I: pbuilder: network access will be disabled during build I: Current time: Wed Jan 1 06:02:25 +14 2025 I: pbuilder-time-stamp: 1735660945 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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_4.1.3+dfsg-2.dsc] I: copying [./htsjdk_4.1.3+dfsg.orig.tar.xz] I: copying [./htsjdk_4.1.3+dfsg-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./htsjdk_4.1.3+dfsg-2.dsc: unsupported subcommand dpkg-source: info: extracting htsjdk in htsjdk-4.1.3+dfsg dpkg-source: info: unpacking htsjdk_4.1.3+dfsg.orig.tar.xz dpkg-source: info: unpacking htsjdk_4.1.3+dfsg-2.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 171-use-org-kordamp-json.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/1704786/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Dec 31 16:02 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1704786/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1704786/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=cf0b869eae6041709f7736c4c58f3008 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1704786 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.kRLBVa3y/pbuilderrc_FaKJ --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.kRLBVa3y/b2 --logfile b2/build.log htsjdk_4.1.3+dfsg-2.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1704786/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), libjson-java, libcommons-jexl2-java, libcommons-logging-java, libjaxb-api-java, libjaxb-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 ... 19975 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 libjson-java; however: Package libjson-java 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 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: 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{a} dbus-bin{a} dbus-daemon{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} dwz{a} fastjar{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gpg{a} gpg-agent{a} gpgconf{a} gpgsm{a} gpgv{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} libargs4j-java{a} libasm-java{a} libasound2-data{a} libasound2t64{a} libassuan9{a} libatinject-jsr330-api-java{a} libatk-bridge2.0-0t64{a} libatk1.0-0t64{a} libatspi2.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbcel-java{a} libbcpg-java{a} libbcprov-java{a} libbrotli1{a} 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} libcom-err2{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-collections4-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} libcups2t64{a} libdatrie1{a} libdbus-1-3{a} libdconf1{a} libdd-plist-java{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdom4j-java{a} libdrm-amdgpu1{a} libdrm-common{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} libezmorph-java{a} libfastinfoset-java{a} libfelix-framework-java{a} libfelix-gogo-runtime-java{a} libfelix-resolver-java{a} libffi8{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} libfreetype6{a} libfribidi0{a} libgbm1{a} libgcrypt20{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} libgnutls30t64{a} libgoogle-gson-java{a} libgpg-error0{a} libgradle-core-java{a} libgradle-plugins-java{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk-3-0t64{a} libgtk-3-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhawtjni-runtime-java{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhttpclient-java{a} libhttpcore-java{a} libicu72{a} libidn2-0{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-java{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjunixsocket-java{a} libjunixsocket-jni{a} libjzlib-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libkryo-java{a} libksba8{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblightcouch-java{a} libllvm19{a} liblog4j2-java{a} liblogback-java{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmaven-file-management-java{a} libmaven-parent-java{a} libmaven-resolver-1.6-java{a} libmaven-resolver-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven3-core-java{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libminlog-java{a} libmodule-runtime-perl{a} libmongodb-java{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} libnsl2{a} libnspr4{a} libnss3{a} libobjenesis-java{a} libosgi-annotation-java{a} libosgi-compendium-java{a} libosgi-core-java{a} libp11-kit0{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} libpython3.12-minimal{a} libpython3.12-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} libstax-ex-java{a} libstreambuffer-java{a} libsub-quote-perl{a} libsystemd-shared{a} libtasn1-6{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libtry-tiny-perl{a} libtxw2-java{a} libuchardet0{a} libunistring5{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} libwayland-server0{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} libxom-java{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} mesa-libgallium{a} ncbi-vdb-data{a} netbase{a} openjdk-21-doc{a} openjdk-21-jdk{a} openjdk-21-jdk-headless{a} openjdk-21-jre{a} openjdk-21-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} scala-library{a} sensible-utils{a} shared-mime-info{a} sopv-gpgv{a} systemd{a} systemd-sysv{a} testng{a} tzdata{a} unzip{a} wdiff{a} x11-common{a} xkb-data{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf at-spi2-core chrony curl debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra gnupg-utils gpg-wks-client javascript-common krb5-locales 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 libgpg-error-l10n libgtk-3-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjson-perl libkmod2 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 linux-sysctl-defaults lynx mesa-vulkan-drivers ntpsec openntpd pristine-tar psmisc python3-apt python3-argcomplete python3-debian python3-magic python3-requests python3-unidiff python3-xdg strace systemd-cryptsetup systemd-timesyncd wget xdg-user-dirs 0 packages upgraded, 421 newly installed, 0 to remove and 0 not upgraded. Need to get 351 MB of archives. After unpacking 1232 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libapparmor1 arm64 3.1.7-1+b3 [41.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libsystemd-shared arm64 257.1-5 [1909 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 systemd arm64 257.1-5 [3368 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 systemd-sysv arm64 257.1-5 [60.2 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 libdbus-1-3 arm64 1.16.0-1 [168 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 dbus-bin arm64 1.16.0-1 [77.7 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 dbus-session-bus-common all 1.16.0-1 [51.1 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 dbus-daemon arm64 1.16.0-1 [150 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 dbus-system-bus-common all 1.16.0-1 [52.2 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 dbus arm64 1.16.0-1 [69.4 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 binfmt-support arm64 2.2.2-7+b1 [68.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.8-3 [810 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.8-3 [1941 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.8-1 [26.9 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024b-4 [256 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2~rc1-2 [23.7 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 25 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.8-3 [1906 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.8-3 [677 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.8-1 [9788 B] Get: 35 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.8-1 [27.9 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libgpg-error0 arm64 1.51-3 [78.5 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libgcrypt20 arm64 1.11.0-7 [742 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 gpgv arm64 2.2.45-2 [199 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-6 [872 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.3.2-2 [1347 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20241223 [164 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-3 [198 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libpam-systemd arm64 257.1-5 [271 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-13 [91.4 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [311 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.4-1 [1411 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 shared-mime-info arm64 2.4-5+b1 [755 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.44-3 [273 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.4.0-0.1+b1 [112 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.4.0-0.1+b1 [268 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.12+dfsg-1+b1 [131 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 gtk-update-icon-cache arm64 4.16.7+ds-1 [49.8 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 hicolor-icon-theme all 0.18-1 [12.0 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 adwaita-icon-theme all 47.0-2 [463 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 ca-certificates-java all 20240118 [11.6 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 java-common all 0.76 [6776 B] Get: 72 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libnspr4 arm64 2:4.36-1 [102 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libnss3 arm64 2:3.106-1 [1292 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libpcsclite1 arm64 2.3.1-1 [55.3 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jre-headless arm64 21.0.6~6ea-1 [40.6 MB] Get: 77 http://deb.debian.org/debian unstable/main arm64 default-jre-headless arm64 2:1.21-76 [3192 B] Get: 78 http://deb.debian.org/debian unstable/main arm64 ant all 1.10.15-1 [2163 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 ant-optional all 1.10.15-1 [456 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libantlr-java all 2.7.7+dfsg-14 [458 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 antlr all 2.7.7+dfsg-14 [8376 B] Get: 82 http://deb.debian.org/debian unstable/main arm64 at-spi2-common all 2.54.0-1 [170 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-3 [723 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 unzip arm64 6.0-28+b1 [158 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 java-wrappers all 0.5 [8848 B] Get: 90 http://deb.debian.org/debian unstable/main arm64 libhamcrest-java all 2.2-2 [121 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 junit4 all 4.13.2-5 [350 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libfelix-framework-java all 4.6.1-2.1 [569 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libfelix-gogo-runtime-java all 0.16.2-1.1 [114 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libosgi-annotation-java all 8.1.0-1 [9436 B] Get: 95 http://deb.debian.org/debian unstable/main arm64 libosgi-core-java all 8.0.0-2 [182 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libfelix-resolver-java all 1.16.0-1 [180 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libhawtjni-runtime-java all 1.18-1 [36.3 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libjansi-native-java all 1.8-2 [26.0 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libjansi1-java all 1.18-3 [66.5 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libjline2-java all 2.14.6-5 [151 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libosgi-compendium-java all 7.0.0-1 [477 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libslf4j-java all 1.7.32-1 [144 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libxz-java all 1.9-1 [143 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libyaml-snake-java all 1.33-2 [321 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 bnd all 5.0.1-5 [10.1 MB] Get: 106 http://deb.debian.org/debian unstable/main arm64 dbus-user-session arm64 1.16.0-1 [51.0 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libdconf1 arm64 0.40.0-4+b3 [40.4 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 dconf-service arm64 0.40.0-4+b3 [31.1 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 dconf-gsettings-backend arm64 0.40.0-4+b3 [27.4 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 dctrl-tools arm64 2.24-3+b1 [125 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.23 [90.6 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 117 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-3 [1532 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.23 [919 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libatk1.0-0t64 arm64 2.54.0-1 [49.7 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libatspi2.0-0t64 arm64 2.54.0-1 [72.9 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libatk-bridge2.0-0t64 arm64 2.54.0-1 [64.4 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1+b1 [318 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1+b1 [387 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b3 [27.2 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 libcairo-gobject2 arm64 1.18.2-2 [130 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 libcloudproviders0 arm64 0.3.6-1+b1 [27.7 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 libcolord2 arm64 1.4.7-1+b2 [130 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libavahi-common-data arm64 0.8-15 [112 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 libavahi-common3 arm64 0.8-15 [43.3 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 libavahi-client3 arm64 0.8-15 [46.8 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.19.0-3+b3 [46.9 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.8-2 [1363 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 libcups2t64 arm64 2.4.10-2+b1 [236 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 libepoxy0 arm64 1.5.10-2 [200 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.1.0-2 [443 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-1.1+b1 [463 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.55.0+ds-3 [212 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.55.0+ds-3 [52.1 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.55.0+ds-3 [33.4 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 libwayland-client0 arm64 1.23.0-1+b1 [26.0 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 libwayland-cursor0 arm64 1.23.0-1+b1 [11.5 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 libwayland-egl1 arm64 1.23.0-1+b1 [5768 B] Get: 170 http://deb.debian.org/debian unstable/main arm64 libxcomposite1 arm64 1:0.4.6-1 [16.4 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 libxfixes3 arm64 1:6.0.0-2+b3 [20.4 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 libxcursor1 arm64 1:1.2.2-1+b1 [37.1 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 libxdamage1 arm64 1:1.1.6-1+b2 [15.6 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 libxinerama1 arm64 2:1.1.4-3+b3 [16.1 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 xkb-data all 2.42-1 [790 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 libxkbcommon0 arm64 1.7.0-2 [106 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 libxrandr2 arm64 2:1.5.4-1+b2 [36.0 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 libgtk-3-common all 3.24.43-4 [4657 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 libgtk-3-0t64 arm64 3.24.43-4 [2546 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 libglvnd0 arm64 1.7.0-1+b2 [41.6 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 libdrm-common all 2.4.123-1 [8084 B] Get: 182 http://deb.debian.org/debian unstable/main arm64 libdrm2 arm64 2.4.123-1 [38.0 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 libglapi-mesa arm64 24.2.8-1 [48.2 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 libx11-xcb1 arm64 2:1.8.10-2 [241 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 libxcb-dri2-0 arm64 1.17.0-2+b1 [107 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 libxcb-dri3-0 arm64 1.17.0-2+b1 [107 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 libxcb-glx0 arm64 1.17.0-2+b1 [123 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 libxcb-present0 arm64 1.17.0-2+b1 [106 kB] Get: 189 http://deb.debian.org/debian unstable/main arm64 libxcb-randr0 arm64 1.17.0-2+b1 [117 kB] Get: 190 http://deb.debian.org/debian unstable/main arm64 libxcb-sync1 arm64 1.17.0-2+b1 [109 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 libxcb-xfixes0 arm64 1.17.0-2+b1 [110 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 libxshmfence1 arm64 1.3-1+b2 [9076 B] Get: 193 http://deb.debian.org/debian unstable/main arm64 libxxf86vm1 arm64 1:1.1.4-1+b3 [19.2 kB] Get: 194 http://deb.debian.org/debian unstable/main arm64 libdrm-amdgpu1 arm64 2.4.123-1 [21.6 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 libdrm-radeon1 arm64 2.4.123-1 [21.3 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20240808-1 [89.2 kB] Get: 197 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 libllvm19 arm64 1:19.1.6-1 [23.3 MB] Get: 199 http://deb.debian.org/debian unstable/main arm64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 libsensors5 arm64 1:3.6.0-10+b1 [34.3 kB] Get: 201 http://deb.debian.org/debian unstable/main arm64 mesa-libgallium arm64 24.2.8-1 [7689 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 libvulkan1 arm64 1.3.296.0-1 [123 kB] Get: 203 http://deb.debian.org/debian unstable/main arm64 libwayland-server0 arm64 1.23.0-1+b1 [33.4 kB] Get: 204 http://deb.debian.org/debian unstable/main arm64 libgbm1 arm64 24.2.8-1 [42.0 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 libgl1-mesa-dri arm64 24.2.8-1 [43.6 kB] Get: 206 http://deb.debian.org/debian unstable/main arm64 libglx-mesa0 arm64 24.2.8-1 [152 kB] Get: 207 http://deb.debian.org/debian unstable/main arm64 libglx0 arm64 1.7.0-1+b2 [31.1 kB] Get: 208 http://deb.debian.org/debian unstable/main arm64 libgl1 arm64 1.7.0-1+b2 [90.9 kB] Get: 209 http://deb.debian.org/debian unstable/main arm64 libasound2-data all 1.2.12-1 [21.0 kB] Get: 210 http://deb.debian.org/debian unstable/main arm64 libasound2t64 arm64 1.2.12-1+b1 [336 kB] Get: 211 http://deb.debian.org/debian unstable/main arm64 libgif7 arm64 5.2.2-1+b1 [44.2 kB] Get: 212 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+23.1 [216 kB] Get: 213 http://deb.debian.org/debian unstable/main arm64 libxtst6 arm64 2:1.2.3-1.1+b3 [26.0 kB] Get: 214 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jre arm64 21.0.6~6ea-1 [193 kB] Get: 215 http://deb.debian.org/debian unstable/main arm64 default-jre arm64 2:1.21-76 [1068 B] Get: 216 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jdk-headless arm64 21.0.6~6ea-1 [81.8 MB] Get: 217 http://deb.debian.org/debian unstable/main arm64 default-jdk-headless arm64 2:1.21-76 [1124 B] Get: 218 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jdk arm64 21.0.6~6ea-1 [3435 kB] Get: 219 http://deb.debian.org/debian unstable/main arm64 default-jdk arm64 2:1.21-76 [1076 B] Get: 220 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 221 http://deb.debian.org/debian unstable/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 222 http://deb.debian.org/debian unstable/main arm64 libjs-jquery-ui-theme-base all 1.12.1+dfsg-1.1 [44.3 kB] Get: 223 http://deb.debian.org/debian unstable/main arm64 openjdk-21-doc all 21.0.6~6ea-1 [13.2 MB] Get: 224 http://deb.debian.org/debian unstable/main arm64 default-jdk-doc arm64 2:1.21-76 [3264 B] Get: 225 http://deb.debian.org/debian unstable/main arm64 libassuan9 arm64 3.0.1-2 [58.1 kB] Get: 226 http://deb.debian.org/debian unstable/main arm64 gpgconf arm64 2.2.45-2 [114 kB] Get: 227 http://deb.debian.org/debian unstable/main arm64 libksba8 arm64 1.6.7-2+b1 [125 kB] Get: 228 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 229 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 230 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.19+dfsg-1 [175 kB] Get: 231 http://deb.debian.org/debian unstable/main arm64 libnpth0t64 arm64 1.8-2 [22.8 kB] Get: 232 http://deb.debian.org/debian unstable/main arm64 dirmngr arm64 2.2.45-2 [343 kB] Get: 233 http://deb.debian.org/debian unstable/main arm64 gnupg-l10n all 2.2.45-2 [705 kB] Get: 234 http://deb.debian.org/debian unstable/main arm64 gpg arm64 2.2.45-2 [481 kB] Get: 235 http://deb.debian.org/debian unstable/main arm64 pinentry-curses arm64 1.2.1-5 [76.6 kB] Get: 236 http://deb.debian.org/debian unstable/main arm64 gpg-agent arm64 2.2.45-2 [230 kB] Get: 237 http://deb.debian.org/debian unstable/main arm64 gpgsm arm64 2.2.45-2 [232 kB] Get: 238 http://deb.debian.org/debian unstable/main arm64 gnupg all 2.2.45-2 [376 kB] Get: 239 http://deb.debian.org/debian unstable/main arm64 sopv-gpgv all 0.1.1-1 [10.7 kB] Get: 240 http://deb.debian.org/debian unstable/main arm64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 241 http://deb.debian.org/debian unstable/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 242 http://deb.debian.org/debian unstable/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 243 http://deb.debian.org/debian unstable/main arm64 libfile-touch-perl all 0.12-2 [8816 B] Get: 244 http://deb.debian.org/debian unstable/main arm64 libio-pty-perl arm64 1:1.20-1+b2 [34.0 kB] Get: 245 http://deb.debian.org/debian unstable/main arm64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 246 http://deb.debian.org/debian unstable/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 247 http://deb.debian.org/debian unstable/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b4 [34.9 kB] Get: 248 http://deb.debian.org/debian unstable/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b2 [10.6 kB] Get: 249 http://deb.debian.org/debian unstable/main arm64 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get: 250 http://deb.debian.org/debian unstable/main arm64 libdevel-callchecker-perl arm64 0.009-1+b1 [16.3 kB] Get: 251 http://deb.debian.org/debian unstable/main arm64 libparams-classify-perl arm64 0.015-2+b4 [22.3 kB] Get: 252 http://deb.debian.org/debian unstable/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 253 http://deb.debian.org/debian unstable/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 254 http://deb.debian.org/debian unstable/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 255 http://deb.debian.org/debian unstable/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 256 http://deb.debian.org/debian unstable/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 257 http://deb.debian.org/debian unstable/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 258 http://deb.debian.org/debian unstable/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 259 http://deb.debian.org/debian unstable/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 260 http://deb.debian.org/debian unstable/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 261 http://deb.debian.org/debian unstable/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 262 http://deb.debian.org/debian unstable/main arm64 liburi-perl all 5.30-1 [105 kB] Get: 263 http://deb.debian.org/debian unstable/main arm64 libhtml-parser-perl arm64 3.83-1+b1 [97.5 kB] Get: 264 http://deb.debian.org/debian unstable/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 265 http://deb.debian.org/debian unstable/main arm64 libclone-perl arm64 0.47-1+b1 [13.7 kB] Get: 266 http://deb.debian.org/debian unstable/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get: 267 http://deb.debian.org/debian unstable/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 268 http://deb.debian.org/debian unstable/main arm64 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 269 http://deb.debian.org/debian unstable/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 270 http://deb.debian.org/debian unstable/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 271 http://deb.debian.org/debian unstable/main arm64 perl-openssl-defaults arm64 7+b2 [6712 B] Get: 272 http://deb.debian.org/debian unstable/main arm64 libnet-ssleay-perl arm64 1.94-2 [323 kB] Get: 273 http://deb.debian.org/debian unstable/main arm64 libio-socket-ssl-perl all 2.089-1 [223 kB] Get: 274 http://deb.debian.org/debian unstable/main arm64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 275 http://deb.debian.org/debian unstable/main arm64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 276 http://deb.debian.org/debian unstable/main arm64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 277 http://deb.debian.org/debian unstable/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 278 http://deb.debian.org/debian unstable/main arm64 libwww-perl all 6.77-1 [183 kB] Get: 279 http://deb.debian.org/debian unstable/main arm64 patchutils arm64 0.4.2-1+b1 [71.3 kB] Get: 280 http://deb.debian.org/debian unstable/main arm64 wdiff arm64 1.2.2-6+b1 [119 kB] Get: 281 http://deb.debian.org/debian unstable/main arm64 devscripts all 2.24.9 [1075 kB] Get: 282 http://deb.debian.org/debian unstable/main arm64 fastjar arm64 2:0.98-7+b1 [74.9 kB] Get: 283 http://deb.debian.org/debian unstable/main arm64 ivy all 2.5.2-1 [1295 kB] Get: 284 http://deb.debian.org/debian unstable/main arm64 libasm-java all 9.7.1-1 [391 kB] Get: 285 http://deb.debian.org/debian unstable/main arm64 libbsf-java all 1:2.4.0-8 [76.3 kB] Get: 286 http://deb.debian.org/debian unstable/main arm64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 287 http://deb.debian.org/debian unstable/main arm64 libapache-pom-java all 33-2 [5852 B] Get: 288 http://deb.debian.org/debian unstable/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 289 http://deb.debian.org/debian unstable/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 290 http://deb.debian.org/debian unstable/main arm64 libjansi-java all 2.4.1-2 [100 kB] Get: 291 http://deb.debian.org/debian unstable/main arm64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 292 http://deb.debian.org/debian unstable/main arm64 libqdox-java all 1.12.1-4 [173 kB] Get: 293 http://deb.debian.org/debian unstable/main arm64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 294 http://deb.debian.org/debian unstable/main arm64 libxpp3-java all 1.1.4c-3 [292 kB] Get: 295 http://deb.debian.org/debian unstable/main arm64 libxstream-java all 1.4.21-1 [567 kB] Get: 296 http://deb.debian.org/debian unstable/main arm64 groovy all 2.4.21-10 [12.8 MB] Get: 297 http://deb.debian.org/debian unstable/main arm64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 298 http://deb.debian.org/debian unstable/main arm64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 299 http://deb.debian.org/debian unstable/main arm64 libcommons-codec-java all 1.17.1-1 [303 kB] Get: 300 http://deb.debian.org/debian unstable/main arm64 libcommons-io-java all 2.17.0-1 [488 kB] Get: 301 http://deb.debian.org/debian unstable/main arm64 libcommons-compress-java all 1.27.1-2 [641 kB] Get: 302 http://deb.debian.org/debian unstable/main arm64 libcommons-lang-java all 2.6-10 [273 kB] Get: 303 http://deb.debian.org/debian unstable/main arm64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 304 http://deb.debian.org/debian unstable/main arm64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 305 http://deb.debian.org/debian unstable/main arm64 libguava-java all 32.0.1-1 [2708 kB] Get: 306 http://deb.debian.org/debian unstable/main arm64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 307 http://deb.debian.org/debian unstable/main arm64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 308 http://deb.debian.org/debian unstable/main arm64 libjarjar-java all 1.4+svn142-12 [205 kB] Get: 309 http://deb.debian.org/debian unstable/main arm64 libjcip-annotations-java all 20060626-6 [11.8 kB] Get: 310 http://deb.debian.org/debian unstable/main arm64 libjna-jni arm64 5.15.0-1 [62.4 kB] Get: 311 http://deb.debian.org/debian unstable/main arm64 libjna-java all 5.15.0-1 [238 kB] Get: 312 http://deb.debian.org/debian unstable/main arm64 libbcprov-java all 1.77-1 [5300 kB] Get: 313 http://deb.debian.org/debian unstable/main arm64 libjunixsocket-jni arm64 2.6.1-1+b1 [18.3 kB] Get: 314 http://deb.debian.org/debian unstable/main arm64 libeclipse-jdt-annotation-java all 2.2.700+eclipse4.29-2 [25.5 kB] Get: 315 http://deb.debian.org/debian unstable/main arm64 libjunixsocket-java all 2.6.1-1 [264 kB] Get: 316 http://deb.debian.org/debian unstable/main arm64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 317 http://deb.debian.org/debian unstable/main arm64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get: 318 http://deb.debian.org/debian unstable/main arm64 libmongodb-java all 3.6.3-2 [1901 kB] Get: 319 http://deb.debian.org/debian unstable/main arm64 liblog4j2-java all 2.19.0-2 [2310 kB] Get: 320 http://deb.debian.org/debian unstable/main arm64 libjzlib-java all 1.1.3-3 [79.4 kB] Get: 321 http://deb.debian.org/debian unstable/main arm64 libjsch-java all 0.2.19-1 [513 kB] Get: 322 http://deb.debian.org/debian unstable/main arm64 libminlog-java all 1.3.1-1 [7808 B] Get: 323 http://deb.debian.org/debian unstable/main arm64 libobjenesis-java all 3.3-3 [41.3 kB] Get: 324 http://deb.debian.org/debian unstable/main arm64 libreflectasm-java all 1.11.9+dfsg-4 [25.0 kB] Get: 325 http://deb.debian.org/debian unstable/main arm64 libkryo-java all 2.20-7 [158 kB] Get: 326 http://deb.debian.org/debian unstable/main arm64 liblogback-java all 1:1.2.11-6 [701 kB] Get: 327 http://deb.debian.org/debian unstable/main arm64 libnative-platform-jni arm64 0.14-6+b1 [11.7 kB] Get: 328 http://deb.debian.org/debian unstable/main arm64 libnative-platform-java all 0.14-6 [69.8 kB] Get: 329 http://deb.debian.org/debian unstable/main arm64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 330 http://deb.debian.org/debian unstable/main arm64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 331 http://deb.debian.org/debian unstable/main arm64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 332 http://deb.debian.org/debian unstable/main arm64 libnekohtml-java all 1.9.22.noko2-0.1 [125 kB] Get: 333 http://deb.debian.org/debian unstable/main arm64 libxbean-reflect-java all 4.5-9 [132 kB] Get: 334 http://deb.debian.org/debian unstable/main arm64 libgradle-core-java all 4.4.1-21 [4318 kB] Get: 335 http://deb.debian.org/debian unstable/main arm64 libbcpg-java all 1.77-1 [428 kB] Get: 336 http://deb.debian.org/debian unstable/main arm64 libbsh-java all 2.0b4-20 [291 kB] Get: 337 http://deb.debian.org/debian unstable/main arm64 libdd-plist-java all 1.20-1.1 [72.6 kB] Get: 338 http://deb.debian.org/debian unstable/main arm64 libjaxen-java all 1.1.6-5 [214 kB] Get: 339 http://deb.debian.org/debian unstable/main arm64 libdom4j-java all 2.1.4-1 [312 kB] Get: 340 http://deb.debian.org/debian unstable/main arm64 libcommons-lang3-java all 3.17.0-1 [641 kB] Get: 341 http://deb.debian.org/debian unstable/main arm64 libbcel-java all 6.10.0-1 [674 kB] Get: 342 http://deb.debian.org/debian unstable/main arm64 libjformatstring-java all 0.10~20131207-2.1 [34.5 kB] Get: 343 http://deb.debian.org/debian unstable/main arm64 libfindbugs-java all 3.1.0~preview2-4 [3535 kB] Get: 344 http://deb.debian.org/debian unstable/main arm64 libaopalliance-java all 20070526-7 [8572 B] Get: 345 http://deb.debian.org/debian unstable/main arm64 libguice-java all 5.1.0-1 [932 kB] Get: 346 http://deb.debian.org/debian unstable/main arm64 libjatl-java all 0.2.3-1.1 [29.0 kB] Get: 347 http://deb.debian.org/debian unstable/main arm64 libjcifs-java all 1.3.19-2 [394 kB] Get: 348 http://deb.debian.org/debian unstable/main arm64 libjavaewah-java all 1.2.3-1 [159 kB] Get: 349 http://deb.debian.org/debian unstable/main arm64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 350 http://deb.debian.org/debian unstable/main arm64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 351 http://deb.debian.org/debian unstable/main arm64 libjetty9-java all 9.4.56-1 [2964 kB] Get: 352 http://deb.debian.org/debian unstable/main arm64 libjgit-java all 6.7.0-2 [3152 kB] Get: 353 http://deb.debian.org/debian unstable/main arm64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 354 http://deb.debian.org/debian unstable/main arm64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 355 http://deb.debian.org/debian unstable/main arm64 libmaven-resolver-1.6-java all 1.6.3-3 [558 kB] Get: 356 http://deb.debian.org/debian unstable/main arm64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 357 http://deb.debian.org/debian unstable/main arm64 libmaven-parent-java all 43-2 [6252 B] Get: 358 http://deb.debian.org/debian unstable/main arm64 libmaven-resolver-java all 1.9.22-1 [729 kB] Get: 359 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-utils-java all 3.4.2-1 [137 kB] Get: 360 http://deb.debian.org/debian unstable/main arm64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 361 http://deb.debian.org/debian unstable/main arm64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 362 http://deb.debian.org/debian unstable/main arm64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 363 http://deb.debian.org/debian unstable/main arm64 libplexus-interpolation-java all 1.27-1 [76.8 kB] Get: 364 http://deb.debian.org/debian unstable/main arm64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 365 http://deb.debian.org/debian unstable/main arm64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 366 http://deb.debian.org/debian unstable/main arm64 libcdi-api-java all 1.2-4 [55.3 kB] Get: 367 http://deb.debian.org/debian unstable/main arm64 libsisu-inject-java all 0.3.5-1 [352 kB] Get: 368 http://deb.debian.org/debian unstable/main arm64 libsisu-plexus-java all 0.3.5-1 [183 kB] Get: 369 http://deb.debian.org/debian unstable/main arm64 libmaven3-core-java all 3.9.9-1 [1661 kB] Get: 370 http://deb.debian.org/debian unstable/main arm64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 371 http://deb.debian.org/debian unstable/main arm64 libpolyglot-maven-java all 0.8~tobrien+git20120905-10 [74.9 kB] Get: 372 http://deb.debian.org/debian unstable/main arm64 librhino-java all 1.7.15-1 [1382 kB] Get: 373 http://deb.debian.org/debian unstable/main arm64 libsimple-http-java all 4.1.21-1.1 [211 kB] Get: 374 http://deb.debian.org/debian unstable/main arm64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 375 http://deb.debian.org/debian unstable/main arm64 libjsoup-java all 1.15.3-1 [431 kB] Get: 376 http://deb.debian.org/debian unstable/main arm64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 377 http://deb.debian.org/debian unstable/main arm64 libjcommander-java all 1.71-4 [73.0 kB] Get: 378 http://deb.debian.org/debian unstable/main arm64 testng all 6.9.12-4 [795 kB] Get: 379 http://deb.debian.org/debian unstable/main arm64 libgradle-plugins-java all 4.4.1-21 [5244 kB] Get: 380 http://deb.debian.org/debian unstable/main arm64 gradle all 4.4.1-21 [400 kB] Get: 381 http://deb.debian.org/debian unstable/main arm64 maven-repo-helper all 1.11 [142 kB] Get: 382 http://deb.debian.org/debian unstable/main arm64 gradle-debian-helper all 2.4 [24.5 kB] Get: 383 http://deb.debian.org/debian unstable/main arm64 jarwrapper all 0.80 [9692 B] Get: 384 http://deb.debian.org/debian unstable/main arm64 javahelper all 0.80 [80.4 kB] Get: 385 http://deb.debian.org/debian unstable/main arm64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 386 http://deb.debian.org/debian unstable/main arm64 libargs4j-java all 2.33-2 [138 kB] Get: 387 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 388 http://deb.debian.org/debian unstable/main arm64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 389 http://deb.debian.org/debian unstable/main arm64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 390 http://deb.debian.org/debian unstable/main arm64 libsnappy1v5 arm64 1.2.1-1+b1 [28.7 kB] Get: 391 http://deb.debian.org/debian unstable/main arm64 libsnappy-jni arm64 1.1.10.7-1 [6476 B] Get: 392 http://deb.debian.org/debian unstable/main arm64 libsnappy-java all 1.1.10.7-1 [87.6 kB] Get: 393 http://deb.debian.org/debian unstable/main arm64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 394 http://deb.debian.org/debian unstable/main arm64 libistack-commons-java all 3.0.6-5 [145 kB] Get: 395 http://deb.debian.org/debian unstable/main arm64 libcodemodel-java all 2.6+jaxb2.3.0.1-11 [164 kB] Get: 396 http://deb.debian.org/debian unstable/main arm64 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get: 397 http://deb.debian.org/debian unstable/main arm64 libcommons-collections4-java all 4.4-2 [682 kB] Get: 398 http://deb.debian.org/debian unstable/main arm64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 399 http://deb.debian.org/debian unstable/main arm64 libdtd-parser-java all 1.2-1 [64.9 kB] Get: 400 http://deb.debian.org/debian unstable/main arm64 libezmorph-java all 1.0.6-4 [75.9 kB] Get: 401 http://deb.debian.org/debian unstable/main arm64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 402 http://deb.debian.org/debian unstable/main arm64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 403 http://deb.debian.org/debian unstable/main arm64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 404 http://deb.debian.org/debian unstable/main arm64 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB] Get: 405 http://deb.debian.org/debian unstable/main arm64 libxsom-java all 2.3.0.1-11 [401 kB] Get: 406 http://deb.debian.org/debian unstable/main arm64 libfastinfoset-java all 1.2.12-3 [343 kB] Get: 407 http://deb.debian.org/debian unstable/main arm64 librngom-java all 2.3.0.1-11 [292 kB] Get: 408 http://deb.debian.org/debian unstable/main arm64 libtxw2-java all 2.3.0.1-11 [134 kB] Get: 409 http://deb.debian.org/debian unstable/main arm64 libjaxb-java all 2.3.0.1-11 [1980 kB] Get: 410 http://deb.debian.org/debian unstable/main arm64 libjimfs-java all 1.1-6 [191 kB] Get: 411 http://deb.debian.org/debian unstable/main arm64 libxom-java all 1.3.9-1 [174 kB] Get: 412 http://deb.debian.org/debian unstable/main arm64 libjson-java all 3.1.0+dfsg-2 [142 kB] Get: 413 http://deb.debian.org/debian unstable/main arm64 libmbedcrypto16 arm64 3.6.2-3 [341 kB] Get: 414 http://deb.debian.org/debian unstable/main arm64 libmbedx509-7 arm64 3.6.2-3 [146 kB] Get: 415 http://deb.debian.org/debian unstable/main arm64 libmbedtls21 arm64 3.6.2-3 [222 kB] Get: 416 http://deb.debian.org/debian unstable/main arm64 ncbi-vdb-data all 3.0.9+dfsg-2 [74.0 kB] Get: 417 http://deb.debian.org/debian unstable/main arm64 libncbi-vdb3 arm64 3.0.9+dfsg-2 [1110 kB] Get: 418 http://deb.debian.org/debian unstable/main arm64 libncbi-ngs3 arm64 3.0.9+dfsg-7+b1 [143 kB] Get: 419 http://deb.debian.org/debian unstable/main arm64 libngs-jni arm64 3.0.9+dfsg-7+b1 [25.8 kB] Get: 420 http://deb.debian.org/debian unstable/main arm64 libngs-java arm64 3.0.9+dfsg-7+b1 [112 kB] Get: 421 http://deb.debian.org/debian unstable/main arm64 scala-library all 2.11.12-5 [9588 kB] Fetched 351 MB in 3s (117 MB/s) Preconfiguring packages ... 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 ... 19975 files and directories currently installed.) Preparing to unpack .../libapparmor1_3.1.7-1+b3_arm64.deb ... Unpacking libapparmor1:arm64 (3.1.7-1+b3) ... Selecting previously unselected package libsystemd-shared:arm64. Preparing to unpack .../libsystemd-shared_257.1-5_arm64.deb ... Unpacking libsystemd-shared:arm64 (257.1-5) ... Selecting previously unselected package systemd. Preparing to unpack .../systemd_257.1-5_arm64.deb ... Unpacking systemd (257.1-5) ... Setting up libapparmor1:arm64 (3.1.7-1+b3) ... Setting up libsystemd-shared:arm64 (257.1-5) ... Setting up systemd (257.1-5) ... 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. /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 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 ... 20932 files and directories currently installed.) Preparing to unpack .../00-systemd-sysv_257.1-5_arm64.deb ... Unpacking systemd-sysv (257.1-5) ... Selecting previously unselected package libdbus-1-3:arm64. Preparing to unpack .../01-libdbus-1-3_1.16.0-1_arm64.deb ... Unpacking libdbus-1-3:arm64 (1.16.0-1) ... Selecting previously unselected package dbus-bin. 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Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package binfmt-support. Preparing to unpack .../09-binfmt-support_2.2.2-7+b1_arm64.deb ... Unpacking binfmt-support (2.2.2-7+b1) ... Selecting previously unselected package libpython3.12-minimal:arm64. Preparing to unpack .../10-libpython3.12-minimal_3.12.8-3_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.8-3) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../11-python3.12-minimal_3.12.8-3_arm64.deb ... Unpacking python3.12-minimal (3.12.8-3) ... Setting up libpython3.12-minimal:arm64 (3.12.8-3) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-3) ... Selecting previously unselected package python3-minimal. (Reading database ... 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Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../13-libnsl2_1.3.0-3+b3_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../14-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../15-libreadline8t64_8.2-6_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 (8.2-6) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../16-libpython3.12-stdlib_3.12.8-3_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.8-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../17-python3.12_3.12.8-3_arm64.deb ... Unpacking python3.12 (3.12.8-3) ... 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Selecting previously unselected package libgpg-error0:arm64. Preparing to unpack .../001-libgpg-error0_1.51-3_arm64.deb ... Unpacking libgpg-error0:arm64 (1.51-3) ... Selecting previously unselected package libgcrypt20:arm64. Preparing to unpack .../002-libgcrypt20_1.11.0-7_arm64.deb ... Unpacking libgcrypt20:arm64 (1.11.0-7) ... Selecting previously unselected package gpgv. Preparing to unpack .../003-gpgv_2.2.45-2_arm64.deb ... Unpacking gpgv (2.2.45-2) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../004-libproc2-0_2%3a4.0.4-6_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../005-procps_2%3a4.0.4-6_arm64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../006-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. 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Setting up libpixman-1-0:arm64 (0.44.0-3) ... Setting up libjcommander-java (1.71-4) ... Setting up libdtd-parser-java (1.2-1) ... Setting up wdiff (1.2.2-6+b1) ... Setting up libsharpyuv0:arm64 (1.4.0-0.1+b1) ... Setting up libslf4j-java (1.7.32-1) ... Setting up libfile-which-perl (1.27-2) ... Setting up systemd-sysv (257.1-5) ... Setting up libxau6:arm64 (1:1.0.11-1) ... Setting up libxdmcp6:arm64 (1:1.1.5-1) ... Setting up libplexus-utils2-java (3.4.2-1) ... Setting up libnpth0t64:arm64 (1.8-2) ... Setting up libkeyutils1:arm64 (1.6.3-4) ... Setting up libplexus-classworlds-java (2.7.0-1) ... Setting up libxcb1:arm64 (1.17.0-2+b1) ... Setting up libqdox-java (1.12.1-4) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up libxcb-xfixes0:arm64 (1.17.0-2+b1) ... Setting up liblerc4:arm64 (4.0.0+ds-5) ... Setting up libjsr305-java (0.1~+svn49-11) ... Setting up libsimple-http-java (4.1.21-1.1) ... Setting up bsdextrautils (2.40.2-13) ... Setting up hicolor-icon-theme (0.18-1) ... Setting up libgpg-error0:arm64 (1.51-3) ... Setting up java-common (0.76) ... Setting up libdynaloader-functions-perl (0.004-1) ... Setting up libdatrie1:arm64 (0.2.13-3+b1) ... 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+b2) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libxcb-render0:arm64 (1.17.0-2+b1) ... Setting up liblogback-java (1:1.2.11-6) ... Setting up libclone-perl:arm64 (0.47-1+b1) ... Setting up libminlog-java (1.3.1-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglvnd0:arm64 (1.7.0-1+b2) ... Setting up libgoogle-gson-java (2.10.1-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libxcb-glx0:arm64 (1.17.0-2+b1) ... Setting up unzip (6.0-28+b1) ... Setting up libdebhelper-perl (13.23) ... Setting up libbrotli1:arm64 (1.1.0-2+b6) ... Setting up libedit2:arm64 (3.1-20240808-1) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up libasm-java (9.7.1-1) ... Setting up libjs-jquery-ui-theme-base (1.12.1+dfsg-1.1) ... Setting up x11-common (1:7.7+23.1) ... Running in chroot, ignoring request. Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libtry-tiny-perl (0.32-1) ... Setting up libsensors-config (1:3.6.0-10) ... Setting up libdeflate0:arm64 (1.22-1) ... Setting up perl-openssl-defaults:arm64 (7+b2) ... Setting up libdd-plist-java (1.20-1.1) ... Setting up gettext-base (0.22.5-3) ... Setting up m4 (1.4.19-4) ... Setting up libel-api-java (3.0.0-3) ... Setting up libgcrypt20:arm64 (1.11.0-7) ... Setting up scala-library (2.11.12-5) ... Setting up xkb-data (2.42-1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libplexus-component-annotations-java (2.1.1-1) ... Setting up libxcb-shm0:arm64 (1.17.0-2+b1) ... Setting up libcom-err2:arm64 (1.47.2~rc1-2) ... Setting up file (1:5.45-3+b1) ... Setting up libpolyglot-maven-java (0.8~tobrien+git20120905-10) ... Setting up libfelix-gogo-runtime-java (0.16.2-1.1) ... Setting up libjzlib-java (1.1.3-3) ... Setting up libjbig0:arm64 (2.1-6.1+b2) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libsnappy1v5:arm64 (1.2.1-1+b1) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Dec 31 16:04:52 UTC 2024. Universal Time is now: Tue Dec 31 16:04:52 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:arm64 (1.17.0-2+b1) ... 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 (1.2.12-1) ... Setting up libreflectasm-java (1.11.9+dfsg-4) ... Setting up librhino-java (1.7.15-1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:arm64 (4.13.3-1) ... Setting up libbsf-java (1:2.4.0-8) ... Setting up libosgi-annotation-java (8.1.0-1) ... Setting up libjformatstring-java (0.10~20131207-2.1) ... Setting up libasound2t64:arm64 (1.2.12-1+b1) ... Setting up libjavaewah-java (1.2.3-1) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Setting up libjaxen-java (1.1.6-5) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libepoxy0:arm64 (1.5.10-2) ... Setting up libnspr4:arm64 (2:4.36-1) ... Setting up gnupg-l10n (2.2.45-2) ... Setting up libxcb-sync1:arm64 (1.17.0-2+b1) ... Setting up libeclipse-jdt-annotation-java (2.2.700+eclipse4.29-2) ... Setting up libjansi-java (2.4.1-2) ... Setting up libapache-pom-java (33-2) ... Setting up libavahi-common-data:arm64 (0.8-15) ... Setting up libxpp3-java (1.1.4c-3) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libdbus-1-3:arm64 (1.16.0-1) ... Setting up libwebsocket-api-java (1.1-2) ... Setting up libfribidi0:arm64 (1.0.16-1) ... Setting up libproc2-0:arm64 (2:4.0.4-6) ... Setting up libplexus-interpolation-java (1.27-1) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.44-3) ... 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 autopoint (0.22.5-3) ... Setting up binfmt-support (2.2.2-7+b1) ... 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 (0.22-3+b2) ... Setting up libjunixsocket-jni (2.6.1-1+b1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libfelix-framework-java (4.6.1-2.1) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up libpcsclite1:arm64 (2.3.1-1) ... Setting up libsensors5:arm64 (1:3.6.0-10+b1) ... Setting up libmongodb-java (3.6.3-2) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... 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 (24.2.8-1) ... Setting up libbsh-java (2.0b4-20) ... Setting up libjsp-api-java (2.3.4-3) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Setting up libvulkan1:arm64 (1.3.296.0-1) ... Setting up autoconf (2.72-3) ... Setting up libwebp7:arm64 (1.4.0-0.1+b1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libxcb-dri2-0:arm64 (1.17.0-2+b1) ... Setting up libgif7:arm64 (5.2.2-1+b1) ... Setting up libjarjar-java (1.4+svn142-12) ... Setting up libffi8:arm64 (3.4.6-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libxshmfence1:arm64 (1.3-1+b2) ... Setting up libjsoup-java (1.15.3-1) ... Setting up at-spi2-common (2.54.0-1) ... Setting up gpgv (2.2.45-2) ... Setting up libtiff6:arm64 (4.5.1+git230720-5) ... Setting up libxcb-randr0:arm64 (1.17.0-2+b1) ... Setting up dbus-session-bus-common (1.16.0-1) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libassuan9:arm64 (3.0.1-2) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up procps (2:4.0.4-6) ... Setting up libxbean-reflect-java (4.5-9) ... Setting up libservlet-api-java (4.0.1-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libtasn1-6:arm64 (4.19.0-3+b3) ... Setting up libx11-6:arm64 (2:1.8.10-2) ... Setting up ncbi-vdb-data (3.0.9+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+b1) ... Setting up libclass-xsaccessor-perl (1.19-4+b4) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libwayland-egl1:arm64 (1.23.0-1+b1) ... Setting up libmbedcrypto16:arm64 (3.6.2-3) ... 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 (1.16.0-1) ... useradd: Warning: missing or non-executable shell '/usr/sbin/nologin' 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-14) ... Setting up libyaml-snake-java (1.33-2) ... Setting up openssl (3.3.2-2) ... Setting up libdrm-common (2.4.123-1) ... Setting up libcdi-api-java (1.2-4) ... Setting up libsnappy-jni (1.1.10.7-1) ... Setting up libezmorph-java (1.0.6-4) ... Setting up libxcomposite1:arm64 (1:0.4.6-1) ... Setting up readline-common (8.2-6) ... Setting up libhawtjni-runtime-java (1.18-1) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up liburi-perl (5.30-1) ... Setting up dbus-bin (1.16.0-1) ... Setting up libargs4j-java (2.33-2) ... Setting up libfile-touch-perl (0.12-2) ... Setting up dctrl-tools (2.24-3+b1) ... Setting up libjatl-java (0.2.3-1.1) ... Setting up libxkbcommon0:arm64 (1.7.0-2) ... Setting up libwayland-client0:arm64 (1.23.0-1+b1) ... Setting up libnet-ssleay-perl:arm64 (1.94-2) ... 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 libksba8:arm64 (1.6.7-2+b1) ... Setting up pinentry-curses (1.2.1-5) ... Setting up libdom4j-java (2.1.4-1) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libxcb-dri3-0:arm64 (1.17.0-2+b1) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libnative-platform-java (0.14-6) ... Setting up libllvm19:arm64 (1:19.1.6-1) ... Setting up libwayland-server0:arm64 (1.23.0-1+b1) ... Setting up libosgi-core-java (8.0.0-2) ... Setting up libx11-xcb1:arm64 (2:1.8.10-2) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libxstream-java (1.4.21-1) ... Setting up libnekohtml-java (1.9.22.noko2-0.1) ... Setting up gettext (0.22.5-3) ... Setting up libjetty9-java (9.4.56-1) ... Setting up libxdamage1:arm64 (1:1.1.6-1+b2) ... Setting up java-wrappers (0.5) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libosgi-compendium-java (7.0.0-1) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b3) ... Setting up jarwrapper (0.80) ... Setting up libtool (2.4.7-8) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libstax-ex-java (1.7.8-3) ... Setting up libmaven-parent-java (43-2) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:arm64 (0.8-15) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:arm64 (2:1.3.4-1+b2) ... Setting up libnet-http-perl (6.23-1) ... Setting up libsisu-inject-java (0.3.5-1) ... Setting up libidn2-0:arm64 (2.3.7-2+b1) ... Setting up libnss3:arm64 (2:3.106-1) ... Setting up dbus-daemon (1.16.0-1) ... Setting up libxom-java (1.3.9-1) ... Setting up libdevel-callchecker-perl:arm64 (0.009-1+b1) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libjunixsocket-java (2.6.1-1) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up libxxf86vm1:arm64 (1:1.1.4-1+b3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1+b1) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up libthai0:arm64 (0.1.29-2+b1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.5-1) ... Setting up libglib2.0-0t64:arm64 (2.82.4-1) ... Setting up libmbedx509-7:arm64 (3.6.2-3) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libxfixes3:arm64 (1:6.0.0-2+b3) ... Setting up testng (6.9.12-4) ... Setting up dbus (1.16.0-1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up shared-mime-info (2.4-5+b1) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up libxinerama1:arm64 (2:1.1.4-3+b3) ... Setting up libstreambuffer-java (1.5.4-1.1) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libxrandr2:arm64 (2:1.5.4-1+b2) ... Setting up libcommons-collections4-java (4.4-2) ... Setting up libjna-jni (5.15.0-1) ... Setting up libcommons-lang3-java (3.17.0-1) ... Setting up libmbedtls21:arm64 (3.6.2-3) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libfelix-resolver-java (1.16.0-1) ... Setting up librngom-java (2.3.0.1-11) ... Setting up libdrm2:arm64 (2.4.123-1) ... Setting up libjansi-native-java (1.8-2) ... Setting up groff-base (1.23.0-7) ... Setting up libwayland-cursor0:arm64 (1.23.0-1+b1) ... Setting up libhtml-parser-perl:arm64 (3.83-1+b1) ... Setting up libjna-java (5.15.0-1) ... Setting up gpgconf (2.2.45-2) ... Setting up libpam-systemd:arm64 (257.1-5) ... Setting up libcommons-beanutils-java (1.9.4-2) ... Setting up libjansi1-java (1.18-3) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libharfbuzz0b:arm64 (10.1.0-2) ... Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-1+b1) ... Setting up libsnappy-java (1.1.10.7-1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1+b1) ... Setting up libxsom-java (2.3.0.1-11) ... 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 (1.17.1-1) ... Setting up libjline2-java (2.14.6-5) ... Setting up libavahi-client3:arm64 (0.8-15) ... Setting up libio-socket-ssl-perl (2.089-1) ... Setting up gpg (2.2.45-2) ... Setting up libhttp-message-perl (7.00-2) ... Setting up libdrm-amdgpu1:arm64 (2.4.123-1) ... Setting up libgnutls30t64:arm64 (3.8.8-2) ... Setting up gtk-update-icon-cache (4.16.7+ds-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up gpg-agent (2.2.45-2) ... 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 libatk1.0-0t64:arm64 (2.54.0-1) ... Setting up openjdk-21-jre-headless:arm64 (21.0.6~6ea-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libxi6:arm64 (2:1.8.2-1) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libcommons-io-java (2.17.0-1) ... Setting up libdrm-radeon1:arm64 (2.4.123-1) ... Setting up libxtst6:arm64 (2:1.2.3-1.1+b3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libxcursor1:arm64 (1:1.2.2-1+b1) ... Setting up libparams-classify-perl:arm64 (0.015-2+b4) ... Setting up gpgsm (2.2.45-2) ... Setting up libpango-1.0-0:arm64 (1.55.0+ds-3) ... Setting up libncbi-vdb3:arm64 (3.0.9+dfsg-2) ... Setting up libcloudproviders0:arm64 (0.3.6-1+b1) ... Setting up man-db (2.13.0-1) ... 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 libcairo2:arm64 (1.18.2-2) ... Setting up libldap-2.5-0:arm64 (2.5.19+dfsg-1) ... Setting up libcolord2:arm64 (1.4.7-1+b2) ... Setting up libmaven-resolver-1.6-java (1.6.3-3) ... Setting up libdconf1:arm64 (0.40.0-4+b3) ... Setting up dirmngr (2.2.45-2) ... Created symlink '/etc/systemd/user/sockets.target.wants/dirmngr.socket' -> '/usr/lib/systemd/user/dirmngr.socket'. Setting up openjdk-21-doc (21.0.6~6ea-1) ... Setting up dbus-user-session (1.16.0-1) ... Setting up libmaven-resolver-java (1.9.22-1) ... Setting up libbcel-java (6.10.0-1) ... Setting up adwaita-icon-theme (47.0-2) ... 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 libatspi2.0-0t64:arm64 (2.54.0-1) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libnsl2:arm64 (1.3.0-3+b3) ... Setting up gnupg (2.2.45-2) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libcairo-gobject2:arm64 (1.18.2-2) ... Setting up libmaven-shared-utils-java (3.4.2-1) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up libpangoft2-1.0-0:arm64 (1.55.0+ds-3) ... Setting up libcups2t64:arm64 (2.4.10-2+b1) ... Setting up libpangocairo-1.0-0:arm64 (1.55.0+ds-3) ... Setting up libncbi-ngs3:arm64 (3.0.9+dfsg-7+b1) ... Setting up libatk-bridge2.0-0t64:arm64 (2.54.0-1) ... Setting up mesa-libgallium:arm64 (24.2.8-1) ... Setting up libngs-jni:arm64 (3.0.9+dfsg-7+b1) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libfindbugs-java (3.1.0~preview2-4) ... Setting up libpython3.12-stdlib:arm64 (3.12.8-3) ... Setting up libcommons-compress-java (1.27.1-2) ... Setting up libgbm1:arm64 (24.2.8-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up liblog4j2-java (2.19.0-2) ... Setting up python3.12 (3.12.8-3) ... Setting up libgl1-mesa-dri:arm64 (24.2.8-1) ... Setting up debhelper (13.23) ... Setting up dconf-service (0.40.0-4+b3) ... Setting up default-jdk-doc (2:1.21-76) ... Setting up libjsch-java (0.2.19-1) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libngs-java:arm64 (3.0.9+dfsg-7+b1) ... Setting up libpython3-stdlib:arm64 (3.12.8-1) ... Setting up libjgit-java (6.7.0-2) ... Setting up libglx-mesa0:arm64 (24.2.8-1) ... Setting up libglx0:arm64 (1.7.0-1+b2) ... Setting up dconf-gsettings-backend:arm64 (0.40.0-4+b3) ... Setting up python3 (3.12.8-1) ... Setting up sopv-gpgv (0.1.1-1) ... update-alternatives: using /usr/bin/sopv-gpgv to provide /usr/bin/sopv (sopv) in auto mode Setting up libgl1:arm64 (1.7.0-1+b2) ... Setting up libgtk-3-common (3.24.43-4) ... Setting up libgtk-3-0t64:arm64 (3.24.43-4) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libwww-perl (6.77-1) ... Setting up devscripts (2.24.9) ... Setting up libguava-java (32.0.1-1) ... Setting up javahelper (0.80) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libguice-java (5.1.0-1) ... Setting up libmaven3-core-java (3.9.9-1) ... 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 (2.40-4) ... Processing triggers for systemd (257.1-5) ... 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:FIRMAPROFESIONAL_CA_ROOT-A_WEB.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:SecureSign_Root_CA12.pem Adding debian:SecureSign_Root_CA14.pem Adding debian:SecureSign_Root_CA15.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: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_CYBER_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem Adding debian:Telekom_Security_TLS_RSA_Root_2023.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-14) ... Setting up openjdk-21-jre:arm64 (21.0.6~6ea-1) ... Setting up ivy (2.5.2-1) ... Setting up ant (1.10.15-1) ... Setting up junit4 (4.13.2-5) ... 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 openjdk-21-jdk-headless:arm64 (21.0.6~6ea-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre-headless (2:1.21-76) ... Setting up maven-repo-helper (1.11) ... Setting up default-jre (2:1.21-76) ... Setting up ant-optional (1.10.15-1) ... Setting up openjdk-21-jdk:arm64 (21.0.6~6ea-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up bnd (5.0.1-5) ... Setting up default-jdk-headless (2:1.21-76) ... Setting up libgradle-core-java (4.4.1-21) ... Setting up libgradle-plugins-java (4.4.1-21) ... Setting up libjson-java (3.1.0+dfsg-2) ... Setting up gradle (4.4.1-21) ... Setting up libistack-commons-java (3.0.6-5) ... Setting up default-jdk (2:1.21-76) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-11) ... Setting up gradle-debian-helper (2.4) ... Setting up libtxw2-java (2.3.0.1-11) ... Setting up libjaxb-java (2.3.0.1-11) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/1704786/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/1704786/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/htsjdk-4.1.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../htsjdk_4.1.3+dfsg-2_source.changes dpkg-buildpackage: info: source package htsjdk dpkg-buildpackage: info: source version 4.1.3+dfsg-2 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-4.1.3\+dfsg/.gradle /build/reproducible-path/htsjdk-4.1.3\+dfsg/buildSrc/.gradle .m2 dh_autoreconf_clean -O--buildsystem=gradle jh_clean -O--buildsystem=gradle rm -fr debian/_jh_manifest* debian/_jh_build* Duplicate specification "u=s" for option "u" Duplicate specification "unlink|u" for option "u" 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 execute_after_dh_clean make[1]: Entering directory '/build/reproducible-path/htsjdk-4.1.3+dfsg' # Restoring test file we skipped. if [ -e VariantContextBuilderTest.java ]; then \ mv VariantContextBuilderTest.java src/test/java/htsjdk/variant/variantcontext/; \ fi make[1]: Leaving directory '/build/reproducible-path/htsjdk-4.1.3+dfsg' 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 debian/rules execute_before_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/htsjdk-4.1.3+dfsg' # Skipping this test file to avoid exception: # org.gradle.api.GradleException: failed to read class file /build/reproducible-path/htsjdk-4.1.3+dfsg/build/classes/java/test/htsjdk/variant/variantcontext/VariantContextBuilderTestCBuilderScheme.class mv src/test/java/htsjdk/variant/variantcontext/VariantContextBuilderTest.java . make[1]: Leaving directory '/build/reproducible-path/htsjdk-4.1.3+dfsg' dh_auto_configure -O--buildsystem=gradle jh_linkjars -O--buildsystem=gradle Duplicate specification "u=s" for option "u" Duplicate specification "unlink|u" for option "u" debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/htsjdk-4.1.3+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 "21.0.6-ea" 2025-01-21 OpenJDK Runtime Environment (build 21.0.6-ea+6-Debian-1) OpenJDK 64-Bit Server VM (build 21.0.6-ea+6-Debian-1, mixed mode, sharing) Initialized native services in: /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-21-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 2.315 secs. The client will now receive all logging from the daemon (pid: 1762462). The daemon log file: /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/daemon/4.4.1/daemon-1762462.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-4.1.3+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@48106eba Creating new cache for resourceHashesCache, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@48106eba Creating new cache for fileHashes, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@280c1b61 Starting Build Compiling initialization script '/build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer. Creating new cache for metadata-1.1/results, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@8a5133d Compiling initialization script '/build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer. Compiling settings file '/build/reproducible-path/htsjdk-4.1.3+dfsg/settings.gradle' using SubsetScriptTransformer. Compiling settings file '/build/reproducible-path/htsjdk-4.1.3+dfsg/settings.gradle' using BuildScriptTransformer. Settings evaluated using settings file '/build/reproducible-path/htsjdk-4.1.3+dfsg/settings.gradle'. Projects loaded. Root project using build file '/build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/build.gradle'. Compiling build file '/build/reproducible-path/htsjdk-4.1.3+dfsg/build.gradle' using SubsetScriptTransformer. Compiling build file '/build/reproducible-path/htsjdk-4.1.3+dfsg/build.gradle' using BuildScriptTransformer. Starting process 'command 'dpkg-parsechangelog''. Working directory: /build/reproducible-path/htsjdk-4.1.3+dfsg Command: dpkg-parsechangelog -S Version Successfully started process 'command 'dpkg-parsechangelog'' build for version:4.1.3 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-4.1.3+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@1c4f67fd 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-4.1.3+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@280c1b61 Creating new cache for taskHistory, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@7d3c248c Creating new cache for outputFiles, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@4b622c4d :compileJava (Thread[#55,Task worker for ':',5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.004 secs. Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@6c40e7d0 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:1.3.0 -> 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:1.25.0 -> org.apache.commons:commons-compress:jar:debian Replacing org.tukaani:xz:jar:1.9 -> org.tukaani:xz:jar:debian Replacing org.json:json:jar:20231013 -> org.kordamp.json:json-lib-core: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 commons-codec:commons-codec:jar:debian Passing through commons-io:commons-io:jar:debian Passing through commons-beanutils:commons-beanutils:jar:debian Passing through junit:junit:jar:4.x Passing through net.sf.ezmorph:ezmorph:jar:debian Passing through org.apache.commons:commons-collections4:jar:debian Passing through org.apache.commons:commons-lang3:jar:debian Passing through org.slf4j:slf4j-api:jar:debian Passing through org.slf4j:slf4j-parent:jar:debian Passing through xom:xom:jar:debian Passing through com.sun.activation:javax.activation:jar:debian Passing through com.sun.activation:all:jar:debian Passing through commons-collections:commons-collections:jar:3.x Passing through org.hamcrest:hamcrest:jar:debian Passing through commons-lang:commons-lang:jar:debian Passing through xerces:xercesImpl:jar:debian Passing through jaxen:jaxen:jar:debian Passing through xml-apis:xml-apis-1.4:jar:debian Up-to-date check for task ':compileJava' took 5.732 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. /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/DiskBackedQueue.java:258: warning: [removal] finalize() in Object has been deprecated and marked for removal protected void finalize() throws Throwable { ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/DiskBackedQueue.java:260: warning: [removal] finalize() in Object has been deprecated and marked for removal super.finalize(); // NB: intellij wanted me to do this. Need I? I'm not extending anything ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/FileAppendStreamLRUCache.java:59: warning: [removal] runFinalization() in System has been deprecated and marked for removal System.runFinalization(); ^ 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. 3 warnings :compileJava (Thread[#55,Task worker for ':',5,main]) completed. Took 29.104 secs. :processResources (Thread[#55,Task worker for ':',5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. Up-to-date check for task ':processResources' took 0.007 secs. It is not up-to-date because: No history is available. :processResources (Thread[#55,Task worker for ':',5,main]) completed. Took 0.061 secs. :classes (Thread[#55,Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes (Thread[#55,Task worker for ':',5,main]) completed. Took 0.0 secs. :debianMavenPom (Thread[#55,Task worker for ':',5,main]) started. :debianMavenPom Putting task artifact state for task ':debianMavenPom' into context took 0.0 secs. Up-to-date check for task ':debianMavenPom' took 0.007 secs. It is not up-to-date because: No history is available. Generating pom file /build/reproducible-path/htsjdk-4.1.3+dfsg/build/debian/htsjdk.pom :debianMavenPom (Thread[#55,Task worker for ':',5,main]) completed. Took 0.161 secs. :jar (Thread[#55,Task worker for ':',5,main]) started. :jar Putting task artifact state for task ':jar' into context took 0.0 secs. Up-to-date check for task ':jar' took 0.065 secs. It is not up-to-date because: No history is available. :jar (Thread[#55,Task worker for ':',5,main]) completed. Took 0.745 secs. :javadoc (Thread[#55,Task worker for ':',5,main]) started. :javadoc Putting task artifact state for task ':javadoc' into context took 0.0 secs. Up-to-date check for task ':javadoc' took 0.885 secs. It is not up-to-date because: No history is available. Starting process 'command '/usr/lib/jvm/java-21-openjdk-arm64/bin/javadoc''. Working directory: /build/reproducible-path/htsjdk-4.1.3+dfsg Command: /usr/lib/jvm/java-21-openjdk-arm64/bin/javadoc @/build/reproducible-path/htsjdk-4.1.3+dfsg/build/tmp/javadoc/javadoc.options Successfully started process 'command '/usr/lib/jvm/java-21-openjdk-arm64/bin/javadoc'' /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java:211: warning: invalid input: '<' * Closes inner SamIterator. ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java:211: warning: invalid input: '<' * Closes inner SamIterator. ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java:52: warning: invalid input: 'instead' * @deprecated Use {@link #setAttribute(String, String) instead ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java:52: warning: invalid input: 'instead' * @deprecated Use {@link #setAttribute(String, String) instead ^ /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:140: warning: invalid input: '<' * @param compressionLevel 1 <= compressionLevel <= 9 ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:140: warning: invalid input: '<' * @param compressionLevel 1 <= compressionLevel <= 9 ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:148: warning: invalid input: '<' * @param compressionLevel 1 <= compressionLevel <= 9 ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:148: warning: invalid input: '<' * @param compressionLevel 1 <= compressionLevel <= 9 ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:158: warning: invalid input: '<' * @param compressionLevel 1 <= compressionLevel <= 9 ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:158: warning: invalid input: '<' * @param compressionLevel 1 <= compressionLevel <= 9 ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:167: warning: invalid input: '<' * @param compressionLevel 1 <= compressionLevel <= 9 ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:167: warning: invalid input: '<' * @param compressionLevel 1 <= compressionLevel <= 9 ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:64: warning: invalid input: '<' * @param compressionLevel 1 <= compressionLevel <= 9 ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:64: warning: invalid input: '<' * @param compressionLevel 1 <= compressionLevel <= 9 ^ /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+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-4.1.3+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. * @return a new CompressionHeader ^ /build/reproducible-path/htsjdk-4.1.3+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. * @return a new {@link ContainerHeader} object with container header values filled out but empty body (no slices and blocks). ^ /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/FormatUtil.java:97: warning: invalid input: '&' /** Formats date & time */ ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/FormatUtil.java:97: warning: invalid input: '&' /** Formats date & time */ ^ /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+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-4.1.3+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeLikelihoods.java:443: warning: invalid input: '<' * @throws IllegalArgumentException if altAlleles or ploidy <= 0 ^ /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+dfsg/src/main/java/htsjdk/beta/plugin/HtsCodec.java:79: warning: reference not found: htsjdk.beta.plugin.features *
  • For {@link HtsContentType#FEATURES} codecs, see the {@link htsjdk.beta.plugin.features} package
    • ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/beta/plugin/HtsContentType.java:18: warning: reference not found: htsjdk.beta.plugin.features *
  • For {@link HtsContentType#FEATURES} codecs, see the {@link htsjdk.beta.plugin.features} package
    • ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/beta/plugin/HtsContentType.java:46: warning: reference not found: htsjdk.beta.plugin.features * Features content type (see {@link htsjdk.beta.plugin.features} for related formats) ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/beta/plugin/HtsContentType.java:46: warning: reference not found: htsjdk.beta.plugin.features * Features content type (see {@link htsjdk.beta.plugin.features} for related formats) ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/io/HtsPath.java:55: warning: invalid input: '<' * : ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/io/HtsPath.java:68: warning: invalid input: '&' * uric_no_slash = unreserved | escaped | ";" | "?" | ":" | "@" | "&" | "=" | "+" | "$" | "," ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/io/IOPath.java:55: warning: invalid input: '{@code java.nio File System * returns the reason code). ^ 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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+dfsg/src/main/java/htsjdk/io/IOPath.java:55: warning: invalid input: '{@code java.nio File System * returns the reason code). ^ 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-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/IOUtil.java:167: warning: invalid input: '<' * @param compressionLevel 0 <= compressionLevel <= 9 ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/IOUtil.java:167: warning: invalid input: '<' * @param compressionLevel 0 <= compressionLevel <= 9 ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/cram/io/ITF8.java:17: warning: invalid input: '<' * If highest bit < 8: ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/tribble/index/linear/LinearIndex.java:166: warning: invalid input: '<' * <= ((i + 1) * binWidth)) ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/tribble/readers/LongLineBufferedReader.java:75: warning: invalid input: '<' * @throws IllegalArgumentException If sz is <= 0 ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/tribble/readers/LongLineBufferedReader.java:453: warning: invalid input: '<' * @throws IllegalArgumentException If readAheadLimit is < 0 ^ /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/main/java/htsjdk/samtools/SAMFileHeader.java:291: warning: invalid input: 'instead' * @deprecated Use {@link #setAttribute(String, String) instead ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/SAMFileHeader.java:291: warning: invalid input: 'instead' * @deprecated Use {@link #setAttribute(String, String) instead ^ /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/main/java/htsjdk/samtools/SAMLineParser.java:221: warning: invalid input: '<' * can be <=0. ^ /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:166: warning: invalid input: '<' * abs(insertSize) must be <= this ^ /build/reproducible-path/htsjdk-4.1.3+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.' * @return 1-based inclusive leftmost position of the clipped sequence, or 0 if there is no position. ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:166: warning: invalid input: '<' * abs(insertSize) must be <= this ^ /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+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.' * @return 1-based inclusive leftmost position of the clipped sequence, or 0 if there is no position. ^ /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:39: warning: invalid input: '<' * if A < B, then B > A ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning: invalid input: '<' * if A < B && B < C, then A < C ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning: invalid input: '&' * if A < B && B < C, then A < C ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning: invalid input: '&' * if A < B && B < C, then A < C ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning: invalid input: '<' * if A < B && B < C, then A < C ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning: invalid input: '<' * if A < B && B < C, then A < C ^ /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:646: warning: invalid input: '<' * @return negative if mapq1 < mapq2, etc. ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:647: warning: invalid input: '<' * Note that MAPQ(0) < MAPQ(255) < MAPQ(1) ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:647: warning: invalid input: '<' * Note that MAPQ(0) < MAPQ(255) < MAPQ(1) ^ /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+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. * @return a Slice corresponding to the given records ^ /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+dfsg/src/main/java/htsjdk/beta/plugin/variants/VariantsBundle.java:20: warning: reference not found: BundleResourceType#PRIMARY_CT_VARIANT_CONTEXTS * htsjdk.beta.plugin.variants.VariantsBundle} has a primary resource with content type {@link ^ /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+dfsg/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java:52: warning: invalid input: 'instead' * @deprecated Use {@link #setAttribute(String, String) instead ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/SAMFileHeader.java:291: warning: invalid input: 'instead' * @deprecated Use {@link #setAttribute(String, String) instead ^ /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+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-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java:211: warning: invalid input: '<' * Closes inner SamIterator. ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/beta/plugin/HtsContentType.java:46: warning: reference not found: htsjdk.beta.plugin.features * Features content type (see {@link htsjdk.beta.plugin.features} for related formats) ^ 100 warnings :javadoc (Thread[#55,Task worker for ':',5,main]) completed. Took 24.256 secs. BUILD SUCCESSFUL in 1m 6s 5 actionable tasks: 5 executed make[1]: Leaving directory '/build/reproducible-path/htsjdk-4.1.3+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-4.1.3+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 "21.0.6-ea" 2025-01-21 OpenJDK Runtime Environment (build 21.0.6-ea+6-Debian-1) OpenJDK 64-Bit Server VM (build 21.0.6-ea+6-Debian-1, mixed mode, sharing) Initialized native services in: /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-21-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 2.227 secs. The client will now receive all logging from the daemon (pid: 1774021). The daemon log file: /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/daemon/4.4.1/daemon-1774021.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-4.1.3+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@4b47697a Creating new cache for resourceHashesCache, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@4b47697a Creating new cache for fileHashes, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@4b065447 Starting Build Creating new cache for metadata-1.1/results, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@7c96608 Settings evaluated using settings file '/build/reproducible-path/htsjdk-4.1.3+dfsg/settings.gradle'. Projects loaded. Root project using build file '/build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/build.gradle'. Starting process 'command 'dpkg-parsechangelog''. Working directory: /build/reproducible-path/htsjdk-4.1.3+dfsg Command: dpkg-parsechangelog -S Version Successfully started process 'command 'dpkg-parsechangelog'' build for version:4.1.3 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-4.1.3+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@273f8b63 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-4.1.3+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@4b065447 Creating new cache for taskHistory, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@4c57c17c Creating new cache for outputFiles, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@2e4cf05 :compileJava (Thread[#55,Task worker for ':',5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.168 secs. Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@2e4926d2 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:1.3.0 -> 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:1.25.0 -> org.apache.commons:commons-compress:jar:debian Replacing org.tukaani:xz:jar:1.9 -> org.tukaani:xz:jar:debian Replacing org.json:json:jar:20231013 -> org.kordamp.json:json-lib-core: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 commons-codec:commons-codec:jar:debian Passing through commons-io:commons-io:jar:debian Passing through commons-beanutils:commons-beanutils:jar:debian Passing through junit:junit:jar:4.x Passing through net.sf.ezmorph:ezmorph:jar:debian Passing through org.apache.commons:commons-collections4:jar:debian Passing through org.apache.commons:commons-lang3:jar:debian Passing through org.slf4j:slf4j-api:jar:debian Passing through org.slf4j:slf4j-parent:jar:debian Passing through xom:xom:jar:debian Passing through com.sun.activation:javax.activation:jar:debian Passing through com.sun.activation:all:jar:debian Passing through commons-collections:commons-collections:jar:3.x Passing through org.hamcrest:hamcrest:jar:debian Passing through commons-lang:commons-lang:jar:debian Passing through xerces:xercesImpl:jar:debian Passing through jaxen:jaxen:jar:debian Passing through xml-apis:xml-apis-1.4:jar:debian Skipping task ':compileJava' as it is up-to-date (took 2.833 secs). :compileJava UP-TO-DATE :compileJava (Thread[#55,Task worker for ':',5,main]) completed. Took 3.096 secs. :processResources (Thread[#36,Daemon worker,5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. Skipping task ':processResources' as it is up-to-date (took 0.017 secs). :processResources UP-TO-DATE :processResources (Thread[#36,Daemon worker,5,main]) completed. Took 0.028 secs. :classes (Thread[#36,Daemon worker,5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes UP-TO-DATE :classes (Thread[#36,Daemon worker,5,main]) completed. Took 0.0 secs. :compileTestJava (Thread[#36,Daemon worker,5,main]) started. :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.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:59) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter.execute(DefaultTaskGraphExecuter.java:128) at org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23) at org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43) at org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:46) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30) at org.gradle.initialization.DefaultGradleLauncher$ExecuteTasks.run(DefaultGradleLauncher.java:314) 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.initialization.DefaultGradleLauncher.runTasks(DefaultGradleLauncher.java:204) at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:134) at org.gradle.initialization.DefaultGradleLauncher.executeTasks(DefaultGradleLauncher.java:109) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:78) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:75) at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:152) at org.gradle.internal.invocation.GradleBuildController.doBuild(GradleBuildController.java:100) at org.gradle.internal.invocation.GradleBuildController.run(GradleBuildController.java:75) at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28) at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35) at org.gradle.tooling.internal.provider.ValidatingBuildActionRunner.run(ValidatingBuildActionRunner.java:32) at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$1.run(RunAsBuildOperationBuildActionRunner.java:43) at org.gradle.internal.progress.DefaultBuildOperationExecutor$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.launcher.exec.RunAsBuildOperationBuildActionRunner.run(RunAsBuildOperationBuildActionRunner.java:40) at org.gradle.tooling.internal.provider.SubscribableBuildActionRunner.run(SubscribableBuildActionRunner.java:51) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:47) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:30) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:39) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:80) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:53) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:57) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:32) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:36) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:43) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:29) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:69) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:30) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:59) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:44) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:45) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:30) at org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:67) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:37) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:74) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:72) at org.gradle.util.Swapper.swap(Swapper.java:38) at org.gradle.launcher.daemon.server.exec.ForwardClientInput.execute(ForwardClientInput.java:72) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:50) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:62) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:82) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50) at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:295) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) Malformed class file [SamFlagField.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) at org.gradle.api.internal.changedetection.state.ClasspathEntrySnapshotBuilder.visitFileSnapshot(ClasspathEntrySnapshotBuilder.java:62) at org.gradle.api.internal.changedetection.state.FileTree.visit(FileTree.java:36) at org.gradle.api.internal.changedetection.state.AbstractClasspathSnapshotBuilder.visitFileTreeSnapshot(AbstractClasspathSnapshotBuilder.java:66) at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$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.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:59) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter.execute(DefaultTaskGraphExecuter.java:128) at org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23) at org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43) at org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:46) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30) at org.gradle.initialization.DefaultGradleLauncher$ExecuteTasks.run(DefaultGradleLauncher.java:314) 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.initialization.DefaultGradleLauncher.runTasks(DefaultGradleLauncher.java:204) at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:134) at org.gradle.initialization.DefaultGradleLauncher.executeTasks(DefaultGradleLauncher.java:109) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:78) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:75) at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:152) at org.gradle.internal.invocation.GradleBuildController.doBuild(GradleBuildController.java:100) at org.gradle.internal.invocation.GradleBuildController.run(GradleBuildController.java:75) at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28) at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35) at org.gradle.tooling.internal.provider.ValidatingBuildActionRunner.run(ValidatingBuildActionRunner.java:32) at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$1.run(RunAsBuildOperationBuildActionRunner.java:43) at org.gradle.internal.progress.DefaultBuildOperationExecutor$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.launcher.exec.RunAsBuildOperationBuildActionRunner.run(RunAsBuildOperationBuildActionRunner.java:40) at org.gradle.tooling.internal.provider.SubscribableBuildActionRunner.run(SubscribableBuildActionRunner.java:51) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:47) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:30) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:39) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:80) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:53) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:57) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:32) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:36) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:43) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:29) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:69) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:30) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:59) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:44) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:45) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:30) at org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:67) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:37) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:74) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:72) at org.gradle.util.Swapper.swap(Swapper.java:38) at org.gradle.launcher.daemon.server.exec.ForwardClientInput.execute(ForwardClientInput.java:72) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:50) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:62) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:82) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50) at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:295) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) Malformed class file [SamReaderFactory$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.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:59) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter.execute(DefaultTaskGraphExecuter.java:128) at org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23) at org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43) at org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:46) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30) at org.gradle.initialization.DefaultGradleLauncher$ExecuteTasks.run(DefaultGradleLauncher.java:314) 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.initialization.DefaultGradleLauncher.runTasks(DefaultGradleLauncher.java:204) at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:134) at org.gradle.initialization.DefaultGradleLauncher.executeTasks(DefaultGradleLauncher.java:109) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:78) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:75) at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:152) at org.gradle.internal.invocation.GradleBuildController.doBuild(GradleBuildController.java:100) at org.gradle.internal.invocation.GradleBuildController.run(GradleBuildController.java:75) at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28) at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35) at org.gradle.tooling.internal.provider.ValidatingBuildActionRunner.run(ValidatingBuildActionRunner.java:32) at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$1.run(RunAsBuildOperationBuildActionRunner.java:43) at org.gradle.internal.progress.DefaultBuildOperationExecutor$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.launcher.exec.RunAsBuildOperationBuildActionRunner.run(RunAsBuildOperationBuildActionRunner.java:40) at org.gradle.tooling.internal.provider.SubscribableBuildActionRunner.run(SubscribableBuildActionRunner.java:51) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:47) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:30) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:39) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:80) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:53) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:57) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:32) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:36) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:43) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:29) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:69) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:30) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:59) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:44) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:45) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:30) at org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:67) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:37) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:74) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:72) at org.gradle.util.Swapper.swap(Swapper.java:38) at org.gradle.launcher.daemon.server.exec.ForwardClientInput.execute(ForwardClientInput.java:72) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:50) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:62) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:82) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50) at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:295) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) Malformed class file [SRALazyRecord$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.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:59) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter.execute(DefaultTaskGraphExecuter.java:128) at org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23) at org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43) at org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:46) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30) at org.gradle.initialization.DefaultGradleLauncher$ExecuteTasks.run(DefaultGradleLauncher.java:314) 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.initialization.DefaultGradleLauncher.runTasks(DefaultGradleLauncher.java:204) at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:134) at org.gradle.initialization.DefaultGradleLauncher.executeTasks(DefaultGradleLauncher.java:109) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:78) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:75) at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:152) at org.gradle.internal.invocation.GradleBuildController.doBuild(GradleBuildController.java:100) at org.gradle.internal.invocation.GradleBuildController.run(GradleBuildController.java:75) at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28) at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35) at org.gradle.tooling.internal.provider.ValidatingBuildActionRunner.run(ValidatingBuildActionRunner.java:32) at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$1.run(RunAsBuildOperationBuildActionRunner.java:43) at org.gradle.internal.progress.DefaultBuildOperationExecutor$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.launcher.exec.RunAsBuildOperationBuildActionRunner.run(RunAsBuildOperationBuildActionRunner.java:40) at org.gradle.tooling.internal.provider.SubscribableBuildActionRunner.run(SubscribableBuildActionRunner.java:51) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:47) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:30) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:39) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:80) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:53) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:57) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:32) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:36) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:43) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:29) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:69) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:30) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:59) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:44) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:45) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:30) at org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:67) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:37) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:74) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:72) at org.gradle.util.Swapper.swap(Swapper.java:38) at org.gradle.launcher.daemon.server.exec.ForwardClientInput.execute(ForwardClientInput.java:72) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:50) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:62) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:82) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50) at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:295) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) Malformed class file [SRALazyRecord$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.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:59) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter.execute(DefaultTaskGraphExecuter.java:128) at org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23) at org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43) at org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:46) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30) at org.gradle.initialization.DefaultGradleLauncher$ExecuteTasks.run(DefaultGradleLauncher.java:314) 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.initialization.DefaultGradleLauncher.runTasks(DefaultGradleLauncher.java:204) at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:134) at org.gradle.initialization.DefaultGradleLauncher.executeTasks(DefaultGradleLauncher.java:109) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:78) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:75) at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:152) at org.gradle.internal.invocation.GradleBuildController.doBuild(GradleBuildController.java:100) at org.gradle.internal.invocation.GradleBuildController.run(GradleBuildController.java:75) at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28) at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35) at org.gradle.tooling.internal.provider.ValidatingBuildActionRunner.run(ValidatingBuildActionRunner.java:32) at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$1.run(RunAsBuildOperationBuildActionRunner.java:43) at org.gradle.internal.progress.DefaultBuildOperationExecutor$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.launcher.exec.RunAsBuildOperationBuildActionRunner.run(RunAsBuildOperationBuildActionRunner.java:40) at org.gradle.tooling.internal.provider.SubscribableBuildActionRunner.run(SubscribableBuildActionRunner.java:51) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:47) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:30) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:39) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:80) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:53) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:57) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:32) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:36) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:43) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:29) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:69) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:30) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:59) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:44) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:45) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:30) at org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:67) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:37) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:74) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:72) at org.gradle.util.Swapper.swap(Swapper.java:38) at org.gradle.launcher.daemon.server.exec.ForwardClientInput.execute(ForwardClientInput.java:72) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:50) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:62) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:82) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50) at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:295) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) Malformed class file [SRALazyRecord$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.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:59) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter.execute(DefaultTaskGraphExecuter.java:128) at org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23) at org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43) at org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:46) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30) at org.gradle.initialization.DefaultGradleLauncher$ExecuteTasks.run(DefaultGradleLauncher.java:314) 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.initialization.DefaultGradleLauncher.runTasks(DefaultGradleLauncher.java:204) at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:134) at org.gradle.initialization.DefaultGradleLauncher.executeTasks(DefaultGradleLauncher.java:109) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:78) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:75) at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:152) at org.gradle.internal.invocation.GradleBuildController.doBuild(GradleBuildController.java:100) at org.gradle.internal.invocation.GradleBuildController.run(GradleBuildController.java:75) at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28) at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35) at org.gradle.tooling.internal.provider.ValidatingBuildActionRunner.run(ValidatingBuildActionRunner.java:32) at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$1.run(RunAsBuildOperationBuildActionRunner.java:43) at org.gradle.internal.progress.DefaultBuildOperationExecutor$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.launcher.exec.RunAsBuildOperationBuildActionRunner.run(RunAsBuildOperationBuildActionRunner.java:40) at org.gradle.tooling.internal.provider.SubscribableBuildActionRunner.run(SubscribableBuildActionRunner.java:51) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:47) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:30) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:39) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:80) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:53) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:57) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:32) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:36) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:43) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:29) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:69) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:30) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:59) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:44) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:45) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:30) at org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:67) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:37) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:74) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:72) at org.gradle.util.Swapper.swap(Swapper.java:38) at org.gradle.launcher.daemon.server.exec.ForwardClientInput.execute(ForwardClientInput.java:72) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:50) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:62) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:82) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50) at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:295) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) Malformed class file [ContentDigests$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.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:59) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter.execute(DefaultTaskGraphExecuter.java:128) at org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23) at org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43) at org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:46) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30) at org.gradle.initialization.DefaultGradleLauncher$ExecuteTasks.run(DefaultGradleLauncher.java:314) 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.initialization.DefaultGradleLauncher.runTasks(DefaultGradleLauncher.java:204) at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:134) at org.gradle.initialization.DefaultGradleLauncher.executeTasks(DefaultGradleLauncher.java:109) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:78) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:75) at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:152) at org.gradle.internal.invocation.GradleBuildController.doBuild(GradleBuildController.java:100) at org.gradle.internal.invocation.GradleBuildController.run(GradleBuildController.java:75) at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28) at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35) at org.gradle.tooling.internal.provider.ValidatingBuildActionRunner.run(ValidatingBuildActionRunner.java:32) at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$1.run(RunAsBuildOperationBuildActionRunner.java:43) at org.gradle.internal.progress.DefaultBuildOperationExecutor$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.launcher.exec.RunAsBuildOperationBuildActionRunner.run(RunAsBuildOperationBuildActionRunner.java:40) at org.gradle.tooling.internal.provider.SubscribableBuildActionRunner.run(SubscribableBuildActionRunner.java:51) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:47) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:30) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:39) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:80) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:53) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:57) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:32) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:36) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:43) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:29) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:69) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:30) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:59) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:44) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:45) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:30) at org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:67) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:37) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:74) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:72) at org.gradle.util.Swapper.swap(Swapper.java:38) at org.gradle.launcher.daemon.server.exec.ForwardClientInput.execute(ForwardClientInput.java:72) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:50) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:62) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:82) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50) at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:295) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) Malformed class file [SERIES.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) at org.gradle.api.internal.changedetection.state.ClasspathEntrySnapshotBuilder.visitFileSnapshot(ClasspathEntrySnapshotBuilder.java:62) at org.gradle.api.internal.changedetection.state.FileTree.visit(FileTree.java:36) at org.gradle.api.internal.changedetection.state.AbstractClasspathSnapshotBuilder.visitFileTreeSnapshot(AbstractClasspathSnapshotBuilder.java:66) at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$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.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:59) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter.execute(DefaultTaskGraphExecuter.java:128) at org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23) at org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43) at org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:46) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30) at org.gradle.initialization.DefaultGradleLauncher$ExecuteTasks.run(DefaultGradleLauncher.java:314) 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.initialization.DefaultGradleLauncher.runTasks(DefaultGradleLauncher.java:204) at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:134) at org.gradle.initialization.DefaultGradleLauncher.executeTasks(DefaultGradleLauncher.java:109) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:78) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:75) at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:152) at org.gradle.internal.invocation.GradleBuildController.doBuild(GradleBuildController.java:100) at org.gradle.internal.invocation.GradleBuildController.run(GradleBuildController.java:75) at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28) at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35) at org.gradle.tooling.internal.provider.ValidatingBuildActionRunner.run(ValidatingBuildActionRunner.java:32) at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$1.run(RunAsBuildOperationBuildActionRunner.java:43) at org.gradle.internal.progress.DefaultBuildOperationExecutor$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.launcher.exec.RunAsBuildOperationBuildActionRunner.run(RunAsBuildOperationBuildActionRunner.java:40) at org.gradle.tooling.internal.provider.SubscribableBuildActionRunner.run(SubscribableBuildActionRunner.java:51) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:47) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:30) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:39) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:80) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:53) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:57) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:32) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:36) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:43) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:29) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:69) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:30) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:59) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:44) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:45) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:30) at org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:67) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:37) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:74) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:72) at org.gradle.util.Swapper.swap(Swapper.java:38) at org.gradle.launcher.daemon.server.exec.ForwardClientInput.execute(ForwardClientInput.java:72) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:50) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:62) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:82) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50) at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:295) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) Malformed class file [SAMSequenceDictionaryExtractor$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.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:59) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter.execute(DefaultTaskGraphExecuter.java:128) at org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23) at org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43) at org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:46) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30) at org.gradle.initialization.DefaultGradleLauncher$ExecuteTasks.run(DefaultGradleLauncher.java:314) 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.initialization.DefaultGradleLauncher.runTasks(DefaultGradleLauncher.java:204) at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:134) at org.gradle.initialization.DefaultGradleLauncher.executeTasks(DefaultGradleLauncher.java:109) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:78) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:75) at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:152) at org.gradle.internal.invocation.GradleBuildController.doBuild(GradleBuildController.java:100) at org.gradle.internal.invocation.GradleBuildController.run(GradleBuildController.java:75) at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28) at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35) at org.gradle.tooling.internal.provider.ValidatingBuildActionRunner.run(ValidatingBuildActionRunner.java:32) at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$1.run(RunAsBuildOperationBuildActionRunner.java:43) at org.gradle.internal.progress.DefaultBuildOperationExecutor$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.launcher.exec.RunAsBuildOperationBuildActionRunner.run(RunAsBuildOperationBuildActionRunner.java:40) at org.gradle.tooling.internal.provider.SubscribableBuildActionRunner.run(SubscribableBuildActionRunner.java:51) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:47) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:30) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:39) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:80) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:53) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:57) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:32) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:36) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:43) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:29) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:69) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:30) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:59) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:44) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:45) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:30) at org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:67) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:37) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:74) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:72) at org.gradle.util.Swapper.swap(Swapper.java:38) at org.gradle.launcher.daemon.server.exec.ForwardClientInput.execute(ForwardClientInput.java:72) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:50) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:62) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:82) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50) at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:295) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) Malformed class file [BCF2Type.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) at org.gradle.api.internal.changedetection.state.ClasspathEntrySnapshotBuilder.visitFileSnapshot(ClasspathEntrySnapshotBuilder.java:62) at org.gradle.api.internal.changedetection.state.FileTree.visit(FileTree.java:36) at org.gradle.api.internal.changedetection.state.AbstractClasspathSnapshotBuilder.visitFileTreeSnapshot(AbstractClasspathSnapshotBuilder.java:66) at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$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.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:59) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter.execute(DefaultTaskGraphExecuter.java:128) at org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23) at org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43) at org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:46) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30) at org.gradle.initialization.DefaultGradleLauncher$ExecuteTasks.run(DefaultGradleLauncher.java:314) 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.initialization.DefaultGradleLauncher.runTasks(DefaultGradleLauncher.java:204) at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:134) at org.gradle.initialization.DefaultGradleLauncher.executeTasks(DefaultGradleLauncher.java:109) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:78) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:75) at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:152) at org.gradle.internal.invocation.GradleBuildController.doBuild(GradleBuildController.java:100) at org.gradle.internal.invocation.GradleBuildController.run(GradleBuildController.java:75) at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28) at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35) at org.gradle.tooling.internal.provider.ValidatingBuildActionRunner.run(ValidatingBuildActionRunner.java:32) at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$1.run(RunAsBuildOperationBuildActionRunner.java:43) at org.gradle.internal.progress.DefaultBuildOperationExecutor$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.launcher.exec.RunAsBuildOperationBuildActionRunner.run(RunAsBuildOperationBuildActionRunner.java:40) at org.gradle.tooling.internal.provider.SubscribableBuildActionRunner.run(SubscribableBuildActionRunner.java:51) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:47) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:30) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:39) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:80) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:53) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:57) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:32) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:36) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:43) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:29) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:69) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:30) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:59) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:44) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:45) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:30) at org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:67) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:37) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:74) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:72) at org.gradle.util.Swapper.swap(Swapper.java:38) at org.gradle.launcher.daemon.server.exec.ForwardClientInput.execute(ForwardClientInput.java:72) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:50) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:62) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:82) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50) at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:295) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) Malformed class file [VariantContext$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.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:59) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter.execute(DefaultTaskGraphExecuter.java:128) at org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23) at org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43) at org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:46) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30) at org.gradle.initialization.DefaultGradleLauncher$ExecuteTasks.run(DefaultGradleLauncher.java:314) 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.initialization.DefaultGradleLauncher.runTasks(DefaultGradleLauncher.java:204) at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:134) at org.gradle.initialization.DefaultGradleLauncher.executeTasks(DefaultGradleLauncher.java:109) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:78) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:75) at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:152) at org.gradle.internal.invocation.GradleBuildController.doBuild(GradleBuildController.java:100) at org.gradle.internal.invocation.GradleBuildController.run(GradleBuildController.java:75) at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28) at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35) at org.gradle.tooling.internal.provider.ValidatingBuildActionRunner.run(ValidatingBuildActionRunner.java:32) at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$1.run(RunAsBuildOperationBuildActionRunner.java:43) at org.gradle.internal.progress.DefaultBuildOperationExecutor$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.launcher.exec.RunAsBuildOperationBuildActionRunner.run(RunAsBuildOperationBuildActionRunner.java:40) at org.gradle.tooling.internal.provider.SubscribableBuildActionRunner.run(SubscribableBuildActionRunner.java:51) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:47) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:30) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:39) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:80) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:53) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:57) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:32) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:36) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:43) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:29) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:69) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:30) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:59) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:44) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:45) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:30) at org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:67) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:37) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:74) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:72) at org.gradle.util.Swapper.swap(Swapper.java:38) at org.gradle.launcher.daemon.server.exec.ForwardClientInput.execute(ForwardClientInput.java:72) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:50) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:62) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:82) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50) at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:295) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) Replacing org.testng:testng:jar:7.8.0 -> org.testng:testng:jar:debian Replacing com.google.jimfs:jimfs:jar:1.3.0 -> com.google.jimfs:jimfs:jar:debian Passing through com.google.jimfs:jimfs-parent:jar:debian Replacing com.google.guava:guava:jar:33.0.0-jre -> com.google.guava:guava:jar:debian Passing through com.google.guava:guava-parent:jar:debian Replacing org.apache.commons:commons-lang3:jar:3.14.0 -> 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 3.987 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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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[#36,Daemon worker,5,main]) completed. Took 20.022 secs. :processTestResources (Thread[#36,Daemon worker,5,main]) started. :processTestResources Putting task artifact state for task ':processTestResources' into context took 0.0 secs. Up-to-date check for task ':processTestResources' took 0.67 secs. It is not up-to-date because: No history is available. :processTestResources (Thread[#36,Daemon worker,5,main]) completed. Took 3.418 secs. :testClasses (Thread[#36,Daemon worker,5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. :testClasses (Thread[#36,Daemon worker,5,main]) completed. Took 0.0 secs. :testWithDefaultReference (Thread[#36,Daemon worker,5,main]) started. :testWithDefaultReference Putting task artifact state for task ':testWithDefaultReference' into context took 0.001 secs. Up-to-date check for task ':testWithDefaultReference' took 0.331 secs. It is not up-to-date because: Task.upToDateWhen is false. Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/htsjdk-4.1.3+dfsg Command: /usr/lib/jvm/java-21-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-classpath2778221578531568030txt -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 2025-01-01 06:08:13 Defaults Found file for property samjdk.reference_fasta: /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. 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[68](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR WARNING 2025-01-01 06:08:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:08:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:08:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:08:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:08:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:08:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:08:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:08:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:08:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:08:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:08:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:08:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:08:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:08:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:08:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:08:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:08:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:08:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:08:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:08:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. Finished 2200 tests Finished 2400 tests Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[317](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-01-01 06:09:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:09:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[318](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-01-01 06:09:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:09:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[319](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-01-01 06:09:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:09:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[320](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-01-01 06:09:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:09:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[321](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-01-01 06:09:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:09:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[322](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-01-01 06:09:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:09:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[323](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-01-01 06:09:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:09:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[324](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-01-01 06:09:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:09:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[325](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-01-01 06:09:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:09:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[326](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-01-01 06:09:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:09:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[327](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-01-01 06:09:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:09:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Finished 2600 tests Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[499](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-01-01 06:10:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:10:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[500](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-01-01 06:10:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:10:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[501](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-01-01 06:10:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:10:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[502](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-01-01 06:10:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:10:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[503](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-01-01 06:10:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:10:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[504](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-01-01 06:10:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:10:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[505](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-01-01 06:10:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:10:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[506](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-01-01 06:10:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:10:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[507](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-01-01 06:10:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:10:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[508](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-01-01 06:10:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:10:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[509](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-01-01 06:10:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:10:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingMultiSampleVCF STANDARD_ERROR WARNING 2025-01-01 06:10:13 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Finished 2800 tests Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSingleSampleVCF STANDARD_ERROR WARNING 2025-01-01 06:10:13 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 2025-01-01 06:10:13 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream 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:572) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at java.base/java.lang.Thread.run(Thread.java:1583) Gradle suite > Gradle test > htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.demonstrateTestWriteToPipeDoesNotHang_2 STANDARD_ERROR java.lang.RuntimeException: oops at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.lambda$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:572) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at java.base/java.lang.Thread.run(Thread.java:1583) 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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[4](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testFirstCompleteContigRead runtime: 5ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[6](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstElementOfIterator runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[4](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[0](/build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testFirstSequence runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[2](/build/reproducible-path/htsjdk-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testFirstSequenceExtended runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[0](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testLastCompleteContigRead runtime: 20ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[1](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testLastCompleteContigRead runtime: 18ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[2](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testLastCompleteContigRead runtime: 3ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[3](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testLastCompleteContigRead runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[4](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testLastCompleteContigRead runtime: 12ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[6](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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[7](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testLastCompleteContigRead runtime: 9ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[8](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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.testLastOfChr20[0](/build/reproducible-path/htsjdk-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testNextElementOfIterator runtime: 4ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[1](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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[3](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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[4](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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[5](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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[8](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReadStartingInCenterOfFirstLine runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[1](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testReadStartingInCenterOfFirstLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[2](/build/reproducible-path/htsjdk-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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[4](/build/reproducible-path/htsjdk-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[1](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 4ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[3](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testReset runtime: 9ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[5](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testReset runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[6](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 4ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[8](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 3ms Finished 13000 tests Gradle suite > Gradle test > htsjdk.tribble.AsciiFeatureCodecTest.testMakeIndexableSourceFromUnknownStream STANDARD_ERROR WARNING 2025-01-01 06:11:25 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@2e18776e, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR WARNING 2025-01-01 06:11:25 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 2025-01-01 06:11:25 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 2025-01-01 06:11:25 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 2025-01-01 06:11:25 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.10915193121134190622.bai #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.14025822354882502218.bai #BAMIndexWriterTest diff /tmp/javaBai.10915193121134190622.bai /tmp/cBai.14025822354882502218.bai Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteText STANDARD_OUT #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.628786773551402514.bai.txt #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.16293835400718825741java.bai #BAMIndexWriterTest diff /tmp/javaBai.16293835400718825741java.bai.txt /tmp/cBai.628786773551402514.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 1ms 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.4347185914760970728.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testCustomDeflater STANDARD_OUT Creating file /tmp/testCustomDeflater.8138926958834228597.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testOverflow STANDARD_OUT Creating file /tmp/BCOST.4240615682733432565.gz Finished 13400 tests Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testAllEncodingStrategyCombinations[0](src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.500-unMapped.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.fasta, false, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[0](src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.500-unMapped.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.fasta, false, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[1](src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10m-10m100.cram, src/test/resources/htsjdk/samtools/reference/human_g1k_v37.20.21.fasta.gz, false, false) STANDARD_ERROR WARNING 2025-01-01 06:12:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:12:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:12:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:12:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[1](src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10m-10m100.cram, src/test/resources/htsjdk/samtools/reference/human_g1k_v37.20.21.fasta.gz, false, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[2](src/test/resources/htsjdk/samtools/cram/NA12878.unmapped.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.fasta, false, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[3](src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram, src/test/resources/htsjdk/samtools/reference/human_g1k_v37.20.21.fasta.gz, true, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, true, false) STANDARD_ERROR WARNING 2025-01-01 06:13:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:13:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:13:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:13:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:13:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:13:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:13:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:13:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:13:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:13:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:13:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:13:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, true, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[5](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, true, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[6](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest_2_containers_aligned_to_pos_1.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, true, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[7](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest_3_containers_aligned_to_pos_1.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, true, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromContainer STANDARD_ERROR WARNING 2025-01-01 06:14:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:14:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromStream STANDARD_ERROR WARNING 2025-01-01 06:14:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:14:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.fullVerificationTest[0](c1#bounds) STANDARD_ERROR WARNING 2025-01-01 06:14:08 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 WARNING 2025-01-01 06:14:08 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. WARNING 2025-01-01 06:14:08 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 WARNING 2025-01-01 06:14:08 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 2025-01-01 06:14:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:14:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Finished 13600 tests 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 2025-01-01 06:14:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:14:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testObsoleteDataSeriesNotWritten STANDARD_ERROR WARNING 2025-01-01 06:14:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:14:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testContigNotFoundInRef STANDARD_ERROR WARNING 2025-01-01 06:14:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:14:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testNullsAndBeyondRef STANDARD_ERROR WARNING 2025-01-01 06:14:12 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 WARNING 2025-01-01 06:14:12 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. WARNING 2025-01-01 06:14:12 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 WARNING 2025-01-01 06:14:12 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 2025-01-01 06:14:12 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 WARNING 2025-01-01 06:14:12 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. WARNING 2025-01-01 06:14:12 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 WARNING 2025-01-01 06:14:12 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 2025-01-01 06:18:07 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. WARNING 2025-01-01 06:18:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:18:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCramIteratorWithoutCallingHasNextFirst STANDARD_ERROR WARNING 2025-01-01 06:18:07 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 WARNING 2025-01-01 06:18:07 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. WARNING 2025-01-01 06:18:07 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 WARNING 2025-01-01 06:18:07 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 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:28 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;@41ac0e66, [Ljava.lang.String;@647b4b7c) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.6714735157294447983.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@ef7fd95, [Ljava.lang.String;@5d0e4725) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:28 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 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:28 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 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:28 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;@3729b016, [Ljava.lang.String;@1b446a85) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:28 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;@7b2be584, [Ljava.lang.String;@11699ae4) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.6714735157294447983.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4c6a0447, [Ljava.lang.String;@617e5a82) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:28 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;@fd42d8e, [Ljava.lang.String;@1f114ad) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.6714735157294447983.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@9131b3b, [Ljava.lang.String;@2a2caf4) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:28 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;@e99574e, [Ljava.lang.String;@3d3012de) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.6714735157294447983.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@29ba56ca, [Ljava.lang.String;@3bfd8c9a) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:28 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;@185da494, [Ljava.lang.String;@4ad8aa84) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.6714735157294447983.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5503c500, [Ljava.lang.String;@4fd52dcc) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:28 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;@42d04382, [Ljava.lang.String;@64bb1204) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.6714735157294447983.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@e7f820f, [Ljava.lang.String;@2794a8e4) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:28 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;@5b37e611, [Ljava.lang.String;@61dbed8d) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.6714735157294447983.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@37169359, [Ljava.lang.String;@1d687203) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:28 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;@391ea594, [Ljava.lang.String;@81c4eed) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.6714735157294447983.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@71bf7c89, [Ljava.lang.String;@41c25b2d) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:28 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;@228c27f6, [Ljava.lang.String;@190e41ac) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.6714735157294447983.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2711b04, [Ljava.lang.String;@757a3f6a) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:28 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;@74270858) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:28 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;@53de3503) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:28 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;@543d3e89) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:28 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;@7fb87880) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:28 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;@5bc47e1a) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:28 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;@5770fcfb) STANDARD_ERROR WARNING 2025-01-01 06:23:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:28 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;@26401931) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 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;@31c30b5) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 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 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 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 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:29 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;@93813b1, [Ljava.lang.String;@55b0b268) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 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;@22ae507f, [Ljava.lang.String;@37ede1b) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.6714735157294447983.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7c6a2ad0, [Ljava.lang.String;@4218739a) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:29 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;@41b5b50a, [Ljava.lang.String;@12c44940) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.6714735157294447983.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6fe0d19c, [Ljava.lang.String;@67aabcdf) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:29 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;@8e326c9, [Ljava.lang.String;@49be7782) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.6714735157294447983.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@246c5046, [Ljava.lang.String;@583f2732) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:29 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;@74abef, [Ljava.lang.String;@78eb4972) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.6714735157294447983.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@103eaac5, [Ljava.lang.String;@2fc7110f) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:29 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;@13c006c1, [Ljava.lang.String;@4dbf6641) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.6714735157294447983.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7843245c, [Ljava.lang.String;@2f40da47) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:29 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;@71efcae1, [Ljava.lang.String;@284d08e2) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.6714735157294447983.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@e12b5ec, [Ljava.lang.String;@668e6aca) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:29 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;@1465866e, [Ljava.lang.String;@573eed5b) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.6714735157294447983.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6862af09, [Ljava.lang.String;@5de1fc53) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:29 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;@13688667, [Ljava.lang.String;@deebe2c) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.6714735157294447983.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@48300584, [Ljava.lang.String;@7a146f30) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:29 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;@53cfd60f) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 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;@6161231c) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 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;@36f6000) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 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;@3bb6f3a6) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 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;@39cea39f) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 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;@3c531c8e) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 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;@3474ae38) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 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;@23663de0) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 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;@69305802) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 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;@487d7dd0) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 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;@485d0aed) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 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;@646071e5) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 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;@7cedafcb) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 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;@7a601f9f) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 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;@6e7ffac1) STANDARD_ERROR WARNING 2025-01-01 06:23:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:29 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;@79dd72e8) STANDARD_ERROR WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:30 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;@49e6d28e) STANDARD_ERROR WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:30 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;@677043b3) STANDARD_ERROR WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:30 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;@71650154) STANDARD_ERROR WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:30 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;@313aa0d7) STANDARD_ERROR WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:30 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;@f5f22fe) STANDARD_ERROR WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:30 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;@62a9f5a6) STANDARD_ERROR WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Finished 14000 tests 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;@6313c866) STANDARD_ERROR WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:30 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;@378acd3e) STANDARD_ERROR WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@6f949959) STANDARD_ERROR WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:30 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;@4a598db4) STANDARD_ERROR WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:30 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;@423f1736) STANDARD_ERROR WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:30 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;@45c974c1) STANDARD_ERROR WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:30 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;@66a1eaf) STANDARD_ERROR WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:30 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;@1effd264) STANDARD_ERROR WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.6714735157294447983.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@202cd8ab) STANDARD_ERROR WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:30 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;@5ef33d84, 5) STANDARD_ERROR WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMMergerTest.test STANDARD_ERROR WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.cram.ref.CRAMReferenceRegionTest.testGetReferenceBasesByRegionExceedsContigLength STANDARD_ERROR WARNING 2025-01-01 06:23:31 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 2025-01-01 06:23:31 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+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 2025-01-01 06:23:31 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+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 2025-01-01 06:23:31 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+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 2025-01-01 06:23:32 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:32 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testIgnoreObsoleteDataseriesOnRead STANDARD_ERROR WARNING 2025-01-01 06:23:32 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:32 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 Finished 14600 tests 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 Gradle suite > Gradle test > htsjdk.samtools.DownsamplingIteratorTests.testBasicFunction STANDARD_ERROR Could not delete file /tmp/pbuilder2/DiskBackedQueueTest/diskbackedqueue.18324409963121517318.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 2025-01-01 06:23:47 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 2025-01-01 06:23:48 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 2025-01-01 06:23:49 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 2025-01-01 06:23:49 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 2025-01-01 06:23:49 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 2025-01-01 06:23:49 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 WARNING 2025-01-01 06:23:49 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 2025-01-01 06:23:49 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 WARNING 2025-01-01 06:23:49 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 2025-01-01 06:23:49 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 WARNING 2025-01-01 06:23:49 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 2025-01-01 06:23:49 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 2025-01-01 06:23:49 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 2025-01-01 06:23:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:49 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;@1c0b3f4b, [Ljava.lang.String;@322ff057) STANDARD_ERROR WARNING 2025-01-01 06:23:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.16473239743262422872.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@58a97ffe, [Ljava.lang.String;@44657b73) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 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 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:50 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 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 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;@37edd0b) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:50 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;@3b853ec9) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:50 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;@19b52e79) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:50 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;@67254512) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:50 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;@23ad7322) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:50 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;@bed5ba6) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:50 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;@5974dbe7) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:50 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;@7bd05bdc) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:50 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;@4a2f817c, [Ljava.lang.String;@4871b9e0) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:50 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;@33e87e79, [Ljava.lang.String;@587aef89) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.16473239743262422872.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@527611b5, [Ljava.lang.String;@7f65ed4f) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 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;@26628c06, [Ljava.lang.String;@6ae995c9) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.16473239743262422872.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5f8212a6, [Ljava.lang.String;@f2574c) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 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;@77287a85, [Ljava.lang.String;@45be9b69) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.16473239743262422872.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@35483670, [Ljava.lang.String;@411b3a54) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 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;@6e60bb60, [Ljava.lang.String;@54ce3b07) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.16473239743262422872.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@204731a8, [Ljava.lang.String;@391732c2) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 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;@7a892dcc, [Ljava.lang.String;@60794000) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.16473239743262422872.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3baeba2e, [Ljava.lang.String;@554dc5ec) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 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;@32744a9f, [Ljava.lang.String;@375215ee) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.16473239743262422872.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3bec470d, [Ljava.lang.String;@579bf1bb) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 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;@461617e8, [Ljava.lang.String;@71daa08e) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.16473239743262422872.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@da0422b, [Ljava.lang.String;@13281f0b) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 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;@3f2e7d26, [Ljava.lang.String;@69afd28f) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.16473239743262422872.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5acddcb4, [Ljava.lang.String;@359b1164) STANDARD_ERROR WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 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 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:50 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 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 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 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:51 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 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 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;@75968c8c) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:51 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;@724b9b03) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:51 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;@3220d0a7) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:51 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;@5df71c4) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:51 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;@e40c0b) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:51 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;@7e851978, [Ljava.lang.String;@5f7bad7a) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:51 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;@6690404b, [Ljava.lang.String;@65f5fbe5) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.16473239743262422872.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@646ffce0, [Ljava.lang.String;@5af60d66) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 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;@92cc638, [Ljava.lang.String;@30959cbf) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.16473239743262422872.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@70a56a2d, [Ljava.lang.String;@1c6da538) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 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;@674a2369, [Ljava.lang.String;@338f36bc) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.16473239743262422872.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@31b715b9, [Ljava.lang.String;@7e4b0c96) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 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;@73e100bd, [Ljava.lang.String;@55a12c39) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.16473239743262422872.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7156f5d0, [Ljava.lang.String;@3406fcfd) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 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;@56ccb058, [Ljava.lang.String;@56e07d15) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.16473239743262422872.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@462de3fa, [Ljava.lang.String;@2541e51) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 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;@1731da6f, [Ljava.lang.String;@a454086) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.16473239743262422872.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1b74e114, [Ljava.lang.String;@73746858) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 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;@715a752d, [Ljava.lang.String;@215c409a) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.16473239743262422872.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@49b6449b, [Ljava.lang.String;@1df73b19) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 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;@253c6ef3, [Ljava.lang.String;@761eb71a) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.16473239743262422872.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5966ea35, [Ljava.lang.String;@6757e78d) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 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;@5543bab7) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:51 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;@2e4d45f5) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:51 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;@9c0e6bf) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:51 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;@ae95132) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:51 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;@3b37d090) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:51 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;@6034511a) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:51 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;@49bc1d7e) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.16473239743262422872.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@7a21fe14) STANDARD_ERROR WARNING 2025-01-01 06:23:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:51 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;@65daee65) STANDARD_ERROR WARNING 2025-01-01 06:23:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:52 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;@10004e63) STANDARD_ERROR WARNING 2025-01-01 06:23:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:52 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;@3362c0e6) STANDARD_ERROR WARNING 2025-01-01 06:23:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:52 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;@d8c385e) STANDARD_ERROR WARNING 2025-01-01 06:23:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:52 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;@23d38f7) STANDARD_ERROR WARNING 2025-01-01 06:23:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:52 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;@22d84f34) STANDARD_ERROR WARNING 2025-01-01 06:23:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:52 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;@29b35a50) STANDARD_ERROR WARNING 2025-01-01 06:23:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:52 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;@6484cb49) STANDARD_ERROR WARNING 2025-01-01 06:23:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:52 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;@1d02d1bc) STANDARD_ERROR WARNING 2025-01-01 06:23:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:52 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 2025-01-01 06:23:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:52 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;@54407588, 5) STANDARD_ERROR WARNING 2025-01-01 06:23:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:23:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:23:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Finished 16400 tests Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForDecodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@6a6741b8, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4715d445], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR WARNING 2025-01-01 06:23:52 HtsCodecResolver The specified format string (BOGUS_FORMAT) does not correspond to any registered codec for content type (ALIGNED_READS) Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[1]([], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR WARNING 2025-01-01 06:23:52 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@54a8123c, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@69405a8e, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1a3c1d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@5821d08d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@18f6231], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR WARNING 2025-01-01 06:23:52 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@54a8123c, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@69405a8e, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1a3c1d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@5821d08d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@18f6231], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR WARNING 2025-01-01 06:23:52 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@54a8123c, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@69405a8e, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1a3c1d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@5821d08d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@18f6231], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR WARNING 2025-01-01 06:23:52 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 file10911492679581176135.bad Finished 17200 tests Gradle suite > Gradle test > htsjdk.samtools.util.IntervalTreeTest.performanceTest STANDARD_OUT Time to construct a tree with 50000 nodes: 55 milliseconds Queried for the same 100-length mapping 170145650 times in 10 seconds. Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR INFO 2025-01-01 06:24:05 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 2025-01-01 06:24:05 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) INFO 2025-01-01 06:24:05 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) Finished 17600 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[280](chr3:14174511-14175398 + ., null) STANDARD_ERROR INFO 2025-01-01 06:24:05 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 2025-01-01 06:24:05 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 2025-01-01 06:24:05 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 2025-01-01 06:24:05 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 2025-01-01 06:24:05 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 2025-01-01 06:24:05 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 2025-01-01 06:24:05 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 2025-01-01 06:24:05 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) INFO 2025-01-01 06:24:05 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 2025-01-01 06:24:05 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 2025-01-01 06:24:05 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) INFO 2025-01-01 06:24:05 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 2025-01-01 06:24:05 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) INFO 2025-01-01 06:24:05 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 2025-01-01 06:24:05 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR INFO 2025-01-01 06:24:05 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 2025-01-01 06:24:06 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) INFO 2025-01-01 06:24:06 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 2025-01-01 06:24:06 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 2025-01-01 06:24:06 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 2025-01-01 06:24:06 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 2025-01-01 06:24:06 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 2025-01-01 06:24:06 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 2025-01-01 06:24:06 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 2025-01-01 06:24:06 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 2025-01-01 06:24:06 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) INFO 2025-01-01 06:24:06 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 2025-01-01 06:24:06 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 2025-01-01 06:24:06 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) INFO 2025-01-01 06:24:06 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 2025-01-01 06:24:06 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) INFO 2025-01-01 06:24:06 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 2025-01-01 06:24:06 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 2025-01-01 06:24:06 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Finished 18400 tests Finished 18600 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 a c Finished 18800 tests Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[0](@HD VN:1.0 SO:UNSORTED ) STANDARD_ERROR WARNING 2025-01-01 06:24:36 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 2025-01-01 06:24:36 SAMTextHeaderCodec Found non-conforming header SO tag: FALSE. Treating as 'unknown'. Finished 19000 tests Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[2](@HD VN:1.0 SO:COORDINATE ) STANDARD_ERROR WARNING 2025-01-01 06:24:36 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 2025-01-01 06:24:36 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 2025-01-01 06:24:36 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.specialFileWriterTest STANDARD_ERROR WARNING 2025-01-01 06:24:36 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null WARNING 2025-01-01 06:24:36 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 2025-01-01 06:24:36 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.11660997865893651983..cram INFO 2025-01-01 06:24:36 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-01-01 06:24:36 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): src/test/resources/htsjdk/samtools/cram/ce.fa INFO 2025-01-01 06:24:36 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false INFO 2025-01-01 06:24:36 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+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 2025-01-01 06:24:36 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension10785391260522002189.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.3489360623748220295.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 2025-01-01 06:24:36 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension2184268410665075612.cram INFO 2025-01-01 06:24:36 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-01-01 06:24:36 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): src/test/resources/htsjdk/samtools/cram/ce.fa INFO 2025-01-01 06:24:36 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false INFO 2025-01-01 06:24:36 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+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 2025-01-01 06:24:36 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension2645762509483766438 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForUnknownFileExtension STANDARD_ERROR INFO 2025-01-01 06:24:36 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension544094731469059410.png Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[0](sam) STANDARD_ERROR INFO 2025-01-01 06:24:36 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://594b42fc-e53d-4254-bdf7-968d5f4cab88/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 2025-01-01 06:24:36 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://5d619e1b-c88b-4400-bcc9-15a71b0fb803/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 2025-01-01 06:24:36 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://b6e6d455-c89b-4d58-a784-c0180ea4bca6/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 2025-01-01 06:24:36 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://9721f573-5f5f-4c0d-aa7b-a0d853a4b15d/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 2025-01-01 06:24:36 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://ffff65d9-8a73-4225-926c-57b832446273/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 2025-01-01 06:24:36 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://401ba148-591c-4494-a38e-6b95ae44688b/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 2025-01-01 06:24:49 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.sra.SRAAccessionTest STANDARD_ERROR ngs-java: DLL download was disabled Gradle suite > Gradle test > htsjdk.samtools.sra.SRAAccessionTest.testIsValidAcc[0](SRR000123, true) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.sra.SRAAccessionTest.testIsValidAcc[1](DRR010511, true) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.sra.SRAAccessionTest.testIsValidAcc[2](src/test/resources/htsjdk/samtools/sra/test_archive.sra, true) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.sra.SRAAccessionTest.testIsValidAcc[3](src/test/resources/htsjdk/samtools/compressed.bam, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.sra.SRAAccessionTest.testIsValidAcc[4](src/test/resources/htsjdk/samtools/uncompressed.sam, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.sra.SRALazyRecordTest.testCloneAndEquals[0](SRR2096940) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.sra.SRALazyRecordTest.testSerialization[0](SRR2096940) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.sra.SRAQueryTest.testQueryCounts[0](SRR2096940, CM000681.1, 0, 59128983, true, 10591, 0) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.sra.SRAQueryTest.testQueryCounts[1](SRR2096940, CM000681.1, 55627015, 59128983, true, 10591, 0) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.sra.SRAQueryTest.testQueryCounts[2](SRR2096940, CM000681.1, 55627016, 59128983, true, 0, 0) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.sra.SRAQueryTest.testQueryCounts[3](SRR2096940, CM000681.1, 55627016, 59128983, false, 10591, -1) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.sra.SRAQueryTest.testReferenceAlignedCounts[0](SRR2096940, CM000681.1, 0, 10591) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.sra.SRAQueryTest.testReferenceAlignedCounts[1](SRR2096940, CM000681.1, 55627015, 10591) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.sra.SRAQueryTest.testReferenceAlignedCounts[2](SRR2096940, CM000681.1, 55627016, 0) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.sra.SRAReferenceTest.testReference[0](SRR2096940, CM000681.1, 95001, 95050, AGATGATTCAGTCTCACCAAGAACACTGAAAGTCACATGGCTACCAGCAT) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.sra.SRAReferenceTest.testReferenceMt[0](SRR353866, [AAAB01001871.1:1-50 = TGACGCGCATGAATGGATTAACGAGATTCCCTCTGTCCCTATCTACTATC, AAAB01001871.1:901-950 = ACCAAGCGTACGATTGTTCACCCTTTCAAGGGAACGTGAGCTGGGTTTAG, AAAB01008987.1:1-50 = TTTTGGACGATGTTTTTGGTGAACAGAAAACGAGCTCAATCATCCAGAGC, AAAB01008859.1:1-50 = CAAAACGATGCCACAGATCAGAAGTTAATTAACGCACATTCTCCACCCAC]) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.SamFilesTest.testIndexSymlinking[2](src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai) STANDARD_ERROR WARNING 2025-01-01 06:24:50 SamFiles The index file /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam WARNING 2025-01-01 06:24:50 SamFiles The index file /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.customReaderFactoryTest STANDARD_ERROR INFO 2025-01-01 06:24:51 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory INFO 2025-01-01 06:24:51 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory INFO 2025-01-01 06:24:51 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar INFO 2025-01-01 06:24:51 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 2025-01-01 06:24:51 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 2025-01-01 06:24:51 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 2025-01-01 06:24:52 SamReaderFactoryTest Finished queries in 48ms Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURL STANDARD_ERROR WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLNoIndexFile STANDARD_ERROR WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLStream STANDARD_ERROR WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromMalformedSeekableStream STANDARD_ERROR WARNING 2025-01-01 06:24:52 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 2025-01-01 06:24:52 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 2025-01-01 06:24:52 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 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:24:52 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 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:24:52 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 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:24:52 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 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:24:52 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 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:24:52 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 2025-01-01 06:24:52 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:24:52 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 2025-01-01 06:24:52 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:24:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testBamIntegers[1](inttest_large_coordinates.bam) STANDARD_ERROR WARNING 2025-01-01 06:24:52 BAMRecordCodec Reference length is too large for BAM bin field. WARNING 2025-01-01 06:24:52 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 2025-01-01 06:24:52 BAMRecordCodec Reference length is too large for BAM bin field. WARNING 2025-01-01 06:24:52 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 Finished 20000 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlockReadStreamTest.testSliceBlocksReadStreamsRoundTrip SKIPPED Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlocksTest.testSliceBlocksRoundTrip SKIPPED Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests STANDARD_ERROR WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 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 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 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 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:24:52 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 2025-01-01 06:24:52 CRAMReferenceRegion The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20 WARNING 2025-01-01 06:24:52 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 Finished 36000 tests Gradle Test Executor 1 finished executing tests. Results: SUCCESS (35867 tests, 35832 successes, 0 failures, 35 skipped) Finished generating test XML results (0.23 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/test-results/testWithDefaultReference Generating HTML test report... Finished generating test html results (0.313 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/reports/tests/testWithDefaultReference :testWithDefaultReference (Thread[#36,Daemon worker,5,main]) completed. Took 16 mins 45.981 secs. :testWithOptimisticVCF4_4 (Thread[#36,Daemon worker,5,main]) started. :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 0.039 secs. It is not up-to-date because: Task.upToDateWhen is false. Starting process 'Gradle Test Executor 2'. Working directory: /build/reproducible-path/htsjdk-4.1.3+dfsg Command: /usr/lib/jvm/java-21-openjdk-arm64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false -Dsamjdk.optimistic_vcf_4_4=true @/tmp/gradle-worker-classpath6285001198308272017txt -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 STANDARD_ERROR SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. Gradle Test Executor 2 finished executing tests. Results: SUCCESS (0 tests, 0 successes, 0 failures, 0 skipped) Finished generating test XML results (0.0 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/test-results/testWithOptimisticVCF4_4 Generating HTML test report... Finished generating test html results (0.003 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/reports/tests/testWithOptimisticVCF4_4 :testWithOptimisticVCF4_4 (Thread[#36,Daemon worker,5,main]) completed. Took 1.577 secs. :test (Thread[#36,Daemon worker,5,main]) started. :test Putting task artifact state for task ':test' into context took 0.0 secs. Up-to-date check for task ':test' took 0.062 secs. It is not up-to-date because: Task.upToDateWhen is false. Starting process 'Gradle Test Executor 3'. Working directory: /build/reproducible-path/htsjdk-4.1.3+dfsg Command: /usr/lib/jvm/java-21-openjdk-arm64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false @/tmp/gradle-worker-classpath6789239096872992422txt -Xms1G -Xmx2G -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 3' Successfully started process 'Gradle Test Executor 3' Gradle Test Executor 3 started executing tests. Gradle Test Executor 3 STANDARD_ERROR SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. 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[20](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-01-01 06:25:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:25:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[21](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-01-01 06:25:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:25:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[22](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-01-01 06:25:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:25:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[23](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-01-01 06:25:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:25:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[24](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-01-01 06:25:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:25:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[25](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-01-01 06:25:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:25:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[26](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-01-01 06:25:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:25:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[27](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-01-01 06:25:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:25:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[28](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-01-01 06:25:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:25:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[29](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-01-01 06:25:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:25:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[30](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR WARNING 2025-01-01 06:25:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:25:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[73](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR WARNING 2025-01-01 06:25:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:25:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:25:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:25:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:25:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:25:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:25:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:25:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:25:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:25:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:25:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:25:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:25:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:25:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:25:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:25:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:25:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:25:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:25:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:25:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. Finished 2200 tests Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[236](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-01-01 06:26:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:26:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[237](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-01-01 06:26:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:26:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[238](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-01-01 06:26:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:26:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[239](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-01-01 06:26:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:26:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[240](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-01-01 06:26:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:26:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[241](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-01-01 06:26:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:26:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[242](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-01-01 06:26:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:26:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[243](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-01-01 06:26:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:26:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[244](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-01-01 06:26:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:26:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[245](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-01-01 06:26:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:26:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[246](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR WARNING 2025-01-01 06:26:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:26:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Finished 2400 tests Finished 2600 tests Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingMultiSampleVCF STANDARD_ERROR WARNING 2025-01-01 06:26:14 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Finished 2800 tests Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSingleSampleVCF STANDARD_ERROR WARNING 2025-01-01 06:26:14 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 2025-01-01 06:26:14 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream 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:572) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at java.base/java.lang.Thread.run(Thread.java:1583) Gradle suite > Gradle test > htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.demonstrateTestWriteToPipeDoesNotHang_2 STANDARD_ERROR java.lang.RuntimeException: oops at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.lambda$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:572) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at java.base/java.lang.Thread.run(Thread.java:1583) 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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[4](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[7](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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[5](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testFirstSequenceExtended runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[0](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testLastCompleteContigRead runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[4](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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[5](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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[6](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testLastCompleteContigRead runtime: 3ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[8](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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.testLastOfChr20[0](/build/reproducible-path/htsjdk-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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[6](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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[7](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testReadStartingInCenterOfFirstLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[2](/build/reproducible-path/htsjdk-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testReadStartingInCenterOfMiddleLine runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[0](/build/reproducible-path/htsjdk-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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[1](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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[2](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+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[3](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 4ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[4](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[8](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 2ms Finished 13000 tests Gradle suite > Gradle test > htsjdk.tribble.AsciiFeatureCodecTest.testMakeIndexableSourceFromUnknownStream STANDARD_ERROR WARNING 2025-01-01 06:26:59 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@200e7a18, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR WARNING 2025-01-01 06:26:59 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 2025-01-01 06:26:59 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 2025-01-01 06:26:59 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 2025-01-01 06:26:59 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 Gradle is still running, please be patient... Finished 13200 tests Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteBinary STANDARD_OUT #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.16652828692735069903.bai #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.8638459811425031467.bai #BAMIndexWriterTest diff /tmp/javaBai.16652828692735069903.bai /tmp/cBai.8638459811425031467.bai Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteText STANDARD_OUT #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.11264834002743367072.bai.txt #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.9873963235908844018java.bai #BAMIndexWriterTest diff /tmp/javaBai.9873963235908844018java.bai.txt /tmp/cBai.11264834002743367072.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.5132154257023551793.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testCustomDeflater STANDARD_OUT Creating file /tmp/testCustomDeflater.6321652583714792115.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testOverflow STANDARD_OUT Creating file /tmp/BCOST.8706041714658523121.gz Finished 13400 tests Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testAllEncodingStrategyCombinations[0](src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.500-unMapped.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.fasta, false, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[0](src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.500-unMapped.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.fasta, false, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[1](src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10m-10m100.cram, src/test/resources/htsjdk/samtools/reference/human_g1k_v37.20.21.fasta.gz, false, false) STANDARD_ERROR WARNING 2025-01-01 06:27:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:27:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:27:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:27:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[1](src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10m-10m100.cram, src/test/resources/htsjdk/samtools/reference/human_g1k_v37.20.21.fasta.gz, false, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[2](src/test/resources/htsjdk/samtools/cram/NA12878.unmapped.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.fasta, false, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[3](src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram, src/test/resources/htsjdk/samtools/reference/human_g1k_v37.20.21.fasta.gz, true, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, true, false) STANDARD_ERROR WARNING 2025-01-01 06:29:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:29:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:29:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:29:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:29:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:29:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:29:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:29:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:29:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:29:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:29:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:29:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, true, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[5](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, true, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[6](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest_2_containers_aligned_to_pos_1.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, true, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[7](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest_3_containers_aligned_to_pos_1.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, true, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromContainer STANDARD_ERROR WARNING 2025-01-01 06:29:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:29:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromStream STANDARD_ERROR WARNING 2025-01-01 06:29:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:29:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.fullVerificationTest[0](c1#bounds) STANDARD_ERROR WARNING 2025-01-01 06:29:13 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 WARNING 2025-01-01 06:29:13 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. WARNING 2025-01-01 06:29:13 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 WARNING 2025-01-01 06:29:13 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 2025-01-01 06:29:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:29:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Finished 13600 tests 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 2025-01-01 06:29:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:29:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testObsoleteDataSeriesNotWritten STANDARD_ERROR WARNING 2025-01-01 06:29:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:29:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testContigNotFoundInRef STANDARD_ERROR WARNING 2025-01-01 06:29:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:29:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testNullsAndBeyondRef STANDARD_ERROR WARNING 2025-01-01 06:29:18 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 WARNING 2025-01-01 06:29:18 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. WARNING 2025-01-01 06:29:18 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 WARNING 2025-01-01 06:29:18 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 2025-01-01 06:29:18 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 WARNING 2025-01-01 06:29:18 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. WARNING 2025-01-01 06:29:18 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 WARNING 2025-01-01 06:29:18 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 2025-01-01 06:33:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:33:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCramIteratorWithoutCallingHasNextFirst STANDARD_ERROR WARNING 2025-01-01 06:33:01 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 WARNING 2025-01-01 06:33:01 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. WARNING 2025-01-01 06:33:01 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 WARNING 2025-01-01 06:33:01 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 is still running, please be patient... Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:47 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;@2662e7ae, [Ljava.lang.String;@4b766324) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.11489194670309372209.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3f69725e, [Ljava.lang.String;@6a739e85) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:47 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 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:47 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 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:47 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;@1a1ae0c5, [Ljava.lang.String;@47b1356) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:47 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;@b83c874, [Ljava.lang.String;@2429e374) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.11489194670309372209.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@632bdef, [Ljava.lang.String;@7f8a2564) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:47 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;@37de2174, [Ljava.lang.String;@7cba1a5) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.11489194670309372209.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@72c451a2, [Ljava.lang.String;@605b148f) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:47 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;@5bb5a965, [Ljava.lang.String;@22a31a2b) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.11489194670309372209.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@745ba91e, [Ljava.lang.String;@6813f7eb) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:47 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;@7216fd42, [Ljava.lang.String;@7ef4eed1) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.11489194670309372209.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@74d60183, [Ljava.lang.String;@221e9642) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:47 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;@3e48bdf4, [Ljava.lang.String;@b05c3e8) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.11489194670309372209.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@394fd4bc, [Ljava.lang.String;@42f751f0) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:47 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;@34fe73b9, [Ljava.lang.String;@43a8c5b5) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.11489194670309372209.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4994d182, [Ljava.lang.String;@74662e60) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:47 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;@81c4614, [Ljava.lang.String;@20856b40) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.11489194670309372209.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6c534185, [Ljava.lang.String;@18ceea2b) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:47 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;@4abe0c65, [Ljava.lang.String;@2385f6aa) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.11489194670309372209.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@45f6e7bd, [Ljava.lang.String;@37daa4ab) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:47 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;@6ae34ae5) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:47 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;@1940be4f) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:47 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;@46c17534) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:47 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;@40fa2902) STANDARD_ERROR WARNING 2025-01-01 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:47 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;@1169a0f) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:48 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;@6f26a795) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:48 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;@311506c2) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:48 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;@5e083fb8) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:48 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 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:48 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 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:48 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;@50f6684c, [Ljava.lang.String;@16ccf2af) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:48 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;@62ff1d6c, [Ljava.lang.String;@33b33818) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.11489194670309372209.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7627a2af, [Ljava.lang.String;@1b63b14c) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:48 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;@49db7365, [Ljava.lang.String;@5fd90786) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.11489194670309372209.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2f04a52a, [Ljava.lang.String;@52379885) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:48 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;@7400a65f, [Ljava.lang.String;@3c1ef8e7) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.11489194670309372209.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@70dfa55f, [Ljava.lang.String;@744e7ccf) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:48 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;@4ffbbea2, [Ljava.lang.String;@5eb4c24a) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.11489194670309372209.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6952815d, [Ljava.lang.String;@60adf019) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:48 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;@6be496e4, [Ljava.lang.String;@55e892b9) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.11489194670309372209.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6f90dec, [Ljava.lang.String;@e2132d9) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:48 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;@72a00826, [Ljava.lang.String;@359e1047) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.11489194670309372209.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@643b1ef3, [Ljava.lang.String;@47332a5a) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:48 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;@446f7045, [Ljava.lang.String;@326749ab) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.11489194670309372209.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@12c3c6f5, [Ljava.lang.String;@302fcde) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:48 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;@23efb2c8, [Ljava.lang.String;@6748d0ba) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.11489194670309372209.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6ceaf7e7, [Ljava.lang.String;@41e709d6) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:48 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;@4b4a8dae) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:48 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;@56a2227f) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:48 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;@3cf04c1e) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:48 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;@61800f54) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:48 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;@5850de9b) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:48 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;@5af1d0f9) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:48 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;@7ef246d4) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:48 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;@548393c1) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:48 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;@7fcef8fe) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:48 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;@2cd04841) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:48 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;@3f186718) STANDARD_ERROR WARNING 2025-01-01 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:48 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;@47f6c369) STANDARD_ERROR WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:49 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;@798192d0) STANDARD_ERROR WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:49 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;@4328d8d1) STANDARD_ERROR WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:49 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;@3a774a35) STANDARD_ERROR WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:49 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;@6bb26b42) STANDARD_ERROR WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:49 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;@41ac3a51) STANDARD_ERROR WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:49 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;@5cb9e4ed) STANDARD_ERROR WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:49 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;@4ecb255b) STANDARD_ERROR WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:49 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;@589f7b7d) STANDARD_ERROR WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:49 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;@1c20f3c1) STANDARD_ERROR WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:49 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;@7b022dfa) STANDARD_ERROR WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Finished 14000 tests 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;@11d34dd4) STANDARD_ERROR WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:49 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;@dd42db6) STANDARD_ERROR WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@45554788) STANDARD_ERROR WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:49 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;@776185ec) STANDARD_ERROR WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:49 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;@1044d2d4) STANDARD_ERROR WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:49 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;@4794f694) STANDARD_ERROR WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:49 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;@2666b1ec) STANDARD_ERROR WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:49 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;@f5f1eb2) STANDARD_ERROR WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.11489194670309372209.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@3c82a005) STANDARD_ERROR WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:49 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;@369a7ae1, 5) STANDARD_ERROR WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMMergerTest.test STANDARD_ERROR WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.cram.ref.CRAMReferenceRegionTest.testGetReferenceBasesByRegionExceedsContigLength STANDARD_ERROR WARNING 2025-01-01 06:37:50 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 2025-01-01 06:37:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testIgnoreObsoleteDataseriesOnRead STANDARD_ERROR WARNING 2025-01-01 06:37:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:37:51 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 Finished 14600 tests 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 Could not delete file /tmp/pbuilder2/DiskBackedQueueTest/diskbackedqueue.466036756995640519.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 2025-01-01 06:38:06 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 2025-01-01 06:38:06 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 2025-01-01 06:38:08 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 2025-01-01 06:38:08 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 2025-01-01 06:38:08 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 2025-01-01 06:38:08 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 WARNING 2025-01-01 06:38:08 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 2025-01-01 06:38:08 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 WARNING 2025-01-01 06:38:08 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 2025-01-01 06:38:08 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 WARNING 2025-01-01 06:38:08 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 2025-01-01 06:38:08 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 2025-01-01 06:38:08 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 2025-01-01 06:38:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:08 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;@55ecdc3c, [Ljava.lang.String;@2dcb866b) STANDARD_ERROR WARNING 2025-01-01 06:38:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.8018710971585352341.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@150a0059, [Ljava.lang.String;@387ef849) STANDARD_ERROR WARNING 2025-01-01 06:38:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:08 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 2025-01-01 06:38:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:08 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 2025-01-01 06:38:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:08 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;@cd8e035) STANDARD_ERROR WARNING 2025-01-01 06:38:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:08 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;@3e738cbf) STANDARD_ERROR WARNING 2025-01-01 06:38:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:08 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;@7234b46c) STANDARD_ERROR WARNING 2025-01-01 06:38:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:08 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;@3ab3c3c9) STANDARD_ERROR WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:09 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;@6a843b11) STANDARD_ERROR WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:09 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;@2904a839) STANDARD_ERROR WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:09 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;@59b1f68f) STANDARD_ERROR WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:09 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;@77f79704) STANDARD_ERROR WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:09 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;@3deae77e, [Ljava.lang.String;@c88a9d) STANDARD_ERROR WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:09 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;@561e40b0, [Ljava.lang.String;@2cdad72) STANDARD_ERROR WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.8018710971585352341.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@63febc96, [Ljava.lang.String;@2150c5e3) STANDARD_ERROR WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 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;@7dd6d519, [Ljava.lang.String;@62bc4f38) STANDARD_ERROR WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.8018710971585352341.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2c53dedf, [Ljava.lang.String;@2b80ea94) STANDARD_ERROR WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 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;@761288f1, [Ljava.lang.String;@6921877f) STANDARD_ERROR WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.8018710971585352341.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@757e7374, [Ljava.lang.String;@407f3104) STANDARD_ERROR WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 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;@5e854cbe, [Ljava.lang.String;@5466f05e) STANDARD_ERROR WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.8018710971585352341.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@67f38b50, [Ljava.lang.String;@57f48d43) STANDARD_ERROR WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 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;@154fa3ef, [Ljava.lang.String;@37f0f331) STANDARD_ERROR WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.8018710971585352341.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@67516506, [Ljava.lang.String;@5b0db18) STANDARD_ERROR WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 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;@61670dac, [Ljava.lang.String;@58ec0691) STANDARD_ERROR WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.8018710971585352341.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7d24c83, [Ljava.lang.String;@8a4650e) STANDARD_ERROR WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 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;@56641e45, [Ljava.lang.String;@5270540d) STANDARD_ERROR WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.8018710971585352341.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@434b7903, [Ljava.lang.String;@3db2847c) STANDARD_ERROR WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 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;@242ddd23, [Ljava.lang.String;@d34b7a9) STANDARD_ERROR WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.8018710971585352341.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3f3efd2b, [Ljava.lang.String;@1426b4d9) STANDARD_ERROR WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 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 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:09 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 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 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 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:09 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 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 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;@4212fe9) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 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;@4f086203) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 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;@6741c04d) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 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;@5ea947f) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 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;@3932c0c9) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 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;@7ce768b6, [Ljava.lang.String;@435d1dc8) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 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;@58661332, [Ljava.lang.String;@184be39) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.8018710971585352341.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4eba7717, [Ljava.lang.String;@289a32b1) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 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;@79b3a1e, [Ljava.lang.String;@29f66fb7) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.8018710971585352341.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1237156d, [Ljava.lang.String;@76884feb) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 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;@61296a29, [Ljava.lang.String;@201ee0) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.8018710971585352341.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4d74078d, [Ljava.lang.String;@1e75f916) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 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;@259ad17, [Ljava.lang.String;@62ae9f35) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.8018710971585352341.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1d5f43d3, [Ljava.lang.String;@3c9465c1) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 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;@53a398a7, [Ljava.lang.String;@2a117961) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.8018710971585352341.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@33b14da, [Ljava.lang.String;@39f7cee4) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 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;@8e44a4f, [Ljava.lang.String;@54a2033a) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.8018710971585352341.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@40b4e041, [Ljava.lang.String;@639923bc) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 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;@73ec4608, [Ljava.lang.String;@6b6d4d6d) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.8018710971585352341.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@312e2e2, [Ljava.lang.String;@6ab3d955) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 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;@74111960, [Ljava.lang.String;@1c273587) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.8018710971585352341.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6d3f4bc4, [Ljava.lang.String;@1b325111) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 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;@2539a37e) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 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;@856f2f7) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 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;@4905e0f2) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 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;@1bfad540) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 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;@3cf9e2ad) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 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;@169665db) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 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;@28eded72) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.8018710971585352341.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@1f05c900) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 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;@4ac0f5e1) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 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;@72b784cd) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 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;@779fb0df) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 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;@7bb9b101) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 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;@6f0adc15) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 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;@4747fb08) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 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;@11cfd38e) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 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;@25482bc) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 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;@45e1805a) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 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 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 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;@13bfe521, 5) STANDARD_ERROR WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:38:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Finished 16400 tests Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForDecodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@5ece826e, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@6f622ca4], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR WARNING 2025-01-01 06:38:11 HtsCodecResolver The specified format string (BOGUS_FORMAT) does not correspond to any registered codec for content type (ALIGNED_READS) Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[1]([], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR WARNING 2025-01-01 06:38:11 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@2e5102d7, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@632b01c8, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@6e05be98, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@55da30e2, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@72af1369], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR WARNING 2025-01-01 06:38:11 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@2e5102d7, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@632b01c8, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@6e05be98, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@55da30e2, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@72af1369], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR WARNING 2025-01-01 06:38:11 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@2e5102d7, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@632b01c8, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@6e05be98, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@55da30e2, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@72af1369], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR WARNING 2025-01-01 06:38:11 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 file259349210724204805.bad Finished 17200 tests Gradle suite > Gradle test > htsjdk.samtools.util.IntervalTreeTest.performanceTest STANDARD_OUT Time to construct a tree with 50000 nodes: 36 milliseconds Queried for the same 100-length mapping 208959532 times in 10 seconds. Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR INFO 2025-01-01 06:38:24 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 2025-01-01 06:38:24 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) INFO 2025-01-01 06:38:24 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 2025-01-01 06:38:24 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) Finished 17600 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[281](chr3:50911035-50911051 + ., null) STANDARD_ERROR INFO 2025-01-01 06:38:24 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 2025-01-01 06:38:24 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 2025-01-01 06:38:24 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 2025-01-01 06:38:24 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 2025-01-01 06:38:24 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 2025-01-01 06:38:24 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 2025-01-01 06:38:24 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) INFO 2025-01-01 06:38:24 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 2025-01-01 06:38:24 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 2025-01-01 06:38:24 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) INFO 2025-01-01 06:38:24 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 2025-01-01 06:38:24 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) INFO 2025-01-01 06:38:24 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 2025-01-01 06:38:24 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR INFO 2025-01-01 06:38:24 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 2025-01-01 06:38:24 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) INFO 2025-01-01 06:38:24 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 2025-01-01 06:38:24 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 2025-01-01 06:38:24 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 2025-01-01 06:38:24 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 2025-01-01 06:38:24 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 2025-01-01 06:38:24 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 2025-01-01 06:38:24 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 2025-01-01 06:38:24 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 2025-01-01 06:38:24 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) INFO 2025-01-01 06:38:24 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 2025-01-01 06:38:24 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 2025-01-01 06:38:24 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) INFO 2025-01-01 06:38:24 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 2025-01-01 06:38:24 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) INFO 2025-01-01 06:38:24 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 2025-01-01 06:38:24 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 2025-01-01 06:38:24 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Finished 18400 tests Finished 18600 tests Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaCoordinateMultiIterator STANDARD_OUT read_28833_29006_6945 0 chr21 28833 255 36M * 0 0 AAGCTGGAGATTACCATACTTAGGCTCATGTAGCCA ?.QC5:&34LA#;K;A'5L*!.;.LJ?)FO?'?D2< RG:Z:1 read_28833_29006_6945 0 chr21 30000 255 36M * 0 0 AAGCTGGAGATTACCATACTTAGGCTCATGTAGCCA ?.QC5:&34LA#;K;A'5L*!.;.LJ?)FO?'?D2< RG:Z:1 read_28701_28881_323b 0 chrX 28834 255 36M * 0 0 GCCCTATCGCCAGATCAATCGTCGCTGTGGAACTAG $>8BE+:L!M$K(L*MQ>PO8N*8>;;=5IA>B,*O RG:Z:1 read_28701_28881_323b 0 chrX 28835 255 36M * 0 0 GCCCTATCGCCAGATCAATCGTCGCTGTGGAACTAG $>8BE+:L!M$K(L*MQ>PO8N*8>;;=5IA>B,*O RG:Z:1 read_28701_28881_323c 0 chrX 28835 255 36M * 0 0 CTCAACGTATTCATACAGGCCCTTTTCGAATAGCTG %$=LPJ?D6&@R!"KJCOI+05?>>J9CJ)'@-O>K RG:Z:1 Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaReadOrderMultiIterator STANDARD_OUT a b c d e Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaUnsortedMultiIterator STANDARD_OUT d e c b a Finished 18800 tests Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[0](@HD VN:1.0 SO:UNSORTED ) STANDARD_ERROR WARNING 2025-01-01 06:38:54 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 2025-01-01 06:38:54 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 2025-01-01 06:38:54 SAMTextHeaderCodec Found non-conforming header SO tag: COORDINATE. Treating as 'unknown'. Finished 19000 tests Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[3](@HD VN:1.0 SO:uNknOWn ) STANDARD_ERROR WARNING 2025-01-01 06:38:54 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 2025-01-01 06:38:54 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.specialFileWriterTest STANDARD_ERROR WARNING 2025-01-01 06:38:54 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null WARNING 2025-01-01 06:38:54 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 2025-01-01 06:38:54 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.10815543449925356378..cram INFO 2025-01-01 06:38:54 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-01-01 06:38:54 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-01-01 06:38:54 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeSamOrBamForCramExtension STANDARD_ERROR INFO 2025-01-01 06:38:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension7571250220971129778.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.14625212646296138176.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 2025-01-01 06:38:54 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension5707666141791773180.cram INFO 2025-01-01 06:38:54 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-01-01 06:38:54 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-01-01 06:38:54 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForNoExtension STANDARD_ERROR INFO 2025-01-01 06:38:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension11895534327651119238 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForUnknownFileExtension STANDARD_ERROR INFO 2025-01-01 06:38:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension5238174716143756571.png Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[0](sam) STANDARD_ERROR INFO 2025-01-01 06:38:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://040c1150-cf29-4bb2-963a-2ab76e9a7949/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 2025-01-01 06:38:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://31623644-5b6a-4471-9451-d7633f5cb483/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 2025-01-01 06:38:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://2b538596-cec6-42f1-811c-995e340d058a/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 2025-01-01 06:38:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://021547eb-1894-4761-bccb-cb97d3a45091/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 2025-01-01 06:38:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://f91c5c6c-bacb-4050-bc20-fb31a5d671d8/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 2025-01-01 06:38:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://46a0a549-2529-48ae-a667-704324f37dcf/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 2025-01-01 06:39:08 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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai) STANDARD_ERROR WARNING 2025-01-01 06:39:08 SamFiles The index file /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam WARNING 2025-01-01 06:39:08 SamFiles The index file /build/reproducible-path/htsjdk-4.1.3+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-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.customReaderFactoryTest STANDARD_ERROR INFO 2025-01-01 06:39:09 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory INFO 2025-01-01 06:39:09 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory INFO 2025-01-01 06:39:09 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar INFO 2025-01-01 06:39:09 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 2025-01-01 06:39:09 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 2025-01-01 06:39:09 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 2025-01-01 06:39:09 SamReaderFactoryTest Finished queries in 45ms Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURL STANDARD_ERROR WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLNoIndexFile STANDARD_ERROR WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLStream STANDARD_ERROR WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromMalformedSeekableStream STANDARD_ERROR WARNING 2025-01-01 06:39:09 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 2025-01-01 06:39:09 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 2025-01-01 06:39:09 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 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:39:09 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 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:39:09 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 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:39:09 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 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:39:09 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 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:39:09 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 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:39:09 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 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-01-01 06:39:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testBamIntegers[1](inttest_large_coordinates.bam) STANDARD_ERROR WARNING 2025-01-01 06:39:09 BAMRecordCodec Reference length is too large for BAM bin field. WARNING 2025-01-01 06:39:09 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 2025-01-01 06:39:09 BAMRecordCodec Reference length is too large for BAM bin field. WARNING 2025-01-01 06:39:09 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 Finished 20000 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlocksTest.testSliceBlocksRoundTrip SKIPPED Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests STANDARD_ERROR WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 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 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 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 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. WARNING 2025-01-01 06:39:10 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 2025-01-01 06:39:10 CRAMReferenceRegion The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20 WARNING 2025-01-01 06:39:10 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 Finished 36000 tests Gradle Test Executor 3 finished executing tests. Results: SUCCESS (35850 tests, 35831 successes, 0 failures, 19 skipped) Finished generating test XML results (0.125 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/test-results/test Generating HTML test report... Finished generating test html results (0.215 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/reports/tests/test :test (Thread[#36,Daemon worker,5,main]) completed. Took 14 mins 15.324 secs. BUILD SUCCESSFUL in 31m 40s 7 actionable tasks: 5 executed, 2 up-to-date make[1]: Leaving directory '/build/reproducible-path/htsjdk-4.1.3+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-4.1.3\+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 Duplicate specification "author|A=s" for option "A" Duplicate specification "A" for option "A" Installing javadoc from build/docs/javadoc into package libhtsjdk-java-doc install -m0755 -d debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java cp -r build/docs/javadoc debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/ cat > debian/libhtsjdk-java-doc.doc-base.javadoc dh_installdocs -O--buildsystem=gradle install -m0755 -d debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java install -p -m0644 debian/libhtsjdk-java.README.Debian debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java/README.Debian install -p -m0644 debian/copyright debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java/copyright install -m0755 -d debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc install -p -m0644 debian/copyright debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/copyright install -m0755 -d debian/libhtsjdk-java-doc/usr/share/doc-base/ install -p -m0644 debian/libhtsjdk-java-doc.doc-base.javadoc debian/libhtsjdk-java-doc/usr/share/doc-base/libhtsjdk-java-doc.libhtsjdk-java-doc dh_installchangelogs -O--buildsystem=gradle install -m0755 -d debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java install -p -m0644 debian/.debhelper/generated/libhtsjdk-java/dh_installchangelogs.dch.trimmed debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java/changelog.Debian install -m0755 -d debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc install -p -m0644 debian/.debhelper/generated/libhtsjdk-java-doc/dh_installchangelogs.dch.trimmed debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/changelog.Debian dh_installsystemduser -O--buildsystem=gradle dh_lintian -O--buildsystem=gradle install -m0755 -d debian/libhtsjdk-java-doc/usr/share/lintian/overrides install -p -m0644 debian/libhtsjdk-java-doc.lintian-overrides debian/libhtsjdk-java-doc/usr/share/lintian/overrides/libhtsjdk-java-doc dh_perl -O--buildsystem=gradle dh_link -O--buildsystem=gradle rm -f debian/libhtsjdk-java-doc.debhelper.log debian/libhtsjdk-java.debhelper.log debian/rules override_jh_installlibs make[1]: Entering directory '/build/reproducible-path/htsjdk-4.1.3+dfsg' jh_installlibs --version-strip='[+]dfsg[.0-9]*' install -m0755 -d debian/libhtsjdk-java/usr/share/java install -p -m0644 ./build/libs/htsjdk-4.1.3.jar debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.3.jar rm -f debian/libhtsjdk-java/usr/share/java/htsjdk.jar ln -s htsjdk-4.1.3.jar debian/libhtsjdk-java/usr/share/java/htsjdk.jar make[1]: Leaving directory '/build/reproducible-path/htsjdk-4.1.3+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/json-lib.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 Duplicate specification "V:s" for option "V" Duplicate specification "version|V" for option "V" Updating symlinked /build/reproducible-path/htsjdk-4.1.3+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.3.jar (via debian/libhtsjdk-java/usr/share/java/htsjdk.jar) Reading manifest from /build/reproducible-path/htsjdk-4.1.3+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.3.jar Updating manifest in /build/reproducible-path/htsjdk-4.1.3+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.3.jar jh_manifest -O--buildsystem=gradle Duplicate specification "version|V" for option "V" Duplicate specification "version|V" for option "V" find debian/libhtsjdk-java -name '*.jar' Found usr/share/java/htsjdk-4.1.3.jar Found symlink usr/share/java/htsjdk.jar Reading manifest from debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.3.jar No update of debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.3.jar required. find debian/libhtsjdk-java-doc -name '*.jar' jh_exec -O--buildsystem=gradle jh_depends -O--buildsystem=gradle Searching /build/reproducible-path/htsjdk-4.1.3+dfsg/debian/libhtsjdk-java for libhtsjdk-java Searching /build/reproducible-path/htsjdk-4.1.3+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.3.jar Found Jars: /usr/share/java/commons-compress.jar /usr/share/java/commons-jexl2.jar /usr/share/java/json-lib.jar /usr/share/java/ngs-java.jar /usr/share/java/rhino.jar /usr/share/java/snappy-java.jar Checking: /build/reproducible-path/htsjdk-4.1.3+dfsg/debian/libhtsjdk-java/usr/share/java/commons-compress-1.27.1.jar Checking: /build/reproducible-path/htsjdk-4.1.3+dfsg/debian/libhtsjdk-java-doc/usr/share/java/commons-compress-1.27.1.jar Checking: /build/reproducible-path/htsjdk-4.1.3+dfsg/debian/libhtsjdk-java/usr/share/java/commons-jexl2.jar Checking: /build/reproducible-path/htsjdk-4.1.3+dfsg/debian/libhtsjdk-java-doc/usr/share/java/commons-jexl2.jar Checking: /build/reproducible-path/htsjdk-4.1.3+dfsg/debian/libhtsjdk-java/usr/share/java/json-lib-3.1.0.jar Checking: /build/reproducible-path/htsjdk-4.1.3+dfsg/debian/libhtsjdk-java-doc/usr/share/java/json-lib-3.1.0.jar Checking: /build/reproducible-path/htsjdk-4.1.3+dfsg/debian/libhtsjdk-java/usr/share/java/ngs-java-3.0.9.jar Checking: /build/reproducible-path/htsjdk-4.1.3+dfsg/debian/libhtsjdk-java-doc/usr/share/java/ngs-java-3.0.9.jar Checking: /build/reproducible-path/htsjdk-4.1.3+dfsg/debian/libhtsjdk-java/usr/share/java/js-1.7.14.jar Checking: /build/reproducible-path/htsjdk-4.1.3+dfsg/debian/libhtsjdk-java-doc/usr/share/java/js-1.7.14.jar Checking: /build/reproducible-path/htsjdk-4.1.3+dfsg/debian/libhtsjdk-java/usr/share/java/snappy-java-1.1.10.7.jar Checking: /build/reproducible-path/htsjdk-4.1.3+dfsg/debian/libhtsjdk-java-doc/usr/share/java/snappy-java-1.1.10.7.jar Found Debs: libcommons-compress-java libcommons-jexl2-java libjson-java libngs-java librhino-java libsnappy-java Adding substvars: java:Depends=libcommons-compress-java, libcommons-jexl2-java, libjson-java, libngs-java, librhino-java, libsnappy-java java:Recommends= Searching /build/reproducible-path/htsjdk-4.1.3+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-4.1.3.pom debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/4.1.3/htsjdk-4.1.3.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/4.1.3/htsjdk-4.1.3.jar rm -f debian/libhtsjdk-java/usr/share/java/htsjdk.jar ln -s htsjdk-4.1.3.jar debian/libhtsjdk-java/usr/share/java/htsjdk.jar install -m0755 -d debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/4.1.3 rm -f debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/4.1.3/htsjdk-4.1.3.jar ln -s ../../../../../../java/htsjdk.jar debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/4.1.3/htsjdk-4.1.3.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-4.1.3.jar debian/libhtsjdk-java/usr/share/java/htsjdk.jar rm -f debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/4.1.3/htsjdk-4.1.3.jar ln -s ../../../../../../java/htsjdk.jar debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/4.1.3/htsjdk-4.1.3.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 1735551212 as canonical time Normalizing debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.3.jar using File::StripNondeterminism::handlers::jar Using 1735551212 as canonical time Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ByteArrayStopEncoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/SubexponentialIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/GammaIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CoreCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanByteEncoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/BetaIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/BetaIntegerCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanParamsCalculator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanParams.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanCanoncialCodeGenerator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanBitCode.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/GolombRiceIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/GolombLongEncoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/GolombIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Substitution.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/SoftClip.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Scores.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/RefSkip.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/ReadFeature.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/ReadBase.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Padding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Insertion.html using File::StripNondeterminism::handlers::javadoc Normalizing 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File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TPair64.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TIntv.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TIndex.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/RemoteURLHelper.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/ParsingUtils.html using 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File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/HardyWeinbergCalculation.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/package-summary.html using File::StripNondeterminism:: 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 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File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/ContentDigests.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/Utils.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/SliceFactory.html using File::StripNondeterminism::handlers::javadoc Normalizing 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File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CompressionHeaderFactory.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/RAWExternalCompressor.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/RANSExternalCompressor.html using File::StripNondeterminism::handlers::javadoc Normalizing 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using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/GeneralUtils.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/BinomialCoefficientUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCFVersion.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Utils.html using 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File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsInterval.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/VariantsResolver.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/ReadsResolver.html using File::StripNondeterminism::handlers::javadoc Normalizing 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using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceIndexCreator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceIndex.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaReferenceWriterBuilder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaReferenceWriter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqWriterFactory.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqWriter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqRecord.html using File::StripNondeterminism::handlers::javadoc 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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 jdk/variant/variantcontext/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextUtils.JexlVCMatchExp.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextUtils.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextComparator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextBuilder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.Validation.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.Type.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/StructuralVariantType.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/SimpleAllele.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.LazyParser.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.LazyData.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/JexlMissingValueTreatment.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeType.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypesContext.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeLikelihoods.GenotypeLikelihoodsAllelePair.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeLikelihoods.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeJEXLContext.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeBuilder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/Genotype.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/FastGenotype.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/CommonInfo.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/Allele.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/VariantContextFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/SnpFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/PassingVariantFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/JavascriptVariantFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/HeterozygosityFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/GenotypeQualityFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/FilteringVariantContextIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/FilteringIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/CompoundFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/package-tree.html using File::StripNondeterminism::handlers::javadoc dh_compress -O--buildsystem=gradle cd debian/libhtsjdk-java cd debian/libhtsjdk-java-doc chmod a-x usr/share/doc/libhtsjdk-java/changelog.Debian gzip -9nf usr/share/doc/libhtsjdk-java/changelog.Debian cd '/build/reproducible-path/htsjdk-4.1.3+dfsg' chmod a-x usr/share/doc/libhtsjdk-java-doc/changelog.Debian gzip -9nf usr/share/doc/libhtsjdk-java-doc/changelog.Debian cd '/build/reproducible-path/htsjdk-4.1.3+dfsg' dh_fixperms -O--buildsystem=gradle find debian/libhtsjdk-java ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhtsjdk-java-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhtsjdk-java/usr/share/doc -type f -a -true -a ! -regex 'debian/libhtsjdk-java/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhtsjdk-java/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhtsjdk-java-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 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhtsjdk-java-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhtsjdk-java-doc/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhtsjdk-java-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 dh_missing -O--buildsystem=gradle dh_installdeb -O--buildsystem=gradle install -m0755 -d debian/libhtsjdk-java/DEBIAN install -m0755 -d debian/libhtsjdk-java-doc/DEBIAN dh_gencontrol -O--buildsystem=gradle install -m0755 -d debian/libhtsjdk-java/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-doc/DEBIAN/control chmod 0644 -- debian/libhtsjdk-java/DEBIAN/control dh_md5sums -O--buildsystem=gradle install -m0755 -d debian/libhtsjdk-java/DEBIAN install -m0755 -d debian/libhtsjdk-java-doc/DEBIAN cd debian/libhtsjdk-java >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libhtsjdk-java-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libhtsjdk-java/DEBIAN/md5sums chmod 0644 -- debian/libhtsjdk-java-doc/DEBIAN/md5sums dh_builddeb -O--buildsystem=gradle dpkg-deb --root-owner-group --build debian/libhtsjdk-java .. dpkg-deb --root-owner-group --build debian/libhtsjdk-java-doc .. dpkg-deb: building package 'libhtsjdk-java' in '../libhtsjdk-java_4.1.3+dfsg-2_all.deb'. dpkg-deb: building package 'libhtsjdk-java-doc' in '../libhtsjdk-java-doc_4.1.3+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary -O../htsjdk_4.1.3+dfsg-2_arm64.buildinfo dpkg-genchanges --build=binary -O../htsjdk_4.1.3+dfsg-2_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: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1704786/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1704786/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1704786 and its subdirectories I: Current time: Wed Jan 1 06:39:38 +14 2025 I: pbuilder-time-stamp: 1735663178