:1534009-9935421 ...
    Testing query chr22_random:1798866-3566302 ...
    Testing query chr9_random:2863862-4098636 ...
    Testing query chr7_random:6695702-7166373 ...
    Testing query chr19_random:7774915-8904502 ...
    Testing query chr4_random:1354793-3060860 ...
    Testing query chr16_random:680783-7967813 ...
    Testing query chr22_random:1679274-1962853 ...
    Testing query chr5:1405068-3861785 ...
    Testing query chr8_random:6642950-9011653 ...
    Testing query chr16:1873173-7921837 ...
    Testing query chr7_random:2750681-9520458 ...
    Testing query chr16_random:885218-3713066 ...
    Testing query chr10_random:4952036-9328892 ...
    Testing query chr1_random:1556041-9207413 ...
    Testing query chrX:3509058-4668683 ...
    Testing query chr22_random:5775297-9086853 ...
    Testing query chr1:1171026-6903635 ...
    Testing query chr17_random:706069-7256916 ...
    Testing query chr1:7825983-8559769 ...
    Testing query chr7_random:7709758-9250068 ...
    Testing query chr6:4475592-7218806 ...
    Testing query chr5_random:7263397-7305993 ...
    Testing query chr16_random:5376132-9863064 ...
    Testing query chr5:4383593-4921390 ...
    Testing query chr12:5541381-6329888 ...
    Testing query chr7_random:297473-6191920 ...
    Testing query chr7_random:5797186-6007720 ...
    Testing query chr14:6288978-7147625 ...
    Testing query chrY:3280527-6071425 ...
    Testing query chr2_random:341241-9849655 ...
    Testing query chr18_random:2756400-5124352 ...
    Testing query chr18_random:3245587-6421468 ...
    Testing query chr7_random:1108885-7011416 ...
    Testing query chr19:55506-8032351 ...
    Testing query chr9_random:507759-1925801 ...
    Testing query chr21_random:5641470-6291456 ...
    Testing query chr16_random:2647045-6473932 ...
    Testing query chr3:8883638-9872842 ...
    Testing query chr17:2328196-3652679 ...
    Testing query chr22_random:2297511-5498425 ...
    Testing query chrX_random:3773240-4693054 ...
    Testing query chr13:1575245-9070298 ...
    Testing query chr8_random:5301468-7005527 ...
    Testing query chr4:6535020-9656212 ...
    Testing query chr18:5782944-8199590 ...
    Testing query chr5_random:1102579-7463246 ...
    Testing query chr5:2779653-6802521 ...
    Testing query chr10:99615-2172940 ...
    Testing query chr7:2762506-2870870 ...
    Testing query chr15_random:981768-8907527 ...
    Testing query chr16:436530-5189740 ...
    Testing query chr15:9551545-9569163 ...
    Testing query chr17_random:432471-8074112 ...
    Testing query chr8:4845184-5039976 ...
    Testing query chr7:3531770-6086719 ...
    Testing query chr17:2693356-7185572 ...
    Testing query chr6:6650063-9646384 ...
    Testing query chrY:121317-4718433 ...
    Testing query chr1_random:1003027-1831870 ...
    Testing query chr21:8788645-9420609 ...
    Testing query chr13_random:987064-4341370 ...
    Testing query chr13_random:842466-5111480 ...
    Testing query chrM:7654248-8310027 ...
    Testing query chr2:1532378-3980671 ...
    Testing query chr16_random:2308350-8259941 ...
    Testing query chr18_random:7619793-8200073 ...
    Testing query chr16:908998-6962421 ...
    Testing query chr1_random:4760134-7897692 ...
    Testing query chr4_random:351969-2613223 ...
    Testing query chr16:3482498-9633584 ...
    Testing query chr22:7907949-9933800 ...
    Testing query chr15:5854248-7275283 ...
    Testing query chr14:3664791-8748133 ...
    Testing query chrX:896137-9572469 ...
    Testing query chrX:1865390-3062428 ...
    Testing query chr6:595893-8247348 ...
    Testing query chr9_random:1425130-4402172 ...
    Testing query chr7_random:463001-1378501 ...
    Testing query chr10:5465621-8140677 ...
    Testing query chr22:4007755-6030817 ...
    Testing query chr19:2152758-4285738 ...
    Testing query chrX_random:6197638-7278734 ...
    Testing query chr8_random:2506286-3132074 ...
    Testing query chr3:5088917-6346018 ...
    Testing query chr21_random:709245-2447062 ...
    Testing query chr7_random:2297450-2733491 ...
    Testing query chrX_random:75616-6715390 ...
    Testing query chr14:1451557-9217186 ...
    Testing query chr22:4216648-4273083 ...
    Testing query chr22_random:2900019-9495009 ...
    Testing query chr4:6062237-9450155 ...
    Testing query chr3_random:2205998-8038523 ...
    Testing query chr19:4006735-8497976 ...
    Testing query chrM:4367909-8743630 ...
    Testing query chr1:3235237-5886681 ...
    Testing query chr18:2455071-8918070 ...
    Testing query chr3:715763-7415212 ...
    Testing query chr2_random:3698070-6718252 ...
    Testing query chr10:4035923-8780337 ...
    Testing query chr1_random:4369783-9221375 ...
    Testing query chr11:3488452-9565235 ...
    Testing query chrX:3524615-7110878 ...
    Testing query chr19_random:7779323-8424172 ...
    Testing query chr15_random:910898-4876910 ...
    Testing query chr15_random:1015024-3678499 ...
    Testing query chr9:3393986-9417756 ...
    Testing query chr18_random:857279-9200045 ...
    Testing query chr18:1396324-2772435 ...
    Testing query chr12:5614369-9031405 ...
    Testing query chr5:3780359-4070909 ...
    Testing query chr17:4508678-5389778 ...
    Testing query chr21_random:6972726-7854603 ...
    Testing query chr12:3182535-8039198 ...
    Testing query chr10:3951103-7166395 ...
    Testing query chr5_random:6532707-9837900 ...
    Testing query chr13_random:7985015-9743703 ...
    Testing query chr20:6134113-9969678 ...
    Testing query chrY:1542908-4899134 ...
    Testing query chr19_random:324180-7673324 ...
    Testing query chr22_random:4465119-8807791 ...
    Testing query chr14:4342424-6275354 ...
    Testing query chr21:3393386-7099240 ...
    Testing query chr3_random:2130566-2642809 ...
    Testing query chr1_random:2534189-6047752 ...
    Testing query chrM:3319509-8627744 ...
    Testing query chr4_random:7027413-8546790 ...
    Testing query chr18:5213087-7307044 ...
    Testing query chrX_random:5138706-7179617 ...
    Testing query chr21:1746459-3369825 ...
    Testing query chr17_random:4364489-9952653 ...
    Testing query chr21_random:2852383-6343308 ...
    Testing query chr16:1718072-7027200 ...
    Testing query chr7:2836942-5941970 ...
    Testing query chr21_random:6013526-6739121 ...
    Testing query chr6:2041720-8080188 ...
    Testing query chr20:5614189-8320637 ...
    Testing query chr18:7510033-9259036 ...
    Testing query chr7_random:5464431-5858425 ...
    Testing query chrX_random:2642097-9170108 ...
    Testing query chr21_random:2372613-7228145 ...
    Testing query chr7:7643929-8629915 ...
    Testing query chrM:1496669-3662785 ...
    Testing query chrM:5816559-7988640 ...
    Testing query chr4_random:3216837-5344216 ...
    Testing query chr8_random:7939352-9193364 ...
    Testing query chr11_random:4477474-7119222 ...
    Testing query chr22:1795085-7018163 ...
    Testing query chr2:489045-5507534 ...
    Testing query chr20:228222-2645827 ...
    Testing query chr2_random:6696262-7193942 ...
    Testing query chrX:624678-2022130 ...
    Testing query chr11_random:7420609-7476969 ...
    Testing query chr7_random:35741-8947140 ...
    Testing query chr9:2887670-8574309 ...
    Testing query chr9_random:5022666-8213630 ...
    Testing query chr16_random:2811399-8122673 ...
    Testing query chr19:2563169-2938289 ...
    Testing query chr15_random:3165794-8354108 ...
    Testing query chr1_random:4114915-9235471 ...
    Testing query chr10_random:983161-9480146 ...
    Testing query chr2:5984445-9861542 ...
    Testing query chr21:2955353-3709382 ...
    Testing query chr18:4220403-7713605 ...
    Testing query chr9:5837376-6191557 ...
    Testing query chr18:3760903-6211242 ...
    Testing query chr4:2604919-6869284 ...
    Testing query chr14:8243966-8657979 ...
    Testing query chrX:8572226-9566286 ...
    Testing query chr15_random:1776922-9379642 ...
    Testing query chr11:6484864-9835462 ...
    Testing query chr13_random:2265643-8434104 ...
    Testing query chr18_random:2936640-6667223 ...
    Testing query chr21_random:6212251-8673018 ...
    Testing query chr1_random:1062720-2585432 ...
    Testing query chr21_random:5965453-7655829 ...
    Testing query chrX_random:2147524-2773583 ...
    Testing query chr13_random:368974-2821747 ...
    Testing query chr5_random:1943780-5626512 ...
    Testing query chr20:30472-8431478 ...
    Testing query chr10_random:1574710-2300026 ...
    Testing query chr16_random:5290469-9294719 ...
    Testing query chr22:2213818-3185623 ...
    Testing query chr18:2186838-5554932 ...
    Testing query chr1_random:4416515-6829118 ...
    Testing query chr17_random:4168349-9033195 ...
    Testing query chr4_random:7231065-9006087 ...
    Testing query chr3:6627861-7098084 ...
    Testing query chr21:4791386-7462661 ...
    Testing query chr6:5486440-6497547 ...
    Testing query chr7:7583780-8490132 ...
    Testing query chr15:4167629-9516050 ...
    Testing query chr13:412129-3106131 ...
    Testing query chr6:2242528-3392002 ...
    Testing query chr13:4573366-8565166 ...
    Testing query chr14:1012727-4265512 ...
    Testing query chrX:8331093-8914945 ...
    Testing query chr19:3587675-9174187 ...
    Testing query chr7:296443-1800051 ...
    Testing query chr3:5277077-9767087 ...
    Testing query chr21:7692109-7739057 ...
    Testing query chr11:3448455-8411453 ...
    Testing query chr1_random:2275881-3676442 ...
    Testing query chr4_random:6322956-7587151 ...
    Testing query chr22_random:4609088-7067795 ...
    Testing query chr11:1103974-5115622 ...
    Testing query chr17:8733322-9618772 ...
    Testing query chr5_random:1779768-6935553 ...
    Testing query chr8_random:2538535-9879832 ...
    Testing query chr22:768294-3209930 ...
    Testing query chr22:943981-2330158 ...
    Testing query chr12:4987241-7314877 ...
    Testing query chr2:3120747-6311500 ...
    Testing query chrX:1829150-5592634 ...
    Testing query chr7:795351-9692074 ...
    Testing query chr9:5469158-7108447 ...
    Testing query chr18:1967306-6204810 ...
    Testing query chr4_random:8969152-9598463 ...
    Testing query chr4_random:1579186-2839628 ...
    Testing query chr15:5974419-7281533 ...
    Testing query chr8_random:3609626-6631230 ...
    Testing query chr17:3094989-6618173 ...
    Testing query chr15:1799279-6576530 ...
    Testing query chr3:5157964-8423765 ...
    Testing query chr22_random:2813926-5797993 ...
    Testing query chr2:2248206-3931961 ...
    Testing query chr7:3205910-9801772 ...
    Testing query chr21_random:623490-6775587 ...
    Testing query chrM:8166786-8509161 ...
    Testing query chr17:1804940-2950404 ...
    Testing query chr10_random:2511464-6816559 ...
    Testing query chr21_random:153036-5827934 ...
    Testing query chr2_random:8263243-9685626 ...
    Testing query chr21:1111482-5812333 ...
    Testing query chr8:4290604-9166817 ...
    Testing query chr13:3398929-7913910 ...
    Testing query chr10:4553797-9072246 ...
    Testing query chr20:7207944-7471721 ...
    Testing query chrY:1982521-2897985 ...
    Testing query chr10_random:5100074-7818426 ...
    Testing query chr15:4365944-8388476 ...
    Testing query chr13:50044-8373169 ...
    Testing query chr12:5115399-7648840 ...
    Testing query chr4:2962742-8829366 ...
    Testing query chr6_random:1322565-9235978 ...
    Testing query chr12:6057343-7930326 ...
    Testing query chr3:1612029-2982153 ...
    Testing query chr15:6582900-8591795 ...
    Testing query chr21:5009971-6424414 ...
    Testing query chr6:706279-8162934 ...
    Testing query chr16:3267535-9670332 ...
    Testing query chr16:2694606-3346697 ...
    Testing query chrY:9108749-9339860 ...
    Testing query chr18:1265164-5476362 ...
    Testing query chr8_random:1135765-3131623 ...
    Testing query chr1_random:4068577-5850392 ...
    Testing query chr10_random:8086436-9515610 ...
    Testing query chr12:786080-9272524 ...
    Testing query chr2_random:3529918-9107547 ...
    Testing query chrX:33039-720704 ...
    Testing query chrY:7759964-8753893 ...
    Testing query chr18_random:9023306-9399435 ...
    Testing query chr6:5281117-9258674 ...
    Testing query chr2_random:3737881-7335740 ...
    Testing query chr18_random:486302-3415910 ...
    Testing query chr9_random:4036001-4224366 ...
    Testing query chr1_random:676459-981484 ...
    Testing query chr21:213055-9194219 ...
    Testing query chr3:5273397-7935759 ...
    Testing query chr7:5844019-5928029 ...
    Testing query chr22:4400032-4947008 ...
    Testing query chr1_random:6368632-9050986 ...
    Testing query chr6_random:3521181-8577335 ...
    Testing query chr11_random:4864475-5742060 ...
    Testing query chr9:691952-3618418 ...
    Testing query chr16:5899296-6778697 ...
    Testing query chr16:865613-6607475 ...
    Testing query chr17_random:4739682-6923211 ...
    Testing query chrY:2356621-4914419 ...
    Testing query chr3_random:1842297-6259766 ...
    Testing query chr3_random:5126637-7321281 ...
    Testing query chrX:4209013-9761426 ...
    Testing query chr5_random:4596157-5675945 ...
    Testing query chr21_random:3696079-6024271 ...
    Testing query chr3_random:5067064-8876286 ...
    Testing query chr21_random:5565110-6689301 ...
    Testing query chr21_random:15781-4584722 ...
    Testing query chr1:3346110-7059075 ...
    Testing query chrX:5966696-6933232 ...
    Testing query chr17:5021510-8070334 ...
    Testing query chr6:1149206-6788407 ...
    Testing query chr3_random:3744515-8291994 ...
    Testing query chr2:22996-4588290 ...
    Testing query chr17_random:5326761-6699939 ...
    Testing query chr11_random:2696057-3080563 ...
    Testing query chr9:6885746-7594235 ...
    Testing query chr2:4534733-7295296 ...
    Testing query chr13_random:3998213-9469962 ...
    Testing query chr1_random:5426791-6149949 ...
    Testing query chr9_random:530950-725978 ...
    Testing query chr11:4184033-9403368 ...
    Testing query chr15_random:1456012-6938955 ...
    Testing query chr4:527074-2332486 ...
    Testing query chr15:6231961-6744661 ...
    Testing query chr4_random:1429017-4799661 ...
    Testing query chrX_random:1288951-8906564 ...
    Testing query chr5:203973-5396390 ...
    Testing query chr22_random:6924137-9556382 ...
    Testing query chr13:3692768-5792536 ...
    Testing query chr7_random:4736121-7190035 ...
    Testing query chr19_random:1067060-5424230 ...
    Testing query chr5:4645403-9655346 ...
    Testing query chr21:6194788-9692460 ...
    Testing query chr3_random:6249249-8849610 ...
    Testing query chr1_random:116005-4931104 ...
    Testing query chr9_random:2264542-9177908 ...
    Testing query chr5:1920701-3940100 ...
    Testing query chr19:3510626-6120416 ...
    Testing query chr8_random:1385330-9139475 ...
    Testing query chr5_random:4560385-9932819 ...
    Testing query chr10_random:1546770-4255829 ...
    Testing query chrY:1634712-6195051 ...
    Testing query chr21:1934284-3805640 ...
    Testing query chr10:1098075-1222293 ...
    Testing query chrX:3147440-5915627 ...
    Testing query chr12:644340-9578661 ...
    Testing query chr7:3815107-7552297 ...
    Testing query chr7_random:979254-6592345 ...
    Testing query chr15_random:4031375-9529529 ...
    Testing query chr20:809453-6417655 ...
    Testing query chr3_random:1311668-6592135 ...
    Testing query chr16_random:4796848-9917504 ...
    Testing query chr2:2316239-8809758 ...
    Testing query chr22_random:3700813-7193581 ...
    Testing query chr2_random:5629881-8301170 ...
    Testing query chr2:4292815-5793077 ...
    Testing query chr16:4963697-5732378 ...
    Testing query chr20:1818167-2602981 ...
    Testing query chr13_random:857910-3186701 ...
    Testing query chr8:7828099-7863231 ...
    Testing query chr2:3039751-5869790 ...
    Testing query chr7_random:948462-2258714 ...
    Testing query chr12:2176474-8835346 ...
    Testing query chr4_random:4818082-9335116 ...
    Testing query chr9_random:949590-4937462 ...
    Testing query chr3_random:139177-2147902 ...
    Testing query chr15_random:4086655-7110200 ...
    Testing query chr7:1707937-7031178 ...
    Testing query chr15:6704897-7523233 ...
    Testing query chr8_random:3261310-3388805 ...
    Testing query chr11:4627964-9758513 ...
    Testing query chr3_random:1269243-5807226 ...
    Testing query chr9_random:564250-7036410 ...
    Testing query chr8_random:5129373-5437488 ...
    Testing query chr18:2171501-3304941 ...
    Testing query chr17_random:5747642-6505556 ...
    Testing query chrY:3819311-5517038 ...
    Testing query chr11_random:4980823-9419145 ...
    Testing query chrX:3246258-6297440 ...
    Testing query chr1_random:810216-9835846 ...
    Testing query chr9_random:227030-6294798 ...
    Testing query chr1_random:301295-1576363 ...
    Testing query chr21:4560202-9527465 ...
    Testing query chr11:3926303-4702504 ...
    Testing query chr13_random:4053954-7799426 ...
    Testing query chr8_random:1615788-4228091 ...
    Testing query chrX:5354321-7998054 ...
    Testing query chr5:428791-7222158 ...
    Testing query chrY:5600982-5656729 ...
    Testing query chr4_random:3857931-8313241 ...
    Testing query chr15:1925774-5199208 ...
    Testing query chr11_random:1107850-6997032 ...
    Testing query chr14:2769511-5526141 ...
    Testing query chr22:1129798-7717631 ...
    Testing query chr22_random:2940332-5279177 ...
    Testing query chr9:1067427-1150594 ...
    Testing query chr8:5146545-9541542 ...
    Testing query chr15:7089597-8473958 ...
    Testing query chr12:5527737-5802706 ...
    Testing query chr7:1551097-6396733 ...
    Testing query chr2_random:3022570-3558123 ...
    Testing query chr5_random:385945-6563916 ...
    Testing query chr19_random:3546106-9160937 ...
    Testing query chr15_random:3701260-8137083 ...
    Testing query chr5:1805515-5128679 ...
    Testing query chr10_random:748486-5680503 ...
    Testing query chr18:1342370-7881611 ...
    Testing query chr18_random:770908-6308398 ...
    Testing query chr19:7484581-8473209 ...
    Testing query chr7:4518548-7588072 ...
    Testing query chr9_random:7255308-8443827 ...
    Testing query chrX:5799987-8117438 ...
    Testing query chr14:7540848-8413963 ...
    Testing query chr19_random:2328053-2556284 ...
    Testing query chr16_random:7230921-7518347 ...
    Testing query chr19_random:276347-1547597 ...
    Testing query chr13:765679-7048818 ...
    Testing query chrM:2605992-5897739 ...
    Testing query chrX:7913839-8348655 ...
    Testing query chr2_random:7115229-7577760 ...
    Testing query chr21:7618516-8976664 ...
    Testing query chr10_random:5113402-9511617 ...
    Testing query chr3_random:2749825-6235208 ...
    Testing query chr7_random:4542464-5736534 ...
    Testing query chr22:3287391-8684233 ...
    Testing query chr1:6551268-8138439 ...
    Testing query chr18_random:7072081-7642659 ...
    Testing query chr1_random:375703-2560467 ...
    Testing query chr21:5140483-9431223 ...
    Testing query chr19:320517-7295855 ...
    Testing query chr12:585392-5511186 ...
    Testing query chr18_random:8083366-8235379 ...
    Testing query chr10:126713-1547118 ...
    Testing query chr10:5632955-8746379 ...
    Testing query chr10_random:3676138-6848091 ...
    Testing query chr9:4589897-9207905 ...
    Testing query chr6_random:7846883-9764185 ...
    Testing query chr18_random:4290690-8214747 ...
    Testing query chr13_random:2540819-4559633 ...
    Testing query chr11_random:3861379-5778337 ...
    Testing query chr16_random:1701866-3678380 ...
    Testing query chr15:6359944-8126244 ...
    Testing query chr9_random:3748170-8007098 ...
    Testing query chr9:7943740-9455802 ...
    Testing query chr19_random:1042691-5523628 ...
    Testing query chr1_random:1492517-5228447 ...
    Testing query chr6:5705000-6113711 ...
    Testing query chr20:323999-8013692 ...
    Testing query chr10_random:2403788-4666817 ...
    Testing query chr12:809220-4859122 ...
    Testing query chr7:4626441-6767688 ...
    Testing query chr9:1227373-9861818 ...
    Testing query chr9_random:1646320-4830906 ...
    Testing query chr5:1816686-8010796 ...
    Testing query chr18_random:2978620-4099625 ...
    Testing query chr2:2092284-6363784 ...
    Testing query chr11:6697928-8978854 ...
    Testing query chr15:4328362-7736553 ...
    Testing query chr19:2684370-4694361 ...
    Testing query chr8_random:1549783-2052889 ...
    Testing query chr10_random:343773-5114298 ...
    Testing query chr22:239978-7311092 ...
    Testing query chr10:59830-4498628 ...
    Testing query chr6_random:4394006-8726576 ...
    Testing query chr2:2521493-6006376 ...
    Testing query chrY:174190-248602 ...
    Testing query chr5_random:3175374-3810594 ...
    Testing query chr21:458207-4328406 ...
    Testing query chr7:746735-8755260 ...
    Testing query chr1:8376346-9926832 ...
    Testing query chrX:1558302-6671795 ...
    Testing query chr3:90115-6523026 ...
    Testing query chr17_random:1954593-2055586 ...
    Testing query chr9:2137572-9471850 ...
    Testing query chr18_random:7412031-7927783 ...
    Testing query chr7:2153207-4745373 ...
    Testing query chrX:4532293-8914932 ...
    Testing query chr11:2910609-3421044 ...
    Testing query chr9:6096367-7279687 ...
    Testing query chr3:2070513-7395995 ...
    Testing query chr8_random:835918-1827839 ...
    Testing query chr18:248820-4981110 ...
    Testing query chr11_random:4573607-7438971 ...
    Testing query chrX:4061785-7455437 ...
    Testing query chr3:5179852-5811856 ...
    Testing query chr7_random:3320586-3880101 ...
    Testing query chr22:1201575-8615117 ...
    Testing query chr4:6832003-9027563 ...
    Testing query chr5_random:2075108-2231968 ...
    Testing query chrX_random:59800-714902 ...
    Testing query chrX_random:2828941-5491980 ...
    Testing query chr8:1038109-7255118 ...
    Testing query chr19:564478-5162536 ...
    Testing query chr21:6696589-7247970 ...
    Testing query chr6:918960-1474816 ...
    Testing query chrM:5636321-9968137 ...
    Testing query chr7_random:5485027-5682623 ...
    Testing query chrY:4149126-7271874 ...
    Testing query chrX_random:2119447-7981903 ...
    Testing query chr8:392266-4278110 ...
    Testing query chr15:126791-8741531 ...
    Testing query chrY:1970354-3699838 ...
    Testing query chr16:4070891-8181737 ...
    Testing query chr18_random:1308317-5408953 ...
    Testing query chr9:1486842-2579174 ...
    Testing query chr9_random:3614823-8021197 ...
    Testing query chr19_random:4100590-7401362 ...
    Testing query chr13:9198949-9562213 ...
    Testing query chr13_random:3477250-5979150 ...
    Testing query chr8:702816-7724269 ...
    Testing query chrX:1173848-9916277 ...
    Testing query chr19_random:1528939-7213477 ...
    Testing query chrY:4055178-8006125 ...
    Testing query chr21_random:5600720-8897721 ...
    Testing query chr13:5754292-7802376 ...
    Testing query chr6_random:2337681-6172508 ...
    Testing query chr2:5799739-7134812 ...
    Testing query chrX_random:3353632-6262401 ...
    Testing query chr21:945894-5132876 ...
    Testing query chr18_random:2350673-9531784 ...
    Testing query chr22_random:5048930-8474866 ...
    Testing query chr19:6352226-8501858 ...
    Testing query chr20:3392059-9830746 ...
    Testing query chr16_random:4090981-7752074 ...
    Testing query chr11_random:5905570-6251642 ...
    Testing query chr13:360298-9358487 ...
    Testing query chr6_random:882947-4758560 ...
    Testing query chr11:2340078-2932391 ...
    Testing query chr22_random:2213551-2534609 ...
    Testing query chr21:5841676-5846763 ...
    Testing query chr11_random:4038782-7000307 ...
    Testing query chr6_random:25409-5762752 ...
    Testing query chr16:5928354-8501435 ...
    Testing query chrY:694230-6280406 ...
    Testing query chr11:7243231-8376959 ...
    Testing query chr16_random:7306380-8046651 ...
    Testing query chr16:1271045-7843225 ...
    Testing query chr15:3261152-4143715 ...
    Testing query chr16:3643483-7977448 ...
    Testing query chrM:2682115-4251696 ...
    Testing query chrM:8447185-9660353 ...
    Testing query chr17_random:4662108-9040099 ...
    Testing query chr15:2717869-3422290 ...
    Testing query chr9_random:2276674-4258729 ...
    Testing query chrX_random:975097-5521164 ...
    Testing query chr11:2146529-8617542 ...
    Testing query chr10_random:1180053-8007684 ...
    Testing query chr3_random:3693000-4565796 ...
    Testing query chr11:145445-2682401 ...
    Testing query chr8_random:6750591-7945127 ...
    Testing query chr1:8320362-9511438 ...
    Testing query chr8:7013549-9472948 ...
    Testing query chr13_random:3536637-5003209 ...
    Testing query chr9:6558793-7284938 ...
    Testing query chr21_random:2580219-9412760 ...
    Testing query chr10:406321-2977770 ...
    Testing query chr21:492284-7994828 ...
    Testing query chr8:2657319-7983432 ...
    Testing query chrX:4732048-8043746 ...
    Testing query chr20:3307597-9305376 ...
    Testing query chr2_random:755380-8957174 ...
    Testing query chrY:2933069-9880634 ...
    Testing query chr6:774738-5674081 ...
    Testing query chr22_random:715809-9050909 ...
    Testing query chr4:1349527-3344979 ...
    Testing query chr6:8028105-9684178 ...
    Testing query chr5_random:4787471-8881473 ...
    Testing query chr10_random:2634703-3696440 ...
    Testing query chr11_random:829085-1727870 ...
    Testing query chr15_random:592933-9165180 ...
    Testing query chr4_random:4418610-8898086 ...
    Testing query chrX_random:2431444-6884713 ...
    Testing query chr8_random:6475456-8480814 ...
    Testing query chr7:3815530-7026545 ...
    Testing query chr19:7331585-7602899 ...
    Testing query chr1_random:874465-3320587 ...
    Testing query chr13_random:733794-6825035 ...
    Testing query chr15_random:9014536-9668872 ...
    Testing query chr17_random:6591609-9129777 ...
    Testing query chrM:656068-4356620 ...
    Testing query chr8:405654-9125605 ...
    Testing query chrX:2091850-6675177 ...
    Testing query chr17_random:7703315-8296743 ...
    Testing query chr5:6509082-7915180 ...
    Testing query chr22:2553656-7681295 ...
    Testing query chr14:3268086-7514168 ...
    Testing query chr8:4422671-6192314 ...
    Testing query chr1:65591-912831 ...
    Testing query chr3_random:5754696-6365576 ...
    Testing query chr19:3761804-6226235 ...
    Testing query chr15_random:437782-2343429 ...
    Testing query chr21_random:6464723-8352688 ...
    Testing query chr2:2429164-5768260 ...
    Testing query chr4:470318-7002218 ...
    Testing query chr4:3690943-5461445 ...
    Testing query chr22_random:5183905-6703677 ...
    Testing query chr6:956010-4837181 ...
    Testing query chr22_random:4644999-6726863 ...
    Testing query chr3:461910-2847795 ...
    Testing query chrM:1898841-4804510 ...
    Testing query chr17_random:4508018-9521979 ...
    Testing query chr5_random:324986-2917264 ...
    Testing query chr21_random:5399136-5748620 ...
    Testing query chr22:2778077-4812793 ...
    Testing query chr10:4969555-6126688 ...
    Testing query chr18:1713300-5060476 ...
    Testing query chr13_random:3333348-5290509 ...
    Testing query chr11_random:4081564-5917103 ...
    Testing query chr4_random:5054748-8642850 ...
    Testing query chr1:2326146-4227874 ...
    Testing query chr18:1537257-7925976 ...
    Testing query chr22_random:8252153-8805544 ...
    Testing query chr3_random:1198809-9011283 ...
    Testing query chr17_random:6967406-8885184 ...
    Testing query chr13:1386877-2947412 ...
    Testing query chrM:6757870-7928951 ...
    Testing query chr21:4074861-7649457 ...
    Testing query chrX_random:1019101-6500619 ...
    Testing query chrX:1825987-5504513 ...
    Testing query chr21_random:3186073-5713305 ...
    Testing query chr4:6259611-8028235 ...
    Testing query chr4:1743818-8599191 ...
    Testing query chr17:1858282-6524491 ...
    Testing query chr15_random:4438074-7157093 ...
    Testing query chr3_random:397131-735889 ...
    Testing query chr8:6928096-9944821 ...
    Testing query chr4_random:1300717-4919221 ...
    Testing query chr5_random:338852-4544685 ...
    Testing query chr7_random:9056136-9688355 ...
    Testing query chr13:2503131-3346435 ...
    Testing query chr15_random:4163332-8152391 ...
    Testing query chr11_random:3309623-7440495 ...
    Testing query chr5_random:9256148-9879716 ...
    Testing query chr17_random:1285404-9731324 ...
    Testing query chr11:8839451-9081378 ...
    Testing query chr13:8871343-9845159 ...
    Testing query chr22:4961912-7272246 ...
    Testing query chr7_random:1546612-1704922 ...
    Testing query chr4_random:3988885-5892099 ...
    Testing query chr16:3240803-6856154 ...
    Testing query chr16:217614-7256181 ...
    Testing query chr8_random:9247976-9386452 ...
    Testing query chr3_random:6627763-9791298 ...
    Testing query chr2:2529288-4212123 ...
    Testing query chrX_random:2988973-8007994 ...
    Testing query chr15:7917609-9330719 ...
    Testing query chr11_random:3494062-5554433 ...
    Testing query chr10_random:550231-9169795 ...
    Testing query chrM:2348914-4789264 ...
    Testing query chr10_random:1774094-2022615 ...
    Testing query chrY:1233622-1787356 ...
    Testing query chr16:1423379-2759956 ...
    Testing query chr15_random:2179216-5955676 ...
    Testing query chr13_random:4485355-8258869 ...
    Testing query chr16:1540718-7599890 ...
    Testing query chr16:3470124-5210468 ...
    Testing query chr5_random:2480219-3389498 ...
    Testing query chrX_random:2150354-9183393 ...
    Testing query chr4_random:7326066-8687796 ...
    Testing query chr9_random:778644-7335950 ...
    Testing query chr3_random:117405-711777 ...
    Testing query chr3_random:1627027-5946622 ...
    Testing query chr14:1896619-3058485 ...
    Testing query chr4:361451-8469991 ...
    Testing query chr13:8016007-9409673 ...
    Testing query chr15_random:4902505-9345392 ...
    Testing query chr11_random:7321862-9499733 ...
    Testing query chr4:1033220-5712150 ...
    Testing query chr8:3549734-9090035 ...
    Testing query chrM:5081509-5962772 ...
    Testing query chrX_random:97240-6137606 ...
    Testing query chr8_random:4271059-4291635 ...
    Testing query chrX_random:530035-1682825 ...
    Testing query chr15:2788773-5483281 ...
    Testing query chrX_random:4759178-9377757 ...
    Testing query chrM:3245025-4297984 ...
    Testing query chr19_random:3021529-4576251 ...
    Testing query chr4_random:1397040-5761345 ...
    Testing query chrM:561371-7187972 ...
    Testing query chr22:5413646-8736775 ...
    Testing query chr17_random:1425366-7019792 ...
    Testing query chr3_random:572179-7205526 ...
    Testing query chr5:4328737-9239750 ...
    Testing query chr22:5069432-6659616 ...
    Testing query chr13:48249-7303858 ...
    Testing query chr3:305799-6869287 ...
    Testing query chr21:3873459-5093561 ...
    Testing query chr19:5939843-9027189 ...
    Testing query chr2:5873453-6683127 ...
    Testing query chr22_random:3713598-5598641 ...
    Testing query chr20:179927-8450235 ...
    Testing query chr13_random:8308459-9668938 ...
    Testing query chr11:1199780-7649669 ...
    Testing query chr19:4137076-6447341 ...
    Testing query chrM:78280-8559488 ...
    Testing query chr4:623887-7069138 ...
    Testing query chr16:3039657-4345359 ...
    Testing query chr17:3391405-4744719 ...
    Testing query chr20:2910861-7899348 ...
    Testing query chr19_random:913985-2128081 ...
    Testing query chr22:1426695-8605324 ...
    Testing query chr12:1887213-4358077 ...
    Testing query chrX:5563613-8375913 ...
    Testing query chr7_random:136737-595720 ...
    Testing query chr22:3649338-3715557 ...
    Testing query chr22_random:1857324-2876705 ...
    Testing query chr3_random:1299041-9034999 ...
    Testing query chr15:978485-8350193 ...
    Testing query chr19_random:4068601-6523086 ...
    Testing query chr2:201488-4273604 ...
    Testing query chr19_random:5966187-9871009 ...
    Testing query chrM:1330413-9761840 ...
    Testing query chr7:4263424-8956444 ...
    Testing query chr5:710131-1481160 ...
    Testing query chr22_random:3228001-4696776 ...
    Testing query chr3:64585-1673488 ...
    Testing query chr16:8045346-8459636 ...
    Testing query chr13_random:1741393-4393228 ...
    Testing query chr22_random:2624571-7878001 ...
    Testing query chr20:4312366-7263897 ...
    Testing query chr2_random:792986-9926045 ...
    Testing query chr4:876557-8032416 ...
    Testing query chr7_random:9474728-9775529 ...
    Testing query chrY:196281-2297210 ...
    Testing query chr11_random:1815604-1988691 ...
    Testing query chr17:327462-9941596 ...
    Testing query chr4:1225057-5716342 ...
    Testing query chrX_random:5518830-9291836 ...
    Testing query chr19_random:8850582-9837888 ...
    Testing query chr10_random:906079-4133872 ...
    Testing query chrX:1487717-2363048 ...
    Testing query chrX:315413-7567516 ...
    Testing query chr8_random:6478215-9426080 ...
    Testing query chr20:2999407-4776774 ...
    Testing query chr5_random:1309090-5902755 ...
    Testing query chr4_random:4737388-7952008 ...
    Testing query chr21_random:3092337-5111212 ...
    Testing query chr12:4888197-9051400 ...
    Testing query chr13_random:4483564-5744770 ...
    Testing query chr22_random:54755-6638497 ...
    Testing query chr13_random:5891419-7679795 ...
    Testing query chr12:1730038-8775120 ...
    Testing query chr10:3971454-8725046 ...
    Testing query chr13_random:2420218-3946730 ...
    Testing query chr16_random:6268326-9602951 ...
    Testing query chr15_random:6201359-7624324 ...
    Testing query chr8_random:1897294-5156982 ...
    Testing query chr1:2597385-4514890 ...
    Testing query chrX_random:338730-7953560 ...
    Testing query chr7:5484367-7925032 ...
    Testing query chr5_random:6298235-7470139 ...
    Testing query chr21_random:3834366-4459713 ...
    Testing query chr5:2361767-8905807 ...
    Testing query chrM:3162105-9086123 ...
    Testing query chrX_random:4940689-6482079 ...
    Testing query chr4:4948264-5128137 ...
    Testing query chr3:4207686-7342748 ...
    Testing query chr19_random:2021389-9994958 ...
    Testing query chr18:3680011-9706840 ...
    Testing query chr17_random:5951397-8238603 ...
    Testing query chr15_random:4175461-7481270 ...
    Testing query chr4:498362-9165782 ...
    Testing query chr21:4179687-5159563 ...
    Testing query chr1:5178637-7992880 ...
    Testing query chr15_random:6053128-8149868 ...
    Testing query chr5:4008322-7971530 ...
    Testing query chr19_random:1097409-1939223 ...
    Testing query chr15:7469377-8821183 ...
    Testing query chr11_random:1627957-5387469 ...
    Testing query chr9:5855393-7238773 ...
    Testing query chr22:3055704-4751301 ...
    Testing query chr18_random:2752026-7569770 ...
    Testing query chr6:2659325-3383321 ...
    Testing query chr19_random:6031799-9193165 ...
    Testing query chr10:2867928-7456748 ...
    Testing query chr17:803521-2016747 ...
    Testing query chr11_random:2756837-9309974 ...
    Testing query chr9_random:4932323-6215308 ...
    Testing query chr19_random:1738738-9429398 ...
    Testing query chr4_random:162435-8328176 ...
    Testing query chr17:138893-2694455 ...
    Testing query chrX_random:4137996-9339319 ...
    Testing query chr19:2497402-8914940 ...
    Testing query chr13_random:3513964-5910759 ...
    Testing query chrX:1099583-2639169 ...
    Testing query chr11_random:6266637-8387131 ...
    Testing query chr8_random:3059827-5229064 ...
    Testing query chr6:380960-2560436 ...
    Testing query chr15_random:5618328-6876961 ...
    Testing query chr2_random:3878460-5680854 ...
    Testing query chr8_random:2477614-4148075 ...
    Testing query chr18_random:5415785-8338387 ...
    Testing query chr10_random:8209397-8355863 ...
    Testing query chr11_random:4475489-6604223 ...
    Testing query chr1_random:754948-7226484 ...
    Testing query chr9:2946100-8357028 ...
    Testing query chr15:7199317-8245905 ...
    Testing query chr7_random:7269507-8820498 ...
    Testing query chr16:1621267-2368637 ...
    Testing query chr7_random:2996833-9854987 ...
    Testing query chrM:6484003-6911983 ...
    Testing query chr13:1771424-4738191 ...
    Testing query chr13_random:1828228-4302873 ...
    Testing query chrM:2962858-5957962 ...
    Testing query chr6_random:4242794-9824359 ...
    Testing query chr13:415874-9331256 ...
    Testing query chr8:7417568-9299672 ...
    Testing query chr5_random:6880184-8188312 ...
    Testing query chr10_random:1892176-5188920 ...
    Testing query chr21_random:4076206-6101050 ...
    Testing query chr20:5126731-9990106 ...
    Testing query chr4:3133535-3261569 ...

Gradle suite > Gradle test > htsjdk.samtools.BAMFileReaderTest.testGetIndexTypeOK STANDARD_OUT
    chrM length=	16571	Aligned= 23	Unaligned= 0
    chr1 length=	247249719	Aligned= 885	Unaligned= 0
    chr2 length=	242951149	Aligned= 837	Unaligned= 0
    chr3 length=	199501827	Aligned= 683	Unaligned= 0
    chr4 length=	191273063	Aligned= 633	Unaligned= 0
    chr5 length=	180857866	Aligned= 611	Unaligned= 0
    chr6 length=	170899992	Aligned= 585	Unaligned= 0
    chr7 length=	158821424	Aligned= 521	Unaligned= 0
    chr8 length=	146274826	Aligned= 507	Unaligned= 0
    chr9 length=	140273252	Aligned= 388	Unaligned= 0
    chr10 length=	135374737	Aligned= 477	Unaligned= 0
    chr11 length=	134452384	Aligned= 467	Unaligned= 0
    chr12 length=	132349534	Aligned= 459	Unaligned= 0
    chr13 length=	114142980	Aligned= 327	Unaligned= 0
    chr14 length=	106368585	Aligned= 310	Unaligned= 0
    chr15 length=	100338915	Aligned= 280	Unaligned= 0
    chr16 length=	88827254	Aligned= 278	Unaligned= 0
    chr17 length=	78774742	Aligned= 269	Unaligned= 0
    chr18 length=	76117153	Aligned= 265	Unaligned= 0
    chr19 length=	63811651	Aligned= 178	Unaligned= 0
    chr20 length=	62435964	Aligned= 228	Unaligned= 0
    chr21 length=	46944323	Aligned= 123	Unaligned= 0
    chr22 length=	49691432	Aligned= 121	Unaligned= 0
    chrX length=	154913754	Aligned= 237	Unaligned= 0
    chrY length=	57772954	Aligned= 29	Unaligned= 0
    chr1_random length=	1663265	Aligned= 0	Unaligned= 0
    chr2_random length=	185571	Aligned= 0	Unaligned= 0
    chr3_random length=	749256	Aligned= 0	Unaligned= 0
    chr4_random length=	842648	Aligned= 0	Unaligned= 0
    chr5_random length=	143687	Aligned= 0	Unaligned= 0
    chr6_random length=	1875562	Aligned= 0	Unaligned= 0
    chr7_random length=	549659	Aligned= 0	Unaligned= 0
    chr8_random length=	943810	Aligned= 0	Unaligned= 0
    chr9_random length=	1146434	Aligned= 0	Unaligned= 0
    chr10_random length=	113275	Aligned= 0	Unaligned= 0
    chr11_random length=	215294	Aligned= 0	Unaligned= 0
    chr13_random length=	186858	Aligned= 0	Unaligned= 0
    chr15_random length=	784346	Aligned= 0	Unaligned= 0
    chr16_random length=	105485	Aligned= 0	Unaligned= 0
    chr17_random length=	2617613	Aligned= 0	Unaligned= 0
    chr18_random length=	4262	Aligned= 0	Unaligned= 0
    chr19_random length=	301858	Aligned= 0	Unaligned= 0
    chr21_random length=	1679693	Aligned= 0	Unaligned= 0
    chr22_random length=	257318	Aligned= 0	Unaligned= 0
    chrX_random length=	1719168	Aligned= 0	Unaligned= 0
    NoCoordinateCount= 279
Finished 400 tests

Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteBinary STANDARD_OUT
    #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.1747479980684561059.bai
    #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.11804104086333295410.bai
    #BAMIndexWriterTest diff /tmp/javaBai.1747479980684561059.bai /tmp/cBai.11804104086333295410.bai

Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteText STANDARD_OUT
    #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.4296675977070378954.bai.txt
    #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.17040063018247560354java.bai
    #BAMIndexWriterTest diff /tmp/javaBai.17040063018247560354java.bai.txt /tmp/cBai.4296675977070378954.bai.txt
Finished 600 tests

Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.readPastEndOfFile STANDARD_OUT
    8ms to write

Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.timeTest STANDARD_OUT
    3ms to write

Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedInputStreamTest.testCustomInflater SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testBasic STANDARD_OUT
    Creating file /tmp/BCOST.4954632807742220128.gz

Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testCustomDeflater STANDARD_OUT
    Creating file /tmp/testCustomDeflater.16415492608929428904.gz

Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testOverflow STANDARD_OUT
    Creating file /tmp/BCOST.9677100648622238739.gz
Finished 800 tests

Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromContainer STANDARD_ERROR
    WARNING	2025-06-03 15:20:45	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:20:45	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromStream STANDARD_ERROR
    WARNING	2025-06-03 15:20:45	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:20:45	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.fullVerificationTest[0](c1#bounds) STANDARD_ERROR
    WARNING	2025-06-03 15:20:45	CRAMReferenceRegion	The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12
    WARNING	2025-06-03 15:20:45	Slice	Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0.
    WARNING	2025-06-03 15:20:45	CRAMReferenceRegion	The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12
    WARNING	2025-06-03 15:20:45	Slice	Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0.

Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testCRAMThroughBAMRoundTrip[4](src/test/resources/htsjdk/samtools/cram/test.cram, src/test/resources/htsjdk/samtools/cram/auxf.fa) STANDARD_ERROR
    WARNING	2025-06-03 15:20:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:20:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testCRAMThroughBAMRoundTrip[5](src/test/resources/htsjdk/samtools/cram/test2.cram, src/test/resources/htsjdk/samtools/cram/auxf.fa) STANDARD_ERROR
    WARNING	2025-06-03 15:20:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:20:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testObsoleteDataSeriesNotWritten STANDARD_ERROR
    WARNING	2025-06-03 15:20:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:20:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testContigNotFoundInRef STANDARD_ERROR
    WARNING	2025-06-03 15:20:48	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:20:48	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testNullsAndBeyondRef STANDARD_ERROR
    WARNING	2025-06-03 15:20:48	CRAMReferenceRegion	The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3
    WARNING	2025-06-03 15:20:48	Slice	Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0.
    WARNING	2025-06-03 15:20:48	CRAMReferenceRegion	The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3
    WARNING	2025-06-03 15:20:48	Slice	Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0.

Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testUnsorted STANDARD_ERROR
    WARNING	2025-06-03 15:20:48	CRAMReferenceRegion	The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37
    WARNING	2025-06-03 15:20:48	Slice	Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0.
    WARNING	2025-06-03 15:20:48	CRAMReferenceRegion	The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37
    WARNING	2025-06-03 15:20:48	Slice	Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0.

Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCRAMReader1_ReferenceRequired STANDARD_ERROR
    WARNING	2025-06-03 15:24:50	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:24:50	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCramIteratorWithoutCallingHasNextFirst STANDARD_ERROR
    WARNING	2025-06-03 15:24:50	CRAMReferenceRegion	The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37
    WARNING	2025-06-03 15:24:50	Slice	Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0.
    WARNING	2025-06-03 15:24:50	CRAMReferenceRegion	The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37
    WARNING	2025-06-03 15:24:50	Slice	Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0.
Finished 1000 tests
	Gradle is still running, please be patient...

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[1](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7088d985, [Ljava.lang.String;@65b30cbf) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5baf431a, [Ljava.lang.String;@1138a661) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryAlignmentStart[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, 2) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryAlignmentStart[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, 24) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@8f0bb9c, [Ljava.lang.String;@28ec9d3c) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5703b18d, [Ljava.lang.String;@56ed8401) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7f8c422, [Ljava.lang.String;@14fef042) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@251277c7, [Ljava.lang.String;@468e10c7) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@78307f72, [Ljava.lang.String;@500ab7ad) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@15582e6, [Ljava.lang.String;@4a6e772a) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@51a4e2ef, [Ljava.lang.String;@24396102) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4fbdf1ce, [Ljava.lang.String;@62de2afa) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6f8f7942, [Ljava.lang.String;@53f1a1) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7fd83bee, [Ljava.lang.String;@49d793f3) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@595b1b3e, [Ljava.lang.String;@7079df60) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1dadae69, [Ljava.lang.String;@5c0fbefb) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@79e289b7, [Ljava.lang.String;@1d7d272a) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5f38f5d4, [Ljava.lang.String;@411ec08c) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@69ef4f32, [Ljava.lang.String;@cfe9f49) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@35c3399c, [Ljava.lang.String;@1f964a67) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2b306ecf, [Ljava.lang.String;@5382c776) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@29b3401c) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@3cbfc257) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@12e9a823) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@31091864) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@a2cee93) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@7edf2413) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@5852f258) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@7c3c7291) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryMate[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryMate[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@5e9515fe, [Ljava.lang.String;@28a4c1e9) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@30bd5994, [Ljava.lang.String;@1fe84e57) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6b79c399, [Ljava.lang.String;@135e4946) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@27eceb14, [Ljava.lang.String;@10d28028) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4682b7b9, [Ljava.lang.String;@3be72e7c) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7e6c62b1, [Ljava.lang.String;@31d1d0d9) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6ff6d56d, [Ljava.lang.String;@5d724e38) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
Finished 1200 tests

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6494f524, [Ljava.lang.String;@6893dbc8) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@29a6e90c, [Ljava.lang.String;@6bf9e608) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@246e46d0, [Ljava.lang.String;@268ae346) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@15733ed2, [Ljava.lang.String;@3c5ed10a) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@608a19c, [Ljava.lang.String;@7ee4db53) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4e9cf143, [Ljava.lang.String;@261c2955) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@42df468e, [Ljava.lang.String;@6ee10344) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7fa284e5, [Ljava.lang.String;@6dec6917) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@64bc0bc2, [Ljava.lang.String;@63fb81c3) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@626e0b9b, [Ljava.lang.String;@1d385889) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@558feb61) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@36b7c2d8) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@35bd291d) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@8e5daaf) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@6e58dc03) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@7e15db06) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@71de70d1) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@40d61bac) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@2e326211) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@64aed219) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@ddefa82) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@aeff070) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@60422725) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@13ac6733) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@5ecf902) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@4759af46) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@499d6978) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@16cf28a8) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@48561120) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@6f6d905c) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@650c4c56) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@2ae0b8b7) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@39fa920) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@115d4230) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@409a016d) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@404a26a4) STANDARD_ERROR
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@107936f4) STANDARD_ERROR
    WARNING	2025-06-03 15:27:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@2f6338e5) STANDARD_ERROR
    WARNING	2025-06-03 15:27:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@67767425) STANDARD_ERROR
    WARNING	2025-06-03 15:27:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@5f62f206) STANDARD_ERROR
    WARNING	2025-06-03 15:27:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@2dca71bd) STANDARD_ERROR
    WARNING	2025-06-03 15:27:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@346fcd96, 5) STANDARD_ERROR
    WARNING	2025-06-03 15:27:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMMergerTest.test STANDARD_ERROR
    WARNING	2025-06-03 15:27:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.cram.ref.CRAMReferenceRegionTest.testGetReferenceBasesByRegionExceedsContigLength STANDARD_ERROR
    WARNING	2025-06-03 15:27:38	CRAMReferenceRegion	The bases of length 5000 returned by the reference source do not satisfy the requested fragment length 15000

Gradle suite > Gradle test > htsjdk.samtools.CRAMReferencelessTest.testReadCRAMWithEmbeddedReference STANDARD_ERROR
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Read name 20FUKAAXX100202:2:1:20271:61529, Mate Alignment start (9999748) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Read name 20FUKAAXX100202:2:1:20271:61529, Mate Alignment start (9999748) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 1, Read name 20FUKAAXX100202:3:27:11237:128368, Mate Alignment start (9999703) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 1, Read name 20FUKAAXX100202:3:27:11237:128368, Mate Alignment start (9999703) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 2, Read name 20FUKAAXX100202:3:27:11250:128353, Mate Alignment start (9999703) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 2, Read name 20FUKAAXX100202:3:27:11250:128353, Mate Alignment start (9999703) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 3, Read name 20GAVAAXX100126:4:23:2251:22957, Mate Alignment start (9999692) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 3, Read name 20GAVAAXX100126:4:23:2251:22957, Mate Alignment start (9999692) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 4, Read name 20FUKAAXX100202:2:41:20497:197885, Mate Alignment start (10000344) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 4, Read name 20FUKAAXX100202:2:41:20497:197885, Mate Alignment start (10000344) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 5, Read name 20FUKAAXX100202:7:67:1995:131468, Mate Alignment start (9999746) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 5, Read name 20FUKAAXX100202:7:67:1995:131468, Mate Alignment start (9999746) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 6, Read name 20GAVAAXX100126:2:64:13726:30107, Mate Alignment start (10000306) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 6, Read name 20GAVAAXX100126:2:64:13726:30107, Mate Alignment start (10000306) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 7, Read name 20FUKAAXX100202:4:43:20796:59238, Mate Alignment start (9999709) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 7, Read name 20FUKAAXX100202:4:43:20796:59238, Mate Alignment start (9999709) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 8, Read name 20GAVAAXX100126:1:23:7794:118351, Mate Alignment start (10000299) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 8, Read name 20GAVAAXX100126:1:23:7794:118351, Mate Alignment start (10000299) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 9, Read name 20GAVAAXX100126:4:68:6400:174077, Mate Alignment start (10000335) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 9, Read name 20GAVAAXX100126:4:68:6400:174077, Mate Alignment start (10000335) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 10, Read name 20GAVAAXX100126:5:27:13558:117863, Mate Alignment start (9999715) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 10, Read name 20GAVAAXX100126:5:27:13558:117863, Mate Alignment start (9999715) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 11, Read name 20FUKAAXX100202:1:64:5977:190591, Mate Alignment start (10000296) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 11, Read name 20FUKAAXX100202:1:64:5977:190591, Mate Alignment start (10000296) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 12, Read name 20FUKAAXX100202:8:68:8163:66511, Mate Alignment start (10000285) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 12, Read name 20FUKAAXX100202:8:68:8163:66511, Mate Alignment start (10000285) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 13, Read name 20GAVAAXX100126:2:65:15310:41789, Mate Alignment start (9999670) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 13, Read name 20GAVAAXX100126:2:65:15310:41789, Mate Alignment start (9999670) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 14, Read name 20GAVAAXX100126:7:66:12507:22293, Mate Alignment start (10000236) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 14, Read name 20GAVAAXX100126:7:66:12507:22293, Mate Alignment start (10000236) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 15, Read name 20FUKAAXX100202:4:28:1593:6464, Mate Alignment start (9999607) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 15, Read name 20FUKAAXX100202:4:28:1593:6464, Mate Alignment start (9999607) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 16, Read name 20FUKAAXX100202:3:43:19691:103757, Mate Alignment start (10000257) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 16, Read name 20FUKAAXX100202:3:43:19691:103757, Mate Alignment start (10000257) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 17, Read name 20FUKAAXX100202:5:24:20426:8780, Mate Alignment start (10000318) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 17, Read name 20FUKAAXX100202:5:24:20426:8780, Mate Alignment start (10000318) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 18, Read name 20GAVAAXX100126:3:43:6705:167739, Mate Alignment start (10000257) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 18, Read name 20GAVAAXX100126:3:43:6705:167739, Mate Alignment start (10000257) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 19, Read name 20GAVAAXX100126:3:66:17154:191764, Mate Alignment start (9999760) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 19, Read name 20GAVAAXX100126:3:66:17154:191764, Mate Alignment start (9999760) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 20, Read name 20GAVAAXX100126:6:66:18327:134560, Mate Alignment start (9999694) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 20, Read name 20GAVAAXX100126:6:66:18327:134560, Mate Alignment start (9999694) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 23, Read name 20FUKAAXX100202:5:64:19991:74214, Mate Alignment start (10000274) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 23, Read name 20FUKAAXX100202:5:64:19991:74214, Mate Alignment start (10000274) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 24, Read name 20FUKAAXX100202:2:41:7948:31113, Mate Alignment start (9999705) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 24, Read name 20FUKAAXX100202:2:41:7948:31113, Mate Alignment start (9999705) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 25, Read name 20GAVAAXX100126:8:67:6825:84706, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 25, Read name 20GAVAAXX100126:8:67:6825:84706, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 26, Read name 20FUKAAXX100202:5:46:8200:95675, Mate Alignment start (10000307) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 26, Read name 20FUKAAXX100202:5:46:8200:95675, Mate Alignment start (10000307) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 27, Read name 20FUKAAXX100202:5:46:8201:95696, Mate Alignment start (10000307) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 27, Read name 20FUKAAXX100202:5:46:8201:95696, Mate Alignment start (10000307) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 28, Read name 20FUKAAXX100202:6:5:15635:154535, Mate Alignment start (10000315) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 28, Read name 20FUKAAXX100202:6:5:15635:154535, Mate Alignment start (10000315) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 29, Read name 20FUKAAXX100202:7:41:10752:140666, Mate Alignment start (9999753) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 29, Read name 20FUKAAXX100202:7:41:10752:140666, Mate Alignment start (9999753) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 30, Read name 20GAVAAXX100126:2:23:4627:33063, Mate Alignment start (10000346) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 30, Read name 20GAVAAXX100126:2:23:4627:33063, Mate Alignment start (10000346) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 31, Read name 20GAVAAXX100126:2:23:4640:33082, Mate Alignment start (10000346) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 31, Read name 20GAVAAXX100126:2:23:4640:33082, Mate Alignment start (10000346) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 32, Read name 20GAVAAXX100126:3:25:2015:120007, Mate Alignment start (9999741) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 32, Read name 20GAVAAXX100126:3:25:2015:120007, Mate Alignment start (9999741) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 33, Read name 20GAVAAXX100126:3:25:2028:120028, Mate Alignment start (9999741) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 33, Read name 20GAVAAXX100126:3:25:2028:120028, Mate Alignment start (9999741) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 34, Read name 20FUKAAXX100202:5:41:14163:52829, Mate Alignment start (10000260) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 34, Read name 20FUKAAXX100202:5:41:14163:52829, Mate Alignment start (10000260) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 35, Read name 20GAVAAXX100126:7:46:18099:135243, Mate Alignment start (9999721) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 35, Read name 20GAVAAXX100126:7:46:18099:135243, Mate Alignment start (9999721) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 36, Read name 20GAVAAXX100126:2:47:15498:55100, Mate Alignment start (9999706) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 36, Read name 20GAVAAXX100126:2:47:15498:55100, Mate Alignment start (9999706) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 37, Read name 20FUKAAXX100202:8:21:4919:132430, Mate Alignment start (10000321) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 37, Read name 20FUKAAXX100202:8:21:4919:132430, Mate Alignment start (10000321) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 38, Read name 20FUKAAXX100202:3:67:3748:19953, Mate Alignment start (10000279) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 38, Read name 20FUKAAXX100202:3:67:3748:19953, Mate Alignment start (10000279) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 39, Read name 20FUKAAXX100202:2:2:3418:95829, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 39, Read name 20FUKAAXX100202:2:2:3418:95829, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 40, Read name 20FUKAAXX100202:6:5:5332:102974, Mate Alignment start (10000361) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 40, Read name 20FUKAAXX100202:6:5:5332:102974, Mate Alignment start (10000361) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 41, Read name 20FUKAAXX100202:2:8:7024:145363, Mate Alignment start (10000353) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 41, Read name 20FUKAAXX100202:2:8:7024:145363, Mate Alignment start (10000353) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 42, Read name 20GAVAAXX100126:3:25:20036:5188, Mate Alignment start (9999721) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 42, Read name 20GAVAAXX100126:3:25:20036:5188, Mate Alignment start (9999721) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 43, Read name 20FUKAAXX100202:5:2:4432:167162, Mate Alignment start (9999749) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 43, Read name 20FUKAAXX100202:5:2:4432:167162, Mate Alignment start (9999749) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 44, Read name 20GAVAAXX100126:3:63:6482:2143, Mate Alignment start (10000263) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 44, Read name 20GAVAAXX100126:3:63:6482:2143, Mate Alignment start (10000263) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 45, Read name 20GAVAAXX100126:3:63:6488:2160, Mate Alignment start (10000263) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 45, Read name 20GAVAAXX100126:3:63:6488:2160, Mate Alignment start (10000263) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 48, Read name 20FUKAAXX100202:1:21:2273:66026, Mate Alignment start (10000322) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 48, Read name 20FUKAAXX100202:1:21:2273:66026, Mate Alignment start (10000322) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 49, Read name 20FUKAAXX100202:1:21:2285:66012, Mate Alignment start (10000322) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 49, Read name 20FUKAAXX100202:1:21:2285:66012, Mate Alignment start (10000322) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 50, Read name 20FUKAAXX100202:4:8:13315:108160, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 50, Read name 20FUKAAXX100202:4:8:13315:108160, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 51, Read name 20FUKAAXX100202:2:21:15808:57403, Mate Alignment start (10000379) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 51, Read name 20FUKAAXX100202:2:21:15808:57403, Mate Alignment start (10000379) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 52, Read name 20FUKAAXX100202:8:41:10876:123643, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 52, Read name 20FUKAAXX100202:8:41:10876:123643, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 53, Read name 20FUKAAXX100202:8:41:10891:123658, Mate Alignment start (10000357) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 53, Read name 20FUKAAXX100202:8:41:10891:123658, Mate Alignment start (10000357) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 54, Read name 20FUKAAXX100202:1:8:10582:193735, Mate Alignment start (9999814) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 54, Read name 20FUKAAXX100202:1:8:10582:193735, Mate Alignment start (9999814) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 55, Read name 20FUKAAXX100202:4:23:20668:198863, Mate Alignment start (10000391) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 55, Read name 20FUKAAXX100202:4:23:20668:198863, Mate Alignment start (10000391) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 56, Read name 20FUKAAXX100202:3:27:18714:174324, Mate Alignment start (10000329) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 56, Read name 20FUKAAXX100202:3:27:18714:174324, Mate Alignment start (10000329) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 57, Read name 20GAVAAXX100126:3:3:7922:39057, Mate Alignment start (9999758) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 57, Read name 20GAVAAXX100126:3:3:7922:39057, Mate Alignment start (9999758) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 58, Read name 20GAVAAXX100126:3:26:15712:87893, Mate Alignment start (10000309) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 58, Read name 20GAVAAXX100126:3:26:15712:87893, Mate Alignment start (10000309) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 59, Read name 20GAVAAXX100126:4:23:3530:147535, Mate Alignment start (9999796) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 59, Read name 20GAVAAXX100126:4:23:3530:147535, Mate Alignment start (9999796) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 60, Read name 20GAVAAXX100126:5:24:17054:156839, Mate Alignment start (10000359) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 60, Read name 20GAVAAXX100126:5:24:17054:156839, Mate Alignment start (10000359) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 61, Read name 20GAVAAXX100126:5:24:17070:156829, Mate Alignment start (10000359) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 61, Read name 20GAVAAXX100126:5:24:17070:156829, Mate Alignment start (10000359) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 62, Read name 20GAVAAXX100126:5:28:14493:46327, Mate Alignment start (10000381) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 62, Read name 20GAVAAXX100126:5:28:14493:46327, Mate Alignment start (10000381) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 63, Read name 20GAVAAXX100126:5:28:14509:46338, Mate Alignment start (10000381) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 63, Read name 20GAVAAXX100126:5:28:14509:46338, Mate Alignment start (10000381) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 64, Read name 20FUKAAXX100202:3:3:19592:17448, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 64, Read name 20FUKAAXX100202:3:3:19592:17448, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 65, Read name 20FUKAAXX100202:5:61:14815:105709, Mate Alignment start (9999813) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 65, Read name 20FUKAAXX100202:5:61:14815:105709, Mate Alignment start (9999813) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 66, Read name 20GAVAAXX100126:2:1:17704:50462, Mate Alignment start (9999830) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 66, Read name 20GAVAAXX100126:2:1:17704:50462, Mate Alignment start (9999830) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 67, Read name 20GAVAAXX100126:2:5:19558:132530, Mate Alignment start (10000310) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 67, Read name 20GAVAAXX100126:2:5:19558:132530, Mate Alignment start (10000310) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 68, Read name 20FUKAAXX100202:2:42:6225:11993, Mate Alignment start (10000403) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 68, Read name 20FUKAAXX100202:2:42:6225:11993, Mate Alignment start (10000403) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 69, Read name 20FUKAAXX100202:1:6:12511:73800, Mate Alignment start (10000338) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 69, Read name 20FUKAAXX100202:1:6:12511:73800, Mate Alignment start (10000338) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 70, Read name 20FUKAAXX100202:3:3:7237:174227, Mate Alignment start (9999772) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 70, Read name 20FUKAAXX100202:3:3:7237:174227, Mate Alignment start (9999772) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 71, Read name 20GAVAAXX100126:2:44:2924:108763, Mate Alignment start (9999762) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 71, Read name 20GAVAAXX100126:2:44:2924:108763, Mate Alignment start (9999762) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 72, Read name 20FUKAAXX100202:5:46:18326:99323, Mate Alignment start (9999771) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 72, Read name 20FUKAAXX100202:5:46:18326:99323, Mate Alignment start (9999771) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 73, Read name 20FUKAAXX100202:1:41:13026:43433, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 73, Read name 20FUKAAXX100202:1:41:13026:43433, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 74, Read name 20FUKAAXX100202:7:41:10475:81635, Mate Alignment start (10000316) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 74, Read name 20FUKAAXX100202:7:41:10475:81635, Mate Alignment start (10000316) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 75, Read name 20FUKAAXX100202:6:7:6837:63100, Mate Alignment start (10000335) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 75, Read name 20FUKAAXX100202:6:7:6837:63100, Mate Alignment start (10000335) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 76, Read name 20FUKAAXX100202:8:41:15613:40512, Mate Alignment start (10000400) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 76, Read name 20FUKAAXX100202:8:41:15613:40512, Mate Alignment start (10000400) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 77, Read name 20GAVAAXX100126:4:66:5628:46560, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 77, Read name 20GAVAAXX100126:4:66:5628:46560, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 78, Read name 20GAVAAXX100126:2:43:11751:59743, Mate Alignment start (9999772) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 78, Read name 20GAVAAXX100126:2:43:11751:59743, Mate Alignment start (9999772) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 79, Read name 20GAVAAXX100126:4:6:17284:168594, Mate Alignment start (9999791) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 79, Read name 20GAVAAXX100126:4:6:17284:168594, Mate Alignment start (9999791) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 80, Read name 20FUKAAXX100202:8:41:1273:146353, Mate Alignment start (10000404) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 80, Read name 20FUKAAXX100202:8:41:1273:146353, Mate Alignment start (10000404) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 81, Read name 20FUKAAXX100202:5:43:11657:127515, Mate Alignment start (9999834) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 81, Read name 20FUKAAXX100202:5:43:11657:127515, Mate Alignment start (9999834) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 82, Read name 20FUKAAXX100202:5:43:11665:127498, Mate Alignment start (9999834) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 82, Read name 20FUKAAXX100202:5:43:11665:127498, Mate Alignment start (9999834) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 83, Read name 20FUKAAXX100202:1:48:13750:136932, Mate Alignment start (10000350) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 83, Read name 20FUKAAXX100202:1:48:13750:136932, Mate Alignment start (10000350) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 84, Read name 20FUKAAXX100202:1:2:3754:138352, Mate Alignment start (10000379) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 84, Read name 20FUKAAXX100202:1:2:3754:138352, Mate Alignment start (10000379) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 85, Read name 20GAVAAXX100126:7:46:18080:135229, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 85, Read name 20GAVAAXX100126:7:46:18080:135229, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 86, Read name 20FUKAAXX100202:7:22:18885:27661, Mate Alignment start (9999857) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 86, Read name 20FUKAAXX100202:7:22:18885:27661, Mate Alignment start (9999857) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 87, Read name 20GAVAAXX100126:2:68:19001:156273, Mate Alignment start (9999800) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 87, Read name 20GAVAAXX100126:2:68:19001:156273, Mate Alignment start (9999800) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 88, Read name 20GAVAAXX100126:7:23:12948:100075, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 88, Read name 20GAVAAXX100126:7:23:12948:100075, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 89, Read name 20GAVAAXX100126:3:44:17022:23968, Mate Alignment start (9999797) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 89, Read name 20GAVAAXX100126:3:44:17022:23968, Mate Alignment start (9999797) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 90, Read name 20FUKAAXX100202:1:21:6910:153058, Mate Alignment start (10000324) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 90, Read name 20FUKAAXX100202:1:21:6910:153058, Mate Alignment start (10000324) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 91, Read name 20GAVAAXX100126:4:43:14464:8329, Mate Alignment start (10000409) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 91, Read name 20GAVAAXX100126:4:43:14464:8329, Mate Alignment start (10000409) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 92, Read name 20GAVAAXX100126:4:43:14480:8346, Mate Alignment start (10000408) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 92, Read name 20GAVAAXX100126:4:43:14480:8346, Mate Alignment start (10000408) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 93, Read name 20FUKAAXX100202:6:27:18144:27680, Mate Alignment start (10000498) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 93, Read name 20FUKAAXX100202:6:27:18144:27680, Mate Alignment start (10000498) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 94, Read name 20GAVAAXX100126:8:44:5555:179202, Mate Alignment start (9999834) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 94, Read name 20GAVAAXX100126:8:44:5555:179202, Mate Alignment start (9999834) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 95, Read name 20GAVAAXX100126:5:63:15490:26472, Mate Alignment start (10000395) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 95, Read name 20GAVAAXX100126:5:63:15490:26472, Mate Alignment start (10000395) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 96, Read name 20FUKAAXX100202:6:24:17640:150063, Mate Alignment start (9999667) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 96, Read name 20FUKAAXX100202:6:24:17640:150063, Mate Alignment start (9999667) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 97, Read name 20FUKAAXX100202:2:46:7154:171464, Mate Alignment start (10000326) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 97, Read name 20FUKAAXX100202:2:46:7154:171464, Mate Alignment start (10000326) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 98, Read name 20FUKAAXX100202:2:46:7154:171487, Mate Alignment start (10000326) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 98, Read name 20FUKAAXX100202:2:46:7154:171487, Mate Alignment start (10000326) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 99, Read name 20FUKAAXX100202:3:4:1882:78979, Mate Alignment start (10000344) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 99, Read name 20FUKAAXX100202:3:4:1882:78979, Mate Alignment start (10000344) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 100, Read name 20FUKAAXX100202:4:5:13072:190773, Mate Alignment start (9999748) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 100, Read name 20FUKAAXX100202:4:5:13072:190773, Mate Alignment start (9999748) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 101, Read name 20FUKAAXX100202:8:63:5291:16081, Mate Alignment start (9999671) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 101, Read name 20FUKAAXX100202:8:63:5291:16081, Mate Alignment start (9999671) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 102, Read name 20GAVAAXX100126:5:48:11843:159383, Mate Alignment start (9999699) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 102, Read name 20GAVAAXX100126:5:48:11843:159383, Mate Alignment start (9999699) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 103, Read name 20GAVAAXX100126:6:21:4070:89543, Mate Alignment start (9999671) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 103, Read name 20GAVAAXX100126:6:21:4070:89543, Mate Alignment start (9999671) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 104, Read name 20GAVAAXX100126:7:44:7446:1891, Mate Alignment start (9999669) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 104, Read name 20GAVAAXX100126:7:44:7446:1891, Mate Alignment start (9999669) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 105, Read name 20FUKAAXX100202:6:67:17100:172461, Mate Alignment start (9999764) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 105, Read name 20FUKAAXX100202:6:67:17100:172461, Mate Alignment start (9999764) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 106, Read name 20GAVAAXX100126:6:64:2441:17495, Mate Alignment start (9999764) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 106, Read name 20GAVAAXX100126:6:64:2441:17495, Mate Alignment start (9999764) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 107, Read name 20FUKAAXX100202:1:5:14642:152032, Mate Alignment start (10000246) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 107, Read name 20FUKAAXX100202:1:5:14642:152032, Mate Alignment start (10000246) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 108, Read name 20FUKAAXX100202:4:6:12695:123335, Mate Alignment start (10000333) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 108, Read name 20FUKAAXX100202:4:6:12695:123335, Mate Alignment start (10000333) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 109, Read name 20FUKAAXX100202:1:61:11336:198565, Mate Alignment start (9999704) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 109, Read name 20FUKAAXX100202:1:61:11336:198565, Mate Alignment start (9999704) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 110, Read name 20GAVAAXX100126:7:48:10601:51282, Mate Alignment start (9999727) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 110, Read name 20GAVAAXX100126:7:48:10601:51282, Mate Alignment start (9999727) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 111, Read name 20GAVAAXX100126:8:62:18437:38607, Mate Alignment start (9999701) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 111, Read name 20GAVAAXX100126:8:62:18437:38607, Mate Alignment start (9999701) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 112, Read name 20GAVAAXX100126:4:7:20111:148814, Mate Alignment start (10000281) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 112, Read name 20GAVAAXX100126:4:7:20111:148814, Mate Alignment start (10000281) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 113, Read name 20FUKAAXX100202:8:43:12077:86650, Mate Alignment start (9999682) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 113, Read name 20FUKAAXX100202:8:43:12077:86650, Mate Alignment start (9999682) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 114, Read name 20GAVAAXX100126:5:25:17399:72164, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 114, Read name 20GAVAAXX100126:5:25:17399:72164, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 117, Read name 20FUKAAXX100202:3:48:16538:10482, Mate Alignment start (10000457) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 117, Read name 20FUKAAXX100202:3:48:16538:10482, Mate Alignment start (10000457) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 118, Read name 20GAVAAXX100126:7:46:11904:195602, Mate Alignment start (10000293) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 118, Read name 20GAVAAXX100126:7:46:11904:195602, Mate Alignment start (10000293) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 121, Read name 20GAVAAXX100126:4:21:14134:132604, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 121, Read name 20GAVAAXX100126:4:21:14134:132604, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 122, Read name 20FUKAAXX100202:5:47:2763:24217, Mate Alignment start (9999701) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 122, Read name 20FUKAAXX100202:5:47:2763:24217, Mate Alignment start (9999701) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 123, Read name 20GAVAAXX100126:8:21:2096:123816, Mate Alignment start (9999768) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 123, Read name 20GAVAAXX100126:8:21:2096:123816, Mate Alignment start (9999768) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 126, Read name 20FUKAAXX100202:4:23:7470:195860, Mate Alignment start (10000353) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 126, Read name 20FUKAAXX100202:4:23:7470:195860, Mate Alignment start (10000353) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 127, Read name 20GAVAAXX100126:5:5:9475:54882, Mate Alignment start (10000264) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 127, Read name 20GAVAAXX100126:5:5:9475:54882, Mate Alignment start (10000264) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 128, Read name 20GAVAAXX100126:6:68:9971:99340, Mate Alignment start (10000372) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 128, Read name 20GAVAAXX100126:6:68:9971:99340, Mate Alignment start (10000372) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 129, Read name 20GAVAAXX100126:8:4:2514:172766, Mate Alignment start (9999751) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 129, Read name 20GAVAAXX100126:8:4:2514:172766, Mate Alignment start (9999751) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 130, Read name 20FUKAAXX100202:8:45:1989:15113, Mate Alignment start (10000303) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 130, Read name 20FUKAAXX100202:8:45:1989:15113, Mate Alignment start (10000303) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 131, Read name 20FUKAAXX100202:5:43:9081:11499, Mate Alignment start (9999706) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 131, Read name 20FUKAAXX100202:5:43:9081:11499, Mate Alignment start (9999706) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 132, Read name 20GAVAAXX100126:6:2:3042:60022, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 132, Read name 20GAVAAXX100126:6:2:3042:60022, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 133, Read name 20FUKAAXX100202:1:25:16659:142466, Mate Alignment start (9999713) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 133, Read name 20FUKAAXX100202:1:25:16659:142466, Mate Alignment start (9999713) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 134, Read name 20GAVAAXX100126:7:47:6583:18921, Mate Alignment start (9999712) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 134, Read name 20GAVAAXX100126:7:47:6583:18921, Mate Alignment start (9999712) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 135, Read name 20FUKAAXX100202:8:25:6061:158813, Mate Alignment start (9999688) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 135, Read name 20FUKAAXX100202:8:25:6061:158813, Mate Alignment start (9999688) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 136, Read name 20GAVAAXX100126:8:65:19600:82097, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 136, Read name 20GAVAAXX100126:8:65:19600:82097, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 137, Read name 20GAVAAXX100126:8:65:19610:82077, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 137, Read name 20GAVAAXX100126:8:65:19610:82077, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 138, Read name 20FUKAAXX100202:2:22:8993:175344, Mate Alignment start (9999717) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 138, Read name 20FUKAAXX100202:2:22:8993:175344, Mate Alignment start (9999717) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 139, Read name 20GAVAAXX100126:1:21:7801:54762, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 139, Read name 20GAVAAXX100126:1:21:7801:54762, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 140, Read name 20GAVAAXX100126:4:1:13342:97110, Mate Alignment start (9999743) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 140, Read name 20GAVAAXX100126:4:1:13342:97110, Mate Alignment start (9999743) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 141, Read name 20FUKAAXX100202:3:2:9552:27284, Mate Alignment start (9999718) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 141, Read name 20FUKAAXX100202:3:2:9552:27284, Mate Alignment start (9999718) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 142, Read name 20FUKAAXX100202:4:3:6934:181831, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 142, Read name 20FUKAAXX100202:4:3:6934:181831, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 143, Read name 20GAVAAXX100126:8:7:2115:102977, Mate Alignment start (9999745) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 143, Read name 20GAVAAXX100126:8:7:2115:102977, Mate Alignment start (9999745) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 144, Read name 20FUKAAXX100202:5:45:17899:193943, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 144, Read name 20FUKAAXX100202:5:45:17899:193943, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 145, Read name 20FUKAAXX100202:7:24:21385:130712, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 145, Read name 20FUKAAXX100202:7:24:21385:130712, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 146, Read name 20FUKAAXX100202:7:2:15287:105342, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 146, Read name 20FUKAAXX100202:7:2:15287:105342, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 147, Read name 20FUKAAXX100202:2:61:15800:106937, Mate Alignment start (9999698) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 147, Read name 20FUKAAXX100202:2:61:15800:106937, Mate Alignment start (9999698) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 148, Read name 20GAVAAXX100126:8:41:3599:9555, Mate Alignment start (9999698) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 148, Read name 20GAVAAXX100126:8:41:3599:9555, Mate Alignment start (9999698) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 149, Read name 20FUKAAXX100202:1:44:3588:13144, Mate Alignment start (10000326) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 149, Read name 20FUKAAXX100202:1:44:3588:13144, Mate Alignment start (10000326) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 150, Read name 20GAVAAXX100126:2:8:6126:168407, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 150, Read name 20GAVAAXX100126:2:8:6126:168407, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 151, Read name 20GAVAAXX100126:2:8:6143:168418, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 151, Read name 20GAVAAXX100126:2:8:6143:168418, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 152, Read name 20FUKAAXX100202:3:28:12160:117165, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 152, Read name 20FUKAAXX100202:3:28:12160:117165, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 153, Read name 20GAVAAXX100126:4:45:8053:140082, Mate Alignment start (9999604) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 153, Read name 20GAVAAXX100126:4:45:8053:140082, Mate Alignment start (9999604) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 154, Read name 20GAVAAXX100126:6:28:11134:174564, Mate Alignment start (9999697) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 154, Read name 20GAVAAXX100126:6:28:11134:174564, Mate Alignment start (9999697) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 155, Read name 20GAVAAXX100126:6:28:11146:174578, Mate Alignment start (9999697) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 155, Read name 20GAVAAXX100126:6:28:11146:174578, Mate Alignment start (9999697) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 156, Read name 20FUKAAXX100202:8:2:10382:194128, Mate Alignment start (10000347) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 156, Read name 20FUKAAXX100202:8:2:10382:194128, Mate Alignment start (10000347) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 157, Read name 20FUKAAXX100202:3:61:14021:185070, Mate Alignment start (9999731) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 157, Read name 20FUKAAXX100202:3:61:14021:185070, Mate Alignment start (9999731) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 158, Read name 20FUKAAXX100202:5:62:19690:9570, Mate Alignment start (9999729) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 158, Read name 20FUKAAXX100202:5:62:19690:9570, Mate Alignment start (9999729) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 159, Read name 20GAVAAXX100126:1:63:20142:132241, Mate Alignment start (9999715) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 159, Read name 20GAVAAXX100126:1:63:20142:132241, Mate Alignment start (9999715) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 160, Read name 20GAVAAXX100126:5:5:16399:184379, Mate Alignment start (9999725) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 160, Read name 20GAVAAXX100126:5:5:16399:184379, Mate Alignment start (9999725) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 161, Read name 20GAVAAXX100126:2:8:11075:186130, Mate Alignment start (10000336) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 161, Read name 20GAVAAXX100126:2:8:11075:186130, Mate Alignment start (10000336) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 162, Read name 20FUKAAXX100202:3:64:18891:180836, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 162, Read name 20FUKAAXX100202:3:64:18891:180836, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 163, Read name 20GAVAAXX100126:6:41:1651:77368, Mate Alignment start (9999762) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 163, Read name 20GAVAAXX100126:6:41:1651:77368, Mate Alignment start (9999762) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 164, Read name 20FUKAAXX100202:4:24:12641:3924, Mate Alignment start (9999704) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 164, Read name 20FUKAAXX100202:4:24:12641:3924, Mate Alignment start (9999704) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 165, Read name 20GAVAAXX100126:1:67:21027:67363, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 165, Read name 20GAVAAXX100126:1:67:21027:67363, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 166, Read name 20GAVAAXX100126:6:23:2944:66430, Mate Alignment start (9999718) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 166, Read name 20GAVAAXX100126:6:23:2944:66430, Mate Alignment start (9999718) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 167, Read name 20FUKAAXX100202:5:27:9785:178062, Mate Alignment start (10000338) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 167, Read name 20FUKAAXX100202:5:27:9785:178062, Mate Alignment start (10000338) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 168, Read name 20FUKAAXX100202:7:25:3261:114933, Mate Alignment start (9999772) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 168, Read name 20FUKAAXX100202:7:25:3261:114933, Mate Alignment start (9999772) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 169, Read name 20FUKAAXX100202:7:68:14596:106064, Mate Alignment start (9999731) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 169, Read name 20FUKAAXX100202:7:68:14596:106064, Mate Alignment start (9999731) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 170, Read name 20GAVAAXX100126:3:27:20408:42852, Mate Alignment start (9999751) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 170, Read name 20GAVAAXX100126:3:27:20408:42852, Mate Alignment start (9999751) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 171, Read name 20GAVAAXX100126:5:27:19872:165078, Mate Alignment start (9999729) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 171, Read name 20GAVAAXX100126:5:27:19872:165078, Mate Alignment start (9999729) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 172, Read name 20GAVAAXX100126:8:46:5544:82405, Mate Alignment start (9999696) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 172, Read name 20GAVAAXX100126:8:46:5544:82405, Mate Alignment start (9999696) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 173, Read name 20FUKAAXX100202:6:5:13733:127380, Mate Alignment start (10000378) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 173, Read name 20FUKAAXX100202:6:5:13733:127380, Mate Alignment start (10000378) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 174, Read name 20FUKAAXX100202:6:61:9436:123634, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 174, Read name 20FUKAAXX100202:6:61:9436:123634, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 175, Read name 20FUKAAXX100202:1:4:6802:198636, Mate Alignment start (9999734) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 175, Read name 20FUKAAXX100202:1:4:6802:198636, Mate Alignment start (9999734) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 176, Read name 20FUKAAXX100202:3:61:2345:190213, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 176, Read name 20FUKAAXX100202:3:61:2345:190213, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 177, Read name 20FUKAAXX100202:7:66:18422:38530, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 177, Read name 20FUKAAXX100202:7:66:18422:38530, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 178, Read name 20FUKAAXX100202:1:1:11716:63554, Mate Alignment start (10000217) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 178, Read name 20FUKAAXX100202:1:1:11716:63554, Mate Alignment start (10000217) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 179, Read name 20FUKAAXX100202:7:2:20791:62084, Mate Alignment start (10000415) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 179, Read name 20FUKAAXX100202:7:2:20791:62084, Mate Alignment start (10000415) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 180, Read name 20FUKAAXX100202:8:7:11983:56692, Mate Alignment start (10000329) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 180, Read name 20FUKAAXX100202:8:7:11983:56692, Mate Alignment start (10000329) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 181, Read name 20GAVAAXX100126:4:62:3221:106888, Mate Alignment start (9999712) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 181, Read name 20GAVAAXX100126:4:62:3221:106888, Mate Alignment start (9999712) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 182, Read name 20GAVAAXX100126:4:8:17348:119983, Mate Alignment start (9999711) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 182, Read name 20GAVAAXX100126:4:8:17348:119983, Mate Alignment start (9999711) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 183, Read name 20FUKAAXX100202:4:5:8921:109860, Mate Alignment start (10000352) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 183, Read name 20FUKAAXX100202:4:5:8921:109860, Mate Alignment start (10000352) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 184, Read name 20FUKAAXX100202:3:61:5334:12201, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 184, Read name 20FUKAAXX100202:3:61:5334:12201, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 185, Read name 20FUKAAXX100202:6:25:20343:31574, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 185, Read name 20FUKAAXX100202:6:25:20343:31574, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 186, Read name 20FUKAAXX100202:6:25:20360:31581, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 186, Read name 20FUKAAXX100202:6:25:20360:31581, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 187, Read name 20GAVAAXX100126:3:7:12571:28928, Mate Alignment start (9999729) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 187, Read name 20GAVAAXX100126:3:7:12571:28928, Mate Alignment start (9999729) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 188, Read name 20GAVAAXX100126:7:45:8702:45252, Mate Alignment start (10000303) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 188, Read name 20GAVAAXX100126:7:45:8702:45252, Mate Alignment start (10000303) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 189, Read name 20FUKAAXX100202:4:26:8462:86912, Mate Alignment start (10000373) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 189, Read name 20FUKAAXX100202:4:26:8462:86912, Mate Alignment start (10000373) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 190, Read name 20GAVAAXX100126:8:45:6375:103133, Mate Alignment start (10000350) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 190, Read name 20GAVAAXX100126:8:45:6375:103133, Mate Alignment start (10000350) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 191, Read name 20FUKAAXX100202:4:23:21082:72960, Mate Alignment start (9999741) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 191, Read name 20FUKAAXX100202:4:23:21082:72960, Mate Alignment start (9999741) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 192, Read name 20FUKAAXX100202:4:5:5992:35455, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 192, Read name 20FUKAAXX100202:4:5:5992:35455, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 193, Read name 20GAVAAXX100126:6:4:12978:135278, Mate Alignment start (10000348) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 193, Read name 20GAVAAXX100126:6:4:12978:135278, Mate Alignment start (10000348) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 194, Read name 20GAVAAXX100126:2:5:1838:180237, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 194, Read name 20GAVAAXX100126:2:5:1838:180237, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 195, Read name 20GAVAAXX100126:7:63:11003:164288, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 195, Read name 20GAVAAXX100126:7:63:11003:164288, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 196, Read name 20FUKAAXX100202:3:48:15406:75661, Mate Alignment start (10000347) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 196, Read name 20FUKAAXX100202:3:48:15406:75661, Mate Alignment start (10000347) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 197, Read name 20GAVAAXX100126:8:65:18514:117061, Mate Alignment start (9999703) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 197, Read name 20GAVAAXX100126:8:65:18514:117061, Mate Alignment start (9999703) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 200, Read name 20FUKAAXX100202:4:46:4678:167193, Mate Alignment start (9999725) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 200, Read name 20FUKAAXX100202:4:46:4678:167193, Mate Alignment start (9999725) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 201, Read name 20GAVAAXX100126:4:27:15355:60703, Mate Alignment start (9999746) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 201, Read name 20GAVAAXX100126:4:27:15355:60703, Mate Alignment start (9999746) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 202, Read name 20FUKAAXX100202:4:63:3107:142967, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 202, Read name 20FUKAAXX100202:4:63:3107:142967, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 203, Read name 20GAVAAXX100126:1:46:17524:10808, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 203, Read name 20GAVAAXX100126:1:46:17524:10808, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 204, Read name 20GAVAAXX100126:2:45:9532:172440, Mate Alignment start (10000366) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 204, Read name 20GAVAAXX100126:2:45:9532:172440, Mate Alignment start (10000366) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 205, Read name 20FUKAAXX100202:4:43:4771:2441, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 205, Read name 20FUKAAXX100202:4:43:4771:2441, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 206, Read name 20FUKAAXX100202:1:23:16512:3262, Mate Alignment start (9999728) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 206, Read name 20FUKAAXX100202:1:23:16512:3262, Mate Alignment start (9999728) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 207, Read name 20GAVAAXX100126:6:66:6108:99558, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 207, Read name 20GAVAAXX100126:6:66:6108:99558, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 208, Read name 20FUKAAXX100202:3:23:19248:42689, Mate Alignment start (10000341) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 208, Read name 20FUKAAXX100202:3:23:19248:42689, Mate Alignment start (10000341) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 209, Read name 20FUKAAXX100202:4:67:19946:84115, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 209, Read name 20FUKAAXX100202:4:67:19946:84115, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 210, Read name 20FUKAAXX100202:4:67:19957:84130, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 210, Read name 20FUKAAXX100202:4:67:19957:84130, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 211, Read name 20GAVAAXX100126:8:46:6721:107141, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 211, Read name 20GAVAAXX100126:8:46:6721:107141, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 212, Read name 20FUKAAXX100202:2:44:11476:56122, Mate Alignment start (10000402) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 212, Read name 20FUKAAXX100202:2:44:11476:56122, Mate Alignment start (10000402) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 213, Read name 20FUKAAXX100202:2:62:3370:172539, Mate Alignment start (10000406) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 213, Read name 20FUKAAXX100202:2:62:3370:172539, Mate Alignment start (10000406) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 214, Read name 20FUKAAXX100202:5:27:20510:84577, Mate Alignment start (9999762) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 214, Read name 20FUKAAXX100202:5:27:20510:84577, Mate Alignment start (9999762) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 215, Read name 20FUKAAXX100202:5:43:10418:69609, Mate Alignment start (10000351) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 215, Read name 20FUKAAXX100202:5:43:10418:69609, Mate Alignment start (10000351) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 216, Read name 20FUKAAXX100202:8:22:10804:10935, Mate Alignment start (10000400) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 216, Read name 20FUKAAXX100202:8:22:10804:10935, Mate Alignment start (10000400) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 217, Read name 20FUKAAXX100202:8:28:12970:89358, Mate Alignment start (10000394) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 217, Read name 20FUKAAXX100202:8:28:12970:89358, Mate Alignment start (10000394) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 218, Read name 20GAVAAXX100126:1:3:9885:16197, Mate Alignment start (10000221) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 218, Read name 20GAVAAXX100126:1:3:9885:16197, Mate Alignment start (10000221) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 219, Read name 20GAVAAXX100126:5:41:2927:129979, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 219, Read name 20GAVAAXX100126:5:41:2927:129979, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 220, Read name 20FUKAAXX100202:6:3:13871:76745, Mate Alignment start (9999759) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 220, Read name 20FUKAAXX100202:6:3:13871:76745, Mate Alignment start (9999759) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 221, Read name 20GAVAAXX100126:8:8:9677:53860, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 221, Read name 20GAVAAXX100126:8:8:9677:53860, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 222, Read name 20GAVAAXX100126:2:7:6406:190923, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 222, Read name 20GAVAAXX100126:2:7:6406:190923, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 225, Read name 20GAVAAXX100126:5:45:7084:89817, Mate Alignment start (9999773) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 225, Read name 20GAVAAXX100126:5:45:7084:89817, Mate Alignment start (9999773) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 226, Read name 20FUKAAXX100202:2:8:8921:13714, Mate Alignment start (9999637) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 226, Read name 20FUKAAXX100202:2:8:8921:13714, Mate Alignment start (9999637) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 227, Read name 20FUKAAXX100202:3:25:5393:174013, Mate Alignment start (9999699) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 227, Read name 20FUKAAXX100202:3:25:5393:174013, Mate Alignment start (9999699) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 228, Read name 20GAVAAXX100126:4:61:19483:178175, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 228, Read name 20GAVAAXX100126:4:61:19483:178175, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 229, Read name 20FUKAAXX100202:6:61:13597:167016, Mate Alignment start (9999733) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 229, Read name 20FUKAAXX100202:6:61:13597:167016, Mate Alignment start (9999733) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 230, Read name 20GAVAAXX100126:2:46:9819:189801, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 230, Read name 20GAVAAXX100126:2:46:9819:189801, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 231, Read name 20GAVAAXX100126:1:47:11960:43085, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 231, Read name 20GAVAAXX100126:1:47:11960:43085, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 232, Read name 20FUKAAXX100202:8:61:8547:37887, Mate Alignment start (10000431) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 232, Read name 20FUKAAXX100202:8:61:8547:37887, Mate Alignment start (10000431) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 233, Read name 20GAVAAXX100126:1:64:13278:136055, Mate Alignment start (10000387) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 233, Read name 20GAVAAXX100126:1:64:13278:136055, Mate Alignment start (10000387) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 234, Read name 20GAVAAXX100126:8:8:10069:1815, Mate Alignment start (10000360) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 234, Read name 20GAVAAXX100126:8:8:10069:1815, Mate Alignment start (10000360) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 235, Read name 20FUKAAXX100202:6:43:12464:95867, Mate Alignment start (9999715) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 235, Read name 20FUKAAXX100202:6:43:12464:95867, Mate Alignment start (9999715) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 236, Read name 20GAVAAXX100126:8:4:3360:104730, Mate Alignment start (9999724) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 236, Read name 20GAVAAXX100126:8:4:3360:104730, Mate Alignment start (9999724) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 237, Read name 20GAVAAXX100126:7:23:5527:173596, Mate Alignment start (10000333) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 237, Read name 20GAVAAXX100126:7:23:5527:173596, Mate Alignment start (10000333) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 238, Read name 20FUKAAXX100202:3:63:15601:87681, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 238, Read name 20FUKAAXX100202:3:63:15601:87681, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 239, Read name 20GAVAAXX100126:8:7:19780:99577, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 239, Read name 20GAVAAXX100126:8:7:19780:99577, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 240, Read name 20FUKAAXX100202:7:64:11274:28663, Mate Alignment start (10000350) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 240, Read name 20FUKAAXX100202:7:64:11274:28663, Mate Alignment start (10000350) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 241, Read name 20FUKAAXX100202:5:46:7034:130269, Mate Alignment start (9999775) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 241, Read name 20FUKAAXX100202:5:46:7034:130269, Mate Alignment start (9999775) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 242, Read name 20FUKAAXX100202:6:42:13864:97949, Mate Alignment start (9999770) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 242, Read name 20FUKAAXX100202:6:42:13864:97949, Mate Alignment start (9999770) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 243, Read name 20FUKAAXX100202:7:63:12812:59167, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 243, Read name 20FUKAAXX100202:7:63:12812:59167, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 244, Read name 20FUKAAXX100202:3:42:10889:9286, Mate Alignment start (9999781) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 244, Read name 20FUKAAXX100202:3:42:10889:9286, Mate Alignment start (9999781) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 245, Read name 20FUKAAXX100202:7:44:10464:154941, Mate Alignment start (9999777) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 245, Read name 20FUKAAXX100202:7:44:10464:154941, Mate Alignment start (9999777) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 246, Read name 20GAVAAXX100126:2:62:9149:111864, Mate Alignment start (10000382) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 246, Read name 20GAVAAXX100126:2:62:9149:111864, Mate Alignment start (10000382) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 247, Read name 20GAVAAXX100126:3:6:21157:147419, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 247, Read name 20GAVAAXX100126:3:6:21157:147419, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 248, Read name 20FUKAAXX100202:2:6:7367:104244, Mate Alignment start (10000408) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 248, Read name 20FUKAAXX100202:2:6:7367:104244, Mate Alignment start (10000408) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 249, Read name 20GAVAAXX100126:8:23:12150:79883, Mate Alignment start (10000363) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 249, Read name 20GAVAAXX100126:8:23:12150:79883, Mate Alignment start (10000363) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 250, Read name 20GAVAAXX100126:2:66:8843:33721, Mate Alignment start (10000388) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 250, Read name 20GAVAAXX100126:2:66:8843:33721, Mate Alignment start (10000388) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 251, Read name 20GAVAAXX100126:2:66:8848:33740, Mate Alignment start (10000388) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 251, Read name 20GAVAAXX100126:2:66:8848:33740, Mate Alignment start (10000388) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 252, Read name 20GAVAAXX100126:2:66:8861:33717, Mate Alignment start (10000388) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 252, Read name 20GAVAAXX100126:2:66:8861:33717, Mate Alignment start (10000388) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 253, Read name 20FUKAAXX100202:6:24:9789:119768, Mate Alignment start (9999745) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 253, Read name 20FUKAAXX100202:6:24:9789:119768, Mate Alignment start (9999745) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 254, Read name 20GAVAAXX100126:4:48:13006:180541, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 254, Read name 20GAVAAXX100126:4:48:13006:180541, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 255, Read name 20FUKAAXX100202:4:61:14645:192554, Mate Alignment start (10000352) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 255, Read name 20FUKAAXX100202:4:61:14645:192554, Mate Alignment start (10000352) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 256, Read name 20GAVAAXX100126:2:27:18806:87123, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 256, Read name 20GAVAAXX100126:2:27:18806:87123, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 257, Read name 20GAVAAXX100126:2:66:8554:80197, Mate Alignment start (9999742) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 257, Read name 20GAVAAXX100126:2:66:8554:80197, Mate Alignment start (9999742) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 258, Read name 20FUKAAXX100202:5:44:18607:97922, Mate Alignment start (10000375) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 258, Read name 20FUKAAXX100202:5:44:18607:97922, Mate Alignment start (10000375) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 259, Read name 20FUKAAXX100202:6:7:20029:86575, Mate Alignment start (9999724) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 259, Read name 20FUKAAXX100202:6:7:20029:86575, Mate Alignment start (9999724) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 262, Read name 20GAVAAXX100126:7:28:19343:119692, Mate Alignment start (10000324) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 262, Read name 20GAVAAXX100126:7:28:19343:119692, Mate Alignment start (10000324) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 263, Read name 20GAVAAXX100126:8:3:19154:172785, Mate Alignment start (10000444) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 263, Read name 20GAVAAXX100126:8:3:19154:172785, Mate Alignment start (10000444) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 264, Read name 20FUKAAXX100202:4:2:11323:157919, Mate Alignment start (9999727) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 264, Read name 20FUKAAXX100202:4:2:11323:157919, Mate Alignment start (9999727) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 265, Read name 20FUKAAXX100202:4:24:20755:63383, Mate Alignment start (10000420) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 265, Read name 20FUKAAXX100202:4:24:20755:63383, Mate Alignment start (10000420) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 266, Read name 20GAVAAXX100126:6:41:12737:140458, Mate Alignment start (10000391) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 266, Read name 20GAVAAXX100126:6:41:12737:140458, Mate Alignment start (10000391) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 267, Read name 20FUKAAXX100202:1:41:8855:77865, Mate Alignment start (10000406) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 267, Read name 20FUKAAXX100202:1:41:8855:77865, Mate Alignment start (10000406) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 268, Read name 20FUKAAXX100202:2:7:20289:162172, Mate Alignment start (10000401) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 268, Read name 20FUKAAXX100202:2:7:20289:162172, Mate Alignment start (10000401) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 269, Read name 20FUKAAXX100202:3:5:15184:151247, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 269, Read name 20FUKAAXX100202:3:5:15184:151247, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 270, Read name 20GAVAAXX100126:5:8:18245:6953, Mate Alignment start (10000327) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 270, Read name 20GAVAAXX100126:5:8:18245:6953, Mate Alignment start (10000327) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 271, Read name 20FUKAAXX100202:3:24:9989:45675, Mate Alignment start (9999781) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 271, Read name 20FUKAAXX100202:3:24:9989:45675, Mate Alignment start (9999781) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 272, Read name 20FUKAAXX100202:3:25:21206:43648, Mate Alignment start (9999754) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 272, Read name 20FUKAAXX100202:3:25:21206:43648, Mate Alignment start (9999754) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 273, Read name 20GAVAAXX100126:8:7:10416:22501, Mate Alignment start (9999744) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 273, Read name 20GAVAAXX100126:8:7:10416:22501, Mate Alignment start (9999744) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 274, Read name 20GAVAAXX100126:8:7:10417:22480, Mate Alignment start (9999744) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 274, Read name 20GAVAAXX100126:8:7:10417:22480, Mate Alignment start (9999744) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 275, Read name 20FUKAAXX100202:2:23:12195:137492, Mate Alignment start (10000417) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 275, Read name 20FUKAAXX100202:2:23:12195:137492, Mate Alignment start (10000417) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 276, Read name 20FUKAAXX100202:2:68:14803:9019, Mate Alignment start (10000435) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 276, Read name 20FUKAAXX100202:2:68:14803:9019, Mate Alignment start (10000435) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 277, Read name 20FUKAAXX100202:2:68:1649:5921, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 277, Read name 20FUKAAXX100202:2:68:1649:5921, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 278, Read name 20GAVAAXX100126:6:67:14138:53447, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 278, Read name 20GAVAAXX100126:6:67:14138:53447, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 279, Read name 20GAVAAXX100126:6:27:17917:125886, Mate Alignment start (10000392) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 279, Read name 20GAVAAXX100126:6:27:17917:125886, Mate Alignment start (10000392) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 280, Read name 20GAVAAXX100126:6:27:17919:125864, Mate Alignment start (10000392) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 280, Read name 20GAVAAXX100126:6:27:17919:125864, Mate Alignment start (10000392) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 281, Read name 20GAVAAXX100126:4:23:11820:142520, Mate Alignment start (9999792) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 281, Read name 20GAVAAXX100126:4:23:11820:142520, Mate Alignment start (9999792) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 282, Read name 20FUKAAXX100202:3:22:1789:82621, Mate Alignment start (10000372) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 282, Read name 20FUKAAXX100202:3:22:1789:82621, Mate Alignment start (10000372) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 283, Read name 20GAVAAXX100126:6:21:6652:178712, Mate Alignment start (10000425) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 283, Read name 20GAVAAXX100126:6:21:6652:178712, Mate Alignment start (10000425) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 284, Read name 20FUKAAXX100202:4:43:6140:91204, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 284, Read name 20FUKAAXX100202:4:43:6140:91204, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 285, Read name 20FUKAAXX100202:4:43:6159:91203, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 285, Read name 20FUKAAXX100202:4:43:6159:91203, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 288, Read name 20GAVAAXX100126:4:28:9009:173490, Mate Alignment start (10000424) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 288, Read name 20GAVAAXX100126:4:28:9009:173490, Mate Alignment start (10000424) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 289, Read name 20FUKAAXX100202:8:45:1884:47673, Mate Alignment start (9999784) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 289, Read name 20FUKAAXX100202:8:45:1884:47673, Mate Alignment start (9999784) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 290, Read name 20FUKAAXX100202:8:45:1902:47680, Mate Alignment start (9999784) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 290, Read name 20FUKAAXX100202:8:45:1902:47680, Mate Alignment start (9999784) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 293, Read name 20FUKAAXX100202:5:26:19959:88445, Mate Alignment start (9999764) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 293, Read name 20FUKAAXX100202:5:26:19959:88445, Mate Alignment start (9999764) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 294, Read name 20FUKAAXX100202:6:26:12485:190127, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 294, Read name 20FUKAAXX100202:6:26:12485:190127, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 295, Read name 20FUKAAXX100202:6:26:12497:190143, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 295, Read name 20FUKAAXX100202:6:26:12497:190143, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 296, Read name 20FUKAAXX100202:7:67:18360:176157, Mate Alignment start (10000361) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 296, Read name 20FUKAAXX100202:7:67:18360:176157, Mate Alignment start (10000361) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 297, Read name 20GAVAAXX100126:3:7:6468:165793, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 297, Read name 20GAVAAXX100126:3:7:6468:165793, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 298, Read name 20FUKAAXX100202:3:63:14607:69414, Mate Alignment start (10000374) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 298, Read name 20FUKAAXX100202:3:63:14607:69414, Mate Alignment start (10000374) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 299, Read name 20FUKAAXX100202:4:66:18078:75058, Mate Alignment start (10000422) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 299, Read name 20FUKAAXX100202:4:66:18078:75058, Mate Alignment start (10000422) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 300, Read name 20FUKAAXX100202:4:66:18086:75040, Mate Alignment start (10000422) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 300, Read name 20FUKAAXX100202:4:66:18086:75040, Mate Alignment start (10000422) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 301, Read name 20GAVAAXX100126:6:62:12722:64586, Mate Alignment start (10000424) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 301, Read name 20GAVAAXX100126:6:62:12722:64586, Mate Alignment start (10000424) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 304, Read name 20FUKAAXX100202:2:65:8299:177086, Mate Alignment start (10000414) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 304, Read name 20FUKAAXX100202:2:65:8299:177086, Mate Alignment start (10000414) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 305, Read name 20FUKAAXX100202:5:1:12372:198214, Mate Alignment start (10000442) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 305, Read name 20FUKAAXX100202:5:1:12372:198214, Mate Alignment start (10000442) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 306, Read name 20GAVAAXX100126:7:44:13710:11047, Mate Alignment start (10000383) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 306, Read name 20GAVAAXX100126:7:44:13710:11047, Mate Alignment start (10000383) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 309, Read name 20FUKAAXX100202:6:27:15343:160627, Mate Alignment start (9999796) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 309, Read name 20FUKAAXX100202:6:27:15343:160627, Mate Alignment start (9999796) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 310, Read name 20FUKAAXX100202:8:21:1790:48091, Mate Alignment start (9999943) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 310, Read name 20FUKAAXX100202:8:21:1790:48091, Mate Alignment start (9999943) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 311, Read name 20GAVAAXX100126:4:67:14214:45473, Mate Alignment start (9999769) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 311, Read name 20GAVAAXX100126:4:67:14214:45473, Mate Alignment start (9999769) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 312, Read name 20GAVAAXX100126:7:45:7524:110161, Mate Alignment start (9999815) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 312, Read name 20GAVAAXX100126:7:45:7524:110161, Mate Alignment start (9999815) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 313, Read name 20GAVAAXX100126:5:27:11481:127142, Mate Alignment start (10000390) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 313, Read name 20GAVAAXX100126:5:27:11481:127142, Mate Alignment start (10000390) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 314, Read name 20GAVAAXX100126:6:41:19998:100609, Mate Alignment start (10000440) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 314, Read name 20GAVAAXX100126:6:41:19998:100609, Mate Alignment start (10000440) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 315, Read name 20GAVAAXX100126:2:41:5807:152808, Mate Alignment start (10000365) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 315, Read name 20GAVAAXX100126:2:41:5807:152808, Mate Alignment start (10000365) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 316, Read name 20GAVAAXX100126:5:67:8769:184399, Mate Alignment start (10000413) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 316, Read name 20GAVAAXX100126:5:67:8769:184399, Mate Alignment start (10000413) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 317, Read name 20GAVAAXX100126:1:1:8996:5944, Mate Alignment start (9999798) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 317, Read name 20GAVAAXX100126:1:1:8996:5944, Mate Alignment start (9999798) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 318, Read name 20GAVAAXX100126:5:42:12694:142155, Mate Alignment start (10000420) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 318, Read name 20GAVAAXX100126:5:42:12694:142155, Mate Alignment start (10000420) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 319, Read name 20GAVAAXX100126:7:44:8840:83089, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 319, Read name 20GAVAAXX100126:7:44:8840:83089, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 320, Read name 20FUKAAXX100202:7:26:12026:80165, Mate Alignment start (10000385) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 320, Read name 20FUKAAXX100202:7:26:12026:80165, Mate Alignment start (10000385) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 321, Read name 20GAVAAXX100126:1:4:21009:20022, Mate Alignment start (10000385) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 321, Read name 20GAVAAXX100126:1:4:21009:20022, Mate Alignment start (10000385) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 322, Read name 20FUKAAXX100202:2:68:3792:94879, Mate Alignment start (10000432) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 322, Read name 20FUKAAXX100202:2:68:3792:94879, Mate Alignment start (10000432) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 323, Read name 20GAVAAXX100126:8:25:12361:154123, Mate Alignment start (9999756) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 323, Read name 20GAVAAXX100126:8:25:12361:154123, Mate Alignment start (9999756) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 324, Read name 20GAVAAXX100126:8:25:12382:154125, Mate Alignment start (9999756) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 324, Read name 20GAVAAXX100126:8:25:12382:154125, Mate Alignment start (9999756) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 325, Read name 20GAVAAXX100126:3:65:18493:115113, Mate Alignment start (10000436) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 325, Read name 20GAVAAXX100126:3:65:18493:115113, Mate Alignment start (10000436) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 326, Read name 20FUKAAXX100202:7:67:21244:6474, Mate Alignment start (10000458) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 326, Read name 20FUKAAXX100202:7:67:21244:6474, Mate Alignment start (10000458) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 327, Read name 20FUKAAXX100202:4:46:2349:67300, Mate Alignment start (9999771) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 327, Read name 20FUKAAXX100202:4:46:2349:67300, Mate Alignment start (9999771) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 328, Read name 20FUKAAXX100202:4:64:17702:39209, Mate Alignment start (9999785) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 328, Read name 20FUKAAXX100202:4:64:17702:39209, Mate Alignment start (9999785) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 329, Read name 20FUKAAXX100202:1:43:15726:132914, Mate Alignment start (10000377) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 329, Read name 20FUKAAXX100202:1:43:15726:132914, Mate Alignment start (10000377) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 330, Read name 20FUKAAXX100202:6:64:3811:167383, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 330, Read name 20FUKAAXX100202:6:64:3811:167383, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 331, Read name 20FUKAAXX100202:8:27:7323:75566, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 331, Read name 20FUKAAXX100202:8:27:7323:75566, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 332, Read name 20GAVAAXX100126:2:28:15360:131557, Mate Alignment start (10000418) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 332, Read name 20GAVAAXX100126:2:28:15360:131557, Mate Alignment start (10000418) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 333, Read name 20GAVAAXX100126:2:66:5383:81213, Mate Alignment start (9999769) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 333, Read name 20GAVAAXX100126:2:66:5383:81213, Mate Alignment start (9999769) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 334, Read name 20GAVAAXX100126:6:22:11440:95696, Mate Alignment start (9999766) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 334, Read name 20GAVAAXX100126:6:22:11440:95696, Mate Alignment start (9999766) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 335, Read name 20GAVAAXX100126:6:67:12425:123302, Mate Alignment start (9999799) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 335, Read name 20GAVAAXX100126:6:67:12425:123302, Mate Alignment start (9999799) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 336, Read name 20FUKAAXX100202:1:41:1662:13912, Mate Alignment start (10000331) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 336, Read name 20FUKAAXX100202:1:41:1662:13912, Mate Alignment start (10000331) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 337, Read name 20FUKAAXX100202:3:21:19677:162487, Mate Alignment start (10000332) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 337, Read name 20FUKAAXX100202:3:21:19677:162487, Mate Alignment start (10000332) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 340, Read name 20FUKAAXX100202:6:46:13213:95672, Mate Alignment start (10000321) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 340, Read name 20FUKAAXX100202:6:46:13213:95672, Mate Alignment start (10000321) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 341, Read name 20GAVAAXX100126:2:67:11830:144272, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 341, Read name 20GAVAAXX100126:2:67:11830:144272, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 342, Read name 20GAVAAXX100126:6:25:11700:156967, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 342, Read name 20GAVAAXX100126:6:25:11700:156967, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 343, Read name 20GAVAAXX100126:8:2:1530:90452, Mate Alignment start (10000415) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 343, Read name 20GAVAAXX100126:8:2:1530:90452, Mate Alignment start (10000415) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 344, Read name 20FUKAAXX100202:1:41:15735:31577, Mate Alignment start (9999745) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 344, Read name 20FUKAAXX100202:1:41:15735:31577, Mate Alignment start (9999745) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 345, Read name 20FUKAAXX100202:7:67:19743:72886, Mate Alignment start (10000397) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 345, Read name 20FUKAAXX100202:7:67:19743:72886, Mate Alignment start (10000397) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 346, Read name 20GAVAAXX100126:2:62:5242:113457, Mate Alignment start (10000452) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 346, Read name 20GAVAAXX100126:2:62:5242:113457, Mate Alignment start (10000452) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 347, Read name 20FUKAAXX100202:7:41:10114:15727, Mate Alignment start (9999528) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 347, Read name 20FUKAAXX100202:7:41:10114:15727, Mate Alignment start (9999528) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 348, Read name 20FUKAAXX100202:5:27:14631:113616, Mate Alignment start (10000394) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 348, Read name 20FUKAAXX100202:5:27:14631:113616, Mate Alignment start (10000394) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 349, Read name 20FUKAAXX100202:8:26:8051:103852, Mate Alignment start (10000399) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 349, Read name 20FUKAAXX100202:8:26:8051:103852, Mate Alignment start (10000399) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 350, Read name 20GAVAAXX100126:4:1:11639:105967, Mate Alignment start (9999769) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 350, Read name 20GAVAAXX100126:4:1:11639:105967, Mate Alignment start (9999769) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 351, Read name 20GAVAAXX100126:8:6:11303:64367, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 351, Read name 20GAVAAXX100126:8:6:11303:64367, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 352, Read name 20GAVAAXX100126:8:6:11319:64357, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 352, Read name 20GAVAAXX100126:8:6:11319:64357, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21
Finished 1400 tests
Finished 1600 tests

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testAllCRAMEncodingsRoundTripThroughStream STANDARD_ERROR
    WARNING	2025-06-03 15:27:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testIgnoreObsoleteDataseriesOnRead STANDARD_ERROR
    WARNING	2025-06-03 15:27:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
Finished 1800 tests

Gradle suite > Gradle test > htsjdk.samtools.util.CoordSpanInputSteamTest.test_3_ranges_byte_single_read STANDARD_ERROR
    Adding chunk: 0 - 100
    Adding chunk: 10 - 20
    Adding chunk: 100 - 200
    Adding chunk: 1048575 - 1048576

Gradle suite > Gradle test > htsjdk.samtools.util.CoordSpanInputSteamTest.test_first_3_bytes STANDARD_ERROR
    Adding chunk: 0 - 1
    Adding chunk: 1 - 2
    Adding chunk: 2 - 3

Gradle suite > Gradle test > htsjdk.samtools.util.CoordSpanInputSteamTest.test_range_read STANDARD_ERROR
    Adding chunk: 0 - 100
    Adding chunk: 10 - 20
    Adding chunk: 100 - 200
    Adding chunk: 1048575 - 1048576
    Adding chunk: 0 - 100
    Adding chunk: 10 - 20
    Adding chunk: 100 - 200
    Adding chunk: 1048575 - 1048576

Gradle suite > Gradle test > htsjdk.samtools.cram.build.CramIOTest.testCheckHeaderAndEOF SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.cram.build.CramIOTest.testRejectUnknownCRAMVersion SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.util.DiskBackedQueueTest STANDARD_ERROR
    Resetting tmpdir

Gradle suite > Gradle test STANDARD_ERROR
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
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    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir

Gradle suite > Gradle test > htsjdk.samtools.DownsamplingIteratorTests.testBasicFunction STANDARD_ERROR
    Could not delete file /tmp/pbuilder2/DiskBackedQueueTest/diskbackedqueue.10342644787588597466.tmp
Finished 2000 tests
Finished 2200 tests
Finished 2400 tests
Finished 2600 tests
Finished 2800 tests
Finished 3000 tests

Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testBuildFromFasta[1](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    WARNING	2025-06-03 15:27:51	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testCreate[1](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    WARNING	2025-06-03 15:27:51	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
Finished 3200 tests
Finished 3400 tests
Finished 3600 tests

Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR
    WARNING	2025-06-03 15:27:53	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200

Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicShallowDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR
    WARNING	2025-06-03 15:27:53	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200

Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.codecFilterOutFieldsTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR
    WARNING	2025-06-03 15:27:53	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200

Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.testGZipped[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3.gz) STANDARD_ERROR
    WARNING	2025-06-03 15:27:53	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200
    WARNING	2025-06-03 15:27:53	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200

Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.testGZippedShallow[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3.gz) STANDARD_ERROR
    WARNING	2025-06-03 15:27:53	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200
    WARNING	2025-06-03 15:27:53	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200

Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3WriterTest.testRoundTrip[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3) STANDARD_ERROR
    WARNING	2025-06-03 15:27:53	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200
    WARNING	2025-06-03 15:27:53	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200
Finished 3800 tests

Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombLongEncodingTest.testToString STANDARD_ERROR
    WARNING	2025-06-03 15:27:53	ExperimentalEncoding	Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding which is untested and scheduled for removal from the CRAM spec

Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombRiceIntegerEncodingTest.testToString STANDARD_ERROR
    WARNING	2025-06-03 15:27:53	ExperimentalEncoding	Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[1](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7a15030b, [Ljava.lang.String;@713220d0) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@402adafa, [Ljava.lang.String;@27650402) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryAlignmentStart[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, 2) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryAlignmentStart[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, 24) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@6469e460) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@2a3322ed) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@1c32a0e6) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@2d748564) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@61996cf6) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@b319d51) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@6ac16bdd) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@1fbfd1d6) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@5488f9ea, [Ljava.lang.String;@2b94cc04) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@65701ad0, [Ljava.lang.String;@4ead36e0) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@366702bb, [Ljava.lang.String;@197f72c3) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@37d8b041, [Ljava.lang.String;@3c4369cb) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@36a56cdc, [Ljava.lang.String;@5fe2d78d) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@301ec8c1, [Ljava.lang.String;@59a0faf5) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@487b3e25, [Ljava.lang.String;@267cead9) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@19071978, [Ljava.lang.String;@7d391967) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@bdc229c, [Ljava.lang.String;@2e45ac83) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1de060c7, [Ljava.lang.String;@394e162d) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2ce853b8, [Ljava.lang.String;@785c69ec) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4b9333c9, [Ljava.lang.String;@1287b953) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@58c02614, [Ljava.lang.String;@576a536) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5b9f8bba, [Ljava.lang.String;@5491d8cb) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@30c74afa, [Ljava.lang.String;@4be8f5a4) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4582a95b, [Ljava.lang.String;@4137800e) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7f4bbeaf, [Ljava.lang.String;@499825cf) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMate[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMate[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMateEnsureInternalIteratorsClosed[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMateEnsureInternalIteratorsClosed[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@118b7a71) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@59deac9d) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@58480d4a) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@46e2d5b1) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@458cfd81) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@6fc70a4e, [Ljava.lang.String;@393e9fb1) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@312965c5, [Ljava.lang.String;@6d2981a7) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2429b974, [Ljava.lang.String;@df4488a) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@533a7b8b, [Ljava.lang.String;@51f83f4e) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@253a1f88, [Ljava.lang.String;@6a270c10) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3aa5fb03, [Ljava.lang.String;@6b3050ad) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1c66672, [Ljava.lang.String;@755ab9de) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5c575d99, [Ljava.lang.String;@36f79e83) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@77487e5, [Ljava.lang.String;@282dd29d) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@433b8757, [Ljava.lang.String;@571b725e) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@495b8f28, [Ljava.lang.String;@2d869380) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
Finished 4000 tests

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2c1056bc, [Ljava.lang.String;@4576194e) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7f78d45e, [Ljava.lang.String;@7c1760e5) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@683edb4f, [Ljava.lang.String;@35a448d6) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2c15865c, [Ljava.lang.String;@4d045c13) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@100d4fcd, [Ljava.lang.String;@177b01be) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4b504264, [Ljava.lang.String;@4a4cec98) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@e85d062) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@6d45d904) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@259f472d) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@19b8551) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@b738659) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@57f21d3b) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@591652b) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@73e78369) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@7075fd2e) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@1c9fac72) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@207f438) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@252eed6) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@6e169242) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@11a23c8) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@5b7c3a52) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@4f4551b2) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@2a23d31b) STANDARD_ERROR
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueries[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 12, 7) STANDARD_ERROR
    WARNING	2025-06-03 15:27:56	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:56	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:56	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:56	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:56	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:56	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@57e6f2a9, 5) STANDARD_ERROR
    WARNING	2025-06-03 15:27:56	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:56	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:27:56	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:27:56	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForDecodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@66b3fafe, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@56d9efae], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR
    WARNING	2025-06-03 15:27:56	HtsCodecResolver	The specified format string (BOGUS_FORMAT) does not correspond to any registered codec for content type (ALIGNED_READS)

Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[1]([], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR
    WARNING	2025-06-03 15:27:56	HtsCodecResolver	The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS)

Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[2]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@7106a2c7, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@6c649c4a, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4167f6e4, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@45b4a65, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@23e09c3c], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR
    WARNING	2025-06-03 15:27:56	HtsCodecResolver	The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS)

Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@7106a2c7, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@6c649c4a, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4167f6e4, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@45b4a65, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@23e09c3c], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR
    WARNING	2025-06-03 15:27:56	HtsCodecResolver	The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS)

Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[5]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@7106a2c7, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@6c649c4a, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4167f6e4, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@45b4a65, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@23e09c3c], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR
    WARNING	2025-06-03 15:27:56	HtsCodecResolver	The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS)
Finished 4200 tests
Finished 4400 tests
some stuffFinished 4600 tests

Gradle suite > Gradle test > htsjdk.samtools.util.IOUtilTest.testDeleteSingleWithDeletePaths STANDARD_ERROR
    Could not delete file tmp
    Could not delete file file10312350155809276216.bad
Finished 4800 tests

Gradle suite > Gradle test > htsjdk.samtools.util.IntervalTreeTest.performanceTest STANDARD_OUT
    Time to construct a tree with 50000 nodes: 30 milliseconds
    Queried for the same 100-length mapping 214359980 times in 10 seconds.

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[0](chr3:50911035-50911051	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95)
Finished 5000 tests
Finished 5200 tests

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[279](chr2:111013693-111013832	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95)
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[280](chr3:14174511-14175398	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[281](chr3:50911035-50911051	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[282](chr6:32071709-32071869	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[283](chr6:32072183-32072358	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[284](chr6:32104446-32104606	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[285](chr6:32104920-32105095	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[286](chr7:101995561-101995739	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[288](chr7:142179850-142180013	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95)
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[292](chr15:19335778-19336302	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[293](chr17:33364376-33364428	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95)
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[294](chr17:33546162-33546214	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95)
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[295](chr17:33706667-33706736	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[0](chr3:50911035-50911051	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95)
Finished 5400 tests

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[279](chr2:111013693-111013832	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95)
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[280](chr3:14174511-14175398	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[281](chr3:50911035-50911051	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[282](chr6:32071709-32071869	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[283](chr6:32072183-32072358	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[284](chr6:32104446-32104606	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[285](chr6:32104920-32105095	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[286](chr7:101995561-101995739	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[288](chr7:142179850-142180013	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95)
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[292](chr15:19335778-19336302	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[293](chr17:33364376-33364428	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95)
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[294](chr17:33546162-33546214	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95)
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[295](chr17:33706667-33706736	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95)
Finished 5600 tests

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[0](chr3:50911035-50911051	+	.) STANDARD_OUT
    Diagnosing chr3:50911035-50911051	+	. (len 17)
    chr3:50911035-50911051	+	null intersection null (len 17)=>chr3:50936014-50936030	+	.(+) using chain 3 ; pct matched 0.9411765

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[1](chr2:111013693-111013832	+	.) STANDARD_OUT
    Diagnosing chr2:111013693-111013832	+	. (len 140)
    chr2:111013693-111013832	+	null intersection null (len 140)=>null using chain 1
    chr2:111013693-111013832	+	null intersection null (len 140)=>chr2:108482693-108482783	-	.(-) using chain 53 ; pct matched 0.65
    chr2:111013693-111013832	+	null intersection null (len 140)=>chr2:113152284-113152332	+	.(+) using chain 310 ; pct matched 0.35

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[2](chr3:14174511-14175398	+	.) STANDARD_OUT
    Diagnosing chr3:14174511-14175398	+	. (len 888)
    chr3:14174511-14175398	+	null intersection null (len 888)=>chr3:14199509-14200394	+	.(+) using chain 3 ; pct matched 0.9166667

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[3](chr3:50911035-50911051	+	.) STANDARD_OUT
    Diagnosing chr3:50911035-50911051	+	. (len 17)
    chr3:50911035-50911051	+	null intersection null (len 17)=>chr3:50936014-50936030	+	.(+) using chain 3 ; pct matched 0.9411765

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[4](chr6:32071709-32071869	+	.) STANDARD_OUT
    Diagnosing chr6:32071709-32071869	+	. (len 161)
    chr6:32071709-32071869	+	null intersection null (len 161)=>chr6:31963730-31963890	+	.(+) using chain 6 ; pct matched 0.89440995

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[5](chr6:32072183-32072358	+	.) STANDARD_OUT
    Diagnosing chr6:32072183-32072358	+	. (len 176)
    chr6:32072183-32072358	+	null intersection null (len 176)=>chr6:31964204-31964379	+	.(+) using chain 6 ; pct matched 0.90909094

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[6](chr6:32104446-32104606	+	.) STANDARD_OUT
    Diagnosing chr6:32104446-32104606	+	. (len 161)
    chr6:32104446-32104606	+	null intersection null (len 161)=>chr6:31996468-31996628	+	.(+) using chain 6 ; pct matched 0.89440995

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[7](chr6:32104920-32105095	+	.) STANDARD_OUT
    Diagnosing chr6:32104920-32105095	+	. (len 176)
    chr6:32104920-32105095	+	null intersection null (len 176)=>chr6:31996942-31997117	+	.(+) using chain 6 ; pct matched 0.90909094

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[8](chr7:101995561-101995739	+	.) STANDARD_OUT
    Diagnosing chr7:101995561-101995739	+	. (len 179)
    chr7:101995561-101995739	+	null intersection null (len 179)=>chr7:102208488-102208633	+	.(+) using chain 7 ; pct matched 0.8156425

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[9](chr7:142178782-142178825	+	.) STANDARD_OUT
    Diagnosing chr7:142178782-142178825	+	. (len 44)
    chr7:142178782-142178825	+	null intersection null (len 44)=>null using chain 7

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[10](chr7:142179850-142180013	+	.) STANDARD_OUT
    Diagnosing chr7:142179850-142180013	+	. (len 164)
    chr7:142179850-142179857	+	null intersection null (len 8)=>chr7:142479907-142479914	+	.(+) using chain 31548103 ; pct matched 0.048780486
    chr7:142179946-142180009	+	null intersection null (len 64)=>chr7:142480003-142480066	+	.(+) using chain 30171758 ; pct matched 0.3902439
    chr7:142179850-142180013	+	null intersection null (len 164)=>null using chain 7

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[11](chr7:142181067-142181324	+	.) STANDARD_OUT
    Diagnosing chr7:142181067-142181324	+	. (len 258)
    chr7:142181067-142181324	+	null intersection null (len 258)=>null using chain 7

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[12](chr7:142181720-142181860	+	.) STANDARD_OUT
    Diagnosing chr7:142181720-142181860	+	. (len 141)
    chr7:142181720-142181860	+	null intersection null (len 141)=>null using chain 7

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[13](chr7:142182157-142182313	+	.) STANDARD_OUT
    Diagnosing chr7:142182157-142182313	+	. (len 157)
    chr7:142182157-142182313	+	null intersection null (len 157)=>null using chain 7

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[14](chr15:19335778-19336302	+	.) STANDARD_OUT
    Diagnosing chr15:19335778-19336302	+	. (len 525)
    chr15:19335778-19336302	+	null intersection null (len 525)=>chr15:21071199-21071612	+	.(+) using chain 16 ; pct matched 0.7885714
    chr15:19335778-19336302	+	null intersection null (len 525)=>null using chain 110

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[15](chr17:33364376-33364428	+	.) STANDARD_OUT
    Diagnosing chr17:33364376-33364428	+	. (len 53)
    chr17:33364376-33364428	+	null intersection null (len 53)=>chr17:36289992-36290044	+	.(+) using chain 18 ; pct matched 0.3207547
    chr17:33364385-33364428	+	null intersection null (len 44)=>chr17:36342590-36342625	-	.(-) using chain 363 ; pct matched 0.6792453

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[16](chr17:33546162-33546214	+	.) STANDARD_OUT
    Diagnosing chr17:33546162-33546214	+	. (len 53)
    chr17:33546162-33546214	+	null intersection null (len 53)=>null using chain 18
    chr17:33546162-33546214	+	null intersection null (len 53)=>null using chain 1564
    chr17:33546162-33546214	+	null intersection null (len 53)=>chr17:36289992-36290044	-	.(-) using chain 363 ; pct matched 0.3207547
    chr17:33546162-33546214	+	null intersection null (len 53)=>chr17:36342590-36342625	+	.(+) using chain 1571 ; pct matched 0.6792453

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[17](chr17:33706667-33706736	+	.) STANDARD_OUT
    Diagnosing chr17:33706667-33706736	+	. (len 70)
    chr17:33706667-33706736	+	null intersection null (len 70)=>chr17:36453148-36453217	+	.(+) using chain 18 ; pct matched 0.75714284

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[18](chr17:59772721-59772781	+	.) STANDARD_OUT
    Diagnosing chr17:59772721-59772781	+	. (len 61)
    chr17:59772721-59772781	+	null intersection null (len 61)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[19](chr17:59779355-59779421	+	.) STANDARD_OUT
    Diagnosing chr17:59779355-59779421	+	. (len 67)
    chr17:59779355-59779421	+	null intersection null (len 67)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[20](chr17:59781483-59781540	+	.) STANDARD_OUT
    Diagnosing chr17:59781483-59781540	+	. (len 58)
    chr17:59781483-59781540	+	null intersection null (len 58)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[21](chr17:59783488-59783565	+	.) STANDARD_OUT
    Diagnosing chr17:59783488-59783565	+	. (len 78)
    chr17:59783488-59783565	+	null intersection null (len 78)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[22](chr17:59784584-59784615	+	.) STANDARD_OUT
    Diagnosing chr17:59784584-59784615	+	. (len 32)
    chr17:59784584-59784615	+	null intersection null (len 32)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[23](chr17:59786025-59786136	+	.) STANDARD_OUT
    Diagnosing chr17:59786025-59786136	+	. (len 112)
    chr17:59786025-59786136	+	null intersection null (len 112)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[24](chr17:59787203-59787494	+	.) STANDARD_OUT
    Diagnosing chr17:59787203-59787494	+	. (len 292)
    chr17:59787203-59787494	+	null intersection null (len 292)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[25](chr17:59791235-59791514	+	.) STANDARD_OUT
    Diagnosing chr17:59791235-59791514	+	. (len 280)
    chr17:59791235-59791514	+	null intersection null (len 280)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[26](chr17:59794247-59794502	+	.) STANDARD_OUT
    Diagnosing chr17:59794247-59794502	+	. (len 256)
    chr17:59794247-59794502	+	null intersection null (len 256)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[27](chr17:59801884-59802193	+	.) STANDARD_OUT
    Diagnosing chr17:59801884-59802193	+	. (len 310)
    chr17:59801884-59802193	+	null intersection null (len 310)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[28](chr17:59804685-59804982	+	.) STANDARD_OUT
    Diagnosing chr17:59804685-59804982	+	. (len 298)
    chr17:59804685-59804982	+	null intersection null (len 298)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[29](chr17:59817352-59817382	+	.) STANDARD_OUT
    Diagnosing chr17:59817352-59817382	+	. (len 31)
    chr17:59817352-59817382	+	null intersection null (len 31)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[30](chr17:59817465-59817532	+	.) STANDARD_OUT
    Diagnosing chr17:59817465-59817532	+	. (len 68)
    chr17:59817465-59817532	+	null intersection null (len 68)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[31](chr17:59875754-59875812	+	.) STANDARD_OUT
    Diagnosing chr17:59875754-59875812	+	. (len 59)
    chr17:59875754-59875812	+	null intersection null (len 59)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[32](chr17:59875899-59875944	+	.) STANDARD_OUT
    Diagnosing chr17:59875899-59875944	+	. (len 46)
    chr17:59875899-59875944	+	null intersection null (len 46)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[33](chr17:59879183-59879456	+	.) STANDARD_OUT
    Diagnosing chr17:59879183-59879456	+	. (len 274)
    chr17:59879183-59879456	+	null intersection null (len 274)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[34](chr17:59883988-59884276	+	.) STANDARD_OUT
    Diagnosing chr17:59883988-59884276	+	. (len 289)
    chr17:59883988-59884276	+	null intersection null (len 289)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[35](chr17:59887398-59887512	+	.) STANDARD_OUT
    Diagnosing chr17:59887398-59887512	+	. (len 115)
    chr17:59887398-59887512	+	null intersection null (len 115)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[36](chrX:48774611-48775058	+	.) STANDARD_OUT
    Diagnosing chrX:48774611-48775058	+	. (len 448)
    chrX:48774611-48775058	+	null intersection null (len 448)=>null using chain 8
Finished 5800 tests

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testLiftoverCounter[0](chr3:50911035-50911051	+	., null) STANDARD_ERROR
    INFO	2025-06-03 15:28:10	LiftOver	Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95)
Finished 6000 tests
Finished 6200 tests

Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaCoordinateMultiIterator STANDARD_OUT
    read_28833_29006_6945	0	chr21	28833	255	36M	*	0	0	AAGCTGGAGATTACCATACTTAGGCTCATGTAGCCA	?.QC5:&34LA#;K;A'5L*!.;.LJ?)FO?'?D2<	RG:Z:1

    read_28833_29006_6945	0	chr21	30000	255	36M	*	0	0	AAGCTGGAGATTACCATACTTAGGCTCATGTAGCCA	?.QC5:&34LA#;K;A'5L*!.;.LJ?)FO?'?D2<	RG:Z:1

    read_28701_28881_323b	0	chrX	28834	255	36M	*	0	0	GCCCTATCGCCAGATCAATCGTCGCTGTGGAACTAG	$>8BE+:L!M$K(L*MQ>PO8N*8>;;=5IA>B,*O	RG:Z:1

    read_28701_28881_323b	0	chrX	28835	255	36M	*	0	0	GCCCTATCGCCAGATCAATCGTCGCTGTGGAACTAG	$>8BE+:L!M$K(L*MQ>PO8N*8>;;=5IA>B,*O	RG:Z:1

    read_28701_28881_323c	0	chrX	28835	255	36M	*	0	0	CTCAACGTATTCATACAGGCCCTTTTCGAATAGCTG	%$=LPJ?D6&@R!"KJCOI+05?>>J9CJ)'@-O>K	RG:Z:1


Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaReadOrderMultiIterator STANDARD_OUT
    a
    b
    c
    d
    e

Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaUnsortedMultiIterator STANDARD_OUT
    d
    e
    c
    b
    a
Finished 6400 tests
Finished 6600 tests

Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[0](@HD	VN:1.0	SO:UNSORTED
) STANDARD_ERROR
    WARNING	2025-06-03 15:28:34	SAMTextHeaderCodec	Found non-conforming header SO tag: UNSORTED. Treating as 'unknown'.

Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[1](@HD	VN:1.0	SO:FALSE
) STANDARD_ERROR
    WARNING	2025-06-03 15:28:34	SAMTextHeaderCodec	Found non-conforming header SO tag: FALSE. Treating as 'unknown'.

Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[2](@HD	VN:1.0	SO:COORDINATE
) STANDARD_ERROR
    WARNING	2025-06-03 15:28:34	SAMTextHeaderCodec	Found non-conforming header SO tag: COORDINATE. Treating as 'unknown'.

Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[3](@HD	VN:1.0	SO:uNknOWn
) STANDARD_ERROR
    WARNING	2025-06-03 15:28:34	SAMTextHeaderCodec	Found non-conforming header SO tag: uNknOWn. Treating as 'unknown'.

Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[4](@HD	VN:1.0	SO:cOoRdinate
) STANDARD_ERROR
    WARNING	2025-06-03 15:28:34	SAMTextHeaderCodec	Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'.

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.specialFileWriterTest STANDARD_ERROR
    WARNING	2025-06-03 15:28:34	SAMFileWriterFactory	Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null
    WARNING	2025-06-03 15:28:34	SAMFileWriterFactory	Cannot create index for BAM because output file is not a regular file: file:///dev/null

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeCRAMWriterWithNoReference STANDARD_ERROR
    INFO	2025-06-03 15:28:34	SAMFileWriterFactory	Reference fasta is not provided when writing CRAM file file:///tmp/tmp.17251361361741487238..cram
    INFO	2025-06-03 15:28:34	SAMFileWriterFactory	Will attempt to use a default reference or download as set by defaults:
    INFO	2025-06-03 15:28:34	SAMFileWriterFactory	Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null
    INFO	2025-06-03 15:28:34	SAMFileWriterFactory	Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeSamOrBamForCramExtension STANDARD_ERROR
    INFO	2025-06-03 15:28:34	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension1835310855957523149.cram

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriter[0](sam) STANDARD_ERROR
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriter[1](bam) STANDARD_ERROR
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /tmp/tmp.10939782239141989243.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForCramExtensionNoReference STANDARD_ERROR
    INFO	2025-06-03 15:28:34	SAMFileWriterFactory	Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension12709178603073247359.cram
    INFO	2025-06-03 15:28:34	SAMFileWriterFactory	Will attempt to use a default reference or download as set by defaults:
    INFO	2025-06-03 15:28:34	SAMFileWriterFactory	Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null
    INFO	2025-06-03 15:28:34	SAMFileWriterFactory	Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForNoExtension STANDARD_ERROR
    INFO	2025-06-03 15:28:34	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension9588431482652211133

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForUnknownFileExtension STANDARD_ERROR
    INFO	2025-06-03 15:28:34	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension13756555188097146974.png

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[0](sam) STANDARD_ERROR
    INFO	2025-06-03 15:28:34	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: jimfs://a4453744-6589-48c3-8aa2-4e95a3e7ae0c/work/testMakeWriterPathsam
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathsam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[1](bam) STANDARD_ERROR
    INFO	2025-06-03 15:28:34	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: jimfs://193f36ab-cca5-4bff-b7da-f498d380be3c/work/testMakeWriterPathbam
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathbam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[2](cram) STANDARD_ERROR
    INFO	2025-06-03 15:28:34	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: jimfs://77cc6c5c-db41-4c78-b978-cca734673979/work/testMakeWriterPathcram
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathcram, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPathAndReferencePath[0](sam) STANDARD_ERROR
    INFO	2025-06-03 15:28:34	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: jimfs://590000ef-d7d1-4e61-a89e-bb4e0198e5f1/work/testMakeWriterPathsam
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathsam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPathAndReferencePath[1](bam) STANDARD_ERROR
    INFO	2025-06-03 15:28:34	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: jimfs://71ba114c-2962-4917-b29b-e94eb234e536/work/testMakeWriterPathbam
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathbam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPathAndReferencePath[2](cram) STANDARD_ERROR
    INFO	2025-06-03 15:28:34	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: jimfs://0da2f541-84ab-4dca-a341-27177ccc4952/work/testMakeWriterPathcram
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathcram, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1
Finished 6800 tests
Finished 7000 tests

Gradle suite > Gradle test > htsjdk.samtools.SAMSequenceDictionaryTest.testMergeDictionaries[7](SAMSequenceRecord(name=chr1,length=101,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=0,dict_index=0,assembly=null,alternate_names=[]), false) STANDARD_ERROR
    ERROR	2025-06-03 15:28:46	SAMSequenceDictionary	Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2.

Gradle suite > Gradle test > htsjdk.samtools.SamFilesTest.testIndexSymlinking[2](src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai) STANDARD_ERROR
    WARNING	2025-06-03 15:28:46	SamFiles	The index file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam
    WARNING	2025-06-03 15:28:46	SamFiles	The index file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam
Finished 7200 tests

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.customReaderFactoryTest STANDARD_ERROR
    INFO	2025-06-03 15:28:47	CustomReaderFactory	Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory
    INFO	2025-06-03 15:28:47	CustomReaderFactory	Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory
    INFO	2025-06-03 15:28:47	CustomReaderFactory	Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from  this jar
    INFO	2025-06-03 15:28:47	SamReaderFactoryTest	Opening customr reader for src/test/resources/htsjdk/samtools/uncompressed.sam

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.exhaustInputResourcePermutation SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.openPath STANDARD_ERROR
    INFO	2025-06-03 15:28:47	SamReaderFactoryTest	Reading from src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam ...

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.queryInputResourcePermutation SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.queryStreamingPathBamWithFileIndex STANDARD_ERROR
    INFO	2025-06-03 15:28:47	SamReaderFactoryTest	Query from data=PATH:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam;index=FILE:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai ...
    INFO	2025-06-03 15:28:47	SamReaderFactoryTest	Finished queries in 58ms

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURL STANDARD_ERROR
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLNoIndexFile STANDARD_ERROR
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLStream STANDARD_ERROR
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromMalformedSeekableStream STANDARD_ERROR
    WARNING	2025-06-03 15:28:47	SamReaderFactory	Unable to detect file format from input URL or stream, assuming SAM format.

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromSeekableStream STANDARD_ERROR
    WARNING	2025-06-03 15:28:47	SamReaderFactory	Unable to detect file format from input URL or stream, assuming SAM format.

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromURL STANDARD_ERROR
    WARNING	2025-06-03 15:28:47	SamReaderFactory	Unable to detect file format from input URL or stream, assuming SAM format.

Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[0](cram/test.cram, cram/auxf.fa, 0:12-13, Jim) STANDARD_ERROR
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[1](cram_with_bai_index.cram, hg19mini.fasta, 3:700-0, k) STANDARD_ERROR
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[2](cram_with_crai_index.cram, hg19mini.fasta, 2:350-0, i) STANDARD_ERROR
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testIterateCRAMWithIndex[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testIterateCRAMWithIndex[1](cram_with_crai_index.cram, hg19mini.fasta) STANDARD_ERROR
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testReferenceRequiredForCRAM[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testReferenceRequiredForCRAM[1](cram_with_crai_index.cram, hg19mini.fasta) STANDARD_ERROR
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testBamIntegers[1](inttest_large_coordinates.bam) STANDARD_ERROR
    WARNING	2025-06-03 15:28:47	BAMRecordCodec	Reference length is too large for BAM bin field.
    WARNING	2025-06-03 15:28:47	BAMRecordCodec	Reads on references longer than 536870912bp will have bin set to 0.

Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testSamIntegers[1](inttest_large_coordinates.sam) STANDARD_ERROR
    WARNING	2025-06-03 15:28:47	BAMRecordCodec	Reference length is too large for BAM bin field.
    WARNING	2025-06-03 15:28:47	BAMRecordCodec	Reads on references longer than 536870912bp will have bin set to 0.

Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testCRAMConversion SKIPPED

Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testSamtoolsIsAvailable SKIPPED

Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testSamtoolsVersion SKIPPED
Finished 7400 tests
Finished 7600 tests

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlockReadStreamTest.testSliceBlocksReadStreamsRoundTrip SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlocksTest.testSliceBlocksRoundTrip SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests STANDARD_ERROR
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index.

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.sliceStateTest[6]([htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772, htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111, htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0, htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f, htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee, htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d, htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c, htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb, htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a, htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09], true, UNMAPPED_UNPLACED, 0, 0) STANDARD_ERROR
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index.

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.sliceStateTest[7]([htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772, htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111, htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0, htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f, htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee, htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d, htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c, htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb, htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a, htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09], false, UNMAPPED_UNPLACED, 0, 0) STANDARD_ERROR
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:28:48	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index.

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.testValidateReferenceMD5Fails STANDARD_ERROR
    WARNING	2025-06-03 15:28:48	CRAMReferenceRegion	The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20
    WARNING	2025-06-03 15:28:48	Slice	Slice mapped outside of reference bases length 20: slice reference context=SINGLE_REFERENCE: 0, start=1, span=20, counter=0.

Gradle suite > Gradle test > htsjdk.samtools.util.SortingCollectionTest STANDARD_ERROR
    Resetting tmpdir

Gradle suite > Gradle test STANDARD_ERROR
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
Finished 7800 tests
Finished 8000 tests
Finished 8200 tests
Finished 8400 tests
Finished 8600 tests
Finished 8800 tests
Finished 9000 tests
Finished 9200 tests
Finished 9400 tests
Finished 9600 tests
Finished 9800 tests
Finished 10000 tests

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[233](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[234](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[235](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[236](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[237](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[238](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[239](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[240](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[241](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[242](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[243](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[277](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[278](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[279](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[280](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[281](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[282](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[283](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[284](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[285](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[286](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[287](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2025-06-03 15:28:51	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
Finished 10200 tests

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[511](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR
    WARNING	2025-06-03 15:29:57	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:29:57	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:29:57	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:29:57	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:29:57	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:29:57	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:29:57	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:29:57	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:29:57	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:29:57	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:29:57	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:29:57	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:29:57	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:29:57	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:29:57	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:29:57	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:29:57	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:29:57	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:29:57	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index.
    WARNING	2025-06-03 15:29:57	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index.
Finished 10400 tests

Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingMultiSampleVCF STANDARD_ERROR
    WARNING	2025-06-03 15:29:58	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSingleSampleVCF STANDARD_ERROR
    WARNING	2025-06-03 15:29:58	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSitesOnlyVCF STANDARD_ERROR
    WARNING	2025-06-03 15:29:58	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
Finished 10600 tests
Finished 10800 tests

Gradle suite > Gradle test > htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.demonstrateTestWriteToPipeDoesNotHang_1 STANDARD_ERROR
    java.lang.RuntimeException: oops
    	at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.lambda$demonstrateTestWriteToPipeDoesNotHang_1$0(VariantContextWriterBuilderUnitTest.java:497)
    	at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.lambda$testWriteToPipe$2(VariantContextWriterBuilderUnitTest.java:522)
    	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
    	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
    	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    	at java.base/java.lang.Thread.run(Thread.java:840)

Gradle suite > Gradle test > htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.demonstrateTestWriteToPipeDoesNotHang_2 STANDARD_ERROR
    java.lang.RuntimeException: oops
    	at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.lambda$demonstrateTestWriteToPipeDoesNotHang_2$1(VariantContextWriterBuilderUnitTest.java:503)
    	at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.lambda$testWriteToPipe$2(VariantContextWriterBuilderUnitTest.java:522)
    	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
    	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
    	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    	at java.base/java.lang.Thread.run(Thread.java:840)
Finished 11000 tests
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WARNING: A terminally deprecated method in java.lang.System has been called
Gradle Test Executor 3 finished executing tests.
WARNING: System::setSecurityManager has been called by org.gradle.api.internal.tasks.testing.worker.TestWorker (file:/usr/share/gradle/lib/plugins/gradle-testing-base-4.4.1.jar)
WARNING: Please consider reporting this to the maintainers of org.gradle.api.internal.tasks.testing.worker.TestWorker
WARNING: System::setSecurityManager will be removed in a future release
Finished 35600 tests
Finished 35800 tests
Results: SUCCESS (35800 tests, 35790 successes, 0 failures, 10 skipped)
Finished generating test XML results (0.274 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/test-results/test
Generating HTML test report...
Finished generating test html results (0.182 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/reports/tests/test
:test (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 11 mins 45.223 secs.

BUILD SUCCESSFUL in 23m 55s
7 actionable tasks: 5 executed, 2 up-to-date
make[1]: Leaving directory '/build/reproducible-path/htsjdk-4.1.0+dfsg'
   create-stamp debian/debhelper-build-stamp
   dh_testroot -O--buildsystem=gradle
   dh_prep -O--buildsystem=gradle
	rm -f -- debian/libhtsjdk-java.substvars debian/libhtsjdk-java-doc.substvars
	rm -fr -- debian/.debhelper/generated/libhtsjdk-java/ debian/libhtsjdk-java/ debian/tmp/ debian/.debhelper/generated/libhtsjdk-java-doc/ debian/libhtsjdk-java-doc/
   dh_auto_install -O--buildsystem=gradle
	install -m0755 -d /build/reproducible-path/htsjdk-4.1.0\+dfsg/debian/tmp
   dh_install -O--buildsystem=gradle
	install -m0755 -d debian/libhtsjdk-java/usr/share/libhtsjdk-java
	cp --reflink=auto -a ./scripts/explain_sam_flags.py debian/libhtsjdk-java/usr/share/libhtsjdk-java/
   jh_installjavadoc -O--buildsystem=gradle
	Installing javadoc from build/docs/javadoc into package libhtsjdk-java-doc
	install -m0755 -d debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java
	cp -r build/docs/javadoc debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/
	cat > debian/libhtsjdk-java-doc.doc-base.javadoc
   dh_installdocs -O--buildsystem=gradle
	install -m0755 -d debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java
	install -p -m0644 debian/libhtsjdk-java.README.Debian debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java/README.Debian
	install -p -m0644 debian/copyright debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java/copyright
	install -m0755 -d debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc
	install -p -m0644 debian/copyright debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/copyright
	install -m0755 -d debian/libhtsjdk-java-doc/usr/share/doc-base/
	install -p -m0644 debian/libhtsjdk-java-doc.doc-base.javadoc debian/libhtsjdk-java-doc/usr/share/doc-base/libhtsjdk-java-doc.libhtsjdk-java-doc
   dh_installchangelogs -O--buildsystem=gradle
	install -m0755 -d debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java
	install -p -m0644 debian/.debhelper/generated/libhtsjdk-java/dh_installchangelogs.dch.trimmed debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java/changelog.Debian
	install -m0755 -d debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc
	install -p -m0644 debian/.debhelper/generated/libhtsjdk-java-doc/dh_installchangelogs.dch.trimmed debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/changelog.Debian
   dh_installsystemduser -O--buildsystem=gradle
   dh_lintian -O--buildsystem=gradle
	install -m0755 -d debian/libhtsjdk-java-doc/usr/share/lintian/overrides
	install -p -m0644 debian/libhtsjdk-java-doc.lintian-overrides debian/libhtsjdk-java-doc/usr/share/lintian/overrides/libhtsjdk-java-doc
   dh_perl -O--buildsystem=gradle
   dh_link -O--buildsystem=gradle
	rm -f debian/libhtsjdk-java-doc.debhelper.log debian/libhtsjdk-java.debhelper.log
   debian/rules override_jh_installlibs
make[1]: Entering directory '/build/reproducible-path/htsjdk-4.1.0+dfsg'
jh_installlibs --version-strip='[+]dfsg[.0-9]*'
	install -m0755 -d debian/libhtsjdk-java/usr/share/java
	install -p -m0644 ./build/libs/htsjdk-4.1.0.jar debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.0.jar
	rm -f debian/libhtsjdk-java/usr/share/java/htsjdk.jar
	ln -s htsjdk-4.1.0.jar debian/libhtsjdk-java/usr/share/java/htsjdk.jar
make[1]: Leaving directory '/build/reproducible-path/htsjdk-4.1.0+dfsg'
   jh_classpath -O--buildsystem=gradle
	jh_manifest -plibhtsjdk-java "--classpath=/usr/share/java/commons-compress.jar /usr/share/java/commons-jexl2.jar /usr/share/java/mjson.jar /usr/share/java/ngs-java.jar /usr/share/java/rhino.jar /usr/share/java/snappy-java.jar" debian/libhtsjdk-java/usr/share/java/htsjdk.jar
	Updating symlinked /build/reproducible-path/htsjdk-4.1.0+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.0.jar (via debian/libhtsjdk-java/usr/share/java/htsjdk.jar)
	Reading manifest from /build/reproducible-path/htsjdk-4.1.0+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.0.jar
	Updating manifest in /build/reproducible-path/htsjdk-4.1.0+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.0.jar
   jh_manifest -O--buildsystem=gradle
	find debian/libhtsjdk-java  -name '*.jar'
	Found usr/share/java/htsjdk-4.1.0.jar
	Found symlink usr/share/java/htsjdk.jar
	Reading manifest from debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.0.jar
	No update of debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.0.jar required.
	find debian/libhtsjdk-java-doc  -name '*.jar'
   jh_exec -O--buildsystem=gradle
   jh_depends -O--buildsystem=gradle
Searching /build/reproducible-path/htsjdk-4.1.0+dfsg/debian/libhtsjdk-java for libhtsjdk-java
Searching /build/reproducible-path/htsjdk-4.1.0+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.0.jar
Found Jars: /usr/share/java/commons-compress.jar /usr/share/java/commons-jexl2.jar /usr/share/java/mjson.jar /usr/share/java/ngs-java.jar /usr/share/java/rhino.jar /usr/share/java/snappy-java.jar
Checking:  /build/reproducible-path/htsjdk-4.1.0+dfsg/debian/libhtsjdk-java/usr/share/java/commons-compress-1.25.0.jar
Checking:  /build/reproducible-path/htsjdk-4.1.0+dfsg/debian/libhtsjdk-java-doc/usr/share/java/commons-compress-1.25.0.jar
Checking:  /build/reproducible-path/htsjdk-4.1.0+dfsg/debian/libhtsjdk-java/usr/share/java/commons-jexl2.jar
Checking:  /build/reproducible-path/htsjdk-4.1.0+dfsg/debian/libhtsjdk-java-doc/usr/share/java/commons-jexl2.jar
Checking:  /build/reproducible-path/htsjdk-4.1.0+dfsg/debian/libhtsjdk-java/usr/share/java/mjson.jar
Checking:  /build/reproducible-path/htsjdk-4.1.0+dfsg/debian/libhtsjdk-java-doc/usr/share/java/mjson.jar
Checking:  /build/reproducible-path/htsjdk-4.1.0+dfsg/debian/libhtsjdk-java/usr/share/java/ngs-java-3.0.3.jar
Checking:  /build/reproducible-path/htsjdk-4.1.0+dfsg/debian/libhtsjdk-java-doc/usr/share/java/ngs-java-3.0.3.jar
Checking:  /build/reproducible-path/htsjdk-4.1.0+dfsg/debian/libhtsjdk-java/usr/share/java/js-1.7.14.jar
Checking:  /build/reproducible-path/htsjdk-4.1.0+dfsg/debian/libhtsjdk-java-doc/usr/share/java/js-1.7.14.jar
Checking:  /build/reproducible-path/htsjdk-4.1.0+dfsg/debian/libhtsjdk-java/usr/share/java/snappy-java-1.1.10.5.jar
Checking:  /build/reproducible-path/htsjdk-4.1.0+dfsg/debian/libhtsjdk-java-doc/usr/share/java/snappy-java-1.1.10.5.jar
Found Debs: libcommons-compress-java libcommons-jexl2-java libmjson-java libngs-java librhino-java libsnappy-java
Adding substvars: java:Depends=libcommons-compress-java,  libcommons-jexl2-java,  libmjson-java,  libngs-java,  librhino-java,  libsnappy-java java:Recommends=
Searching /build/reproducible-path/htsjdk-4.1.0+dfsg/debian/libhtsjdk-java-doc for libhtsjdk-java-doc
Searching
Found Jars:
Found Debs:
Adding substvars: java:Depends= java:Recommends=
   mh_installpoms -O--buildsystem=gradle
	mh_installpom   --package=libhtsjdk-java            --has-package-version --usj-name=htsjdk         debian/htsjdk.pom
	mh_cleanpom   --package=libhtsjdk-java    --has-package-version   --rules=debian/maven.rules  --ignore-rules=debian/maven.ignoreRules    debian/htsjdk.pom debian/.debhelper/.mh/pom.xml debian/.debhelper/.mh/pom.properties
	mv debian/.debhelper/.mh/pom.xml debian/.debhelper/.mh/htsjdk-debian.pom
	install -m 644 -D debian/.debhelper/.mh/htsjdk-3.0.2.pom debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/3.0.2/htsjdk-3.0.2.pom
	install -m 644 -D debian/.debhelper/.mh/htsjdk-debian.pom debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/debian/htsjdk-debian.pom
   mh_linkjars --skip-clean-poms -O--buildsystem=gradle
	mh_linkjar --has-package-version            --package=libhtsjdk-java    --skip-clean-pom debian/htsjdk.pom /usr/share/java/htsjdk.jar
	dh_link   -plibhtsjdk-java /usr/share/javahtsjdk.jar usr/share/maven-repo/com/github/samtools/htsjdk/3.0.2/htsjdk-3.0.2.jar
	rm -f debian/libhtsjdk-java/usr/share/java/htsjdk.jar
	ln -s htsjdk-4.1.0.jar debian/libhtsjdk-java/usr/share/java/htsjdk.jar
	install -m0755 -d debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/3.0.2
	rm -f debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/3.0.2/htsjdk-3.0.2.jar
	ln -s ../../../../../../java/htsjdk.jar debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/3.0.2/htsjdk-3.0.2.jar
	dh_link   -plibhtsjdk-java /usr/share/javahtsjdk.jar usr/share/maven-repo/com/github/samtools/htsjdk/debian/htsjdk-debian.jar
	rm -f debian/libhtsjdk-java/usr/share/java/htsjdk.jar
	ln -s htsjdk-4.1.0.jar debian/libhtsjdk-java/usr/share/java/htsjdk.jar
	rm -f debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/3.0.2/htsjdk-3.0.2.jar
	ln -s ../../../../../../java/htsjdk.jar debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/3.0.2/htsjdk-3.0.2.jar
	install -m0755 -d debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/debian
	rm -f debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/debian/htsjdk-debian.jar
	ln -s ../../../../../../java/htsjdk.jar debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/debian/htsjdk-debian.jar
   dh_strip_nondeterminism -O--buildsystem=gradle
	Using 1707687699 as canonical time
	Normalizing debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.0.jar using File::StripNondeterminism::handlers::jar
	Using 1707687699 as canonical time
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/UnsortedFileException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/CodecLineParsingException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexCreator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/MutableIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/Index.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/AbstractIndex.BlockStats.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/DynamicIndexCreator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.IndexType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/Block.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/ChrIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.IndexBalanceApproach.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/AbstractIndex.IndexType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/TribbleIndexCreator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/AbstractIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/LinearIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/LinearIndexCreator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/LinearIndex.ChrIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalTree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalIndexCreator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalTreeIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/Interval.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalTreeIndex.ChrIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixFormat.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/StreamBasedTabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndexMerger.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/AllRefsTabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Writer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.Gff3Directive.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.DecodeDepth.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3FeatureImpl.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3BaseData.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/SequenceRegion.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsDecoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/Upgradeable.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsVersion.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsContentType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/IOUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsHeader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsRecord.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsIntervalUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQuery.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsInterval.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQueryRule.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQueryInterval.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceDecoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceEncoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HapRefDecoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceDecoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceFormats.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceEncoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/VariantsResolver.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsDefaultRegistry.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/ReadsResolver.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsCodecResolver.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsCodecRegistry.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HaploidReferenceResolver.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsEncoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsDecoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsFormats.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsDecoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsEncoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsDecoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsDecoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsEncoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsQuery.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-d	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.Type.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/SimpleAllele.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeJEXLContext.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/FastGenotype.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeBuilder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/JexlMissingValueTreatment.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeLikelihoods.GenotypeLikelihoodsAllelePair.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/Allele.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeLikelihoods.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/StructuralVariantType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/SnpFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/CompoundFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/PassingVariantFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/HeterozygosityFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/VariantContextFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/FilteringIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/FilteringVariantContextIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/JavascriptVariantFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/GenotypeQualityFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.ADAccessor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.GQAccessor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.AtomicInt.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/VariantContextWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.IGFGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.Float.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.Flag.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.GenericInts.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/Options.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.StringOrCharacter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.Accessor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GTWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.FTGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.IntegerTypeGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.OutputType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GenericSiteWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriterManager.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.IntArray.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.StaticallyTypeGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/package-summary.html	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMContainerStreamWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMFileWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSortOrderChecker.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMStartingAtIteratorFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAMException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/BAIEntry.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAIIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAIEntry.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAIIndexMerger.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressorCache.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressionHeader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/ContainerHeader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SubstitutionMatrix.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/AlignmentContext.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/Slice.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/DataSeries.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CRAMEncodingStrategy.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CRAMRecordReadFeatures.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/EncodingDescriptor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SliceBlocksWriteStreams.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressionHeaderEncodingMap.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CramHeader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CRAMCompressionRecord.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/DataSeriesType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/Container.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SliceBlocks.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SliceBlocksReadStreams.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/AlignmentSpan.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/ReadTag.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/EncodingID.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/BlockCompressionMethod.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/BlockContentType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/Block.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/ContentDigests.KNOWN_DIGESTS.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/ContentDigests.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/CramVersions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/MutableInt.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cra	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFEncoderV4_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFCodecV4_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFCodecV4_2.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFEncoderV4_2.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFDecoderV4_2.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFEncoderV3_2.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFCodecV3_2.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFDecoderV3_2.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/ReadsCodecUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMDecoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMDecoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMEncoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMEncoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMCodecV2_1.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMEncoderV2_1.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMDecoderV2_1.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMDecoderV3_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMEncoderV3_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMCodecV3_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/HtsgetBAMCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/HtsgetBAMDecoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMDecoderV1_2.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMCodecV1_2.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMEncoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMDecoderOptions.html using File::StripNondeterminism::handlers::javadoc
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	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSequenceRecord.ht	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/AbstractJavascriptFilter.html using File::StripNondeterminism::handlers::javadoc
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	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/NotPrimaryAlignmentFilter.html using File::StripNondeterminism::handlers::javadoc
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	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/ReadNameFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/MappingQualityFilter.html using File::StripNondeterminism::handlers::javadoc
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	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequence.html using File::StripNondeterminism::handlers::javadoc
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	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaReferenceWriterBuilder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFileFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/SamLocusAndReferenceIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceIndexEntry.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFileWalker.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFile.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/SamLocusAndReferenceIterator.SAMLocusAndReference.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceIndexCreator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqRecord.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqEncoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqWriterFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqConstants.FastqExtensions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/AsyncFastqWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqReader.LineType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqConstants.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/BasicFastqWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/LiftOver.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/LiftOver.PartialLiftover.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/Header.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/MetricBase.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/MetricsFile.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/VersionHeader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/package-summary.html 	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FileAppendStreamLRUCache.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.DefaultingMap.Factory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/EdgingRecordAndOffset.Type.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/TrimmingUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/HttpUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/EdgeReadIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Lazy.LazyInitializer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractLocusIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractRecordAndOffset.AlignmentType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProgressLoggerInterface.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DateParser.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ResourceLimitedMap.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamLocusIterator.LocusInfo.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/RuntimeEOFException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.RevIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IOUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ReferenceSequenceMask.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DelegatingIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SortingCollection.Codec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.Node.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SAMRecordPrefetchingIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CloseableIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Tuple.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamLocusIterator.RecordAndOffset.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/TempStreamFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SequenceUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetRequest.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetPOSTRequest.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetRequestField.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetResponse.Block.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetFormat.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetResponse.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetClass.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetErrorResponse.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetMalformedResponseException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/nio/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/nio/DeleteOnExitPathHook.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/nio/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/FTPStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/FTPUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/FTPReply.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/FTPClient.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/DeflaterFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-d	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/SliceFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CompressionHeaderFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramSpanContainerIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramContainerHeaderIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramContainerIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CRAMReferenceRegion.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/ContainerFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramIO.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/Utils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/ByteArrayLenEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/CRAMCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/EncodingFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/CRAMEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/DataSeriesReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/CramRecordReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/DataSeriesWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/CramRecordWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalByteEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalByteArrayCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ByteArrayStopEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalLongEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalByteArrayEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Deletion.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/SoftClip.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/ReadBase.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/RefSkip.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Padding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/InsertBase.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/BaseQualityScore.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Scores.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/HardClip.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Bases.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Substitution.html using	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/LittleEndianOutputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/MathUtils.RunningStat.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/FTPHelper.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TPair64.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/RemoteURLHelper.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TIntv.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/URLHelper.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/HTTPHelper.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/HardyWeinbergCalculation.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/IntervalList/IntervalListCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/IntervalList/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/IntervalList/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.Exon.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDCodec.StartOffset.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.Exon2.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDFeature.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/SimpleBEDFeature.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTestUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFileValidator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.SortOrder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIterator.RecordRangeInfo.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndex.Header.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CoordinateSortedPairInfoMap.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexBuilder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMBinaryTagAndUnsignedArrayValue.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMSBIIndexer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSequenceDictionary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMCRAIIndexer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordCoordinateComparator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTag.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinList.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSequenceDictionaryCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordComparator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndexMetaData.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CustomReaderFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReaderFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileSource.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndexWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReaderFactory.Option.html using File::StripNondeterminism::handlers::javadoc
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	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DiskBackedQueue.html using File::StripNondeterminism::handlers::javadoc
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	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalList.html using File::StripNondeterminism::handlers::javadoc
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	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/PositionalOutputStream.html using File::StripNondeterminism::handlers::javadoc
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	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractProgressLogger.html using File::StripNondeterminism::handlers::javadoc
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	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/GZIIndex.GZIIndexer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Histogram.html using File::StripNondeterminism::handlers::javadoc
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	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/OverlapDetector.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CloserUtil.html using File::StripNondeterminism::handlers::javadoc
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	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ListMap.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CoordSpanInputSteam.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ComparableTuple.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-javaoc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsEncoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsFormats.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsBundle.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkIOException.html using File::StripNondeterminism::handlers::javadoc
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	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkPluginException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/FASTACodecV1_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/FASTADecoderV1_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VariantsCodecUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFEncoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFDecoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFEncoderV4_1.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFCodecV4_1.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFDecoderV4_1.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFEncoderV3_3.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFDecoderV3_3.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFCodecV3_3.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/VCFCodecV4_3.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/VCFDecoderV4_3.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFDecoderV4_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/package-tree.html using File::StripNondeterminism::handlers::javadoc
ml using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/LinearIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamIndexes.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndexMerger.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMReadGroupRecord.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SQTagUtil.SQBase.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/AbstractSAMHeaderRecord.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.GroupOrder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/TextCigarCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileWriterImpl.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMHeaderRecordComparator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/ValidationStringency.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinWithOffset.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Cigar.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFlagField.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTextHeaderCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CigarOperator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileSpan.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAFileReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BamIndexValidator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamPairUtil.PairOrientation.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/ReservedTagConstants.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndexer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CustomReaderFactory.ICustomReaderFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateScoringStrategy.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFiles.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMQueryMultipleIntervalsIteratorFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTextWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFileValidator.ValidationMetrics.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMProgramRecord.html using File::StripNondeterminism::handlers::javadoc
Gff3Constants.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Feature.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/AsciiLineReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/PositionalBufferedStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/AsciiLineReaderIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixIteratorLineReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/SynchronousLineReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.Iterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineIteratorImpl.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/Positional.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.TPair64.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.TIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LongLineBufferedReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/CountRecords.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/ProfileIndexReading.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/IndexToTable.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/IndicesAreEqual.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/ExampleBinaryCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/Strand.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/URLHelperFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/LittleEndianInputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/ParsingUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/MathUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/serialized-form.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/help-doc.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/overview-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/constant-values.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/index.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/overview-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/deprecated-list.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/allpackages-index.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/allclasses-index.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/index-all.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/resources/glass.png using File::StripNondeterminism::handlers::png
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/resources/x.png using File::StripNondeterminism::handlers::png
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Codec.SitesInfoForDecoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Decoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.Decoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Utils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2LazyGenotypesDecoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Codec.LazyData.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCFVersion.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Type.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Codec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/example/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/example/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/example/PrintVariantsExample.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/SAMSequenceDictionaryExtractor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/VCFHeaderReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/BinomialCoefficientUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/GeneralUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCompoundHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeader.HEADER_FIELDS.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFAltHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFConstants.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFIteratorBuilder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPassThruTextTransformer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFEncoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/AbstractVCFCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderVersion.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineTranslator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFSampleHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFIDHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFStandardHeaderLines.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-dom/common/CRAMVersion.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceSource.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/EnaRefService.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceContextType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/CRAMReferenceSource.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceContext.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/GaveUpException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/CRAMLazyReferenceSource.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/LTF8.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CountingInputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CramIntArray.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CRC32InputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CramInt.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/BitOutputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/ITF8.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/DefaultBitInputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/InputStreamUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/BitInputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/DefaultBitOutputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CRC32OutputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/GZIPExternalCompressor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/BZIP2ExternalCompressor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/LZMAExternalCompressor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/ExternalCompressor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/RAWExternalCompressor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/RANSExternalCompressor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/RANS.ORDER.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/RANS.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/package-summary.html using File::StripNondeterminism::handlers::javadoc
tripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMDecoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMDecoderV1_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMEncoderV1_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMCodecV1_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMDecoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMEncoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMDecoderV1_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMEncoderV1_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMCodecV1_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/IOPathUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/OutputStreamResource.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleResourceBase.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/SignatureStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/Bundle.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/IOPathResource.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/InputStreamResource.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleJSON.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleResourceType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleBuilder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/SeekableStreamResource.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleResource.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/InternalAPI.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/BetaAPI.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/package-summary.html using File::StripNondeterminism::handlers::javadoc
oc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/InflaterFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFTPStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableStreamFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFTPStreamHelper.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/ByteArraySeekableStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/ISeekableStreamFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableMemoryStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableBufferedStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/ReadableSeekableStreamByteChannel.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFileStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/UserPasswordInput.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekablePathStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableHTTPStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/TimeChannel.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/TimeRandomAccessFile.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/AsyncWriterPool.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/Writer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/IOPath.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/HtsPath.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/ValidationUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/ClassFinder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsEncoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsDecoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsEncoderOptions.html using File::StripNondeterminism::handlers::javadoc
 using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2Encoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.SiteWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.DPAccessor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/SortingVariantContextWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/AsyncVariantContextWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GenotypesWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.PLAccessor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TabixFeatureReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.CorruptedIndexFile.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AbstractFeatureReader.ComponentMethods.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/Tribble.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/BinaryFeatureCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AsciiFeatureCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/FeatureCodecHeader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.InvalidHeader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.UnableToReadIndexFile.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.MalformedFeatureFile.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AbstractFeatureCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.TabixReaderFailure.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.InvalidDecodeLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/MutableFeature.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/NameAwareCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AbstractFeatureReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.InternalCodecException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleIndexedFeatureReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/FeatureCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/FeatureReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/SimpleFeature.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.FeatureFileDoesntExist.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/Feature.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/NamedFeature.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/CloseableTribbleIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.UnableToCreateCorrectIndexType.html using File::StripNondeterminism::handlers::javadoc
using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/StringHeader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/PrintReadsExample.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/ExampleSamUsage.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAIndexedSequenceFile.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAAlignmentIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/ReferenceCache.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAAccession.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRALazyRecord.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAUnalignmentIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FormatUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CustomGzipOutputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamConstants.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.DefaultingMap.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Murmur3.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalUtil.IntervalCombiner.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Iso8601Date.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SortingLongCollection.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/GZIIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamRecordWithOrdinal.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AsyncBlockCompressedInputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/WholeGenomeReferenceSequenceMask.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IterableOnceIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractRecordAndOffset.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FileExtensions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedInputStream.FileTermination.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/QualityEncodingDetector.FileContext.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FastqQualityFormat.html using File::StripNondeterminism::handlers::javadoc
handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Bin.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.ReaderImplementation.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CSIIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.Indexing.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordQueryNameComparator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMValidationError.Type.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMBinaryTagAndValue.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateSetIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMBAIIndexer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMLineParser.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFormatException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DefaultSAMRecordFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DiskBasedBAMFileIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SecondaryAlignmentSkippingIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileReader.BAMQueryFilteringIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CigarElement.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/TextTagCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMValidationError.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.PrimitiveSamReaderToSamReaderAdapter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/MergingSamRecordIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BrowseableBAMIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexBuilder.FeatureToBeIndexed.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexContent.BinList.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BamIndexValidator.IndexValidationStringency.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Defaults.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMFileReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.PgIdGenerator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/QueryInterval.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinaryTagCodec.html using File::StripNondeterminism::handlers::javadoc
 File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/ReadFeature.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Insertion.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CoreCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/GammaIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/SubexponentialIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanByteEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/BetaIntegerCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/BetaIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanBitCode.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanParams.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanParamsCalculator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanCanoncialCodeGenerator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/GolombIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/GolombLongEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/GolombRiceIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/SecondaryOrSupplementaryFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/WholeReadClippedFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/SolexaNoiseFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/IntervalKeepPairFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/AlignedFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/InvertFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/SecondaryAlignmentFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/TagFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/FilteringSamIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/InsertSizeFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/FilteringIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/OverclippedReadFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/DuplicateReadFilter.html using File::StripNondeterminism::handlers::javadoc
/api/htsjdk/samtools/util/CigarUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/StopWatch.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Locus.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BufferedLineReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SnappyLoader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/LocationAware.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedOutputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractLocusInfo.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IterableAdapter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalList.IntervalMergerIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalListReferenceSequenceMask.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractAsyncWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamRecordTrackingBuffer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BinaryCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/RuntimeScriptException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FastLineReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Md5CalculatingInputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AsyncBufferedIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/LocusComparator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.Partitioner.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/QualityEncodingDetector.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Interval.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/LocusImpl.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProcessExecutor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.FwdIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProgressLogger.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/MergingIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Locatable.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/TestUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/PeekableIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockGunzipper.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/PeekIterator.html using File::StripNondeterminism::handlers::javadoc
c/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFormatHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCompoundHeaderLine.SupportedHeaderLineType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFRecordCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFContigHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFileReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFTextTransformer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFMetaHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineCount.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCF3Codec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFSimpleHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPercentEncodedTextTransformer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFilterHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFInfoHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPedigreeHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/CommonInfo.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextBuilder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/Genotype.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextUtils.JexlVCMatchExp.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.LazyData.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextComparator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.Validation.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypesContext.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.LazyParser.html using File::StripNondeterminism::handlers::javadoc
   dh_compress -O--buildsystem=gradle
	cd debian/libhtsjdk-java
	cd debian/libhtsjdk-java-doc
	chmod a-x usr/share/doc/libhtsjdk-java/changelog.Debian
	gzip -9nf usr/share/doc/libhtsjdk-java/changelog.Debian
	cd '/build/reproducible-path/htsjdk-4.1.0+dfsg'
	chmod a-x usr/share/doc/libhtsjdk-java-doc/changelog.Debian
	gzip -9nf usr/share/doc/libhtsjdk-java-doc/changelog.Debian
	cd '/build/reproducible-path/htsjdk-4.1.0+dfsg'
   dh_fixperms -O--buildsystem=gradle
	find debian/libhtsjdk-java ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/libhtsjdk-java-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/libhtsjdk-java/usr/share/doc -type f -a -true -a ! -regex 'debian/libhtsjdk-java/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libhtsjdk-java/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/libhtsjdk-java -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libhtsjdk-java-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/libhtsjdk-java-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libhtsjdk-java-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/libhtsjdk-java-doc/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libhtsjdk-java-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
   dh_missing -O--buildsystem=gradle
   dh_installdeb -O--buildsystem=gradle
	install -m0755 -d debian/libhtsjdk-java/DEBIAN
	install -m0755 -d debian/libhtsjdk-java-doc/DEBIAN
   dh_gencontrol -O--buildsystem=gradle
	install -m0755 -d debian/libhtsjdk-java-doc/DEBIAN
	echo misc:Depends= >> debian/libhtsjdk-java-doc.substvars
	echo misc:Pre-Depends= >> debian/libhtsjdk-java-doc.substvars
	dpkg-gencontrol -plibhtsjdk-java-doc -ldebian/changelog -Tdebian/libhtsjdk-java-doc.substvars -cdebian/control -Pdebian/libhtsjdk-java-doc
	install -m0755 -d debian/libhtsjdk-java/DEBIAN
	echo misc:Depends= >> debian/libhtsjdk-java.substvars
	echo misc:Pre-Depends= >> debian/libhtsjdk-java.substvars
	dpkg-gencontrol -plibhtsjdk-java -ldebian/changelog -Tdebian/libhtsjdk-java.substvars -cdebian/control -Pdebian/libhtsjdk-java
	chmod 0644 -- debian/libhtsjdk-java/DEBIAN/control
	chmod 0644 -- debian/libhtsjdk-java-doc/DEBIAN/control
   dh_md5sums -O--buildsystem=gradle
	install -m0755 -d debian/libhtsjdk-java/DEBIAN
	install -m0755 -d debian/libhtsjdk-java-doc/DEBIAN
	cd debian/libhtsjdk-java >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	cd debian/libhtsjdk-java-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/libhtsjdk-java/DEBIAN/md5sums
	chmod 0644 -- debian/libhtsjdk-java-doc/DEBIAN/md5sums
   dh_builddeb -O--buildsystem=gradle
	dpkg-deb --root-owner-group --build debian/libhtsjdk-java ..
	dpkg-deb --root-owner-group --build debian/libhtsjdk-java-doc ..
dpkg-deb: building package 'libhtsjdk-java' in '../libhtsjdk-java_4.1.0+dfsg-1_all.deb'.
dpkg-deb: building package 'libhtsjdk-java-doc' in '../libhtsjdk-java-doc_4.1.0+dfsg-1_all.deb'.
 dpkg-genbuildinfo --build=binary -O../htsjdk_4.1.0+dfsg-1_amd64.buildinfo
 dpkg-genchanges --build=binary -O../htsjdk_4.1.0+dfsg-1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: including full source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/787020/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/787020/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env 
I: removing directory /srv/workspace/pbuilder/787020 and its subdirectories
I: Current time: Tue Jun  3 15:31:52 +14 2025
I: pbuilder-time-stamp: 1748914312