[exp - 140amd64-default-build-as-user][biology/gatk] Failed for gatk-4.6.0.0 in checksum

Go to: [ bottom of page ] [ top of archives ] [ this month ]
From: <pkg-fallout_at_FreeBSD.org>
Date: Wed, 17 Jul 2024 16:22:31 UTC
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/package19/data/140amd64-default-build-as-user/e65776ce3703/logs/gatk-4.6.0.0.log
Build URL:      https://pkg-status.freebsd.org/package19/build.html?mastername=140amd64-default-build-as-user&build=e65776ce3703
Log:

=>> Building biology/gatk
build started at Wed Jul 17 15:19:08 UTC 2024
port directory: /usr/ports/biology/gatk
package name: gatk-4.6.0.0
building for: FreeBSD 140amd64-default-build-as-user-job-07 14.0-RELEASE-p8 FreeBSD 14.0-RELEASE-p8 amd64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r--  1 root wheel 4410 Jul 15 00:06 /usr/ports/biology/gatk/Makefile
Ports top last git commit: e65776ce370
Ports top unclean checkout: no
Port dir last git commit: c3b8a41d7f6
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1-30-g79e3edcd
Host OSVERSION: 1500019
Jail OSVERSION: 1400097
Job Id: 07

---Begin Environment---
SHELL=/bin/sh
OSVERSION=1400097
UNAME_v=FreeBSD 14.0-RELEASE-p8
UNAME_r=14.0-RELEASE-p8
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=/poudriere/data/.m/140amd64-default-build-as-user/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
GID=0
OUTPUT_REDIRECTED_STDERR=4
OUTPUT_REDIRECTED=1
UID=0
PWD=/poudriere/data/.m/140amd64-default-build-as-user/07/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=140amd64-default-build-as-user
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/poudriere/data/.m/140amd64-default-build-as-user/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=14.0 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
FORCE_PACKAGE=yes
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
####  ####
# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
---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--
=======================<phase: check-sanity   >============================
===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534
===>  License BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===== 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
[140amd64-default-build-as-user-job-07] Installing pkg-1.21.3...
[140amd64-default-build-as-user-job-07] 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
===========================================================================
=======================<phase: fetch-depends  >============================
===== 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
[140amd64-default-build-as-user-job-07] Installing git-2.45.2_1...
[140amd64-default-build-as-user-job-07] `-- Installing curl-8.8.0...
[140amd64-default-build-as-user-job-07] |   `-- Installing libnghttp2-1.62.1...
[140amd64-default-build-as-user-job-07] |   `-- Extracting libnghttp2-1.62.1: .......... done
[140amd64-default-build-as-user-job-07] |   `-- Installing libpsl-0.21.5_1...
[140amd64-default-build-as-user-job-07] |   | `-- Installing libidn2-2.3.7...
[140amd64-default-build-as-user-job-07] |   |   `-- Installing indexinfo-0.3.1...
[140amd64-default-build-as-user-job-07] |   |   `-- Extracting indexinfo-0.3.1: .... done
[140amd64-default-build-as-user-job-07] |   |   `-- Installing libunistring-1.2...
[140amd64-default-build-as-user-job-07] |   |   `-- Extracting libunistring-1.2: .......... done
[140amd64-default-build-as-user-job-07] |   | `-- Extracting libidn2-2.3.7: .......... done
[140amd64-default-build-as-user-job-07] |   `-- Extracting libpsl-0.21.5_1: .......... done
[140amd64-default-build-as-user-job-07] |   `-- Installing libssh2-1.11.0_1,3...
[140amd64-default-build-as-user-job-07] |   `-- Extracting libssh2-1.11.0_1,3: .......... done
[140amd64-default-build-as-user-job-07] `-- Extracting curl-8.8.0: .......... done
[140amd64-default-build-as-user-job-07] `-- Installing expat-2.6.2...
[140amd64-default-build-as-user-job-07] `-- Extracting expat-2.6.2: .......... done
[140amd64-default-build-as-user-job-07] `-- Installing gettext-runtime-0.22.5...
[140amd64-default-build-as-user-job-07] `-- Extracting gettext-runtime-0.22.5: .......... done
[140amd64-default-build-as-user-job-07] `-- Installing p5-Authen-SASL-2.17...
[140amd64-default-build-as-user-job-07] |   `-- Installing p5-Digest-HMAC-1.04...
[140amd64-default-build-as-user-job-07] |   | `-- Installing perl5-5.36.3_1...
[140amd64-default-build-as-user-job-07] |   | `-- Extracting perl5-5.36.3_1: .......... done
[140amd64-default-build-as-user-job-07] |   `-- Extracting p5-Digest-HMAC-1.04: .......... done
[140amd64-default-build-as-user-job-07] |   `-- Installing p5-GSSAPI-0.28_2...
[140amd64-default-build-as-user-job-07] |   `-- Extracting p5-GSSAPI-0.28_2: .......... done
[140amd64-default-build-as-user-job-07] `-- Extracting p5-Authen-SASL-2.17: .......... done
[140amd64-default-build-as-user-job-07] `-- Installing p5-CGI-4.66...
[140amd64-default-build-as-user-job-07] |   `-- Installing p5-HTML-Parser-3.82...
[140amd64-default-build-as-user-job-07] |   | `-- Installing p5-HTML-Tagset-3.24...
[140amd64-default-build-as-user-job-07] |   | `-- Extracting p5-HTML-Tagset-3.24: ....... done
[140amd64-default-build-as-user-job-07] |   | `-- Installing p5-HTTP-Message-6.46...
[140amd64-default-build-as-user-job-07] |   |   `-- Installing p5-Clone-0.46...
[140amd64-default-build-as-user-job-07] |   |   `-- Extracting p5-Clone-0.46: ......... done
[140amd64-default-build-as-user-job-07] |   |   `-- Installing p5-Encode-Locale-1.05...
[140amd64-default-build-as-user-job-07] |   |   `-- Extracting p5-Encode-Locale-1.05: ....... done
[140amd64-default-build-as-user-job-07] |   |   `-- Installing p5-HTTP-Date-6.06...
[140amd64-default-build-as-user-job-07] |   |   | `-- Installing p5-TimeDate-2.33,1...
[140amd64-default-build-as-user-job-07] |   |   | `-- Extracting p5-TimeDate-2.33,1: .......... done
[140amd64-default-build-as-user-job-07] |   |   `-- Extracting p5-HTTP-Date-6.06: ....... done
[140amd64-default-build-as-user-job-07] |   |   `-- Installing p5-IO-HTML-1.004...
[140amd64-default-build-as-user-job-07] |   |   `-- Extracting p5-IO-HTML-1.004: ....... done
[140amd64-default-build-as-user-job-07] |   |   `-- Installing p5-LWP-MediaTypes-6.04...
[140amd64-default-build-as-user-job-07] |   |   `-- Extracting p5-LWP-MediaTypes-6.04: ........ done
[140amd64-default-build-as-user-job-07] |   |   `-- Installing p5-URI-5.28...
[140amd64-default-build-as-user-job-07] |   |   `-- Extracting p5-URI-5.28: .......... done
[140amd64-default-build-as-user-job-07] |   | `-- Extracting p5-HTTP-Message-6.46: .......... done
[140amd64-default-build-as-user-job-07] |   `-- Extracting p5-HTML-Parser-3.82: .......... done
[140amd64-default-build-as-user-job-07] `-- Extracting p5-CGI-4.66: .......... done
[140amd64-default-build-as-user-job-07] `-- Installing p5-Error-0.17029...
[140amd64-default-build-as-user-job-07] `-- Extracting p5-Error-0.17029: ......... done
[140amd64-default-build-as-user-job-07] `-- Installing p5-IO-Socket-SSL-2.087...
[140amd64-default-build-as-user-job-07] |   `-- Installing p5-IO-Socket-IP-0.42...
[140amd64-default-build-as-user-job-07] |   `-- Extracting p5-IO-Socket-IP-0.42: ....... done
[140amd64-default-build-as-user-job-07] |   `-- Installing p5-Mozilla-CA-20240313...
[140amd64-default-build-as-user-job-07] |   `-- Extracting p5-Mozilla-CA-20240313: ....... done
[140amd64-default-build-as-user-job-07] |   `-- Installing p5-Net-SSLeay-1.94...
<snip>
Downloading src/test/resources/large/mitochondria_references/blacklist_sites.hg38.chrM.shifted_by_8000_bases.bed.idx (305 B)
Downloading src/test/resources/large/mitochondria_references/control_region_shifted.chrM.interval_list (233 B)
Downloading src/test/resources/large/mitochondria_references/non_control_region.chrM.interval_list (211 B)
Downloading src/test/resources/large/multiSampleSubsetted.bam (32 MB)
Downloading src/test/resources/large/multiSampleSubsetted.bam.bai (36 KB)
Downloading src/test/resources/large/mutect/dream_synthetic_bams/normal.bam (4.4 MB)
Downloading src/test/resources/large/mutect/dream_synthetic_bams/normal.bam.bai (5.3 KB)
Downloading src/test/resources/large/mutect/dream_synthetic_bams/normal_1.bam (3.5 MB)
Downloading src/test/resources/large/mutect/dream_synthetic_bams/normal_1.bam.bai (33 KB)
Downloading src/test/resources/large/mutect/dream_synthetic_bams/normal_2.bam (4.8 MB)
Downloading src/test/resources/large/mutect/dream_synthetic_bams/normal_2.bam.bai (33 KB)
Downloading src/test/resources/large/mutect/dream_synthetic_bams/normal_3.bam (20 MB)
Downloading src/test/resources/large/mutect/dream_synthetic_bams/normal_3.bam.bai (40 KB)
Downloading src/test/resources/large/mutect/dream_synthetic_bams/normal_4.bam (29 MB)
Downloading src/test/resources/large/mutect/dream_synthetic_bams/normal_4.bam.bai (47 KB)
Downloading src/test/resources/large/mutect/dream_synthetic_bams/tumor.bam (4.8 MB)
Downloading src/test/resources/large/mutect/dream_synthetic_bams/tumor.bam.bai (5.3 KB)
Downloading src/test/resources/large/mutect/dream_synthetic_bams/tumor_1.bam (3.9 MB)
Downloading src/test/resources/large/mutect/dream_synthetic_bams/tumor_1.bam.bai (32 KB)
Downloading src/test/resources/large/mutect/dream_synthetic_bams/tumor_2.bam (5.5 MB)
Downloading src/test/resources/large/mutect/dream_synthetic_bams/tumor_2.bam.bai (33 KB)
Downloading src/test/resources/large/mutect/dream_synthetic_bams/tumor_3.bam (21 MB)
Downloading src/test/resources/large/mutect/dream_synthetic_bams/tumor_3.bam.bai (40 KB)
Downloading src/test/resources/large/mutect/dream_synthetic_bams/tumor_4.bam (29 MB)
Downloading src/test/resources/large/mutect/dream_synthetic_bams/tumor_4.bam.bai (46 KB)
Downloading src/test/resources/large/mutect/highDPMTsnippet.bai (96 B)
Downloading src/test/resources/large/mutect/highDPMTsnippet.bam (1.5 MB)
Downloading src/test/resources/large/mutect/mito/alleles.vcf (924 B)
Downloading src/test/resources/large/mutect/mito/alleles.vcf.idx (297 B)
Downloading src/test/resources/large/mutect/mito/mito.bam (1.1 MB)
Downloading src/test/resources/large/mutect/mito/mito.bam.bai (96 B)
Downloading src/test/resources/large/mutect/mito/mito_shifted_8000.dict (135 B)
Downloading src/test/resources/large/mutect/mito/mito_shifted_8000.fasta (17 KB)
Downloading src/test/resources/large/mutect/mito/mito_shifted_8000.fasta.fai (21 B)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-normal-allelic-counts-SM-74NEG-v1-chr20.allelicCounts.tsv (2.2 MB)
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 src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-2-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-2-denoised-copy-ratios-SM-74P4M-v1-chr20.denoisedCR.tsv (191 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/dragstr/compose-str-table-file-gencode-transcripts.dragen.tab.gz (1.7 MB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/dragstr/compose-str-table-file-human_g1k_v37.20.21.dragen.tab.gz (1.6 MB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/dragstr/compose-str-table-file-human_g1k_v37_20.21.dragen.zip (1.5 MB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/dragstr/compose-str-table-file-human_v38.20.21.dragen.tab.gz (1.7 MB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/dragstr/dragen-param-estimator-expected-output.txt (2.7 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/dragstr/dragen-param-estimator-input.tab.gz (1.4 MB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.indel.pos.annot.hdf5 (30 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.indel.pos.vcf (171 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.indel.pos.vcf.idx (114 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.indel.posUn.annot.hdf5 (30 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.indel.posUn.unlabeled.annot.hdf5 (38 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.indel.posUn.vcf.idx (114 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.snp.pos.annot.hdf5 (147 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.snp.pos.vcf (193 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.snp.pos.vcf.idx (114 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.snp.posUn.unlabeled.annot.hdf5 (32 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.snp.posUn.vcf.idx (114 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.snpIndel.pos.annot.hdf5 (174 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.snpIndel.pos.vcf (196 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.snpIndel.pos.vcf.idx (114 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.snpIndel.posUn.annot.hdf5 (174 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.snpIndel.posUn.unlabeled.annot.hdf5 (32 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.snpIndel.posUn.vcf.idx (114 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.indel.pos.annot.hdf5 (31 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.indel.pos.vcf (171 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.indel.pos.vcf.idx (114 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.indel.posUn.unlabeled.annot.hdf5 (33 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.indel.posUn.vcf.idx (114 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.snp.pos.annot.hdf5 (153 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.snp.pos.vcf (193 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.snp.pos.vcf.idx (114 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.snp.posUn.unlabeled.annot.hdf5 (33 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.snp.posUn.vcf.idx (114 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.snpIndel.pos.annot.hdf5 (181 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.snpIndel.pos.vcf (196 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.snpIndel.pos.vcf.idx (114 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.snpIndel.posUn.annot.hdf5 (181 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.snpIndel.posUn.unlabeled.annot.hdf5 (33 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.snpIndel.posUn.vcf.idx (114 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/input/small_callset_low_threshold.sites-only.chr1.1-10M.vcf (2.0 MB)
Downloading 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 (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)
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 (525 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 (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)
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 src/test/resources/large/sv/SVIntegrationTest_hg19.bam (862 KB)
Downloading src/test/resources/large/sv/SVIntegrationTest_hg19.bam.bai (38 KB)
Downloading src/test/resources/large/sv/SVIntegrationTest_hg19_gaps.bed.gz (136 B)
Downloading src/test/resources/large/sv/SVIntegrationTest_hg19_gaps.bed.gz.tbi (157 B)
Downloading src/test/resources/large/sv/SVIntegrationTest_hg19_umap_s100.bed.gz (5.8 KB)
Downloading src/test/resources/large/sv/SVIntegrationTest_hg19_umap_s100.bed.gz.tbi (787 B)
Downloading src/test/resources/large/sv/SVIntegrationTest_hg19_umap_s50.bed.gz (75 KB)
Downloading src/test/resources/large/sv/SVIntegrationTest_hg19_umap_s50.bed.gz.tbi (1.3 KB)
Downloading src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest.bam (209 KB)
Downloading src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest.bam.bai (482 KB)
Downloading src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_Complex.vcf (232 KB)
Downloading src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_NonComplex.vcf (229 KB)
Downloading src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_cpx_reinterpreted_simple_1_seg.vcf (218 KB)
Downloading src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_cpx_reinterpreted_simple_multi_seg.vcf (224 KB)
Downloading src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_merged_simple.vcf (240 KB)
Downloading src/test/resources/large/sv/forBND_SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest.bam (116 KB)
Downloading src/test/resources/large/sv/forBND_SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_NonComplex.vcf (222 KB)
Downloading src/test/resources/large/testFlowModeFlag_expected.bam (1.1 MB)
Downloading src/test/resources/large/testFlowModeFlag_expected.bam.bai (67 KB)
Downloading src/test/resources/large/testFlowModeFlag_expected.bam.sbi (92 B)
Downloading src/test/resources/large/testFlowModeFlag_expected.txt (2.2 KB)
Downloading src/test/resources/large/testProductionGVCF.expected.g.vcf (1.4 MB)
Downloading src/test/resources/large/testProductionGVCF.expected.g.vcf.gz.tbi (369 B)
Downloading src/test/resources/large/variantRecalling/150292-BC05.vcf.gz (311 KB)
Downloading src/test/resources/large/variantRecalling/150292-BC05.vcf.gz.tbi (2.7 KB)
Downloading src/test/resources/large/variantRecalling/chr5.bam1.rename.bam (13 MB)
Downloading src/test/resources/large/variantRecalling/chr5.bam1.rename.bam.bai (62 KB)
Downloading src/test/resources/large/variantRecalling/chr5.bam2.rename.bam (18 MB)
Downloading src/test/resources/large/variantRecalling/chr5.bam2.rename.bam.bai (62 KB)
Downloading src/test/resources/large/variantRecalling/haps_chr5.bam (15 MB)
Downloading src/test/resources/large/variantRecalling/haps_chr5.bam.bai (69 KB)
Downloading src/test/resources/large/variantRecalling/variantRecallerBasic.expected.csv (12 KB)
Downloading src/test/resources/large/very-small-gnomad.vcf (4.6 MB)
Downloading src/test/resources/large/very-small-gnomad.vcf.idx (44 KB)
Downloading src/test/resources/large/whole_exome_illumina_coding_v1.Homo_sapiens_assembly19.targets.interval_list (11 MB)
===> Fetching all distfiles required by gatk-4.6.0.0 for building
===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by gatk-4.6.0.0 for building
=> SHA256 Checksum OK for gatk-4.6.0.0-deps.tar.gz.
=> SHA256 Checksum mismatch for broadinstitute-gatk-4.6.0.0_GH0.tar.gz.
===>  Giving up on fetching files:  broadinstitute-gatk-4.6.0.0_GH0.tar.gz 
Make sure the Makefile and distinfo file (/usr/ports/biology/gatk/distinfo)
are up to date.  If you are absolutely sure you want to override this
check, type "make NO_CHECKSUM=yes [other args]".
*** Error code 1

Stop.
make[1]: stopped in /usr/ports/biology/gatk
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/gatk