From nobody Sun Jul 14 12:32:08 2024 X-Original-To: pkg-fallout@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4WMPpx2qzyz5QW4K for ; Sun, 14 Jul 2024 12:32:09 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R11" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4WMPpw3yWGz4pmb for ; Sun, 14 Jul 2024 12:32:08 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1720960328; a=rsa-sha256; cv=none; b=vDdKQdWl70HdhK2s5+4pP4EXkvElC8/j+Z2D2Y8K6VqfFK5M1zfHnIK/Yn/4ZrnLX3NuGO lVOupf2RxvSpV14SEvDqlpO05WasAVQGDgKiUAlUVJQqDLGFGuBhbYUZQV1Ym2rXfyNbOG 5VnnSDtt8UzhtQIOK2ZhrNcUmvivF8+SBAj20EsdeMFdG7oJIIKzRoOXx+71e0QfmTHSWh /LLuxyqBqbVvaVJRA9DRbrInldYiGsqwjpkbj12y6nmlOHiIU7+74MGEqzAJ0BDg1gg88q oBMITg3mRBo9dzOEoEuzLhpT+RriF2CPvLHT7LNmRRxqXruJ+D+fGEwXztrJzQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1720960328; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=QmpIAlp8C0kIdSOFy8W1xEGk4frvwQQa006ZcYxL+J8=; b=y1UxdPNXV4mf+glzRyo5OkfIREXaMcPqgTCDOxt8Bpyh/V4NOn6A7SpxmhsVtDdd9gC9V3 l6/kO0TZMUz3I7PKklIOqKEySK+VkEQ9/B7kpP2fmDPx5sKnNaoReIqLpSxOKpIHFoatRP VUhAe420MXM+uvo08rAR3IunwbwE+J90oGgfH2H1q6Qpf9C9VGVwmWK7nOrJlbSTs4arTl NTR7YB2yntgC5jv81y8kxSO8z08J4WwxApJVR2g8fghN8HB/Cp/AX7uwjAuDw1hH6Z7N8q +0KrYqyt5WoRjSxLLILEpQmZ6JYHurEa4523FaEiWqMHknpxcdDK1zkySBTJiQ== Received: from beefy16.nyi.freebsd.org (beefy16.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:1f]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4WMPpw3WNyz18VM for ; Sun, 14 Jul 2024 12:32:08 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 1594 by beefy16.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on beefy16.nyi.freebsd.org); Sun, 14 Jul 2024 12:32:08 +0000 To: yuri@FreeBSD.org Subject: [package - 133amd64-default][biology/gatk] Failed for gatk-4.6.0.0 in checksum Cc: pkg-fallout@FreeBSD.org Date: Sun, 14 Jul 2024 12:32:08 +0000 Message-Id: <6693c548.1594.14255be1@beefy16.nyi.freebsd.org> From: List-Id: Fallout logs from package building List-Archive: https://lists.freebsd.org/archives/freebsd-pkg-fallout List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-pkg-fallout@FreeBSD.org You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: yuri@FreeBSD.org Log URL: https://pkg-status.freebsd.org/beefy16/data/133amd64-default/a71eaeb3e54e/logs/gatk-4.6.0.0.log Build URL: https://pkg-status.freebsd.org/beefy16/build.html?mastername=133amd64-default&build=a71eaeb3e54e Log: =>> Building biology/gatk build started at Sun Jul 14 12:09:35 UTC 2024 port directory: /usr/ports/biology/gatk package name: gatk-4.6.0.0 building for: FreeBSD 133amd64-default-job-09 13.3-RELEASE-p4 FreeBSD 13.3-RELEASE-p4 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 3943 Jul 13 01:02 /usr/ports/biology/gatk/Makefile Ports top last git commit: a71eaeb3e54 Ports top unclean checkout: no Port dir last git commit: 290983fbb4b Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.1-30-g79e3edcd Host OSVERSION: 1500019 Jail OSVERSION: 1303001 Job Id: 09 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1303001 UNAME_v=FreeBSD 13.3-RELEASE-p4 UNAME_r=13.3-RELEASE-p4 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.1-30-g79e3edcd MASTERMNT=/usr/local/poudriere/data/.m/133amd64-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/133amd64-default/09/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=133amd64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/133amd64-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.1-30-g79e3edcd SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for gatk-4.6.0.0: WITH_LARGE_FILES=on: Download large LFS files needed for build and tests ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gatk/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gatk/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gatk/work/.cache HOME=/wrkdirs/usr/ports/biology/gatk/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gatk/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gatk/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gatk/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gatk/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gatk/work/.cache HOME=/wrkdirs/usr/ports/biology/gatk/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gatk/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gatk/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="i nstall -m 444" --End MAKE_ENV-- --PLIST_SUB-- JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" OSREL=13.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/gatk" EXAMPLESDIR="share/examples/gatk" DATADIR="share/gatk" WWWDIR="www/gatk" ETCDIR="etc/gatk" --End PLIST_SUB-- --SUB_LIST-- PORTVERSION=4.6.0.0 JAVA=/usr/local/openjdk17/bin/java JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" JAVA_VERSION="17" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/gatk DOCSDIR=/usr/local/share/doc/gatk EXAMPLESDIR=/usr/local/share/examples/gatk WWWDIR=/usr/local/www/gatk ETCDIR=/usr/local/etc/gatk --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 2048 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD3CLAUSE accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gatk-4.6.0.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.21.3.pkg [133amd64-default-job-09] Installing pkg-1.21.3... [133amd64-default-job-09] Extracting pkg-1.21.3: .......... done ===> gatk-4.6.0.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gatk-4.6.0.0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gatk-4.6.0.0 depends on executable: git - not found ===> Installing existing package /packages/All/git-2.45.2_1.pkg [133amd64-default-job-09] Installing git-2.45.2_1... [133amd64-default-job-09] `-- Installing curl-8.8.0... [133amd64-default-job-09] | `-- Installing libnghttp2-1.62.1... [133amd64-default-job-09] | `-- Extracting libnghttp2-1.62.1: .......... done [133amd64-default-job-09] | `-- Installing libpsl-0.21.5_1... [133amd64-default-job-09] | | `-- Installing libidn2-2.3.7... [133amd64-default-job-09] | | `-- Installing indexinfo-0.3.1... 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[133amd64-default-job-09] | | `-- Installing perl5-5.36.3_1... [133amd64-default-job-09] | | `-- Extracting perl5-5.36.3_1: .......... done [133amd64-default-job-09] | `-- Extracting p5-Digest-HMAC-1.04: .......... done [133amd64-default-job-09] | `-- Installing p5-GSSAPI-0.28_2... [133amd64-default-job-09] | `-- Extracting p5-GSSAPI-0.28_2: .......... done [133amd64-default-job-09] `-- Extracting p5-Authen-SASL-2.17: .......... done [133amd64-default-job-09] `-- Installing p5-CGI-4.66... [133amd64-default-job-09] | `-- Installing p5-HTML-Parser-3.82... [133amd64-default-job-09] | | `-- Installing p5-HTML-Tagset-3.24... [133amd64-default-job-09] | | `-- Extracting p5-HTML-Tagset-3.24: ....... done [133amd64-default-job-09] | | `-- Installing p5-HTTP-Message-6.46... [133amd64-default-job-09] | | `-- Installing p5-Clone-0.46... [133amd64-default-job-09] | | `-- Extracting p5-Clone-0.46: ......... done [133amd64-default-job-09] | | `-- Installing p5-Encode-Locale-1.05... [133amd64-default-job-09] | | `-- Extracting p5-Encode-Locale-1.05: ....... done [133amd64-default-job-09] | | `-- Installing p5-HTTP-Date-6.06... [133amd64-default-job-09] | | | `-- Installing p5-TimeDate-2.33,1... [133amd64-default-job-09] | | | `-- Extracting p5-TimeDate-2.33,1: .......... done [133amd64-default-job-09] | | `-- Extracting p5-HTTP-Date-6.06: ....... done [133amd64-default-job-09] | | `-- Installing p5-IO-HTML-1.004... [133amd64-default-job-09] | | `-- Extracting p5-IO-HTML-1.004: ....... done [133amd64-default-job-09] | | `-- Installing p5-LWP-MediaTypes-6.04... [133amd64-default-job-09] | | `-- Extracting p5-LWP-MediaTypes-6.04: ........ done [133amd64-default-job-09] | | `-- Installing p5-URI-5.28... [133amd64-default-job-09] | | `-- Extracting p5-URI-5.28: .......... done [133amd64-default-job-09] | | `-- Extracting p5-HTTP-Message-6.46: .......... done [133amd64-default-job-09] | `-- Extracting p5-HTML-Parser-3.82: .......... done [133amd64-default-job-09] `-- Extracting p5-CGI-4.66: .......... done [133amd64-default-job-09] `-- Installing p5-Error-0.17029... [133amd64-default-job-09] `-- Extracting p5-Error-0.17029: ......... done [133amd64-default-job-09] `-- Installing p5-IO-Socket-SSL-2.087... [133amd64-default-job-09] | `-- Installing p5-IO-Socket-IP-0.42... Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-normal-allelic-counts-with-missing-sites.allelicCounts.tsv (2.2 MB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-1-allelic-counts-SM-74P4M-v1-chr20.allelicCounts.tsv (2.2 MB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-1-allelic-counts-with-missing-sites.allelicCounts.tsv (2.2 MB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-1-denoised-copy-ratios-SM-74P4M-v1-chr20.denoisedCR.tsv (191 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-1-denoised-copy-ratios-with-missing-intervals.denoisedCR.tsv (190 KB) Downloading 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src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/input/small_callset_low_threshold.sites-only.chr1.1-10M.vcf.idx (5.4 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.1-5M.vcf.gz (128 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.1-5M.vcf.gz.tbi (2.1 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.5M-10M.vcf.gz (132 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.5M-10M.vcf.gz.tbi (2.5 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.1-5M.vcf.gz (46 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.1-5M.vcf.gz.tbi (2.0 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.5M-10M.vcf.gz (50 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.5M-10M.vcf.gz.tbi (2.5 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snp.annot.hdf5 (737 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snp.scores.hdf5 (35 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snp.vcf (2.2 MB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snp.vcf.idx (119 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snpIndel.annot.hdf5 (822 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snpIndel.scores.hdf5 (38 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snpIndel.vcf (2.2 MB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snpIndel.vcf.idx (119 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snp.annot.hdf5 (766 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snp.scores.hdf5 (35 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snp.vcf (2.2 MB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snp.vcf.idx (119 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snpIndel.annot.hdf5 (830 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snpIndel.scores.hdf5 (38 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snpIndel.vcf (2.2 MB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snpIndel.vcf.idx (119 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snp.posOnly.IF.snp.calibrationScores.hdf5 (5.0 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snp.posOnly.IF.snp.scorer.pkl (676 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snp.posOnly.IF.snp.trainingScores.hdf5 (6.0 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed.snp.calibrationScores.hdf5 (5.0 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed.snp.scorer.pkl (687 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed.snp.trainingScores.hdf5 (6.0 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.indel.calibrationScores.hdf5 (2.7 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.indel.scorer.pkl (304 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.indel.trainingScores.hdf5 (2.9 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.snp.scorer.pkl (676 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed.indel.calibrationScores.hdf5 (2.7 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed.indel.scorer.pkl (310 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed.indel.trainingScores.hdf5 (2.9 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snp.posOnly.IF.snp.calibrationScores.hdf5 (5.0 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snp.posOnly.IF.snp.scorer.pkl (745 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snp.posOnly.IF.snp.trainingScores.hdf5 (6.0 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed.snp.calibrationScores.hdf5 (5.0 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed.snp.scorer.pkl (702 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed.snp.trainingScores.hdf5 (6.0 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.indel.calibrationScores.hdf5 (2.7 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.indel.scorer.pkl (336 KB) 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src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed.indel.trainingScores.hdf5 (2.9 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/isolation-forest-hyperparameters-different-seed.json (23 B) Downloading src/test/resources/large/readFilter/read_filter_output.sam (5.9 MB) Downloading src/test/resources/large/reblockGVCFs_AS_test.p_falciparum.g.vcf (178 KB) Downloading src/test/resources/large/snpEff2.0.5.AFR.unfiltered.VariantAnnotator.output.vcf (4.2 MB) Downloading src/test/resources/large/snpEff2.0.5.AFR.unfiltered.VariantAnnotator.output.vcf.idx (3.6 KB) Downloading src/test/resources/large/sv/CpxVariantReInterpreterSparkIntegrationTest_complex_assembly.bam (139 KB) Downloading src/test/resources/large/sv/CpxVariantReInterpreterSparkIntegrationTest_complex_assembly.bam.bai (398 KB) Downloading 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src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snp.scores.hdf5 (35 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snp.vcf.idx (119 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snpIndel.annot.hdf5 (822 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snpIndel.scores.hdf5 (38 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snpIndel.vcf.idx (119 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snp.annot.hdf5 (766 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snp.scores.hdf5 (35 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snp.vcf.idx (119 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snpIndel.annot.hdf5 (830 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snpIndel.scores.hdf5 (38 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snpIndel.vcf.idx (119 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snp.posOnly.IF.snp.calibrationScores.hdf5 (5.0 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snp.posOnly.IF.snp.scorer.pkl (506 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snp.posOnly.IF.snp.trainingScores.hdf5 (6.0 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed.snp.calibrationScores.hdf5 (5.0 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed.snp.scorer.pkl (514 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed.snp.trainingScores.hdf5 (6.0 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.indel.calibrationScores.hdf5 (2.7 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.indel.scorer.pkl (236 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.indel.trainingScores.hdf5 (2.9 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.snp.calibrationScores.hdf5 (5.0 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.snp.scorer.pkl (506 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.snp.trainingScores.hdf5 (6.0 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed.indel.calibrationScores.hdf5 (2.7 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed.indel.scorer.pkl (240 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed.indel.trainingScores.hdf5 (2.9 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed.snp.calibrationScores.hdf5 (5.0 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed.snp.trainingScores.hdf5 (6.0 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snp.posOnly.IF.snp.calibrationScores.hdf5 (5.0 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snp.posOnly.IF.snp.scorer.pkl (557 KB) 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(2.7 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.indel.scorer.pkl (259 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.indel.trainingScores.hdf5 (2.9 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.snp.calibrationScores.hdf5 (5.0 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.snp.scorer.pkl (557 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.snp.trainingScores.hdf5 (6.0 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed.indel.calibrationScores.hdf5 (2.7 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed.indel.scorer.pkl (249 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed.indel.trainingScores.hdf5 (2.9 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed.snp.calibrationScores.hdf5 (5.0 KB) Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed.snp.trainingScores.hdf5 (6.0 KB) ===> Fetching all distfiles required by gatk-4.6.0.0 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by gatk-4.6.0.0 for building /usr/ports/Mk/Scripts/checksum.sh: cannot open gatk-4.6.0.0-deps.tar.gz: No such file or directory *** Error code 2 Stop. make: stopped in /usr/ports/biology/gatk