SVGenotyper error: Cannot get platform for read

pjmtelepjmtele Member
edited July 2018 in GenomeSTRiP

I saw the other recent post regarding bam header issues in SVDiscovery, but thought I would post a separate question since this regards a separate script. I've run the CNVDiscovery pipeline on a set of high coverage bams and am now attempting to genotype some lower coverage individuals at these previously discovered structural variants. All of these samples have the necessary metadata and have been run separately through CNVDiscovery, so all bams will play well with at least some of Genome STRiP's functionality.

However, when I run SVGenotyper, I get the following error:

INFO  12:37:45,082 HelpFormatter - ----------------------------------------------------------------------------------------- 
INFO  12:37:45,090 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7.GS-r1748-0-g74bfe0b, Compiled 2018/04/10 10:30:23 
INFO  12:37:45,090 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute 
INFO  12:37:45,090 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk 
INFO  12:37:45,090 HelpFormatter - [Sun Jul 29 12:37:45 CDT 2018] Executing on Linux 2.6.32-696.30.1.el6.x86_64 amd64 
INFO  12:37:45,090 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_144-b01 
INFO  12:37:45,100 HelpFormatter - Program Args: -T SVGenotyperWalker -R /home/hirschc1/pmonnaha/misc-files/gstrip/W22_chr1-10.fasta -O /panfs/roc/scratch/pmonnaha/Maize/gstrip/w22_allSamps_smallWindows/P0120.genotypes.vcf.gz -disableGATKTraversal true -md /home/hirschc1/pmonnaha/misc-files/gstrip/W22_MetaData_E2-0 -md /home/hirschc1/pmonnaha/misc-files/gstrip/W22_MetaData_E2-1 -md /home/hirschc1/pmonnaha/misc-files/gstrip/W22_MetaData_E2-2 -configFile /home/hirschc1/pmonnaha/software/svtoolkit/conf/genstrip_parameters.txt -P input.platformMapFile:/home/hirschc1/pmonnaha/misc-files/gstrip/platform_map.txt -P depth.parityCorrectionThreshold:null -runDirectory /panfs/roc/scratch/pmonnaha/Maize/gstrip/w22_allSamps_smallWindows -genderMapFile /home/hirschc1/pmonnaha/misc-files/gstrip/W22_MetaData_E2-0/sample_gender.report.txt -genderMapFile /home/hirschc1/pmonnaha/misc-files/gstrip/W22_MetaData_E2-1/sample_gender.report.txt -genderMapFile /home/hirschc1/pmonnaha/misc-files/gstrip/W22_MetaData_E2-2/sample_gender.report.txt -ploidyMapFile /home/hirschc1/pmonnaha/misc-files/gstrip/W22_chr1-10.ploidymap.txt -vcf /panfs/roc/scratch/pmonnaha/Maize/gstrip/w22_BigSamps_smallWindows/results/gs_cnv.genotypes.vcf.gz -partitionName P0120 -partition records:11901-12000 -L chr1:1-1 
INFO  12:37:45,104 HelpFormatter - Executing as [email protected] on Linux 2.6.32-696.30.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_144-b01. 
INFO  12:37:45,105 HelpFormatter - Date/Time: 2018/07/29 12:37:45 
INFO  12:37:45,105 HelpFormatter - ----------------------------------------------------------------------------------------- 
INFO  12:37:45,105 HelpFormatter - ----------------------------------------------------------------------------------------- 
INFO  12:37:45,133 29-Jul-2018 GenomeAnalysisEngine - Strictness is SILENT
INFO  12:37:45,405 29-Jul-2018 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO  12:37:45,444 29-Jul-2018 IntervalUtils - Processing 1 bp from intervals
INFO  12:37:45,608 29-Jul-2018 GenomeAnalysisEngine - Preparing for traversal
INFO  12:37:45,609 29-Jul-2018 GenomeAnalysisEngine - Done preparing for traversal
INFO  12:37:45,610 29-Jul-2018 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO  12:37:45,610 29-Jul-2018 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
INFO  12:37:45,610 29-Jul-2018 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
INFO  12:37:45,616 29-Jul-2018 SVGenotyper - Opening reference sequence ...
INFO  12:37:45,616 29-Jul-2018 SVGenotyper - Opened reference sequence.
INFO  12:37:45,618 29-Jul-2018 MetaData - Opening metadata ... 
INFO  12:37:45,618 29-Jul-2018 MetaData - Adding metadata location /home/hirschc1/pmonnaha/misc-files/gstrip/W22_MetaData_E2-0 ...
INFO  12:37:45,619 29-Jul-2018 MetaData - Adding metadata location /home/hirschc1/pmonnaha/misc-files/gstrip/W22_MetaData_E2-1 ...
INFO  12:37:45,619 29-Jul-2018 MetaData - Adding metadata location /home/hirschc1/pmonnaha/misc-files/gstrip/W22_MetaData_E2-2 ...
INFO  12:37:45,623 29-Jul-2018 MetaData - Opened metadata.
INFO  12:37:45,627 29-Jul-2018 SVGenotyper - Initializing input data set ...
INFO  12:37:45,834 29-Jul-2018 SVGenotyper - Initialized data set: 99 files, 162 read groups, 99 samples.
INFO  12:37:46,024 29-Jul-2018 MetaData - Loading insert size distributions ...
INFO  12:37:46,302 29-Jul-2018 MetaData - Loading insert size distributions ...
INFO  12:37:46,395 29-Jul-2018 MetaData - Loading insert size distributions ...
INFO  12:37:46,486 29-Jul-2018 ReadCountCache - Initializing read count cache with 3 files.
##### ERROR --
##### ERROR stack trace 
java.lang.RuntimeException: Cannot get platform for read HISEQ07:449:H3MCMBCXX:1:1116:14082:78574
    at org.broadinstitute.sv.util.ReadPairOrientation.getOrientation(ReadPairOrientation.java:99)
    at org.broadinstitute.sv.genotyping.ReadPairMapper.processSingleRead(ReadPairMapper.java:203)
    at org.broadinstitute.sv.genotyping.ReadPairMapper.searchWindow(ReadPairMapper.java:175)
    at org.broadinstitute.sv.genotyping.ReadPairMapper.getReadPairs(ReadPairMapper.java:157)
    at org.broadinstitute.sv.genotyping.GenotypingReadPairModule.getReadPairs(GenotypingReadPairModule.java:217)
    at org.broadinstitute.sv.genotyping.GenotypingReadPairModule.genotypeSample(GenotypingReadPairModule.java:104)
    at org.broadinstitute.sv.genotyping.GenotypingReadPairModule.genotypeCnp(GenotypingReadPairModule.java:66)
    at org.broadinstitute.sv.genotyping.GenotypingReadPairModule.genotypeCnp(GenotypingReadPairModule.java:40)
    at org.broadinstitute.sv.genotyping.GenotypingAlgorithm.genotypeCnpInternal(GenotypingAlgorithm.java:149)
    at org.broadinstitute.sv.genotyping.GenotypingAlgorithm.genotypeCnp(GenotypingAlgorithm.java:114)
    at org.broadinstitute.sv.genotyping.SVGenotyperWalker.processVCFFile(SVGenotyperWalker.java:273)
    at org.broadinstitute.sv.genotyping.SVGenotyperWalker.map(SVGenotyperWalker.java:217)
    at org.broadinstitute.sv.genotyping.SVGenotyperWalker.map(SVGenotyperWalker.java:57)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:106)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
    at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:98)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:316)
    at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
    at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:141)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
    at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:91)
    at org.broadinstitute.sv.main.SVGenotyper.main(SVGenotyper.java:21)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.7.GS-r1748-0-g74bfe0b):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Cannot get platform for read HISEQ07:449:H3MCMBCXX:1:1116:14082:78574
##### ERROR ---------------------------------------------------------------------------

I saw in a separate post (https://gatkforums.broadinstitute.org/gatk/discussion/1511/svdiscovery-walker) that this issue can be fixed for SVDiscovery Walker by specifying -P input.platformMapFile:platform_map.txt, and that this fix was planned for SVGenotyper as well.

I created the platform map file, but am still receiving the error. Was this option ever implemented SVGenotyper or will I need to re-header the bams?

My call to SVGenotyper is as follows:

classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"
java -Xmx${MEM}g -cp ${classpath} \
     org.broadinstitute.gatk.queue.QCommandLine \
     -S ${SV_DIR}/qscript/SVGenotyper.q \
     -S ${SV_DIR}/qscript/SVQScript.q \
     -cp ${classpath} \
     -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
     -configFile ${SV_DIR}/conf/genstrip_parameters.txt \
     -R /home/hirschc1/pmonnaha/misc-files/gstrip/${REF}_chr1-10.fasta \
     -vcf ${VCF} \
     -I ${BAM_LIST} \
     -O ${OUT}/${NAME} \
     -md /home/hirschc1/pmonnaha/misc-files/gstrip/${REF}_MetaData_E2-0 \
     -md /home/hirschc1/pmonnaha/misc-files/gstrip/${REF}_MetaData_E2-1 \
     -md /home/hirschc1/pmonnaha/misc-files/gstrip/${REF}_MetaData_E2-2 \
     -runDirectory ${OUT} \
     -jobLogDir ${OUT}/logs \
     -jobRunner Drmaa \
     -gatkJobRunner Drmaa \
     -P input.platformMapFile:/home/hirschc1/pmonnaha/misc-files/gstrip/platform_map.txt \
     -P depth.parityCorrectionThreshold:null \
     -retry 10 \
     -parallelRecords 100 \
     -memLimit ${MEM} \
     -jobNative '-l walltime=12:00:00 -A hirschc1' \
     -run

Thanks,
Patrick

Best Answer

Answers

Sign In or Register to comment.