Sat Apr 27 10:27:56 UTC 2024 I: starting to build htsjdk/trixie/arm64 on jenkins on '2024-04-27 10:27' Sat Apr 27 10:27:56 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_17/33421/console.log Sat Apr 27 10:27:56 UTC 2024 I: Downloading source for trixie/htsjdk=4.1.0+dfsg-1 --2024-04-27 10:27:56-- http://deb.debian.org/debian/pool/main/h/htsjdk/htsjdk_4.1.0%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2649 (2.6K) [text/prs.lines.tag] Saving to: ‘htsjdk_4.1.0+dfsg-1.dsc’ 0K .. 100% 333M=0s 2024-04-27 10:27:56 (333 MB/s) - ‘htsjdk_4.1.0+dfsg-1.dsc’ saved [2649/2649] Sat Apr 27 10:27:56 UTC 2024 I: htsjdk_4.1.0+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: htsjdk Binary: libhtsjdk-java, libhtsjdk-java-doc Architecture: all Version: 4.1.0+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Olivier Sallou , Vincent Danjean , Andreas Tille , Pierre Gruet Homepage: https://samtools.github.io/htsjdk/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/htsjdk Vcs-Git: https://salsa.debian.org/med-team/htsjdk.git Testsuite: autopkgtest Testsuite-Triggers: beagle, beagle-doc, chromhmm, chromhmm-example, drop-seq-testdata, drop-seq-tools, fastqc, igv, jalview, picard-tools, pilon, samtools, unzip Build-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 Package-List: libhtsjdk-java deb java optional arch=all libhtsjdk-java-doc deb doc optional arch=all Checksums-Sha1: aa5a3495d2052882432ca07dd78cae9d712024ec 46877396 htsjdk_4.1.0+dfsg.orig.tar.xz 0227e41449a8a346b2a0e708c26eba5d9f608ca9 39392 htsjdk_4.1.0+dfsg-1.debian.tar.xz Checksums-Sha256: 75be49672a4e418ec52a379cd12e86faa59b94d9641485c1346388ed27c815ee 46877396 htsjdk_4.1.0+dfsg.orig.tar.xz ba1a45ebee933ea38e822479d882cf81d9c89416352a2a2d8b7409d26c9e52cc 39392 htsjdk_4.1.0+dfsg-1.debian.tar.xz Files: cbe903b31d19abb821d95896975dca1b 46877396 htsjdk_4.1.0+dfsg.orig.tar.xz ff2eafa8c8358279b9caaecdb142de23 39392 htsjdk_4.1.0+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmXJP/0ACgkQYAMWptwn dHagIA//WRVIY5LetII5bd1Aw5Gy2qvRrNVwGq1FORlvAU+t4kxAieRjwg1Eh6Hq oryUB7ZJWOWBUAfpSqlp2cwqbv03/gPHlUMajeI5iL5Ja6US99KpSIezfwqEXIpg HWbQXWQdoytr0edZqoz5WKXhLJh46g6CL17FCbzikOh647jhUo5KTJhXY8QAVK3k irNa2SFrY4LFwv8S+kvRKhoBAkEHjf8bBFACcU0Pdn1bxlviPA47VLnNZdoGtGcF RGJFJmQi17YCG3j+I3EVHG54VLuok+DKENsIL3xFLyNJGF4zaayUqBY17FsJhOVS SZsgAtSVuA0M/fcoMl5tp7SCoqckJdnr2irrjBVachYv0YCm33HNUb1glklJIN6L pdvuEIKxpA6KhqujR4TNgvTxSZlItYiX6GdV8gLCYNZiFuDYrkoP048Hxi6eJc56 cFQNSDHhBEqhhTGWDQU0dC1yH7YsfAMPJ7G6tCujI4gc/tjECNUOGuvCaQuwHHNu ZQNSSN1k5HFfZoQU/30zx4YdFCb84xvXUu3CNInaVDEKAoKYYHfqbeQXfwsJmwsr l1CuWHNHLc3IAAoYc0YyqeVXWA+qHXdlYNRAUHnBdKe1c0mNsZ0mUBt5XQbzk/b7 Z87z0qdScpOk3LjLNuhBFp3MQ4iE6XWmipqr/+Rd13uyABPWv7I= =5wjM -----END PGP SIGNATURE----- Sat Apr 27 10:27:56 UTC 2024 I: Checking whether the package is not for us Sat Apr 27 10:27:56 UTC 2024 I: Starting 1st build on remote node codethink03-arm64.debian.net. Sat Apr 27 10:27:56 UTC 2024 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Sat Apr 27 11:09:50 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri May 30 04:50:59 -12 2025 I: pbuilder-time-stamp: 1748623859 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/2896947/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='43abbf9bafca4565a8a0f3e60bde7b3d' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2896947' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.nv8vSwtQ/pbuilderrc_9wuH --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.nv8vSwtQ/b1 --logfile b1/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+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 24 13:38 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2896947/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: arm64 Maintainer: Debian Pbuilder Team 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 ... 19937 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} libmagic1{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 55.3 MB of archives. After unpacking 400 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) libssl3 [3.1.5-1 (now)] Install the following packages: 2) adwaita-icon-theme [46.0-1 (testing)] 3) ant [1.10.14-1 (testing)] 4) ant-optional [1.10.14-1 (testing)] 5) antlr [2.7.7+dfsg-13 (testing)] 6) at-spi2-common [2.50.0-1 (testing)] 7) binfmt-support [2.2.2-7 (testing)] 8) bnd [5.0.1-5 (testing)] 9) ca-certificates [20240203 (testing)] 10) ca-certificates-java [20240118 (testing)] 11) dbus-broker [36-1 (testing)] 12) dbus-session-bus-common [1.14.10-4 (testing)] 13) dbus-system-bus-common [1.14.10-4 (testing)] 14) dbus-user-session [1.14.10-4+b1 (testing)] 15) dconf-gsettings-backend [0.40.0-4+b2 (testing)] 16) dconf-service [0.40.0-4+b2 (testing)] 17) dctrl-tools [2.24-3 (testing)] 18) default-jdk [2:1.17-75 (testing)] 19) default-jdk-headless [2:1.17-75 (testing)] 20) default-jre [2:1.17-75 (testing)] 21) default-jre-headless [2:1.17-75 (testing)] 22) devscripts [2.23.7 (testing)] 23) dmsetup [2:1.02.196-1+b1 (testing)] 24) fastjar [2:0.98-7 (testing)] 25) fontconfig [2.15.0-1.1 (testing)] 26) fontconfig-config [2.15.0-1.1 (testing)] 27) fonts-urw-base35 [20200910-8 (testing)] 28) gradle [4.4.1-20 (testing)] 29) gradle-debian-helper [2.4 (testing)] 30) groovy [2.4.21-10 (testing)] 31) gtk-update-icon-cache [3.24.41-1 (testing)] 32) hicolor-icon-theme [0.17-2 (testing)] 33) ivy [2.5.2-1 (testing)] 34) jarwrapper [0.79 (testing)] 35) java-common [0.75 (testing)] 36) java-wrappers [0.4 (testing)] 37) javahelper [0.79 (testing)] 38) junit4 [4.13.2-4 (testing)] 39) libantlr-java [2.7.7+dfsg-13 (testing)] 40) libaopalliance-java [20070526-7 (testing)] 41) libapparmor1 [3.0.13-2 (testing)] 42) libargon2-1 [0~20190702+dfsg-4+b1 (testing)] 43) libargs4j-java [2.33-2 (testing)] 44) libasm-java [9.7-1 (testing)] 45) libasound2 [1.2.10-3 (testing)] 46) libasound2-data [1.2.10-3 (testing)] 47) libatinject-jsr330-api-java [1.0+ds1-5 (testing)] 48) libatk-bridge2.0-0 [2.50.0-1+b1 (testing)] 49) libatk1.0-0 [2.50.0-1+b1 (testing)] 50) libatspi2.0-0 [2.50.0-1+b1 (testing)] 51) libavahi-client3 [0.8-13+b1 (testing)] 52) libavahi-common-data [0.8-13+b1 (testing)] 53) libavahi-common3 [0.8-13+b1 (testing)] 54) libb-hooks-op-check-perl [0.22-2+b2 (testing)] 55) libbcel-java [6.5.0-2 (testing)] 56) libbcpg-java [1.77-1 (testing)] 57) libbcprov-java [1.77-1 (testing)] 58) libbrotli1 [1.1.0-2+b3 (testing)] 59) libbsd0 [0.12.2-1 (testing)] 60) libbsf-java [1:2.4.0-8 (testing)] 61) libbsh-java [2.0b4-20 (testing)] 62) libcairo-gobject2 [1.18.0-1+b1 (testing)] 63) libcairo2 [1.18.0-1+b1 (testing)] 64) libcdi-api-java [1.2-3 (testing)] 65) libclass-method-modifiers-perl [2.15-1 (testing)] 66) libclass-xsaccessor-perl [1.19-4+b2 (testing)] 67) libclone-perl [0.46-1+b1 (testing)] 68) libcloudproviders0 [0.3.5-1 (testing)] 69) libcodemodel-java [2.6+jaxb2.3.0.1-10.1 (testing)] 70) libcolord2 [1.4.7-1+b1 (testing)] 71) libcommons-cli-java [1.6.0-1 (testing)] 72) libcommons-codec-java [1.16.0-1 (testing)] 73) libcommons-collections3-java [3.2.2-3 (testing)] 74) libcommons-io-java [2.16.0-1 (testing)] 75) libcommons-lang-java [2.6-10 (testing)] 76) libcryptsetup12 [2:2.6.1-6+b1 (testing)] 77) libcups2 [2.4.7-1+b1 (testing)] 78) libdatrie1 [0.2.13-3 (testing)] 79) libdbus-1-3 [1.14.10-4+b1 (testing)] 80) libdconf1 [0.40.0-4+b2 (testing)] 81) libdd-plist-java [1.20-1.1 (testing)] 82) libdeflate0 [1.20-1 (testing)] 83) libdevel-callchecker-perl [0.008-2+b1 (testing)] 84) libdevmapper1.02.1 [2:1.02.196-1+b1 (testing)] 85) libdom4j-java [2.1.4-1 (testing)] 86) libdrm-amdgpu1 [2.4.120-2 (testing)] 87) libdrm-common [2.4.120-2 (testing)] 88) libdrm-nouveau2 [2.4.120-2 (testing)] 89) libdrm-radeon1 [2.4.120-2 (testing)] 90) libdrm2 [2.4.120-2 (testing)] 91) libdtd-parser-java [1.2-1 (testing)] 92) libdynaloader-functions-perl [0.003-3 (testing)] 93) libeclipse-jdt-annotation-java [2.2.700+eclipse4.26-2 (testing)] 94) libedit2 [3.1-20230828-1 (testing)] 95) libel-api-java [3.0.0-3 (testing)] 96) libencode-locale-perl [1.05-3 (testing)] 97) libepoxy0 [1.5.10-1+b2 (testing)] 98) liberror-prone-java [2.18.0-1 (testing)] 99) libexpat1 [2.6.2-1 (testing)] 100) libfastinfoset-java [1.2.12-3 (testing)] 101) libfdisk1 [2.39.3-6 (testing)] 102) libfelix-framework-java [4.6.1-2.1 (testing)] 103) libfelix-gogo-runtime-java [0.16.2-1.1 (testing)] 104) libfelix-resolver-java [1.16.0-1 (testing)] 105) libfile-dirlist-perl [0.05-3 (testing)] 106) libfile-homedir-perl [1.006-2 (testing)] 107) libfile-listing-perl [6.16-1 (testing)] 108) libfile-touch-perl [0.12-2 (testing)] 109) libfile-which-perl [1.27-2 (testing)] 110) libfindbugs-java [3.1.0~preview2-3 (testing)] 111) libfontconfig1 [2.15.0-1.1 (testing)] 112) libfontenc1 [1:1.1.8-1 (testing)] 113) libfreetype6 [2.13.2+dfsg-1+b4 (testing)] 114) libfribidi0 [1.0.13-3+b1 (testing)] 115) libgdk-pixbuf-2.0-0 [2.42.10+dfsg-3+b3 (testing)] 116) libgdk-pixbuf2.0-common [2.42.10+dfsg-3 (testing)] 117) libgeronimo-annotation-1.3-spec-java [1.3-1 (testing)] 118) libgeronimo-interceptor-3.0-spec-java [1.0.1-4 (testing)] 119) libgif7 [5.2.2-1 (testing)] 120) libgl1 [1.7.0-1 (testing)] 121) libgl1-mesa-dri [23.3.5-1 (testing)] 122) libglapi-mesa [23.3.5-1 (testing)] 123) libglib2.0-0t64 [2.78.4-7 (testing)] 124) libglvnd0 [1.7.0-1 (testing)] 125) libglx-mesa0 [23.3.5-1 (testing)] 126) libglx0 [1.7.0-1 (testing)] 127) libgoogle-gson-java [2.10.1-1 (testing)] 128) libgradle-core-java [4.4.1-20 (testing)] 129) libgradle-plugins-java [4.4.1-20 (testing)] 130) libgraphite2-3 [1.3.14-2 (testing)] 131) libgtk-3-0 [3.24.41-1 (testing)] 132) libgtk-3-common [3.24.41-1 (testing)] 133) libguava-java [32.0.1-1 (testing)] 134) libguice-java [4.2.3-2 (testing)] 135) libhamcrest-java [2.2-2 (testing)] 136) libharfbuzz0b [8.3.0-2+b1 (testing)] 137) libhawtjni-runtime-java [1.18-1 (testing)] 138) libhtml-parser-perl [3.81-1+b1 (testing)] 139) libhtml-tagset-perl [3.24-1 (testing)] 140) libhtml-tree-perl [5.07-3 (testing)] 141) libhttp-cookies-perl [6.11-1 (testing)] 142) libhttp-date-perl [6.06-1 (testing)] 143) libhttp-message-perl [6.45-1 (testing)] 144) libhttp-negotiate-perl [6.01-2 (testing)] 145) libhttpclient-java [4.5.14-1 (testing)] 146) libhttpcore-java [4.4.16-1 (testing)] 147) libimport-into-perl [1.002005-2 (testing)] 148) libio-html-perl [1.004-3 (testing)] 149) libio-pty-perl [1:1.20-1 (testing)] 150) libio-socket-ssl-perl [2.085-1 (testing)] 151) libipc-run-perl [20231003.0-2 (testing)] 152) libistack-commons-java [3.0.6-5 (testing)] 153) libjansi-java [2.4.1-2 (testing)] 154) libjansi-native-java [1.8-2 (testing)] 155) libjansi1-java [1.18-3 (testing)] 156) libjarjar-java [1.4+svn142-12 (testing)] 157) libjatl-java [0.2.3-1.1 (testing)] 158) libjavaewah-java [1.2.3-1 (testing)] 159) libjaxb-java [2.3.0.1-10.1 (testing)] 160) libjaxen-java [1.1.6-4 (testing)] 161) libjbig0 [2.1-6.1+b1 (testing)] 162) libjcifs-java [1.3.19-2 (testing)] 163) libjcip-annotations-java [20060626-6 (testing)] 164) libjcommander-java [1.71-4 (testing)] 165) libjetty9-java [9.4.54-1 (testing)] 166) libjformatstring-java [0.10~20131207-2.1 (testing)] 167) libjgit-java [4.11.9-2 (testing)] 168) libjline2-java [2.14.6-5 (testing)] 169) libjna-java [5.14.0-1 (testing)] 170) libjna-jni [5.14.0-1 (testing)] 171) libjpeg62-turbo [1:2.1.5-2+b2 (testing)] 172) libjsch-java [0.1.55-1 (testing)] 173) libjson-c5 [0.17-1+b1 (testing)] 174) libjsoup-java [1.15.3-1 (testing)] 175) libjsp-api-java [2.3.4-3 (testing)] 176) libjsr305-java [0.1~+svn49-11 (testing)] 177) libjzlib-java [1.1.3-3 (testing)] 178) libkmod2 [31+20240202-2 (testing)] 179) libkryo-java [2.20-7 (testing)] 180) liblcms2-2 [2.14-2+b1 (testing)] 181) liblerc4 [4.0.0+ds-4+b1 (testing)] 182) libllvm17 [1:17.0.6-5 (testing)] 183) liblogback-java [1:1.2.11-5 (testing)] 184) liblwp-mediatypes-perl [6.04-2 (testing)] 185) liblwp-protocol-https-perl [6.14-1 (testing)] 186) libmaven-file-management-java [3.0.0-1 (testing)] 187) libmaven-parent-java [35-1 (testing)] 188) libmaven-resolver-java [1.6.3-1 (testing)] 189) libmaven-shared-io-java [3.0.0-4 (testing)] 190) libmaven-shared-utils-java [3.3.4-1 (testing)] 191) libmaven3-core-java [3.8.7-2 (testing)] 192) libminlog-java [1.3.0-1.1 (testing)] 193) libmodule-runtime-perl [0.016-2 (testing)] 194) libmoo-perl [2.005005-1 (testing)] 195) libnative-platform-java [0.14-6 (testing)] 196) libnative-platform-jni [0.14-6 (testing)] 197) libnekohtml-java [1.9.22.noko2-0.1 (testing)] 198) libnet-http-perl [6.23-1 (testing)] 199) libnet-ssleay-perl [1.94-1 (testing)] 200) libnspr4 [2:4.35-1.1+b1 (testing)] 201) libnss3 [2:3.99-1 (testing)] 202) libobjenesis-java [3.3-3 (testing)] 203) libosgi-annotation-java [8.1.0-1 (testing)] 204) libosgi-compendium-java [7.0.0-1 (testing)] 205) libosgi-core-java [8.0.0-2 (testing)] 206) libpam-systemd [255.4-1 (testing)] 207) libpango-1.0-0 [1.52.1+ds-1 (testing)] 208) libpangocairo-1.0-0 [1.52.1+ds-1 (testing)] 209) libpangoft2-1.0-0 [1.52.1+ds-1 (testing)] 210) libparams-classify-perl [0.015-2+b2 (testing)] 211) libpcsclite1 [2.0.1-1+b1 (testing)] 212) libpixman-1-0 [0.42.2-1+b1 (testing)] 213) libplexus-archiver-java [4.6.1-1 (testing)] 214) libplexus-cipher-java [2.0-1 (testing)] 215) libplexus-classworlds-java [2.7.0-1 (testing)] 216) libplexus-component-annotations-java [2.1.1-1 (testing)] 217) libplexus-container-default-java [2.1.1-1 (testing)] 218) libplexus-interpolation-java [1.26-1 (testing)] 219) libplexus-io-java [3.3.1-2 (testing)] 220) libplexus-sec-dispatcher-java [2.0-3 (testing)] 221) libplexus-utils2-java [3.4.2-1 (testing)] 222) libpng16-16t64 [1.6.43-5 (testing)] 223) libpolyglot-maven-java [0.8~tobrien+git20120905-10 (testing)] 224) libproc2-0 [2:4.0.4-4 (testing)] 225) libpython3-stdlib [3.11.6-1 (testing)] 226) libpython3.11-minimal [3.11.8-1 (testing)] 227) libpython3.11-stdlib [3.11.8-1 (testing)] 228) libqdox-java [1.12.1-3 (testing)] 229) libreflectasm-java [1.11.9+dfsg-4 (testing)] 230) librelaxng-datatype-java [1.0+ds1-3.1 (testing)] 231) librngom-java [2.3.0.1-10.1 (testing)] 232) librole-tiny-perl [2.002004-1 (testing)] 233) libsensors-config [1:3.6.0-9 (testing)] 234) libsensors5 [1:3.6.0-9 (testing)] 235) libservlet-api-java [4.0.1-2 (testing)] 236) libsharpyuv0 [1.3.2-0.4+b1 (testing)] 237) libsimple-http-java [4.1.21-1.1 (testing)] 238) libsisu-inject-java [0.3.4-2 (testing)] 239) libsisu-plexus-java [0.3.4-3 (testing)] 240) libslf4j-java [1.7.32-1 (testing)] 241) libssl3t64 [3.2.1-3 (testing)] 242) libstax-ex-java [1.7.8-3 (testing)] 243) libstreambuffer-java [1.5.4-1.1 (testing)] 244) libsub-quote-perl [2.006008-1 (testing)] 245) libsystemd-shared [255.4-1 (testing)] 246) libthai-data [0.1.29-2 (testing)] 247) libthai0 [0.1.29-2 (testing)] 248) libtiff6 [4.5.1+git230720-4 (testing)] 249) libtimedate-perl [2.3300-2 (testing)] 250) libtry-tiny-perl [0.31-2 (testing)] 251) libtxw2-java [2.3.0.1-10.1 (testing)] 252) liburi-perl [5.28-1 (testing)] 253) libvulkan1 [1.3.280.0-1 (testing)] 254) libwagon-file-java [3.5.3-1 (testing)] 255) libwagon-http-java [3.5.3-1 (testing)] 256) libwagon-provider-api-java [3.5.3-1 (testing)] 257) libwayland-client0 [1.22.0-2.1+b1 (testing)] 258) libwayland-cursor0 [1.22.0-2.1+b1 (testing)] 259) libwayland-egl1 [1.22.0-2.1+b1 (testing)] 260) libwebp7 [1.3.2-0.4+b1 (testing)] 261) libwebsocket-api-java [1.1-2 (testing)] 262) libwww-perl [6.77-1 (testing)] 263) libwww-robotrules-perl [6.02-1 (testing)] 264) libx11-6 [2:1.8.7-1 (testing)] 265) libx11-data [2:1.8.7-1 (testing)] 266) libx11-xcb1 [2:1.8.7-1 (testing)] 267) libxau6 [1:1.0.9-1 (testing)] 268) libxbean-reflect-java [4.5-8 (testing)] 269) libxcb-dri2-0 [1.15-1 (testing)] 270) libxcb-dri3-0 [1.15-1 (testing)] 271) libxcb-glx0 [1.15-1 (testing)] 272) libxcb-present0 [1.15-1 (testing)] 273) libxcb-randr0 [1.15-1 (testing)] 274) libxcb-render0 [1.15-1 (testing)] 275) libxcb-shm0 [1.15-1 (testing)] 276) libxcb-sync1 [1.15-1 (testing)] 277) libxcb-xfixes0 [1.15-1 (testing)] 278) libxcb1 [1.15-1 (testing)] 279) libxcomposite1 [1:0.4.5-1 (testing)] 280) libxcursor1 [1:1.2.1-1 (testing)] 281) libxdamage1 [1:1.1.6-1 (testing)] 282) libxdmcp6 [1:1.1.2-3 (testing)] 283) libxerces2-java [2.12.2-1 (testing)] 284) libxext6 [2:1.3.4-1+b1 (testing)] 285) libxfixes3 [1:6.0.0-2 (testing)] 286) libxi6 [2:1.8.1-1 (testing)] 287) libxinerama1 [2:1.1.4-3 (testing)] 288) libxkbcommon0 [1.6.0-1 (testing)] 289) libxml-commons-external-java [1.4.01-6 (testing)] 290) libxml-commons-resolver1.1-java [1.2-11 (testing)] 291) libxpp3-java [1.1.4c-3 (testing)] 292) libxrandr2 [2:1.5.4-1 (testing)] 293) libxrender1 [1:0.9.10-1.1 (testing)] 294) libxshmfence1 [1.3-1 (testing)] 295) libxsom-java [2.3.0.1-10.1 (testing)] 296) libxstream-java [1.4.20-1 (testing)] 297) libxtst6 [2:1.2.3-1.1 (testing)] 298) libxxf86vm1 [1:1.1.4-1+b2 (testing)] 299) libxz-java [1.9-1 (testing)] 300) libyaml-snake-java [1.33-2 (testing)] 301) libz3-4 [4.8.12-3.1+b2 (testing)] 302) maven-repo-helper [1.11 (testing)] 303) media-types [10.1.0 (testing)] 304) netbase [6.4 (testing)] 305) openjdk-17-jdk [17.0.10+7-1 (testing)] 306) openjdk-17-jdk-headless [17.0.10+7-1 (testing)] 307) openjdk-17-jre [17.0.10+7-1 (testing)] 308) openjdk-17-jre-headless [17.0.10+7-1 (testing)] 309) openssl [3.2.1-3 (testing)] 310) patchutils [0.4.2-1 (testing)] 311) perl-openssl-defaults [7+b2 (testing)] 312) procps [2:4.0.4-4 (testing)] 313) python3 [3.11.6-1 (testing)] 314) python3-minimal [3.11.6-1 (testing)] 315) python3.11 [3.11.8-1 (testing)] 316) python3.11-minimal [3.11.8-1 (testing)] 317) shared-mime-info [2.4-1 (testing)] 318) systemd [255.4-1 (testing)] 319) systemd-dev [255.4-1 (testing)] 320) systemd-sysv [255.4-1 (testing)] 321) testng [6.9.12-4 (testing)] 322) tzdata [2024a-3 (testing)] 323) unzip [6.0-28 (testing)] 324) wdiff [1.2.2-6 (testing)] 325) x11-common [1:7.7+23 (testing)] 326) xfonts-encodings [1:1.0.4-2.2 (testing)] 327) xfonts-utils [1:7.7+6 (testing)] 328) 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{a} libasound2-data{a} libassuan0{a} libatinject-jsr330-api-java{a} libatk-bridge2.0-0{a} libatk1.0-0{a} libatspi2.0-0{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} libcups2{a} libdatrie1{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-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-3-0{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} libllvm17{a} liblogback-java{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1{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} 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: 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, 404 newly installed, 1 to remove and 0 not upgraded. Need to get 344 MB of archives. After unpacking 1172 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libssl3t64 arm64 3.2.1-3 [2537 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libapparmor1 arm64 3.0.13-2 [41.0 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libargon2-1 arm64 0~20190702+dfsg-4+b1 [20.8 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 dmsetup arm64 2:1.02.196-1+b1 [75.8 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 libdevmapper1.02.1 arm64 2:1.02.196-1+b1 [117 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libjson-c5 arm64 0.17-1+b1 [43.5 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 libcryptsetup12 arm64 2:2.6.1-6+b1 [206 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libfdisk1 arm64 2.39.3-6 [192 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libkmod2 arm64 31+20240202-2 [56.0 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libsystemd-shared arm64 255.4-1 [1720 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 systemd-dev all 255.4-1 [59.7 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 systemd arm64 255.4-1 [3286 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 systemd-sysv arm64 255.4-1 [50.4 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 binfmt-support arm64 2.2.2-7 [61.4 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libpython3.11-minimal arm64 3.11.8-1 [811 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 python3.11-minimal arm64 3.11.8-1 [1848 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.11.6-1 [26.2 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-3 [255 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1781 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 python3.11 arm64 3.11.8-1 [597 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.11.6-1 [9224 B] Get: 28 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.11.6-1 [26.2 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-4 [61.7 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-4 [869 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.2.1-3 [1324 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20240203 [158 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-2+b1 [314 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libmagic1 arm64 1:5.45-2+b1 [100 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-2+b1 [43.2 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-3+b1 [1126 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 dbus-system-bus-common all 1.14.10-4 [80.1 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 dbus-broker arm64 36-1 [150 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libpam-systemd arm64 255.4-1 [242 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.39.3-6 [90.0 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.0-3 [1385 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [307 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.78.4-7 [1364 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b2 [624 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 shared-mime-info arm64 2.4-1 [747 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-2+b2 [172 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.43-5 [272 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.3.2-0.4+b1 [107 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.3.2-0.4+b1 [263 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-4 [307 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.10+dfsg-3+b3 [130 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 gtk-update-icon-cache arm64 3.24.41-1 [45.2 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 adwaita-icon-theme all 46.0-1 [614 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 ca-certificates-java all 20240118 [11.6 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 java-common all 0.75 [6640 B] Get: 64 http://deb.debian.org/debian trixie/main arm64 libavahi-common-data arm64 0.8-13+b1 [112 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libavahi-common3 arm64 0.8-13+b1 [42.4 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libdbus-1-3 arm64 1.14.10-4+b1 [195 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libavahi-client3 arm64 0.8-13+b1 [45.8 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libcups2 arm64 2.4.7-1+b1 [230 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 liblcms2-2 arm64 2.14-2+b1 [144 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.2+dfsg-1+b4 [408 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libfontenc1 arm64 1:1.1.8-1 [22.2 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23 [252 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 xfonts-utils arm64 1:7.7+6 [85.6 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 77 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libnspr4 arm64 2:4.35-1.1+b1 [101 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libnss3 arm64 2:3.99-1 [1293 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libasound2-data all 1.2.10-3 [20.7 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libasound2 arm64 1.2.10-3 [333 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 8.3.0-2+b1 [2178 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libpcsclite1 arm64 2.0.1-1+b1 [50.3 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 openjdk-17-jre-headless arm64 17.0.10+7-1 [42.7 MB] Get: 87 http://deb.debian.org/debian trixie/main arm64 default-jre-headless arm64 2:1.17-75 [3068 B] Get: 88 http://deb.debian.org/debian trixie/main arm64 ant all 1.10.14-1 [2162 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 ant-optional all 1.10.14-1 [455 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libantlr-java all 2.7.7+dfsg-13 [458 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 antlr all 2.7.7+dfsg-13 [8272 B] Get: 92 http://deb.debian.org/debian trixie/main arm64 at-spi2-common all 2.50.0-1 [163 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 unzip arm64 6.0-28 [157 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 java-wrappers all 0.4 [8916 B] Get: 100 http://deb.debian.org/debian trixie/main arm64 libhamcrest-java all 2.2-2 [121 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 junit4 all 4.13.2-4 [349 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libfelix-framework-java all 4.6.1-2.1 [569 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libfelix-gogo-runtime-java all 0.16.2-1.1 [114 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libosgi-annotation-java all 8.1.0-1 [9436 B] Get: 105 http://deb.debian.org/debian trixie/main arm64 libosgi-core-java all 8.0.0-2 [182 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libfelix-resolver-java all 1.16.0-1 [180 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libhawtjni-runtime-java all 1.18-1 [36.3 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libjansi-native-java all 1.8-2 [26.0 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libjansi1-java all 1.18-3 [66.5 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libjline2-java all 2.14.6-5 [151 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libosgi-compendium-java all 7.0.0-1 [477 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libslf4j-java all 1.7.32-1 [144 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libxz-java all 1.9-1 [143 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libyaml-snake-java all 1.33-2 [321 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 bnd all 5.0.1-5 [10.1 MB] Get: 116 http://deb.debian.org/debian trixie/main arm64 dbus-session-bus-common all 1.14.10-4 [79.0 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 dbus-user-session arm64 1.14.10-4+b1 [79.1 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libdconf1 arm64 0.40.0-4+b2 [40.4 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 dconf-service arm64 0.40.0-4+b2 [30.9 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 dconf-gsettings-backend arm64 0.40.0-4+b2 [27.2 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 dctrl-tools arm64 2.24-3 [101 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 129 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libatk1.0-0 arm64 2.50.0-1+b1 [48.2 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 libbsd0 arm64 0.12.2-1 [129 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.7-1 [772 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 libxi6 arm64 2:1.8.1-1 [77.5 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 libatspi2.0-0 arm64 2.50.0-1+b1 [70.6 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 libatk-bridge2.0-0 arm64 2.50.0-1+b1 [62.1 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.15-1 [115 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.15-1 [106 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1 [32.0 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 libcairo2 arm64 1.18.0-1+b1 [478 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 libcairo-gobject2 arm64 1.18.0-1+b1 [129 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 libcloudproviders0 arm64 0.3.5-1 [26.9 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 libcolord2 arm64 1.4.7-1+b1 [129 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 libepoxy0 arm64 1.5.10-1+b2 [199 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.13-3+b1 [71.3 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 fontconfig arm64 2.15.0-1.1 [462 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 libdatrie1 arm64 0.2.13-3 [37.2 kB] Get: 159 http://deb.debian.org/debian trixie/main arm64 libthai0 arm64 0.1.29-2 [48.0 kB] Get: 160 http://deb.debian.org/debian trixie/main arm64 libpango-1.0-0 arm64 1.52.1+ds-1 [204 kB] Get: 161 http://deb.debian.org/debian trixie/main arm64 libpangoft2-1.0-0 arm64 1.52.1+ds-1 [45.4 kB] Get: 162 http://deb.debian.org/debian trixie/main arm64 libpangocairo-1.0-0 arm64 1.52.1+ds-1 [33.1 kB] Get: 163 http://deb.debian.org/debian trixie/main arm64 libwayland-client0 arm64 1.22.0-2.1+b1 [24.8 kB] Get: 164 http://deb.debian.org/debian trixie/main arm64 libwayland-cursor0 arm64 1.22.0-2.1+b1 [11.1 kB] Get: 165 http://deb.debian.org/debian trixie/main arm64 libwayland-egl1 arm64 1.22.0-2.1+b1 [5704 B] Get: 166 http://deb.debian.org/debian trixie/main arm64 libxcomposite1 arm64 1:0.4.5-1 [16.6 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 libxfixes3 arm64 1:6.0.0-2 [22.9 kB] Get: 168 http://deb.debian.org/debian trixie/main arm64 libxcursor1 arm64 1:1.2.1-1 [40.2 kB] Get: 169 http://deb.debian.org/debian trixie/main arm64 libxdamage1 arm64 1:1.1.6-1 [15.2 kB] Get: 170 http://deb.debian.org/debian trixie/main arm64 libxinerama1 arm64 2:1.1.4-3 [17.8 kB] Get: 171 http://deb.debian.org/debian trixie/main arm64 xkb-data all 2.41-2 [795 kB] Get: 172 http://deb.debian.org/debian trixie/main arm64 libxkbcommon0 arm64 1.6.0-1 [103 kB] Get: 173 http://deb.debian.org/debian trixie/main arm64 libxrandr2 arm64 2:1.5.4-1 [35.7 kB] Get: 174 http://deb.debian.org/debian trixie/main arm64 libgtk-3-common all 3.24.41-1 [4633 kB] Get: 175 http://deb.debian.org/debian trixie/main arm64 libgtk-3-0 arm64 3.24.41-1 [2517 kB] Get: 176 http://deb.debian.org/debian trixie/main arm64 libglvnd0 arm64 1.7.0-1 [41.2 kB] Get: 177 http://deb.debian.org/debian trixie/main arm64 libdrm-common all 2.4.120-2 [7688 B] Get: 178 http://deb.debian.org/debian trixie/main arm64 libdrm2 arm64 2.4.120-2 [37.5 kB] Get: 179 http://deb.debian.org/debian trixie/main arm64 libglapi-mesa arm64 23.3.5-1 [45.5 kB] Get: 180 http://deb.debian.org/debian trixie/main arm64 libx11-xcb1 arm64 2:1.8.7-1 [232 kB] Get: 181 http://deb.debian.org/debian trixie/main arm64 libxcb-dri2-0 arm64 1.15-1 [107 kB] Get: 182 http://deb.debian.org/debian trixie/main arm64 libxcb-dri3-0 arm64 1.15-1 [107 kB] Get: 183 http://deb.debian.org/debian trixie/main arm64 libxcb-glx0 arm64 1.15-1 [123 kB] Get: 184 http://deb.debian.org/debian trixie/main arm64 libxcb-present0 arm64 1.15-1 [106 kB] Get: 185 http://deb.debian.org/debian trixie/main arm64 libxcb-randr0 arm64 1.15-1 [117 kB] Get: 186 http://deb.debian.org/debian trixie/main arm64 libxcb-sync1 arm64 1.15-1 [109 kB] Get: 187 http://deb.debian.org/debian trixie/main arm64 libxcb-xfixes0 arm64 1.15-1 [110 kB] Get: 188 http://deb.debian.org/debian trixie/main arm64 libxshmfence1 arm64 1.3-1 [8712 B] Get: 189 http://deb.debian.org/debian trixie/main arm64 libxxf86vm1 arm64 1:1.1.4-1+b2 [20.1 kB] Get: 190 http://deb.debian.org/debian trixie/main arm64 libvulkan1 arm64 1.3.280.0-1 [119 kB] Get: 191 http://deb.debian.org/debian trixie/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [21.0 kB] Get: 192 http://deb.debian.org/debian trixie/main arm64 libdrm-nouveau2 arm64 2.4.120-2 [18.7 kB] Get: 193 http://deb.debian.org/debian trixie/main arm64 libdrm-radeon1 arm64 2.4.120-2 [21.1 kB] Get: 194 http://deb.debian.org/debian trixie/main arm64 libedit2 arm64 3.1-20230828-1 [88.9 kB] Get: 195 http://deb.debian.org/debian trixie/main arm64 libz3-4 arm64 4.8.12-3.1+b2 [6508 kB] Get: 196 http://deb.debian.org/debian trixie/main arm64 libllvm17 arm64 1:17.0.6-5 [21.3 MB] Get: 197 http://deb.debian.org/debian trixie/main arm64 libsensors-config all 1:3.6.0-9 [14.6 kB] Get: 198 http://deb.debian.org/debian trixie/main arm64 libsensors5 arm64 1:3.6.0-9 [33.9 kB] Get: 199 http://deb.debian.org/debian trixie/main arm64 libgl1-mesa-dri arm64 23.3.5-1 [6928 kB] Get: 200 http://deb.debian.org/debian trixie/main arm64 libglx-mesa0 arm64 23.3.5-1 [150 kB] Get: 201 http://deb.debian.org/debian trixie/main arm64 libglx0 arm64 1.7.0-1 [30.7 kB] Get: 202 http://deb.debian.org/debian trixie/main arm64 libgl1 arm64 1.7.0-1 [90.6 kB] Get: 203 http://deb.debian.org/debian trixie/main arm64 libgif7 arm64 5.2.2-1 [43.7 kB] Get: 204 http://deb.debian.org/debian trixie/main arm64 libxtst6 arm64 2:1.2.3-1.1 [27.8 kB] Get: 205 http://deb.debian.org/debian trixie/main arm64 openjdk-17-jre arm64 17.0.10+7-1 [173 kB] Get: 206 http://deb.debian.org/debian trixie/main arm64 default-jre arm64 2:1.17-75 [1056 B] Get: 207 http://deb.debian.org/debian trixie/main arm64 openjdk-17-jdk-headless arm64 17.0.10+7-1 [70.6 MB] Get: 208 http://deb.debian.org/debian trixie/main arm64 default-jdk-headless arm64 2:1.17-75 [1108 B] Get: 209 http://deb.debian.org/debian trixie/main arm64 openjdk-17-jdk arm64 17.0.10+7-1 [2370 kB] Get: 210 http://deb.debian.org/debian trixie/main arm64 default-jdk arm64 2:1.17-75 [1068 B] Get: 211 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 212 http://deb.debian.org/debian trixie/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 213 http://deb.debian.org/debian trixie/main arm64 libjs-jquery-ui-theme-base all 1.12.1+dfsg-1.1 [44.3 kB] Get: 214 http://deb.debian.org/debian trixie/main arm64 openjdk-17-doc all 17.0.10+7-1 [12.8 MB] Get: 215 http://deb.debian.org/debian trixie/main arm64 default-jdk-doc arm64 2:1.17-75 [3148 B] Get: 216 http://deb.debian.org/debian trixie/main arm64 libassuan0 arm64 2.5.6-1 [47.3 kB] Get: 217 http://deb.debian.org/debian trixie/main arm64 gpgconf arm64 2.2.40-1.1+b1 [558 kB] Get: 218 http://deb.debian.org/debian trixie/main arm64 libksba8 arm64 1.6.6-1 [122 kB] Get: 219 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-4+b1 [20.2 kB] Get: 220 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-4+b1 [55.5 kB] Get: 221 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5+b3 [172 kB] Get: 222 http://deb.debian.org/debian trixie/main arm64 libnpth0t64 arm64 1.6-3.1 [17.8 kB] Get: 223 http://deb.debian.org/debian trixie/main arm64 dirmngr arm64 2.2.40-1.1+b1 [771 kB] Get: 224 http://deb.debian.org/debian trixie/main arm64 gnupg-l10n all 2.2.40-1.1 [1093 kB] Get: 225 http://deb.debian.org/debian trixie/main arm64 gnupg-utils arm64 2.2.40-1.1+b1 [881 kB] Get: 226 http://deb.debian.org/debian trixie/main arm64 gpg arm64 2.2.40-1.1+b1 [903 kB] Get: 227 http://deb.debian.org/debian trixie/main arm64 pinentry-curses arm64 1.2.1-3 [75.7 kB] Get: 228 http://deb.debian.org/debian trixie/main arm64 gpg-agent arm64 2.2.40-1.1+b1 [676 kB] Get: 229 http://deb.debian.org/debian trixie/main arm64 gpg-wks-client arm64 2.2.40-1.1+b1 [533 kB] Get: 230 http://deb.debian.org/debian trixie/main arm64 gpg-wks-server arm64 2.2.40-1.1+b1 [525 kB] Get: 231 http://deb.debian.org/debian trixie/main arm64 gpgsm arm64 2.2.40-1.1+b1 [650 kB] Get: 232 http://deb.debian.org/debian trixie/main arm64 gnupg all 2.2.40-1.1 [846 kB] Get: 233 http://deb.debian.org/debian trixie/main arm64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 234 http://deb.debian.org/debian trixie/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 235 http://deb.debian.org/debian trixie/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 236 http://deb.debian.org/debian trixie/main arm64 libfile-touch-perl all 0.12-2 [8816 B] Get: 237 http://deb.debian.org/debian trixie/main arm64 libio-pty-perl arm64 1:1.20-1 [33.8 kB] Get: 238 http://deb.debian.org/debian trixie/main arm64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 239 http://deb.debian.org/debian trixie/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 240 http://deb.debian.org/debian trixie/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b2 [35.2 kB] Get: 241 http://deb.debian.org/debian trixie/main arm64 libb-hooks-op-check-perl arm64 0.22-2+b2 [10.7 kB] Get: 242 http://deb.debian.org/debian trixie/main arm64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 243 http://deb.debian.org/debian trixie/main arm64 libdevel-callchecker-perl arm64 0.008-2+b1 [15.2 kB] Get: 244 http://deb.debian.org/debian trixie/main arm64 libparams-classify-perl arm64 0.015-2+b2 [22.3 kB] Get: 245 http://deb.debian.org/debian trixie/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 246 http://deb.debian.org/debian trixie/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 247 http://deb.debian.org/debian trixie/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 248 http://deb.debian.org/debian trixie/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 249 http://deb.debian.org/debian trixie/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 250 http://deb.debian.org/debian trixie/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 251 http://deb.debian.org/debian trixie/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 252 http://deb.debian.org/debian trixie/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 253 http://deb.debian.org/debian trixie/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 254 http://deb.debian.org/debian trixie/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 255 http://deb.debian.org/debian trixie/main arm64 liburi-perl all 5.28-1 [98.6 kB] Get: 256 http://deb.debian.org/debian trixie/main arm64 libhtml-parser-perl arm64 3.81-1+b1 [97.1 kB] Get: 257 http://deb.debian.org/debian trixie/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 258 http://deb.debian.org/debian trixie/main arm64 libclone-perl arm64 0.46-1+b1 [13.6 kB] Get: 259 http://deb.debian.org/debian trixie/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get: 260 http://deb.debian.org/debian trixie/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 261 http://deb.debian.org/debian trixie/main arm64 libhttp-message-perl all 6.45-1 [82.0 kB] Get: 262 http://deb.debian.org/debian trixie/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 263 http://deb.debian.org/debian trixie/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 264 http://deb.debian.org/debian trixie/main arm64 perl-openssl-defaults arm64 7+b2 [6712 B] Get: 265 http://deb.debian.org/debian trixie/main arm64 libnet-ssleay-perl arm64 1.94-1 [327 kB] Get: 266 http://deb.debian.org/debian trixie/main arm64 libio-socket-ssl-perl all 2.085-1 [218 kB] Get: 267 http://deb.debian.org/debian trixie/main arm64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 268 http://deb.debian.org/debian trixie/main arm64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 269 http://deb.debian.org/debian trixie/main arm64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 270 http://deb.debian.org/debian trixie/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 271 http://deb.debian.org/debian trixie/main arm64 libwww-perl all 6.77-1 [183 kB] Get: 272 http://deb.debian.org/debian trixie/main arm64 patchutils arm64 0.4.2-1 [73.5 kB] Get: 273 http://deb.debian.org/debian trixie/main arm64 wdiff arm64 1.2.2-6 [118 kB] Get: 274 http://deb.debian.org/debian trixie/main arm64 devscripts all 2.23.7 [1068 kB] Get: 275 http://deb.debian.org/debian trixie/main arm64 fastjar arm64 2:0.98-7 [75.5 kB] Get: 276 http://deb.debian.org/debian trixie/main arm64 ivy all 2.5.2-1 [1295 kB] Get: 277 http://deb.debian.org/debian trixie/main arm64 libasm-java all 9.7-1 [394 kB] Get: 278 http://deb.debian.org/debian trixie/main arm64 libbsf-java all 1:2.4.0-8 [76.3 kB] Get: 279 http://deb.debian.org/debian trixie/main arm64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 280 http://deb.debian.org/debian trixie/main arm64 libapache-pom-java all 29-2 [5276 B] Get: 281 http://deb.debian.org/debian trixie/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 282 http://deb.debian.org/debian trixie/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 283 http://deb.debian.org/debian trixie/main arm64 libjansi-java all 2.4.1-2 [100 kB] Get: 284 http://deb.debian.org/debian trixie/main arm64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 285 http://deb.debian.org/debian trixie/main arm64 libqdox-java all 1.12.1-3 [172 kB] Get: 286 http://deb.debian.org/debian trixie/main arm64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 287 http://deb.debian.org/debian trixie/main arm64 libxpp3-java all 1.1.4c-3 [292 kB] Get: 288 http://deb.debian.org/debian trixie/main arm64 libxstream-java all 1.4.20-1 [565 kB] Get: 289 http://deb.debian.org/debian trixie/main arm64 groovy all 2.4.21-10 [12.8 MB] Get: 290 http://deb.debian.org/debian trixie/main arm64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 291 http://deb.debian.org/debian trixie/main arm64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 292 http://deb.debian.org/debian trixie/main arm64 libcommons-compress-java all 1.25.0-1 [635 kB] Get: 293 http://deb.debian.org/debian trixie/main arm64 libcommons-io-java all 2.16.0-1 [484 kB] Get: 294 http://deb.debian.org/debian trixie/main arm64 libcommons-lang-java all 2.6-10 [273 kB] Get: 295 http://deb.debian.org/debian trixie/main arm64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 296 http://deb.debian.org/debian trixie/main arm64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 297 http://deb.debian.org/debian trixie/main arm64 libguava-java all 32.0.1-1 [2708 kB] Get: 298 http://deb.debian.org/debian trixie/main arm64 libcommons-codec-java all 1.16.0-1 [297 kB] Get: 299 http://deb.debian.org/debian trixie/main arm64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 300 http://deb.debian.org/debian trixie/main arm64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 301 http://deb.debian.org/debian trixie/main arm64 libjarjar-java all 1.4+svn142-12 [205 kB] Get: 302 http://deb.debian.org/debian trixie/main arm64 libjcip-annotations-java all 20060626-6 [11.8 kB] Get: 303 http://deb.debian.org/debian trixie/main arm64 libjna-jni arm64 5.14.0-1 [61.5 kB] Get: 304 http://deb.debian.org/debian trixie/main arm64 libjna-java all 5.14.0-1 [237 kB] Get: 305 http://deb.debian.org/debian trixie/main arm64 libjzlib-java all 1.1.3-3 [79.4 kB] Get: 306 http://deb.debian.org/debian trixie/main arm64 libjsch-java all 0.1.55-1 [298 kB] Get: 307 http://deb.debian.org/debian trixie/main arm64 libminlog-java all 1.3.0-1.1 [7928 B] Get: 308 http://deb.debian.org/debian trixie/main arm64 libobjenesis-java all 3.3-3 [41.3 kB] Get: 309 http://deb.debian.org/debian trixie/main arm64 libreflectasm-java all 1.11.9+dfsg-4 [25.0 kB] Get: 310 http://deb.debian.org/debian trixie/main arm64 libkryo-java all 2.20-7 [158 kB] Get: 311 http://deb.debian.org/debian trixie/main arm64 liblogback-java all 1:1.2.11-5 [701 kB] Get: 312 http://deb.debian.org/debian trixie/main arm64 libnative-platform-jni arm64 0.14-6 [11.4 kB] Get: 313 http://deb.debian.org/debian trixie/main arm64 libnative-platform-java all 0.14-6 [69.8 kB] Get: 314 http://deb.debian.org/debian trixie/main arm64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 315 http://deb.debian.org/debian trixie/main arm64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 316 http://deb.debian.org/debian trixie/main arm64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 317 http://deb.debian.org/debian trixie/main arm64 libnekohtml-java all 1.9.22.noko2-0.1 [125 kB] Get: 318 http://deb.debian.org/debian trixie/main arm64 libxbean-reflect-java all 4.5-8 [133 kB] Get: 319 http://deb.debian.org/debian trixie/main arm64 libgradle-core-java all 4.4.1-20 [4293 kB] Get: 320 http://deb.debian.org/debian trixie/main arm64 libbcprov-java all 1.77-1 [5300 kB] Get: 321 http://deb.debian.org/debian trixie/main arm64 libbcpg-java all 1.77-1 [428 kB] Get: 322 http://deb.debian.org/debian trixie/main arm64 libbsh-java all 2.0b4-20 [291 kB] Get: 323 http://deb.debian.org/debian trixie/main arm64 libdd-plist-java all 1.20-1.1 [72.6 kB] Get: 324 http://deb.debian.org/debian trixie/main arm64 libjaxen-java all 1.1.6-4 [214 kB] Get: 325 http://deb.debian.org/debian trixie/main arm64 libdom4j-java all 2.1.4-1 [312 kB] Get: 326 http://deb.debian.org/debian trixie/main arm64 libbcel-java all 6.5.0-2 [634 kB] Get: 327 http://deb.debian.org/debian trixie/main arm64 libjformatstring-java all 0.10~20131207-2.1 [34.5 kB] Get: 328 http://deb.debian.org/debian trixie/main arm64 libfindbugs-java all 3.1.0~preview2-3 [3502 kB] Get: 329 http://deb.debian.org/debian trixie/main arm64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 330 http://deb.debian.org/debian trixie/main arm64 libaopalliance-java all 20070526-7 [8572 B] Get: 331 http://deb.debian.org/debian trixie/main arm64 libguice-java all 4.2.3-2 [1435 kB] Get: 332 http://deb.debian.org/debian trixie/main arm64 libjatl-java all 0.2.3-1.1 [29.0 kB] Get: 333 http://deb.debian.org/debian trixie/main arm64 libjcifs-java all 1.3.19-2 [394 kB] Get: 334 http://deb.debian.org/debian trixie/main arm64 libeclipse-jdt-annotation-java all 2.2.700+eclipse4.26-2 [25.3 kB] Get: 335 http://deb.debian.org/debian trixie/main arm64 libjavaewah-java all 1.2.3-1 [159 kB] Get: 336 http://deb.debian.org/debian trixie/main arm64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 337 http://deb.debian.org/debian trixie/main arm64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 338 http://deb.debian.org/debian trixie/main arm64 libjetty9-java all 9.4.54-1 [2980 kB] Get: 339 http://deb.debian.org/debian trixie/main arm64 libjgit-java all 4.11.9-2 [2534 kB] Get: 340 http://deb.debian.org/debian trixie/main arm64 libcommons-lang3-java all 3.14.0-1 [621 kB] Get: 341 http://deb.debian.org/debian trixie/main arm64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 342 http://deb.debian.org/debian trixie/main arm64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 343 http://deb.debian.org/debian trixie/main arm64 libmaven-resolver-java all 1.6.3-1 [548 kB] Get: 344 http://deb.debian.org/debian trixie/main arm64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 345 http://deb.debian.org/debian trixie/main arm64 libmaven-parent-java all 35-1 [6140 B] Get: 346 http://deb.debian.org/debian trixie/main arm64 libmaven-shared-utils-java all 3.3.4-1 [138 kB] Get: 347 http://deb.debian.org/debian trixie/main arm64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 348 http://deb.debian.org/debian trixie/main arm64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 349 http://deb.debian.org/debian trixie/main arm64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 350 http://deb.debian.org/debian trixie/main arm64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 351 http://deb.debian.org/debian trixie/main arm64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 352 http://deb.debian.org/debian trixie/main arm64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 353 http://deb.debian.org/debian trixie/main arm64 libcdi-api-java all 1.2-3 [54.3 kB] Get: 354 http://deb.debian.org/debian trixie/main arm64 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 355 http://deb.debian.org/debian trixie/main arm64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 356 http://deb.debian.org/debian trixie/main arm64 libmaven3-core-java all 3.8.7-2 [1573 kB] Get: 357 http://deb.debian.org/debian trixie/main arm64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 358 http://deb.debian.org/debian trixie/main arm64 libpolyglot-maven-java all 0.8~tobrien+git20120905-10 [74.9 kB] Get: 359 http://deb.debian.org/debian trixie/main arm64 librhino-java all 1.7.14-2.1 [1357 kB] Get: 360 http://deb.debian.org/debian trixie/main arm64 libsimple-http-java all 4.1.21-1.1 [211 kB] Get: 361 http://deb.debian.org/debian trixie/main arm64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 362 http://deb.debian.org/debian trixie/main arm64 libjsoup-java all 1.15.3-1 [431 kB] Get: 363 http://deb.debian.org/debian trixie/main arm64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 364 http://deb.debian.org/debian trixie/main arm64 libjcommander-java all 1.71-4 [73.0 kB] Get: 365 http://deb.debian.org/debian trixie/main arm64 testng all 6.9.12-4 [795 kB] Get: 366 http://deb.debian.org/debian trixie/main arm64 libgradle-plugins-java all 4.4.1-20 [5206 kB] Get: 367 http://deb.debian.org/debian trixie/main arm64 gradle all 4.4.1-20 [398 kB] Get: 368 http://deb.debian.org/debian trixie/main arm64 maven-repo-helper all 1.11 [142 kB] Get: 369 http://deb.debian.org/debian trixie/main arm64 gradle-debian-helper all 2.4 [24.5 kB] Get: 370 http://deb.debian.org/debian trixie/main arm64 jarwrapper all 0.79 [10.1 kB] Get: 371 http://deb.debian.org/debian trixie/main arm64 javahelper all 0.79 [84.6 kB] Get: 372 http://deb.debian.org/debian trixie/main arm64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 373 http://deb.debian.org/debian trixie/main arm64 libargs4j-java all 2.33-2 [138 kB] Get: 374 http://deb.debian.org/debian trixie/main arm64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 375 http://deb.debian.org/debian trixie/main arm64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 376 http://deb.debian.org/debian trixie/main arm64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 377 http://deb.debian.org/debian trixie/main arm64 libsnappy1v5 arm64 1.1.10-1+b1 [27.1 kB] Get: 378 http://deb.debian.org/debian trixie/main arm64 libsnappy-jni arm64 1.1.10.5-2 [6440 B] Get: 379 http://deb.debian.org/debian trixie/main arm64 libsnappy-java all 1.1.10.5-2 [87.5 kB] Get: 380 http://deb.debian.org/debian trixie/main arm64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 381 http://deb.debian.org/debian trixie/main arm64 libistack-commons-java all 3.0.6-5 [145 kB] Get: 382 http://deb.debian.org/debian trixie/main arm64 libcodemodel-java all 2.6+jaxb2.3.0.1-10.1 [164 kB] Get: 383 http://deb.debian.org/debian trixie/main arm64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 384 http://deb.debian.org/debian trixie/main arm64 libdtd-parser-java all 1.2-1 [64.9 kB] Get: 385 http://deb.debian.org/debian trixie/main arm64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 386 http://deb.debian.org/debian trixie/main arm64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 387 http://deb.debian.org/debian trixie/main arm64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 388 http://deb.debian.org/debian trixie/main arm64 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB] Get: 389 http://deb.debian.org/debian trixie/main arm64 libxsom-java all 2.3.0.1-10.1 [400 kB] Get: 390 http://deb.debian.org/debian trixie/main arm64 libfastinfoset-java all 1.2.12-3 [343 kB] Get: 391 http://deb.debian.org/debian trixie/main arm64 librngom-java all 2.3.0.1-10.1 [290 kB] Get: 392 http://deb.debian.org/debian trixie/main arm64 libtxw2-java all 2.3.0.1-10.1 [134 kB] Get: 393 http://deb.debian.org/debian trixie/main arm64 libjaxb-java all 2.3.0.1-10.1 [1973 kB] Get: 394 http://deb.debian.org/debian trixie/main arm64 libjimfs-java all 1.1-6 [191 kB] Get: 395 http://deb.debian.org/debian trixie/main arm64 libmbedcrypto7t64 arm64 2.28.8-1 [269 kB] Get: 396 http://deb.debian.org/debian trixie/main arm64 libmbedx509-1t64 arm64 2.28.8-1 [131 kB] Get: 397 http://deb.debian.org/debian trixie/main arm64 libmbedtls14t64 arm64 2.28.8-1 [160 kB] Get: 398 http://deb.debian.org/debian trixie/main arm64 libmjson-java all 1.4.0-3 [60.4 kB] Get: 399 http://deb.debian.org/debian trixie/main arm64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get: 400 http://deb.debian.org/debian trixie/main arm64 libncbi-vdb3 arm64 3.0.2+dfsg-2+b1 [985 kB] Get: 401 http://deb.debian.org/debian trixie/main arm64 libncbi-ngs3 arm64 3.0.3+dfsg-6 [141 kB] Get: 402 http://deb.debian.org/debian trixie/main arm64 libngs-jni arm64 3.0.3+dfsg-6 [23.4 kB] Get: 403 http://deb.debian.org/debian trixie/main arm64 libngs-java arm64 3.0.3+dfsg-6 [110 kB] Get: 404 http://deb.debian.org/debian trixie/main arm64 scala-library all 2.11.12-5 [9588 kB] Fetched 344 MB in 4s (81.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). coreutils depends on libssl3 (>= 3.0.0). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19937 files and directories currently installed.) Removing libssl3:arm64 (3.1.5-1) ... Selecting previously unselected package libssl3t64:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19924 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.2.1-3_arm64.deb ... Unpacking libssl3t64:arm64 (3.2.1-3) ... Setting up libssl3t64:arm64 (3.2.1-3) ... Selecting previously unselected package libapparmor1:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19939 files and directories currently installed.) Preparing to unpack .../00-libapparmor1_3.0.13-2_arm64.deb ... Unpacking libapparmor1:arm64 (3.0.13-2) ... Selecting previously unselected package libargon2-1:arm64. Preparing to unpack .../01-libargon2-1_0~20190702+dfsg-4+b1_arm64.deb ... Unpacking libargon2-1:arm64 (0~20190702+dfsg-4+b1) ... Selecting previously unselected package dmsetup. Preparing to unpack .../02-dmsetup_2%3a1.02.196-1+b1_arm64.deb ... Unpacking dmsetup (2:1.02.196-1+b1) ... Selecting previously unselected package libdevmapper1.02.1:arm64. Preparing to unpack .../03-libdevmapper1.02.1_2%3a1.02.196-1+b1_arm64.deb ... Unpacking libdevmapper1.02.1:arm64 (2:1.02.196-1+b1) ... Selecting previously unselected package libjson-c5:arm64. Preparing to unpack .../04-libjson-c5_0.17-1+b1_arm64.deb ... Unpacking libjson-c5:arm64 (0.17-1+b1) ... Selecting previously unselected package libcryptsetup12:arm64. Preparing to unpack .../05-libcryptsetup12_2%3a2.6.1-6+b1_arm64.deb ... Unpacking libcryptsetup12:arm64 (2:2.6.1-6+b1) ... Selecting previously unselected package libfdisk1:arm64. Preparing to unpack .../06-libfdisk1_2.39.3-6_arm64.deb ... Unpacking libfdisk1:arm64 (2.39.3-6) ... Selecting previously unselected package libkmod2:arm64. Preparing to unpack .../07-libkmod2_31+20240202-2_arm64.deb ... Unpacking libkmod2:arm64 (31+20240202-2) ... Selecting previously unselected package libsystemd-shared:arm64. Preparing to unpack .../08-libsystemd-shared_255.4-1_arm64.deb ... Unpacking libsystemd-shared:arm64 (255.4-1) ... Selecting previously unselected package systemd-dev. Preparing to unpack .../09-systemd-dev_255.4-1_all.deb ... Unpacking systemd-dev (255.4-1) ... Selecting previously unselected package systemd. Preparing to unpack .../10-systemd_255.4-1_arm64.deb ... Unpacking systemd (255.4-1) ... Setting up libapparmor1:arm64 (3.0.13-2) ... Setting up libargon2-1:arm64 (0~20190702+dfsg-4+b1) ... Setting up libjson-c5:arm64 (0.17-1+b1) ... Setting up libfdisk1:arm64 (2.39.3-6) ... Setting up libkmod2:arm64 (31+20240202-2) ... Setting up libsystemd-shared:arm64 (255.4-1) ... Setting up systemd-dev (255.4-1) ... Setting up libdevmapper1.02.1:arm64 (2:1.02.196-1+b1) ... Setting up libcryptsetup12:arm64 (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) ... Selecting previously unselected package systemd-sysv. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21032 files and directories currently installed.) Preparing to unpack .../0-systemd-sysv_255.4-1_arm64.deb ... Unpacking systemd-sysv (255.4-1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../1-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package binfmt-support. Preparing to unpack .../2-binfmt-support_2.2.2-7_arm64.deb ... Unpacking binfmt-support (2.2.2-7) ... Selecting previously unselected package libpython3.11-minimal:arm64. Preparing to unpack .../3-libpython3.11-minimal_3.11.8-1_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../4-libexpat1_2.6.2-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../5-python3.11-minimal_3.11.8-1_arm64.deb ... Unpacking python3.11-minimal (3.11.8-1) ... Setting up libpython3.11-minimal:arm64 (3.11.8-1) ... Setting up libexpat1:arm64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.8-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21387 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.6-1_arm64.deb ... Unpacking python3-minimal (3.11.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-3_all.deb ... Unpacking tzdata (2024a-3) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../5-libreadline8t64_8.2-4_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.8-1_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.8-1_arm64.deb ... Unpacking python3.11 (3.11.8-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../8-libpython3-stdlib_3.11.6-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.6-1) ... Setting up python3-minimal (3.11.6-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 22381 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.6-1_arm64.deb ... Unpacking python3 (3.11.6-1) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-4_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-4_arm64.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package openssl. Preparing to unpack .../004-openssl_3.2.1-3_arm64.deb ... Unpacking openssl (3.2.1-3) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../005-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.45-2+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../007-libmagic1_1%3a5.45-2+b1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.45-2+b1_arm64.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../010-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../011-groff-base_1.23.0-3+b1_arm64.deb ... Unpacking groff-base (1.23.0-3+b1) ... Selecting previously unselected package dbus-system-bus-common. Preparing to unpack .../012-dbus-system-bus-common_1.14.10-4_all.deb ... Unpacking dbus-system-bus-common (1.14.10-4) ... Selecting previously unselected package dbus-broker. Preparing to unpack .../013-dbus-broker_36-1_arm64.deb ... Unpacking dbus-broker (36-1) ... Selecting previously unselected package libpam-systemd:arm64. Preparing to unpack .../014-libpam-systemd_255.4-1_arm64.deb ... Unpacking libpam-systemd:arm64 (255.4-1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../015-bsdextrautils_2.39.3-6_arm64.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package man-db. Preparing to unpack .../016-man-db_2.12.0-3_arm64.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package libgdk-pixbuf2.0-common. Preparing to unpack .../017-libgdk-pixbuf2.0-common_2.42.10+dfsg-3_all.deb ... Unpacking libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... Selecting previously unselected package libglib2.0-0t64:arm64. Preparing to unpack .../018-libglib2.0-0t64_2.78.4-7_arm64.deb ... Unpacking libglib2.0-0t64:arm64 (2.78.4-7) ... Selecting previously unselected package libicu72:arm64. 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Setting up liblcms2-2:arm64 (2.14-2+b1) ... Setting up libpixman-1-0:arm64 (0.42.2-1+b1) ... Setting up libjcommander-java (1.71-4) ... Setting up libdtd-parser-java (1.2-1) ... Setting up wdiff (1.2.2-6) ... Setting up libsharpyuv0:arm64 (1.3.2-0.4+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:arm64 (1:1.0.9-1) ... Setting up libplexus-utils2-java (3.4.2-1) ... Setting up libnpth0t64:arm64 (1.6-3.1) ... Setting up libplexus-classworlds-java (2.7.0-1) ... Setting up libqdox-java (1.12.1-3) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up liblerc4:arm64 (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:arm64 (2.28.8-1) ... Setting up java-common (0.75) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libdatrie1:arm64 (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 (1:5.45-2+b1) ... Setting up liblogback-java (1:1.2.11-5) ... Setting up libclone-perl:arm64 (0.46-1+b1) ... Setting up libminlog-java (1.3.0-1.1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglvnd0:arm64 (1.7.0-1) ... 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:arm64 (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 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 libmagic1:arm64 (1:5.45-2+b1) ... Setting up libdeflate0:arm64 (1.20-1) ... Setting up perl-openssl-defaults:arm64 (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 (1:5.45-2+b1) ... Setting up libpolyglot-maven-java (0.8~tobrien+git20120905-10) ... Setting up libfelix-gogo-runtime-java (0.16.2-1.1) ... Setting up libassuan0:arm64 (2.5.6-1) ... Setting up libjzlib-java (1.1.3-3) ... Setting up libjbig0:arm64 (2.1-6.1+b1) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up libsnappy1v5:arm64 (1.1.10-1+b1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-4+b1) ... Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' Local time is now: Fri May 30 16:53:35 UTC 2025. Universal Time is now: Fri May 30 16:53:35 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 (1.2.10-3) ... Setting up libjsch-java (0.1.55-1) ... Setting up libreflectasm-java (1.11.9+dfsg-4) ... Setting up libfontenc1:arm64 (1:1.1.8-1) ... Setting up librhino-java (1.7.14-2.1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:arm64 (4.8.12-3.1+b2) ... Setting up libglib2.0-0t64:arm64 (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 libjavaewah-java (1.2.3-1) ... Setting up libjpeg62-turbo:arm64 (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:arm64 (1.5.10-1+b2) ... Setting up libnspr4:arm64 (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:arm64 (0.8-13+b1) ... Setting up libxpp3-java (1.1.4c-3) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libdbus-1-3:arm64 (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:arm64 (1.0.13-3+b1) ... Setting up libproc2-0:arm64 (2:4.0.4-4) ... Setting up libplexus-interpolation-java (1.26-1) ... Setting up libpng16-16t64:arm64 (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:arm64 (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:arm64 (2.0.1-1+b1) ... Setting up libsensors5:arm64 (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:arm64 (23.3.5-1) ... Setting up libbsh-java (2.0b4-20) ... Setting up libjsp-api-java (2.3.4-3) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-4+b1) ... Setting up libvulkan1:arm64 (1.3.280.0-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:arm64 (1.3.2-0.4+b1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libgif7:arm64 (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:arm64 (1.3-1) ... Setting up libjsoup-java (1.15.3-1) ... Setting up at-spi2-common (2.50.0-1) ... Setting up libtiff6:arm64 (4.5.1+git230720-4) ... Setting up dbus-session-bus-common (1.14.10-4) ... Setting up libuchardet0:arm64 (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 libasound2:arm64 (1.2.10-3) ... 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 libatk1.0-0:arm64 (2.50.0-1+b1) ... Setting up libwayland-egl1:arm64 (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:arm64 (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:arm64 (2.9.14+dfsg-1.3+b2) ... 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) ... Setting up libjatl-java (0.2.3-1.1) ... Setting up libxkbcommon0:arm64 (1.6.0-1) ... Setting up libwayland-client0:arm64 (1.22.0-2.1+b1) ... Setting up libnet-ssleay-perl:arm64 (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:arm64 (1:1.1.2-3) ... Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libmbedx509-1t64:arm64 (2.28.8-1) ... Setting up libjetty9-java (9.4.54-1) ... Setting up libxcb-xfixes0:arm64 (1.15-1) ... Setting up java-wrappers (0.4) ... 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:arm64 (1.15-1) ... Setting up libstax-ex-java (1.7.8-3) ... Setting up libxcb-glx0:arm64 (1.15-1) ... Setting up libmaven-parent-java (35-1) ... Setting up libedit2:arm64 (3.1-20230828-1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:arm64 (0.8-13+b1) ... Setting up libcloudproviders0:arm64 (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:arm64 (2:3.99-1) ... Setting up libxcb-shm0:arm64 (1.15-1) ... Setting up libdevel-callchecker-perl:arm64 (0.008-2+b1) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5+b3) ... Setting up libcolord2:arm64 (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:arm64 (1.15-1) ... Setting up libdconf1:arm64 (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:arm64 (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 libfreetype6:arm64 (2.13.2+dfsg-1+b4) ... Setting up libxcb-sync1:arm64 (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:arm64 (8.2-4) ... Setting up libxcb-dri2-0:arm64 (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:arm64 (2.4.120-2) ... Setting up libjansi-native-java (1.8-2) ... Setting up libmbedtls14t64:arm64 (2.28.8-1) ... Setting up groff-base (1.23.0-3+b1) ... Setting up libwayland-cursor0:arm64 (1.22.0-2.1+b1) ... Setting up libxcb-randr0:arm64 (1.15-1) ... Setting up libhtml-parser-perl:arm64 (3.81-1+b1) ... Setting up gpgconf (2.2.40-1.1+b1) ... Setting up openjdk-17-doc (17.0.10+7-1) ... Setting up libjansi1-java (1.18-3) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libx11-6:arm64 (2:1.8.7-1) ... Setting up libharfbuzz0b:arm64 (8.3.0-2+b1) ... Setting up libgdk-pixbuf-2.0-0:arm64 (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 libllvm17:arm64 (1:17.0.6-5) ... Setting up libxcomposite1:arm64 (1:0.4.5-1) ... Setting up libavahi-client3:arm64 (0.8-13+b1) ... 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:arm64 (2.4.120-2) ... Setting up libxcb-dri3-0:arm64 (1.15-1) ... Setting up gtk-update-icon-cache (3.24.41-1) ... Setting up libx11-xcb1:arm64 (2:1.8.7-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libdrm-nouveau2:arm64 (2.4.120-2) ... Setting up libfindbugs-java (3.1.0~preview2-3) ... Setting up libxdamage1:arm64 (1:1.1.6-1) ... 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:arm64 (1:0.9.10-1.1) ... 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:arm64 (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:arm64 (3.11.8-1) ... Setting up libparams-classify-perl:arm64 (0.015-2+b2) ... Setting up gpgsm (2.2.40-1.1+b1) ... Setting up libgl1-mesa-dri:arm64 (23.3.5-1) ... Setting up libncbi-vdb3:arm64 (3.0.2+dfsg-2+b1) ... Setting up libxext6:arm64 (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:arm64 (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:arm64 (1:6.0.0-2) ... Setting up libxinerama1:arm64 (2:1.1.4-3) ... Setting up libxrandr2:arm64 (2:1.5.4-1) ... Setting up gpg-wks-server (2.2.40-1.1+b1) ... Setting up libcups2:arm64 (2.4.7-1+b1) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libpam-systemd:arm64 (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 libpython3-stdlib:arm64 (3.11.6-1) ... Setting up libncbi-ngs3:arm64 (3.0.3+dfsg-6) ... Setting up python3.11 (3.11.8-1) ... Setting up libjgit-java (4.11.9-2) ... Setting up libngs-jni:arm64 (3.0.3+dfsg-6) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libglx-mesa0:arm64 (23.3.5-1) ... Setting up libxi6:arm64 (2:1.8.1-1) ... Setting up gpg-wks-client (2.2.40-1.1+b1) ... Setting up libglx0:arm64 (1.7.0-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libxtst6:arm64 (2:1.2.3-1.1) ... Setting up libmoo-perl (2.005005-1) ... Setting up libxcursor1:arm64 (1:1.2.1-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.6-1) ... Setting up libatspi2.0-0:arm64 (2.50.0-1+b1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libatk-bridge2.0-0:arm64 (2.50.0-1+b1) ... Setting up dbus-user-session (1.14.10-4+b1) ... Setting up libgl1:arm64 (1.7.0-1) ... Setting up gnupg (2.2.40-1.1) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libngs-java:arm64 (3.0.3+dfsg-6) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up dconf-service (0.40.0-4+b2) ... Setting up libfontconfig1:arm64 (2.15.0-1.1) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up dconf-gsettings-backend:arm64 (0.40.0-4+b2) ... Setting up libpango-1.0-0:arm64 (1.52.1+ds-1) ... Setting up libcairo2:arm64 (1.18.0-1+b1) ... Setting up openjdk-17-jre-headless:arm64 (17.0.10+7-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libcairo-gobject2:arm64 (1.18.0-1+b1) ... Setting up libpangoft2-1.0-0:arm64 (1.52.1+ds-1) ... Setting up libgtk-3-common (3.24.41-1) ... Setting up libpangocairo-1.0-0:arm64 (1.52.1+ds-1) ... Setting up libgtk-3-0:arm64 (3.24.41-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... 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 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:arm64 (17.0.10+7-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/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:arm64 (17.0.10+7-1) ... Setting up maven-repo-helper (1.11) ... Setting up default-jre (2:1.17-75) ... Setting up openjdk-17-jdk:arm64 (17.0.10+7-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/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: Running cd /build/reproducible-path/htsjdk-4.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-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 dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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 "17.0.10" 2024-01-16 OpenJDK Runtime Environment (build 17.0.10+7-Debian-1) OpenJDK 64-Bit Server VM (build 17.0.10+7-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-arm64/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 3.034 secs. The client will now receive all logging from the daemon (pid: 2957809). The daemon log file: /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/daemon/4.4.1/daemon-2957809.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@41a66d06 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@41a66d06 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@402ef48c 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@2bf69304 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@625c131a 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@402ef48c 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@3fc2604d Creating new cache for outputFiles, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@335afe90 :compileJava (Thread[Task worker for ':',5,main]) started. :compileJava executing task ':compileJava' ... Putting task artifact state for task ':compileJava' into context took 0.019 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@72ad5497 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 3.28 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 ':',5,main]) completed. Took 28.041 secs. :processResources (Thread[Task worker for ':',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 0.107 secs. It is not up-to-date because: No history is available. :processResources (Thread[Task worker for ':',5,main]) completed. Took 0.175 secs. :classes (Thread[Task worker for ':',5,main]) started. :classes executing task ':classes' ... Skipping task ':classes' as it has no actions. :classes (Thread[Task worker for ':',5,main]) completed. Took 0.0 secs. :debianMavenPom (Thread[Task worker for ':',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 ':',5,main]) completed. Took 0.175 secs. :jar (Thread[Task worker for ':',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 0.079 secs. It is not up-to-date because: No history is available. :jar (Thread[Task worker for ':',5,main]) completed. Took 1.024 secs. :javadoc (Thread[Task worker for ':',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 0.513 secs. It is not up-to-date because: No history is available. Starting process 'command '/usr/lib/jvm/java-17-openjdk-arm64/bin/javadoc''. Working directory: /build/reproducible-path/htsjdk-4.1.0+dfsg Command: /usr/lib/jvm/java-17-openjdk-arm64/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-arm64/bin/javadoc'' /build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java:211: warning: invalid input: '<' * Closes inner SamIterator. ^ /build/reproducible-path/htsjdk-4.1.0+dfsg/src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java:211: warning: invalid input: '<' * Closes inner 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, not List, 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: '<' * @throws IllegalArgumentException if altAlleles 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/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 *
  • For {@link HtsContentType#FEATURES} codecs, see the {@link htsjdk.beta.plugin.features} package
    • ^ /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 *
  • For {@link HtsContentType#FEATURES} codecs, see the {@link htsjdk.beta.plugin.features} package
    • ^ /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: '<' * : ^ /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 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 ':',5,main]) completed. Took 28.799 secs. BUILD SUCCESSFUL in 1m 13s 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 "17.0.10" 2024-01-16 OpenJDK Runtime Environment (build 17.0.10+7-Debian-1) OpenJDK 64-Bit Server VM (build 17.0.10+7-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-arm64/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 1.547 secs. The client will now receive all logging from the daemon (pid: 2974789). The daemon log file: /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/daemon/4.4.1/daemon-2974789.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@47b9e517 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@47b9e517 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@5fffc5d8 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@2526b4fc 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@752ff9bf 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@5fffc5d8 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@107a9efd Creating new cache for outputFiles, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@95262cf :compileJava (Thread[Task worker for ':',5,main]) started. :compileJava executing task ':compileJava' ... Putting task artifact state for task ':compileJava' into context took 0.023 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@56f0d87a 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 2.467 secs). :compileJava UP-TO-DATE :compileJava (Thread[Task worker for ':',5,main]) completed. Took 2.774 secs. :processResources (Thread[Task worker for ':',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 0.036 secs). :processResources UP-TO-DATE :processResources (Thread[Task worker for ':',5,main]) completed. Took 0.047 secs. :classes (Thread[Task worker for ':',5,main]) started. :classes executing task ':classes' ... Skipping task ':classes' as it has no actions. :classes UP-TO-DATE :classes (Thread[Task worker for ':',5,main]) completed. Took 0.0 secs. :compileTestJava (Thread[Task worker for ':',5,main]) started. :compileTestJava executing task ':compileTestJava' ... Putting task artifact state for task ':compileTestJava' into context took 0.0 secs. 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$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:840) Malformed class file [SamFlagField.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) at org.gradle.api.internal.changedetection.state.ClasspathEntrySnapshotBuilder.visitFileSnapshot(ClasspathEntrySnapshotBuilder.java:62) at org.gradle.api.internal.changedetection.state.FileTree.visit(FileTree.java:36) at org.gradle.api.internal.changedetection.state.AbstractClasspathSnapshotBuilder.visitFileTreeSnapshot(AbstractClasspathSnapshotBuilder.java:66) at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$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$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:840) Malformed class file [SamReaderFactory$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$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:840) Malformed class file [SRALazyRecord$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$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:840) Malformed class file [SRALazyRecord$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$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:840) Malformed class file [ContentDigests$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$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:840) Malformed class file [SERIES.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) at org.gradle.api.internal.changedetection.state.ClasspathEntrySnapshotBuilder.visitFileSnapshot(ClasspathEntrySnapshotBuilder.java:62) at org.gradle.api.internal.changedetection.state.FileTree.visit(FileTree.java:36) at org.gradle.api.internal.changedetection.state.AbstractClasspathSnapshotBuilder.visitFileTreeSnapshot(AbstractClasspathSnapshotBuilder.java:66) at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$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$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:840) Malformed class file [SAMSequenceDictionaryExtractor$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$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:840) Malformed class file [BCF2Type.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) at org.gradle.api.internal.changedetection.state.ClasspathEntrySnapshotBuilder.visitFileSnapshot(ClasspathEntrySnapshotBuilder.java:62) at org.gradle.api.internal.changedetection.state.FileTree.visit(FileTree.java:36) at org.gradle.api.internal.changedetection.state.AbstractClasspathSnapshotBuilder.visitFileTreeSnapshot(AbstractClasspathSnapshotBuilder.java:66) at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$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$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:840) Malformed class file [VariantContext$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) 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 4.543 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/SAMTextWriterTest.java:88: warning: [removal] Character(char) in Character has been deprecated and marked for removal tagMap.put("XC", new Character('q')); ^ /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}, ^ 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 ':',5,main]) completed. Took 34.403 secs. :processTestResources (Thread[Task worker for ':',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 0.902 secs. It is not up-to-date because: No history is available. :processTestResources (Thread[Task worker for ':',5,main]) completed. Took 2.049 secs. :testClasses (Thread[Task worker for ':',5,main]) started. :testClasses executing task ':testClasses' ... Skipping task ':testClasses' as it has no actions. :testClasses (Thread[Task worker for ':',5,main]) completed. Took 0.001 secs. :testWithDefaultReference (Thread[Task worker for ':',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 0.563 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-arm64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false -Dsamjdk.reference_fasta=src/test/resources/htsjdk/samtools/cram/ce.fa @/tmp/gradle-worker-classpath9576976568989013566txt -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 2025-05-30 04:56:31 Defaults Found file for property samjdk.reference_fasta: /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa Finished 200 tests Finished 400 tests Finished 600 tests Finished 800 tests Finished 1000 tests Finished 1200 tests Finished 1400 tests Finished 1600 tests Finished 1800 tests Finished 2000 tests Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[74](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-05-30 04:57:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 04:57:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[75](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-05-30 04:57:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 04:57:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[76](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-05-30 04:57:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 04:57:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[77](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-05-30 04:57:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 04:57:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[78](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-05-30 04:57:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 04:57:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[79](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-05-30 04:57:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 04:57:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[80](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-05-30 04:57:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 04:57:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[81](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-05-30 04:57:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 04:57:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[82](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-05-30 04:57:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 04:57:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[83](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-05-30 04:57:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 04:57:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[84](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-05-30 04:57:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 04:57:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Finished 2200 tests Finished 2400 tests Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[354](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR WARNING 2025-05-30 04:58:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 04:58:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 04:58:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 04:58:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 04:58:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 04:58:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 04:58:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 04:58:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 04:58:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 04:58:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 04:58:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 04:58:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 04:58:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 04:58:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 04:58:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 04:58:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 04:58:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 04:58:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 04:58:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 04:58:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[462](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-05-30 04:59:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 04:59:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[463](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-05-30 04:59:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 04:59:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[464](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-05-30 04:59:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 04:59:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[465](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-05-30 04:59:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 04:59:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[466](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-05-30 04:59:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 04:59:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[467](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-05-30 04:59:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 04:59:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[468](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-05-30 04:59:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 04:59:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[469](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-05-30 04:59:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 04:59:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[470](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-05-30 04:59:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 04:59:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[471](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-05-30 04:59:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 04:59:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[472](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-05-30 04:59:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 04:59:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Finished 2600 tests Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingMultiSampleVCF STANDARD_ERROR WARNING 2025-05-30 04:59:10 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 2025-05-30 04:59:10 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 2025-05-30 04:59:10 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Finished 2800 tests Finished 3000 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 3200 tests Finished 3400 tests Finished 3600 tests Finished 3800 tests Finished 4000 tests Finished 4200 tests Finished 4400 tests Finished 4600 tests Finished 4800 tests Finished 5000 tests Finished 5200 tests Finished 5400 tests Finished 5600 tests Finished 5800 tests Finished 6000 tests Finished 6200 tests Finished 6400 tests Finished 6600 tests Finished 6800 tests Finished 7000 tests Finished 7200 tests Finished 7400 tests Finished 7600 tests 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 Finished 10200 tests Finished 10400 tests Finished 10600 tests Finished 10800 tests Finished 11000 tests Finished 11200 tests Finished 11400 tests Finished 11600 tests Finished 11800 tests Finished 12000 tests Finished 12200 tests Finished 12400 tests Finished 12600 tests Finished 12800 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: 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: 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: 1ms 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: 1ms 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: 6ms 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: 2ms 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: 11ms 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: 7ms 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: 2ms 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: 3ms 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: 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: 6ms 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: 6ms 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: 2ms 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 Finished 13000 tests 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: 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: 5ms 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: 10ms 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: 7ms 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: 8ms 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: 3ms 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 2025-05-30 05:00:11 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@7d5a135e, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR WARNING 2025-05-30 05:00:11 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 2025-05-30 05:00:11 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.voidTestLineEndingLength STANDARD_ERROR WARNING 2025-05-30 05:00:11 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 2025-05-30 05:00:11 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 13200 tests Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteBinary STANDARD_OUT #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.11998119584903580248.bai #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.12568841833897234825.bai #BAMIndexWriterTest diff /tmp/javaBai.11998119584903580248.bai /tmp/cBai.12568841833897234825.bai Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteText STANDARD_OUT #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.8327026769902833432.bai.txt #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.6375932517180698569java.bai #BAMIndexWriterTest diff /tmp/javaBai.6375932517180698569java.bai.txt /tmp/cBai.8327026769902833432.bai.txt Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.readPastEndOfFile STANDARD_OUT 0ms to write Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.timeTest STANDARD_OUT 0ms 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.3289643638295968250.gz Finished 13400 tests Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testCustomDeflater STANDARD_OUT Creating file /tmp/testCustomDeflater.5902305746787500217.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testOverflow STANDARD_OUT Creating file /tmp/BCOST.14283870085185915908.gz Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromContainer STANDARD_ERROR WARNING 2025-05-30 05:03:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:03:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromStream STANDARD_ERROR WARNING 2025-05-30 05:03:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:03:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.fullVerificationTest[0](c1#bounds) STANDARD_ERROR WARNING 2025-05-30 05:03:26 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 WARNING 2025-05-30 05:03:26 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. WARNING 2025-05-30 05:03:26 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 WARNING 2025-05-30 05:03:26 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 2025-05-30 05:03:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:03:33 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 2025-05-30 05:03:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:03:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testObsoleteDataSeriesNotWritten STANDARD_ERROR WARNING 2025-05-30 05:03:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:03:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Finished 13600 tests Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testContigNotFoundInRef STANDARD_ERROR WARNING 2025-05-30 05:03:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:03:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testNullsAndBeyondRef STANDARD_ERROR WARNING 2025-05-30 05:03:37 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 WARNING 2025-05-30 05:03:37 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. WARNING 2025-05-30 05:03:37 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 WARNING 2025-05-30 05:03:37 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 2025-05-30 05:03:37 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 WARNING 2025-05-30 05:03:37 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. WARNING 2025-05-30 05:03:37 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 WARNING 2025-05-30 05:03:37 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. Gradle is still running, please be patient... Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCRAMReader1_ReferenceRequired STANDARD_ERROR INFO 2025-05-30 05:10:22 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 2025-05-30 05:10:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:10:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCramIteratorWithoutCallingHasNextFirst STANDARD_ERROR WARNING 2025-05-30 05:10:22 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 WARNING 2025-05-30 05:10:22 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. WARNING 2025-05-30 05:10:22 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 WARNING 2025-05-30 05:10:22 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. Finished 13800 tests Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 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;@3dbc613f, [Ljava.lang.String;@3223c8aa) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.9693928866850981279.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@452f31c3, [Ljava.lang.String;@2993062) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 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 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:40 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 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 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;@41607d18, [Ljava.lang.String;@3507c5c6) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:40 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;@6170d911, [Ljava.lang.String;@2d189d85) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.9693928866850981279.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3998a17c, [Ljava.lang.String;@7d96fedd) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 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;@44e2910b, [Ljava.lang.String;@993583a) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.9693928866850981279.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@122378b6, [Ljava.lang.String;@204f8d85) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 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;@6c58e073, [Ljava.lang.String;@60fb7f66) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.9693928866850981279.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@47cda05, [Ljava.lang.String;@4f87e0ad) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 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;@63937730, [Ljava.lang.String;@31f28f8e) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.9693928866850981279.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5d4ae780, [Ljava.lang.String;@66122cc6) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 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;@1ef83c02, [Ljava.lang.String;@297182b3) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.9693928866850981279.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7f7b6e2, [Ljava.lang.String;@114e3d01) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 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;@1028d24f, [Ljava.lang.String;@5eae6069) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.9693928866850981279.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1dbfce9d, [Ljava.lang.String;@167cf0c4) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 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;@47bc8898, [Ljava.lang.String;@62c187d0) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.9693928866850981279.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@dfce521, [Ljava.lang.String;@2c510d7f) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 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;@e6e74e6, [Ljava.lang.String;@2c595d1d) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.9693928866850981279.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@11d926cc, [Ljava.lang.String;@3bb31548) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 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;@1915b605) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:40 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;@3c8dbc5c) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:40 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;@d6997ac) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:40 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;@4c753a16) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:40 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;@2a7af7a2) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:40 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;@4715d5) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:40 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;@793f90f7) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:40 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;@fc8eb32) STANDARD_ERROR WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:40 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 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:40 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 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:40 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;@c50362, [Ljava.lang.String;@51245185) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@39bd8d79, [Ljava.lang.String;@5426b02b) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.9693928866850981279.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@156c265e, [Ljava.lang.String;@5d6a636e) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:41 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;@1dd2ccdb, [Ljava.lang.String;@7ab6a94e) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.9693928866850981279.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@646cac44, [Ljava.lang.String;@468f53e9) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:41 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;@5f060936, [Ljava.lang.String;@5a7d4b63) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.9693928866850981279.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6fb35a9c, [Ljava.lang.String;@725688a5) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC 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;@96f8daf, [Ljava.lang.String;@66c79348) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.9693928866850981279.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7b87695f, [Ljava.lang.String;@584735d3) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:41 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;@45246bba, [Ljava.lang.String;@2832229e) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.9693928866850981279.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@66a9ab64, [Ljava.lang.String;@4ae72117) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:41 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;@3dad671, [Ljava.lang.String;@69f78cf) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.9693928866850981279.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@58389819, [Ljava.lang.String;@4ca5132e) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:41 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;@7dc77c59, [Ljava.lang.String;@736673de) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.9693928866850981279.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@12551235, [Ljava.lang.String;@74e639f9) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:41 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;@206f338c, [Ljava.lang.String;@69fb467) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.9693928866850981279.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6c2353af, [Ljava.lang.String;@7cfdc7f2) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:41 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;@711e90b1) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@37322581) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@4311ba09) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@3456c3f1) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@5c409645) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@5663550b) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@5dcd42d1) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@5413b22c) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@4c615b16) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@703716d7) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@7ef224e5) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@4610137d) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@350594b6) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@4f058899) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@5b1577e7) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@ac67c2f) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@7856fddf) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@f46bf85) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@4eea724a) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@2ec0fd1b) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@224ce3d8) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@43c61cc4) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@5cb220d2) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 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;@418b8c3d) STANDARD_ERROR WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Finished 14000 tests 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;@7482d983) STANDARD_ERROR WARNING 2025-05-30 05:15:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:42 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;@7ef96786) STANDARD_ERROR WARNING 2025-05-30 05:15:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:42 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;@22e62c8e) STANDARD_ERROR WARNING 2025-05-30 05:15:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:42 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;@2ce8b314) STANDARD_ERROR WARNING 2025-05-30 05:15:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:42 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;@3bf7d2df) STANDARD_ERROR WARNING 2025-05-30 05:15:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:42 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;@13e2a2be) STANDARD_ERROR WARNING 2025-05-30 05:15:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.9693928866850981279.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@3c839723) STANDARD_ERROR WARNING 2025-05-30 05:15:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:42 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;@5ac3bfc8, 5) STANDARD_ERROR WARNING 2025-05-30 05:15:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMMergerTest.test STANDARD_ERROR WARNING 2025-05-30 05:15:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:15:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.cram.ref.CRAMReferenceRegionTest.testGetReferenceBasesByRegionExceedsContigLength STANDARD_ERROR WARNING 2025-05-30 05:15:43 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 2025-05-30 05:15:43 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 2025-05-30 05:15:43 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 2025-05-30 05:15:43 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 14200 tests Finished 14400 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testAllCRAMEncodingsRoundTripThroughStream STANDARD_ERROR WARNING 2025-05-30 05:15:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testIgnoreObsoleteDataseriesOnRead STANDARD_ERROR WARNING 2025-05-30 05:15:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:15:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN 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 Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Finished 14600 tests Resetting tmpdir Gradle suite > Gradle test > htsjdk.samtools.DownsamplingIteratorTests.testBasicFunction STANDARD_ERROR Could not delete file /tmp/pbuilder1/DiskBackedQueueTest/diskbackedqueue.3371570428180606481.tmp Gradle is still running, please be patient... Finished 14800 tests Finished 15000 tests Finished 15200 tests Finished 15400 tests Finished 15600 tests Finished 15800 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 2025-05-30 05:16:01 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 2025-05-30 05:16:01 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Finished 16000 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 2025-05-30 05:16:03 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 2025-05-30 05:16:03 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 2025-05-30 05:16:03 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 2025-05-30 05:16:03 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 WARNING 2025-05-30 05:16:03 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 2025-05-30 05:16:03 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 WARNING 2025-05-30 05:16:03 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 2025-05-30 05:16:03 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 WARNING 2025-05-30 05:16:03 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombLongEncodingTest.testToString STANDARD_ERROR WARNING 2025-05-30 05:16:03 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 2025-05-30 05:16:03 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec Finished 16200 tests Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest STANDARD_ERROR WARNING 2025-05-30 05:16:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:03 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;@645c5396, [Ljava.lang.String;@3a37b5f4) STANDARD_ERROR WARNING 2025-05-30 05:16:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.12103974098132639278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5d3bee97, [Ljava.lang.String;@5c90ec36) STANDARD_ERROR WARNING 2025-05-30 05:16:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:03 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 2025-05-30 05:16:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:03 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 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:04 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;@4012e98a) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:04 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;@7d596953) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:04 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;@49ccca82) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:04 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;@729bdb47) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:04 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;@56b03736) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:04 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;@79bf9ddb) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:04 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;@7686d227) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:04 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;@14fc757e) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:04 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;@76ffa1c6, [Ljava.lang.String;@2de77e94) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:04 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;@2522c6b5, [Ljava.lang.String;@301c6aa6) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.12103974098132639278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1d0e4455, [Ljava.lang.String;@54179290) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:04 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;@6309e00c, [Ljava.lang.String;@40b1a0a5) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.12103974098132639278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@60c8ca8a, [Ljava.lang.String;@2c573f8b) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:04 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;@25e7dbb3, [Ljava.lang.String;@e981c2c) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.12103974098132639278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5d232e3f, [Ljava.lang.String;@4cdbc919) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:04 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;@5cef736d, [Ljava.lang.String;@7693815c) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.12103974098132639278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@c6a8327, [Ljava.lang.String;@5c48264a) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:04 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;@7f247a1e, [Ljava.lang.String;@26f86b77) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.12103974098132639278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3d444f22, [Ljava.lang.String;@56be66e1) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:04 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;@37d1b792, [Ljava.lang.String;@5116b4d3) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.12103974098132639278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4cce2b2e, [Ljava.lang.String;@79ab14f7) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:04 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;@78373d48, [Ljava.lang.String;@5f5b65a2) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.12103974098132639278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6defc16d, [Ljava.lang.String;@71a1196e) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:04 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;@3b320ad7, [Ljava.lang.String;@e1fea35) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.12103974098132639278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4dfac8ee, [Ljava.lang.String;@5259d0ba) STANDARD_ERROR WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:04 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 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:04 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 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:04 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 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:05 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 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 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;@4bb7645c) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:05 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;@127cca1c) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:05 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;@13f07c74) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:05 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;@2689dd91) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:05 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;@2a48a092) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:05 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;@186433af, [Ljava.lang.String;@52d867b0) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:05 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;@1bdacf4, [Ljava.lang.String;@41ddd3a1) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.12103974098132639278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@520b791c, [Ljava.lang.String;@5b5f6200) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 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;@691097fa, [Ljava.lang.String;@2cab4170) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.12103974098132639278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@64c8ec77, [Ljava.lang.String;@6cba150a) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 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;@66bb464d, [Ljava.lang.String;@dbc0e16) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.12103974098132639278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@58d4e03a, [Ljava.lang.String;@78e4dc1e) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 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;@710d1190, [Ljava.lang.String;@1d0d658c) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.12103974098132639278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7ae3ee8, [Ljava.lang.String;@43b71514) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 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;@490ba7e, [Ljava.lang.String;@466e437c) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.12103974098132639278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@188f3e71, [Ljava.lang.String;@3fa620e) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC 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;@195e7772, [Ljava.lang.String;@1fc3fad3) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.12103974098132639278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7f1d1e02, [Ljava.lang.String;@6434c068) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 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;@62802d13, [Ljava.lang.String;@8038be7) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.12103974098132639278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@209663d4, [Ljava.lang.String;@5f6d076) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 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;@f759191, [Ljava.lang.String;@548bcff8) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.12103974098132639278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4cd08cbb, [Ljava.lang.String;@217787f0) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:05 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;@67e1caab) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:05 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;@3b684afd) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:05 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;@943ec05) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:05 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;@14989392) STANDARD_ERROR WARNING 2025-05-30 05:16:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:05 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;@5e5d14b5) STANDARD_ERROR WARNING 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:06 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;@4859b616) STANDARD_ERROR WARNING 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:06 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;@7390e202) STANDARD_ERROR WARNING 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.12103974098132639278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@12cb5059) STANDARD_ERROR WARNING 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:06 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;@5e025587) STANDARD_ERROR WARNING 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:06 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;@607cb0c8) STANDARD_ERROR WARNING 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:06 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;@54375ee3) STANDARD_ERROR WARNING 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:06 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;@47d44a4) STANDARD_ERROR WARNING 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:06 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;@31095c27) STANDARD_ERROR WARNING 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:06 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;@3391b61) STANDARD_ERROR WARNING 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:06 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;@38e6e591) STANDARD_ERROR WARNING 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:06 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;@36bea67) STANDARD_ERROR WARNING 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:06 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;@32b75921) STANDARD_ERROR WARNING 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:06 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 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:06 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;@732a2016, 5) STANDARD_ERROR WARNING 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:16:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForDecodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@481686dc, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1d30545d], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR WARNING 2025-05-30 05:16:06 HtsCodecResolver The specified format string (BOGUS_FORMAT) does not correspond to any registered codec for content type (ALIGNED_READS) Finished 16400 tests 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 2025-05-30 05:16:06 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@26c58a0d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@5d6c08f7, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4050dbb8, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@3b9f611a, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@5033fe61], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR WARNING 2025-05-30 05:16:06 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@26c58a0d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@5d6c08f7, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4050dbb8, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@3b9f611a, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@5033fe61], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR WARNING 2025-05-30 05:16:06 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@26c58a0d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@5d6c08f7, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4050dbb8, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@3b9f611a, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@5033fe61], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR WARNING 2025-05-30 05:16:06 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) Finished 16600 tests some stuffFinished 16800 tests Finished 17000 tests Gradle suite > Gradle test > htsjdk.samtools.util.IOUtilTest.testDeleteSingleWithDeletePaths STANDARD_ERROR Could not delete file tmp Could not delete file file10784581057765622721.bad Finished 17200 tests Gradle suite > Gradle test > htsjdk.samtools.util.IntervalTreeTest.performanceTest STANDARD_OUT Time to construct a tree with 50000 nodes: 31 milliseconds Queried for the same 100-length mapping 196131250 times in 10 seconds. Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR INFO 2025-05-30 05:16:19 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Finished 17400 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[279](chr2:111013693-111013832 + ., null) STANDARD_ERROR INFO 2025-05-30 05:16:19 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) INFO 2025-05-30 05:16:19 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 2025-05-30 05:16:19 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 2025-05-30 05:16:19 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 2025-05-30 05:16:19 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 2025-05-30 05:16:19 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 2025-05-30 05:16:19 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 2025-05-30 05:16:19 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 2025-05-30 05:16:19 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 2025-05-30 05:16:19 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) INFO 2025-05-30 05:16:19 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 2025-05-30 05:16:19 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 2025-05-30 05:16:19 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) INFO 2025-05-30 05:16:19 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 2025-05-30 05:16:19 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) INFO 2025-05-30 05:16:19 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 2025-05-30 05:16:19 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) Finished 17600 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR INFO 2025-05-30 05:16:19 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Finished 17800 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[279](chr2:111013693-111013832 + ., null) STANDARD_ERROR INFO 2025-05-30 05:16:19 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) INFO 2025-05-30 05:16:19 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 2025-05-30 05:16:19 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 2025-05-30 05:16:19 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 2025-05-30 05:16:19 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 2025-05-30 05:16:19 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 2025-05-30 05:16:19 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 2025-05-30 05:16:19 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 2025-05-30 05:16:19 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 2025-05-30 05:16:19 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) INFO 2025-05-30 05:16:19 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 2025-05-30 05:16:19 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 2025-05-30 05:16:19 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) INFO 2025-05-30 05:16:19 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 2025-05-30 05:16:19 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) INFO 2025-05-30 05:16:19 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 2025-05-30 05:16:19 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.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 18000 tests Finished 18200 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testLiftoverCounter[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR INFO 2025-05-30 05:16:19 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Finished 18400 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 a d e c Finished 18600 tests Finished 18800 tests Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[0](@HD VN:1.0 SO:UNSORTED ) STANDARD_ERROR WARNING 2025-05-30 05:16:51 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 2025-05-30 05:16:51 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 2025-05-30 05:16:51 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 2025-05-30 05:16:51 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 2025-05-30 05:16:51 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.specialFileWriterTest STANDARD_ERROR WARNING 2025-05-30 05:16:51 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null WARNING 2025-05-30 05:16:51 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 2025-05-30 05:16:51 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.776926112161225548..cram INFO 2025-05-30 05:16:51 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-05-30 05:16:51 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): src/test/resources/htsjdk/samtools/cram/ce.fa INFO 2025-05-30 05:16:51 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false INFO 2025-05-30 05:16:51 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 2025-05-30 05:16:51 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension15305882073645600232.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.9100354420730741667.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 2025-05-30 05:16:51 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension13039686395964460801.cram INFO 2025-05-30 05:16:51 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-05-30 05:16:51 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): src/test/resources/htsjdk/samtools/cram/ce.fa INFO 2025-05-30 05:16:51 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false INFO 2025-05-30 05:16:51 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 2025-05-30 05:16:51 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension16921213600533201427 Finished 19000 tests Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForUnknownFileExtension STANDARD_ERROR INFO 2025-05-30 05:16:51 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension15569012167650153155.png Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[0](sam) STANDARD_ERROR INFO 2025-05-30 05:16:51 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://c918d32a-45ab-41ae-b88a-db0ea632935d/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 2025-05-30 05:16:51 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://60472e09-b792-4239-acbe-3cd151dd9eec/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 2025-05-30 05:16:51 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://c415f62c-7e08-43a1-bb34-c734fbfbb4c5/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 2025-05-30 05:16:51 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://c111e770-d257-44d7-86d1-d0d9cd374df3/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 2025-05-30 05:16:51 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://b387f2ed-0eab-4517-ba45-6cc382cafdf8/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 2025-05-30 05:16:51 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://882ad330-4238-491d-b125-faaf4138d17a/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 19200 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 2025-05-30 05:17:05 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 Finished 19400 tests 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 2025-05-30 05:17:06 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 2025-05-30 05:17:06 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 Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.customReaderFactoryTest STANDARD_ERROR INFO 2025-05-30 05:17:07 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory INFO 2025-05-30 05:17:07 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory INFO 2025-05-30 05:17:07 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar INFO 2025-05-30 05:17:07 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 2025-05-30 05:17:07 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 2025-05-30 05:17:07 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 2025-05-30 05:17:07 SamReaderFactoryTest Finished queries in 55ms Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURL STANDARD_ERROR WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLNoIndexFile STANDARD_ERROR WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLStream STANDARD_ERROR WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromMalformedSeekableStream STANDARD_ERROR WARNING 2025-05-30 05:17:07 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 2025-05-30 05:17:07 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 2025-05-30 05:17:07 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 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:17:07 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 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:17:07 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 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Finished 19600 tests Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testIterateCRAMWithIndex[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:17:07 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 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:17:07 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 2025-05-30 05:17:07 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 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:17:07 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 2025-05-30 05:17:07 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 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:17:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testBamIntegers[1](inttest_large_coordinates.bam) STANDARD_ERROR WARNING 2025-05-30 05:17:07 BAMRecordCodec Reference length is too large for BAM bin field. WARNING 2025-05-30 05:17:07 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 2025-05-30 05:17:07 BAMRecordCodec Reference length is too large for BAM bin field. WARNING 2025-05-30 05:17:07 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 19800 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlockReadStreamTest.testSliceBlocksReadStreamsRoundTrip SKIPPED Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlocksTest.testSliceBlocksRoundTrip SKIPPED Finished 20000 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests STANDARD_ERROR WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 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 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 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 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:17:08 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 2025-05-30 05:17:08 CRAMReferenceRegion The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20 WARNING 2025-05-30 05:17:08 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 20200 tests Finished 20400 tests Finished 20600 tests Finished 20800 tests Finished 21000 tests Finished 21200 tests Finished 21400 tests Finished 21600 tests Finished 21800 tests Finished 22000 tests Finished 22200 tests Finished 22400 tests Finished 22600 tests Finished 22800 tests Finished 23000 tests Finished 23200 tests Finished 23400 tests Finished 23600 tests Finished 23800 tests Finished 24000 tests Finished 24200 tests Finished 24400 tests Finished 24600 tests Finished 24800 tests Finished 25000 tests Finished 25200 tests Finished 25400 tests Finished 25600 tests Finished 25800 tests Finished 26000 tests Finished 26200 tests Finished 26400 tests Finished 26600 tests Finished 26800 tests Finished 27000 tests Finished 27200 tests Finished 27400 tests Finished 27600 tests Finished 27800 tests Finished 28000 tests Finished 28200 tests Finished 28400 tests Finished 28600 tests Finished 28800 tests Finished 29000 tests Finished 29200 tests Finished 29400 tests Finished 29600 tests Finished 29800 tests Finished 30000 tests Finished 30200 tests Finished 30400 tests Finished 30600 tests Finished 30800 tests Finished 31000 tests Finished 31200 tests Finished 31400 tests Finished 31600 tests Finished 31800 tests Finished 32000 tests Finished 32200 tests Finished 32400 tests Finished 32600 tests Finished 32800 tests Finished 33000 tests Finished 33200 tests Finished 33400 tests Finished 33600 tests Finished 33800 tests Finished 34000 tests Finished 34200 tests Finished 34400 tests Finished 34600 tests Finished 34800 tests Finished 35000 tests Finished 35200 tests Finished 35400 tests Finished 35600 tests Finished 35800 tests 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 (0.228 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/test-results/testWithDefaultReference Generating HTML test report... Finished generating test html results (0.315 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/reports/tests/testWithDefaultReference :testWithDefaultReference (Thread[Task worker for ':',5,main]) completed. Took 20 mins 44.791 secs. :testWithOptimisticVCF4_4 (Thread[Task worker for ':',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 0.047 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-arm64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false -Dsamjdk.optimistic_vcf_4_4=true @/tmp/gradle-worker-classpath8995434759570513628txt -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 (0.003 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/reports/tests/testWithOptimisticVCF4_4 :testWithOptimisticVCF4_4 (Thread[Task worker for ':',5,main]) completed. Took 2.032 secs. :test (Thread[Task worker for ':',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 0.098 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-arm64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false @/tmp/gradle-worker-classpath10314795968370892853txt -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. Finished 200 tests Finished 400 tests Finished 600 tests Finished 800 tests Finished 1000 tests Finished 1200 tests Finished 1400 tests Finished 1600 tests Finished 1800 tests Finished 2000 tests Finished 2200 tests Finished 2400 tests Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[295](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[296](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[297](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[298](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[299](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[300](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[301](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[302](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[303](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[304](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[305](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[347](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[348](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[349](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[350](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[351](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[352](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[353](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[354](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[355](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[356](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[357](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:18:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[477](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR WARNING 2025-05-30 05:18:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:18:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:18:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:18:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:18:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:18:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:18:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:18:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:18:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:18:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:18:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:18:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:18:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:18:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:18:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:18:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:18:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:18:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:18:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:18:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. Finished 2600 tests Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingMultiSampleVCF STANDARD_ERROR WARNING 2025-05-30 05:18:46 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 2025-05-30 05:18:46 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 2025-05-30 05:18:46 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Finished 2800 tests Finished 3000 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 3200 tests Finished 3400 tests Finished 3600 tests Finished 3800 tests Finished 4000 tests Finished 4200 tests Finished 4400 tests Finished 4600 tests Finished 4800 tests Finished 5000 tests Finished 5200 tests Finished 5400 tests Finished 5600 tests Finished 5800 tests Finished 6000 tests Finished 6200 tests Finished 6400 tests Finished 6600 tests Finished 6800 tests Finished 7000 tests Finished 7200 tests Finished 7400 tests Finished 7600 tests 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 Finished 10200 tests Finished 10400 tests Finished 10600 tests Finished 10800 tests Finished 11000 tests Finished 11200 tests Finished 11400 tests Finished 11600 tests Finished 11800 tests Finished 12000 tests Finished 12200 tests Finished 12400 tests Finished 12600 tests Finished 12800 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: 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: 1ms 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: 4ms 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: 4ms 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: 2ms 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: 8ms 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: 15ms 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: 7ms 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: 5ms 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: 3ms 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: 0ms 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: 3ms 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: 6ms 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: 6ms 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: 2ms 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 Finished 13000 tests 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: 1ms 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: 7ms 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: 7ms 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: 7ms 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: 3ms 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: 3ms Gradle suite > Gradle test > htsjdk.tribble.AsciiFeatureCodecTest.testMakeIndexableSourceFromUnknownStream STANDARD_ERROR WARNING 2025-05-30 05:20:02 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@6dcaa298, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR WARNING 2025-05-30 05:20:02 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 2025-05-30 05:20:02 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.voidTestLineEndingLength STANDARD_ERROR WARNING 2025-05-30 05:20:02 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 2025-05-30 05:20:02 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 13200 tests Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteBinary STANDARD_OUT #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.17664845213816090149.bai #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.5483970478964677291.bai #BAMIndexWriterTest diff /tmp/javaBai.17664845213816090149.bai /tmp/cBai.5483970478964677291.bai Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteText STANDARD_OUT #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.496476064161791017.bai.txt #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.7550185544264298342java.bai #BAMIndexWriterTest diff /tmp/javaBai.7550185544264298342java.bai.txt /tmp/cBai.496476064161791017.bai.txt Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.readPastEndOfFile STANDARD_OUT 1ms to write Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.timeTest STANDARD_OUT 0ms 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.378418794505170167.gz Finished 13400 tests Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testCustomDeflater STANDARD_OUT Creating file /tmp/testCustomDeflater.1683710835170920588.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testOverflow STANDARD_OUT Creating file /tmp/BCOST.4585933757240131918.gz Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromContainer STANDARD_ERROR WARNING 2025-05-30 05:21:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:21:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromStream STANDARD_ERROR WARNING 2025-05-30 05:21:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:21:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.fullVerificationTest[0](c1#bounds) STANDARD_ERROR WARNING 2025-05-30 05:21:04 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 WARNING 2025-05-30 05:21:04 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. WARNING 2025-05-30 05:21:04 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 WARNING 2025-05-30 05:21:04 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 2025-05-30 05:21:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:21:08 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 2025-05-30 05:21:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:21:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testObsoleteDataSeriesNotWritten STANDARD_ERROR WARNING 2025-05-30 05:21:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:21:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Finished 13600 tests Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testContigNotFoundInRef STANDARD_ERROR WARNING 2025-05-30 05:21:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:21:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testNullsAndBeyondRef STANDARD_ERROR WARNING 2025-05-30 05:21:10 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 WARNING 2025-05-30 05:21:10 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. WARNING 2025-05-30 05:21:10 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 WARNING 2025-05-30 05:21:10 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 2025-05-30 05:21:10 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 WARNING 2025-05-30 05:21:10 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. WARNING 2025-05-30 05:21:10 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 WARNING 2025-05-30 05:21:10 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 2025-05-30 05:25:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:25:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCramIteratorWithoutCallingHasNextFirst STANDARD_ERROR WARNING 2025-05-30 05:25:08 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 WARNING 2025-05-30 05:25:08 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. WARNING 2025-05-30 05:25:08 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 WARNING 2025-05-30 05:25:08 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. Gradle is still running, please be patient... Finished 13800 tests Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 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;@aebd2b4, [Ljava.lang.String;@616f5587) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.7490144080838259965.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5f705efc, [Ljava.lang.String;@57289ac5) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 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 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:57 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 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 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;@2233c912, [Ljava.lang.String;@38fc2544) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:57 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;@4156a85d, [Ljava.lang.String;@161c8b24) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.7490144080838259965.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5c9caab7, [Ljava.lang.String;@634f3af4) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 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;@782e8fa4, [Ljava.lang.String;@74fa9bf3) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.7490144080838259965.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2b70215, [Ljava.lang.String;@48d35726) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 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;@746da4dd, [Ljava.lang.String;@61e36931) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.7490144080838259965.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4115db48, [Ljava.lang.String;@74efe6e7) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 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;@288fef56, [Ljava.lang.String;@3ab73311) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.7490144080838259965.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7a176d6a, [Ljava.lang.String;@7ecbddf4) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 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;@37abc95a, [Ljava.lang.String;@717ac9a3) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.7490144080838259965.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@575a47bb, [Ljava.lang.String;@6577dca8) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 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;@9ec7358, [Ljava.lang.String;@3f2853b2) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.7490144080838259965.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@610c4a16, [Ljava.lang.String;@51767571) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 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;@1fc6af08, [Ljava.lang.String;@5b78e7b9) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.7490144080838259965.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@63d13914, [Ljava.lang.String;@5e70354c) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 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;@1225abe, [Ljava.lang.String;@5a6c12b3) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.7490144080838259965.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2b798d1a, [Ljava.lang.String;@58b2b8a) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 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;@73bc1a42) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:57 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;@42cc0692) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:57 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;@5d16fb13) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:57 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;@60f8bea0) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:57 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;@30fb355a) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:57 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;@5144bf2e) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:57 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;@23d06a17) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:57 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;@d9d494b) STANDARD_ERROR WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:57 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 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:57 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 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:58 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;@1a3492e2, [Ljava.lang.String;@2bb23049) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@1a1ce225, [Ljava.lang.String;@3b13deaa) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.7490144080838259965.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3fcf96e2, [Ljava.lang.String;@8b7c671) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:58 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;@420c828a, [Ljava.lang.String;@5e80acd1) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.7490144080838259965.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2d4bcdb4, [Ljava.lang.String;@63c437d7) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:58 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;@51cb03d8, [Ljava.lang.String;@1efb41c5) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.7490144080838259965.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@24e884c8, [Ljava.lang.String;@77def040) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC 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;@21ccca25, [Ljava.lang.String;@185d016e) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.7490144080838259965.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1669323c, [Ljava.lang.String;@1a558d2a) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:58 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;@174e9018, [Ljava.lang.String;@4bb74d28) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.7490144080838259965.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@53366d8f, [Ljava.lang.String;@45e5b029) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:58 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;@7a5d26b9, [Ljava.lang.String;@1a183a58) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.7490144080838259965.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@b0fcad0, [Ljava.lang.String;@3ba6db82) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:58 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;@2e63de40, [Ljava.lang.String;@692ac8eb) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.7490144080838259965.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2ed67cb2, [Ljava.lang.String;@3de029b5) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:58 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;@26f57ba4, [Ljava.lang.String;@3d84083e) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.7490144080838259965.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6ad79a6a, [Ljava.lang.String;@6f00bba7) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:58 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;@7a1b760f) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@2ae74718) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@5173ef54) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@6ab8a913) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@6ba8ff67) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@5918dd35) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@5c7d7046) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@59a9d1aa) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@128575a0) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@4615c9da) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@3a81a5f7) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@49a5bc83) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@19563e1f) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@25272ea1) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@42b91668) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@10a80b70) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@4e31f7b8) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@6f723607) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@3b6f4e5f) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@2b45bfea) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@516b9ee3) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@2092e055) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@559e6db8) STANDARD_ERROR WARNING 2025-05-30 05:30:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:58 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;@14718656) STANDARD_ERROR WARNING 2025-05-30 05:30:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Finished 14000 tests 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;@221ec7f0) STANDARD_ERROR WARNING 2025-05-30 05:30:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:59 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;@12cd7b88) STANDARD_ERROR WARNING 2025-05-30 05:30:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:59 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;@68dae528) STANDARD_ERROR WARNING 2025-05-30 05:30:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:59 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;@7cc6fa63) STANDARD_ERROR WARNING 2025-05-30 05:30:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:59 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;@4baf0f20) STANDARD_ERROR WARNING 2025-05-30 05:30:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:59 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;@7c83d7da) STANDARD_ERROR WARNING 2025-05-30 05:30:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.7490144080838259965.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@2d797a49) STANDARD_ERROR WARNING 2025-05-30 05:30:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:59 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;@6f8c4537, 5) STANDARD_ERROR WARNING 2025-05-30 05:30:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:30:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMMergerTest.test STANDARD_ERROR WARNING 2025-05-30 05:30:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:30:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.cram.ref.CRAMReferenceRegionTest.testGetReferenceBasesByRegionExceedsContigLength STANDARD_ERROR WARNING 2025-05-30 05:31:00 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 14200 tests Finished 14400 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testAllCRAMEncodingsRoundTripThroughStream STANDARD_ERROR WARNING 2025-05-30 05:31:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testIgnoreObsoleteDataseriesOnRead STANDARD_ERROR WARNING 2025-05-30 05:31:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN 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 Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Finished 14600 tests Resetting tmpdir Could not delete file /tmp/pbuilder1/DiskBackedQueueTest/diskbackedqueue.9363157494085915701.tmp Finished 14800 tests Finished 15000 tests Finished 15200 tests Finished 15400 tests Finished 15600 tests Finished 15800 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 2025-05-30 05:31:17 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 2025-05-30 05:31:17 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Finished 16000 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 2025-05-30 05:31:19 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 2025-05-30 05:31:19 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 2025-05-30 05:31:19 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 2025-05-30 05:31:19 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 WARNING 2025-05-30 05:31:19 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 2025-05-30 05:31:19 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 WARNING 2025-05-30 05:31:19 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 2025-05-30 05:31:19 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 WARNING 2025-05-30 05:31:19 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombLongEncodingTest.testToString STANDARD_ERROR WARNING 2025-05-30 05:31:19 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 2025-05-30 05:31:19 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec Finished 16200 tests Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest STANDARD_ERROR WARNING 2025-05-30 05:31:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:19 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;@cd239f3, [Ljava.lang.String;@382c81df) STANDARD_ERROR WARNING 2025-05-30 05:31:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.191124971817241390.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2adc4d35, [Ljava.lang.String;@7f4a1963) STANDARD_ERROR WARNING 2025-05-30 05:31:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 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 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:20 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 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 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;@67487f39) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:20 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;@f91548d) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:20 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;@11c3c4fb) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:20 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;@2be2574a) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:20 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;@2062691b) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:20 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;@55a8946d) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:20 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;@779dad65) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:20 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;@312881c9) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:20 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;@5497a375, [Ljava.lang.String;@747de95b) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:20 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;@37f40de3, [Ljava.lang.String;@579b327a) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.191124971817241390.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2062514a, [Ljava.lang.String;@49df178c) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 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;@2984fe76, [Ljava.lang.String;@10d6db19) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.191124971817241390.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@78147c66, [Ljava.lang.String;@5815ad09) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 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;@23f464ac, [Ljava.lang.String;@63216ee9) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.191124971817241390.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6f4c7cce, [Ljava.lang.String;@51263fbf) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 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;@51e80788, [Ljava.lang.String;@74c3c71f) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.191124971817241390.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3d460fff, [Ljava.lang.String;@2b0a649b) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 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;@d03eb, [Ljava.lang.String;@28e93313) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.191124971817241390.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@60101a3b, [Ljava.lang.String;@6b8e2d0) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 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;@208815a6, [Ljava.lang.String;@4040f4ea) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.191124971817241390.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@20cf7d13, [Ljava.lang.String;@4d490c70) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 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;@18a55a42, [Ljava.lang.String;@2c3568dc) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.191124971817241390.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2e0d337e, [Ljava.lang.String;@57f51b78) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 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;@6b2cc97c, [Ljava.lang.String;@4bd9e39) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.191124971817241390.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@11c75e2e, [Ljava.lang.String;@91b93d1) STANDARD_ERROR WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 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 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:20 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 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:20 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 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:21 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 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 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;@474d74ce) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:21 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;@3c122f01) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:21 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;@412ad937) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:21 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;@529de192) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:21 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;@1ebe3ef) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:21 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;@73415262, [Ljava.lang.String;@16a190f) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:21 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;@343d9d50, [Ljava.lang.String;@7febb04f) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.191124971817241390.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@57e47e58, [Ljava.lang.String;@70b10884) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 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;@628135e7, [Ljava.lang.String;@5cec3b3c) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.191124971817241390.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@19ea3b51, [Ljava.lang.String;@7a156cd0) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 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;@2733d6b9, [Ljava.lang.String;@379e0b8b) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.191124971817241390.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7d893f7c, [Ljava.lang.String;@7784e79a) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 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;@6750d219, [Ljava.lang.String;@4649803b) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.191124971817241390.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@61ac04ff, [Ljava.lang.String;@3826389d) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 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;@5867bc99, [Ljava.lang.String;@35d600e6) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.191124971817241390.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1c21df47, [Ljava.lang.String;@76c0e8e3) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC 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;@1dcec7c8, [Ljava.lang.String;@3215b21d) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.191124971817241390.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@201a6db8, [Ljava.lang.String;@14e54cf9) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 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;@6809ad35, [Ljava.lang.String;@546420e1) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.191124971817241390.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@87679fd, [Ljava.lang.String;@21dbf3a4) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 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;@67f250d2, [Ljava.lang.String;@780cbca4) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.191124971817241390.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@37f174d5, [Ljava.lang.String;@6f6a1a97) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:21 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;@6fb1b59e) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:21 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;@74a4412b) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:21 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;@103efa93) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:21 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;@6eafd34d) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:21 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;@468549b) STANDARD_ERROR WARNING 2025-05-30 05:31:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:21 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;@35b621db) STANDARD_ERROR WARNING 2025-05-30 05:31:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:22 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;@6b467b85) STANDARD_ERROR WARNING 2025-05-30 05:31:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.191124971817241390.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@2f921e77) STANDARD_ERROR WARNING 2025-05-30 05:31:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:22 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;@54310d80) STANDARD_ERROR WARNING 2025-05-30 05:31:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:22 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;@1aa1b787) STANDARD_ERROR WARNING 2025-05-30 05:31:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:22 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;@2f8dda3f) STANDARD_ERROR WARNING 2025-05-30 05:31:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:22 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;@30447efb) STANDARD_ERROR WARNING 2025-05-30 05:31:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:22 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;@1f0e3869) STANDARD_ERROR WARNING 2025-05-30 05:31:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:22 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;@52c9bb1b) STANDARD_ERROR WARNING 2025-05-30 05:31:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:22 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;@53458c6e) STANDARD_ERROR WARNING 2025-05-30 05:31:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:22 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;@69f549aa) STANDARD_ERROR WARNING 2025-05-30 05:31:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:22 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;@fa6fce2) STANDARD_ERROR WARNING 2025-05-30 05:31:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:22 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 2025-05-30 05:31:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:22 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;@33de97d4, 5) STANDARD_ERROR WARNING 2025-05-30 05:31:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:31:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:31:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForDecodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4180751b, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1afdd286], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR WARNING 2025-05-30 05:31:22 HtsCodecResolver The specified format string (BOGUS_FORMAT) does not correspond to any registered codec for content type (ALIGNED_READS) Finished 16400 tests 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 2025-05-30 05:31:22 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@819c21e, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@10a94d2f, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4ba2baa5, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@66be325d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2843af21], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR WARNING 2025-05-30 05:31:22 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@819c21e, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@10a94d2f, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4ba2baa5, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@66be325d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2843af21], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR WARNING 2025-05-30 05:31:22 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@819c21e, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@10a94d2f, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4ba2baa5, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@66be325d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2843af21], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR WARNING 2025-05-30 05:31:22 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) Finished 16600 tests some stuffFinished 16800 tests Finished 17000 tests Gradle suite > Gradle test > htsjdk.samtools.util.IOUtilTest.testDeleteSingleWithDeletePaths STANDARD_ERROR Could not delete file tmp Could not delete file file14261838563345268120.bad Finished 17200 tests Gradle suite > Gradle test > htsjdk.samtools.util.IntervalTreeTest.performanceTest STANDARD_OUT Time to construct a tree with 50000 nodes: 17 milliseconds Queried for the same 100-length mapping 197003978 times in 10 seconds. Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR INFO 2025-05-30 05:31:35 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Finished 17400 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[279](chr2:111013693-111013832 + ., null) STANDARD_ERROR INFO 2025-05-30 05:31:35 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) INFO 2025-05-30 05:31:35 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 2025-05-30 05:31:35 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 2025-05-30 05:31:35 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 2025-05-30 05:31:35 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 2025-05-30 05:31:35 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 2025-05-30 05:31:35 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 2025-05-30 05:31:35 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 2025-05-30 05:31:35 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 2025-05-30 05:31:35 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) INFO 2025-05-30 05:31:35 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 2025-05-30 05:31:35 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 2025-05-30 05:31:35 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) INFO 2025-05-30 05:31:35 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 2025-05-30 05:31:35 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) INFO 2025-05-30 05:31:35 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 2025-05-30 05:31:35 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) Finished 17600 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR INFO 2025-05-30 05:31:35 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Finished 17800 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[279](chr2:111013693-111013832 + ., null) STANDARD_ERROR INFO 2025-05-30 05:31:35 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) INFO 2025-05-30 05:31:35 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 2025-05-30 05:31:35 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 2025-05-30 05:31:35 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 2025-05-30 05:31:35 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 2025-05-30 05:31:35 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 2025-05-30 05:31:35 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 2025-05-30 05:31:35 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 2025-05-30 05:31:35 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 2025-05-30 05:31:35 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) INFO 2025-05-30 05:31:35 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 2025-05-30 05:31:35 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 2025-05-30 05:31:35 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) INFO 2025-05-30 05:31:35 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 2025-05-30 05:31:35 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) INFO 2025-05-30 05:31:35 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 2025-05-30 05:31:35 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.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 18000 tests Finished 18200 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testLiftoverCounter[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR INFO 2025-05-30 05:31:35 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Finished 18400 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 18600 tests Finished 18800 tests Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[0](@HD VN:1.0 SO:UNSORTED ) STANDARD_ERROR WARNING 2025-05-30 05:32:06 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 2025-05-30 05:32:06 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 2025-05-30 05:32:06 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 2025-05-30 05:32:06 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 2025-05-30 05:32:06 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.specialFileWriterTest STANDARD_ERROR WARNING 2025-05-30 05:32:06 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null WARNING 2025-05-30 05:32:06 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 2025-05-30 05:32:06 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.9130620752823605704..cram INFO 2025-05-30 05:32:06 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-05-30 05:32:06 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-05-30 05:32:06 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeSamOrBamForCramExtension STANDARD_ERROR INFO 2025-05-30 05:32:06 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension8220273309462189146.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.13646775313595000002.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 2025-05-30 05:32:06 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension16037318332318990475.cram INFO 2025-05-30 05:32:06 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-05-30 05:32:06 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-05-30 05:32:06 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForNoExtension STANDARD_ERROR INFO 2025-05-30 05:32:06 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension13605565839525493474 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForUnknownFileExtension STANDARD_ERROR INFO 2025-05-30 05:32:06 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension14556870006974348625.png Finished 19000 tests Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[0](sam) STANDARD_ERROR INFO 2025-05-30 05:32:06 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://1a70b3db-67ea-49f4-bba5-cefdf7e5e037/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 2025-05-30 05:32:06 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://2c1f7834-2596-4da2-85be-085881bb869b/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 2025-05-30 05:32:06 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://231554a5-4c56-47e1-bb4d-97acc4b4c2f6/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 2025-05-30 05:32:06 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://f8d910ba-9bac-4dcc-befd-e0f9d2cf98b1/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 2025-05-30 05:32:06 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://36df4179-e15a-4c17-aecc-544de9be5fbf/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 2025-05-30 05:32:06 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://afa90fba-1b2b-4351-9a7b-6507cf0968b3/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 19200 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 2025-05-30 05:32:20 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2. Finished 19400 tests 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 2025-05-30 05:32:20 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 2025-05-30 05:32:20 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 Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.customReaderFactoryTest STANDARD_ERROR INFO 2025-05-30 05:32:21 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory INFO 2025-05-30 05:32:21 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory INFO 2025-05-30 05:32:21 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar INFO 2025-05-30 05:32:21 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 2025-05-30 05:32:21 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 2025-05-30 05:32:21 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 2025-05-30 05:32:22 SamReaderFactoryTest Finished queries in 72ms Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURL STANDARD_ERROR WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLNoIndexFile STANDARD_ERROR WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLStream STANDARD_ERROR WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromMalformedSeekableStream STANDARD_ERROR WARNING 2025-05-30 05:32:22 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 2025-05-30 05:32:22 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 2025-05-30 05:32:22 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 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:32:22 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 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:32:22 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 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Finished 19600 tests Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testIterateCRAMWithIndex[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:32:22 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 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:32:22 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 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:32:22 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 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-05-30 05:32:22 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testBamIntegers[1](inttest_large_coordinates.bam) STANDARD_ERROR WARNING 2025-05-30 05:32:22 BAMRecordCodec Reference length is too large for BAM bin field. WARNING 2025-05-30 05:32:22 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 2025-05-30 05:32:22 BAMRecordCodec Reference length is too large for BAM bin field. WARNING 2025-05-30 05:32:22 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 19800 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlockReadStreamTest.testSliceBlocksReadStreamsRoundTrip SKIPPED Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlocksTest.testSliceBlocksRoundTrip SKIPPED Finished 20000 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests STANDARD_ERROR WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 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 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 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 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. WARNING 2025-05-30 05:32:22 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 2025-05-30 05:32:22 CRAMReferenceRegion The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20 WARNING 2025-05-30 05:32:22 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 20200 tests Finished 20400 tests Finished 20600 tests Finished 20800 tests Finished 21000 tests Finished 21200 tests Finished 21400 tests Finished 21600 tests Finished 21800 tests Finished 22000 tests Finished 22200 tests Finished 22400 tests Finished 22600 tests Finished 22800 tests Finished 23000 tests Finished 23200 tests Finished 23400 tests Finished 23600 tests Finished 23800 tests Finished 24000 tests Finished 24200 tests Finished 24400 tests Finished 24600 tests Finished 24800 tests Finished 25000 tests Finished 25200 tests Finished 25400 tests Finished 25600 tests Finished 25800 tests Finished 26000 tests Finished 26200 tests Finished 26400 tests Finished 26600 tests Finished 26800 tests Finished 27000 tests Finished 27200 tests Finished 27400 tests Finished 27600 tests Finished 27800 tests Finished 28000 tests Finished 28200 tests Finished 28400 tests Finished 28600 tests Finished 28800 tests Finished 29000 tests Finished 29200 tests Finished 29400 tests Finished 29600 tests Finished 29800 tests Finished 30000 tests Finished 30200 tests Finished 30400 tests Finished 30600 tests Finished 30800 tests Finished 31000 tests Finished 31200 tests Finished 31400 tests Finished 31600 tests Finished 31800 tests Finished 32000 tests Finished 32200 tests Finished 32400 tests Finished 32600 tests Finished 32800 tests Finished 33000 tests Finished 33200 tests Finished 33400 tests Finished 33600 tests Finished 33800 tests Finished 34000 tests Finished 34200 tests Finished 34400 tests Finished 34600 tests Finished 34800 tests Finished 35000 tests Finished 35200 tests Finished 35400 tests Finished 35600 tests Finished 35800 tests Gradle Test Executor 3 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 (35800 tests, 35790 successes, 0 failures, 10 skipped) Finished generating test XML results (0.137 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/test-results/test Generating HTML test report... Finished generating test html results (0.214 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/reports/tests/test :test (Thread[Task worker for ':',5,main]) completed. Took 15 mins 12.363 secs. BUILD SUCCESSFUL in 36m 45s 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-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 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 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/help-doc.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/index-all.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 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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/htsjdk/utils/package-tree.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/ValidationUtils.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/annotations/package-tree.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 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/BetaAPI.html using File::StripNondeterminism::handlers::javadoc 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/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkUnsupportedOperationException.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/HtsjdkIOException.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/plugin/package-tree.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/Upgradeable.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/HtsVersion.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/HtsHeader.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 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/HtsDecoderOptions.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/HtsContentType.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/variants/package-tree.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/VariantsFormats.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/VariantsEncoder.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/VariantsDecoder.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/reads/package-tree.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/ReadsQuery.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/ 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/FastqConstants.FastqExtensions.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/fastq/AsyncFastqWriter.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/CRAMException.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/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/BAIEntry.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/package-summary.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/CramVersions.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/CRAMVersion.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/package-summary.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/ReferenceContextType.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/EnaRefService.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/CRAMLazyReferenceSource.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/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 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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/VCFAltHeaderLine.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/AbstractVCFCodec.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/package-summary.html using File::StripNondeterminism::handlers::javadoc 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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/ftp/package-tree.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/ftp/FTPUtils.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/FTPReply.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/nio/package-tree.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/nio/DeleteOnExitPathHook.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-doc/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/util/zip/DeflaterFactory.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-doc/changelog.Debian gzip -9nf usr/share/doc/libhtsjdk-java-doc/changelog.Debian chmod a-x usr/share/doc/libhtsjdk-java/changelog.Debian cd '/build/reproducible-path/htsjdk-4.1.0+dfsg' gzip -9nf usr/share/doc/libhtsjdk-java/changelog.Debian cd '/build/reproducible-path/htsjdk-4.1.0+dfsg' dh_fixperms -O--buildsystem=gradle 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 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s 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/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-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 -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 -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/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 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 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 cd debian/libhtsjdk-java >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums install -m0755 -d debian/libhtsjdk-java-doc/DEBIAN 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-doc .. dpkg-deb: building package 'libhtsjdk-java-doc' in '../libhtsjdk-java-doc_4.1.0+dfsg-1_all.deb'. dpkg-deb --root-owner-group --build debian/libhtsjdk-java .. dpkg-deb: building package 'libhtsjdk-java' in '../libhtsjdk-java_4.1.0+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../htsjdk_4.1.0+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../htsjdk_4.1.0+dfsg-1_arm64.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: 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/2896947 and its subdirectories I: Current time: Fri May 30 05:32:47 -12 2025 I: pbuilder-time-stamp: 1748626367 Sat Apr 27 11:09:51 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink01-arm64.debian.net. Sat Apr 27 11:09:51 UTC 2024 I: Preparing to do remote build '2' on codethink01-arm64.debian.net. Sat Apr 27 11:41:16 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. Sat Apr 27 11:41:17 UTC 2024 I: htsjdk_4.1.0+dfsg-1_arm64.changes: Format: 1.8 Date: Sun, 11 Feb 2024 22:41:39 +0100 Source: htsjdk Binary: libhtsjdk-java libhtsjdk-java-doc Architecture: all Version: 4.1.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Pierre Gruet Description: libhtsjdk-java - Java API for high-throughput sequencing data (HTS) formats libhtsjdk-java-doc - Documentation for the java HTSJDK library Changes: htsjdk (4.1.0+dfsg-1) unstable; urgency=medium . * New upstream version 4.1.0+dfsg * Refreshing patches Checksums-Sha1: 4527260f7634f1bdcddde92be319704ba2dc368e 17711 htsjdk_4.1.0+dfsg-1_arm64.buildinfo cd5a57b07d7d10cdb9bcdd8589cb7cff7b341bea 1043544 libhtsjdk-java-doc_4.1.0+dfsg-1_all.deb 6c80d8437098ebd877b2239a6a94be72a7d84a60 1832576 libhtsjdk-java_4.1.0+dfsg-1_all.deb Checksums-Sha256: bef9b197933a2163ee1b476e294f11fd61494ff1878f006e5234c4393d112eb6 17711 htsjdk_4.1.0+dfsg-1_arm64.buildinfo 96231c377cf6e56a4f668be100a8653e3143c4ed94b7bc209ddee46ba626f9b7 1043544 libhtsjdk-java-doc_4.1.0+dfsg-1_all.deb 53cec3b89440193482f9f544dcce74422ea975f4cb34c8f718d6c4b04b000b9b 1832576 libhtsjdk-java_4.1.0+dfsg-1_all.deb Files: 0498d02b2407f0d039dd59fc75da51ec 17711 science optional htsjdk_4.1.0+dfsg-1_arm64.buildinfo b78f9d715d094b93946f568e5f8f5d8d 1043544 doc optional libhtsjdk-java-doc_4.1.0+dfsg-1_all.deb e2a525d9d62d110f9137837762113747 1832576 java optional libhtsjdk-java_4.1.0+dfsg-1_all.deb Sat Apr 27 11:41:18 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_17-33421.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.nv8vSwtQ/htsjdk_4.1.0+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.nv8vSwtQ/htsjdk_4.1.0+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.nv8vSwtQ/htsjdk_4.1.0+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.nv8vSwtQ/b1/htsjdk_4.1.0+dfsg-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.nv8vSwtQ/b2/htsjdk_4.1.0+dfsg-1_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.502s) 0.502s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.054s) 0.054s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 958ms CPU time consumed: 948ms Sat Apr 27 11:41:20 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Sat Apr 27 11:41:20 UTC 2024 I: htsjdk from trixie built successfully and reproducibly on arm64. Sat Apr 27 11:41:22 UTC 2024 I: Submitting .buildinfo files to external archives: Sat Apr 27 11:41:22 UTC 2024 I: Submitting 20K b1/htsjdk_4.1.0+dfsg-1_arm64.buildinfo.asc Sat Apr 27 11:41:23 UTC 2024 I: Submitting 20K b2/htsjdk_4.1.0+dfsg-1_arm64.buildinfo.asc Sat Apr 27 11:41:24 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Apr 27 11:41:24 UTC 2024 I: Done submitting .buildinfo files. Sat Apr 27 11:41:24 UTC 2024 I: Removing signed htsjdk_4.1.0+dfsg-1_arm64.buildinfo.asc files: removed './b1/htsjdk_4.1.0+dfsg-1_arm64.buildinfo.asc' removed './b2/htsjdk_4.1.0+dfsg-1_arm64.buildinfo.asc'