HI,
Iam running GenomeStrip (lattest version) locally in a Docker-Container with wdl. I can run SVPrepross without any errors for my samples. For saving time I run GenomeStrip only on Chr11/14. When I start CNVDiscoveryPipeline it process 279 jobs fine...another one fail. But when I take a look at the logs the job finish successfully.
My commandline:
set -o pipefail
export SV_DIR=${SV_Dir}
tar -xf ${metaData_archive} && cd svRun &&\
java -Xmx12g -cp ${classpath} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_Dir}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \
-S ${SV_Dir}/qscript/SVQScript.q \
-cp ${classpath} \
-gatk ${SV_Dir}/lib/gatk/GenomeAnalysisTK.jar \
-configFile ${SV_Dir}/conf/genstrip_parameters.txt \
-R ${ref_fasta} \
-I ${input_bam} \
-md metadata \
-jobRunner Shell -gatkJobRunner Shell \
-runDirectory run1 \
-jobLogDir run1/logs \
-l DEBUG \
-intervalList ${intervalList} \
-tilingWindowSize 1000 \
-tilingWindowOverlap 500 \
-maximumReferenceGapLength 1000 \
-boundaryPrecision 100 \
-minimumRefinedLength 500 \
-run
The stderr from wdl (part)
INFO 09:48:19,662 QGraph - Failed: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/root/Translocat [...]
INFO 09:48:19,662 QGraph - Log: /root/TranslocationWorkflow/da98e721-c0ff-438e-86f3-14a63bc1cb46/call-CNVDiscovery/execution/svRun/run1/cnv_stage2/seq_chr11/logs/CNVDiscoveryStage2-231.out
INFO 09:48:19,663 QCommandLine - Script failed: 8 Pend, 0 Run, 1 Fail, 269 Done
DEBUG 10:23:12,115 IOUtils - Deleted /root/TranslocationWorkflow/da98e721-c0ff-438e-86f3-14a63bc1cb46/call-CNVDiscovery/execution/svRun/.queue/tmp/.exec4114067890890442215[...]
ERROR 10:23:12,117 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/root/Transl[...]
ERROR 10:23:12,133 FunctionEdge - Contents of /root/TranslocationWorkflow/da98e721-c0ff-438e-86f3-14a63bc1cb46/call-CNVDiscovery/execution/svRun/run1/logs/CNVDiscoveryPipeline-9.out:
CNVDiscoveryStage2-231.out
INFO 09:39:55,282 HelpFormatter - -----------------------------------------------------------------------------------------
INFO 09:39:55,286 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5.GS-r1678-6-gf101448, Compiled 2017/01/24 12:43:00
INFO 09:39:55,286 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 09:39:55,287 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 09:39:55,294 HelpFormatter - Program Args: -T SVGenotyperWalker -R /root/TranslocationWorkflow/da98e721-c0ff-438e-86f3-14a63bc1cb46/call-CNVDiscovery/inputs/data/reference/meta/metadata/ref/Homo_sapiens_assembly38/Homo_sapiens_assem$
INFO 09:39:55,298 HelpFormatter - Executing as root@d09a132e6dd1 on Linux 3.16.0-4-amd64 amd64; OpenJDK 64-Bit Server VM 1.8.0_111-8u111-b14-2~bpo8+1-b14.
INFO 09:39:55,299 HelpFormatter - Date/Time: 2017/02/21 09:39:55
INFO 09:39:55,299 HelpFormatter - -----------------------------------------------------------------------------------------
INFO 09:39:55,300 HelpFormatter - -----------------------------------------------------------------------------------------
INFO 09:39:55,399 21-Feb-2017 GenomeAnalysisEngine - Strictness is SILENT
INFO 09:39:55,735 21-Feb-2017 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 09:39:55,886 21-Feb-2017 IntervalUtils - Processing 1 bp from intervals
INFO 09:39:55,983 21-Feb-2017 GenomeAnalysisEngine - Preparing for traversal
INFO 09:39:55,984 21-Feb-2017 GenomeAnalysisEngine - Done preparing for traversal
INFO 09:39:55,984 21-Feb-2017 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 09:39:55,985 21-Feb-2017 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 09:39:55,985 21-Feb-2017 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 09:39:55,989 21-Feb-2017 SVGenotyper - Opening reference sequence ...
INFO 09:39:55,990 21-Feb-2017 SVGenotyper - Opened reference sequence.
INFO 09:39:55,990 21-Feb-2017 SVGenotyper - Initializing input data set ...
INFO 09:39:56,070 21-Feb-2017 SVGenotyper - Initialized data set: 1 file, 1 read group, 1 sample.
INFO 09:39:56,071 21-Feb-2017 MetaData - Opening metadata ...
INFO 09:39:56,071 21-Feb-2017 MetaData - Adding metadata directory metadata ...
INFO 09:39:56,072 21-Feb-2017 MetaData - Opened metadata.
INFO 09:39:56,168 21-Feb-2017 MetaData - Loading insert size distributions ...
INFO 09:39:56,276 21-Feb-2017 ReadCountDiskCache - Initializing read count disk cache [metadata/rccache.bin] ...
INFO 09:39:56,277 21-Feb-2017 ReadCountDiskCache - Initialized read count disk cache with 1 file.
INFO 09:39:59,322 21-Feb-2017 ProgressMeter - done 0.0 3.0 s 5.5 w 100.0% 3.0 s 0.0 s
INFO 09:39:59,322 21-Feb-2017 ProgressMeter - Total runtime 3.34 secs, 0.06 min, 0.00 hours
INFO 09:40:00,579 21-Feb-2017 GATKRunReport - Uploaded run statistics report to AWS S3
Any suggestions to fix this ?
Thanks!
Greetings EADG:)