ERROR MESSAGE: Interval X:2699521-154931043 has gender-independent ploidy of NaN

I run a modified version of the discovery script:
java -cp ${classpath} ${mx} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/SVPreprocess.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
--disableJobReport \
-cp ${classpath} \
-configFile /share/apps/genomics/svtoolkit/conf/genstrip_parameters.txt \
-tempDir ${SV_TMPDIR} \
-R /share/apps/genomics/reference/human_g1k_v37.fasta \
-genomeMaskFile /share/apps/genomics/reference/masks/human_g1k_v37.mask.100.fasta \
-copyNumberMaskFile /share/apps/genomics/reference/masks/cn2_mask_g1k_v37.fasta \
-ploidyMapFile /share/apps/genomics/reference/masks/humgen_g1k_v37_ploidy.map \
-genderMapFile gendermap.map \
-runDirectory ${runDir} \
-md ${runDir}/metadata \
-disableGATKTraversal \
-useMultiStep \
-reduceInsertSizeDistributions true \
-computeGCProfiles true \
-computeReadCounts true \
-jobLogDir ${runDir}/logs \
-I ${bam} \
-jobRunner GridEngine \
-jobResReq "tmem=4G" \
-jobResReq "h_vmem=4G" \
-jobResReq "h_rt=06:00:00" \
-run

and it runs OK until:

ERROR 15:14:10,632 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/cluster/project6/gosgene1/whole_genome/nemo/BGI-262/
a/tmpdir' '-cp' '/share/apps/genomics/svtoolkit/lib/SVToolkit.jar:/share/apps/genomics/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/share/apps/genomics/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeR
eadDepthCoverageWalker' '-R' '/share/apps/genomics/reference/human_g1k_v37.fasta' '-I' 'BGI-262_combined_R1.a.fq.gz.bwa.bam.sorted.rmdup.bam' '-O' '/cluster/project6/gosgene1/whole_genome/nemo/BGI-262/a/test1/metadata/depth/BGI-262
_combined_R1.a.fq.gz.bwa.bam.sorted.rmdup.depth.txt' '-disableGATKTraversal' 'true' '-md' 'test1/metadata' '-ploidyMapFile' '/share/apps/genomics/reference/masks/humgen_g1k_v37_ploidy.map' '-genomeMaskFile' '/share/apps/genomics/r
eference/masks/human_g1k_v37.mask.100.fasta' '-minMapQ' '10' '-insertSizeRadius' '10.0'
ERROR 15:14:10,636 FunctionEdge - Contents of /cluster/project6/gosgene1/whole_genome/nemo/BGI-262/a/test1/logs/SVPreprocess-10.out:
INFO 15:13:54,868 HelpFormatter - ---------------------------------------------------------------------------
INFO 15:13:54,870 HelpFormatter - The Genome Analysis Toolkit (GATK) v, Compiled 2015/04/22 10:24:33
INFO 15:13:54,870 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 15:13:54,870 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 15:13:54,874 HelpFormatter - Program Args: -T ComputeReadDepthCoverageWalker -R /share/apps/genomics/reference/human_g1k_v37.fasta -O /cluster/project6/gosgene1/whole_genome/nemo/BGI-262/a/test1/metadata/depth/BGI-262_combined_R
1.a.fq.gz.bwa.bam.sorted.rmdup.depth.txt -disableGATKTraversal true -md test1/metadata -ploidyMapFile /share/apps/genomics/reference/masks/humgen_g1k_v37_ploidy.map -genomeMaskFile /share/apps/genomics/reference/masks/human_g1k_v37.ma
sk.100.fasta -minMapQ 10 -insertSizeRadius 10.0
INFO 15:13:54,876 HelpFormatter - Executing as [email protected] on Linux 2.6.18-371.el5 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_25-b15.
INFO 15:13:54,876 HelpFormatter - Date/Time: 2015/05/12 15:13:54
INFO 15:13:54,876 HelpFormatter - ---------------------------------------------------------------------------
INFO 15:13:54,876 HelpFormatter - ---------------------------------------------------------------------------
INFO 15:13:55,207 GenomeAnalysisEngine - Strictness is SILENT
INFO 15:13:55,308 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 15:13:55,380 GenomeAnalysisEngine - Preparing for traversal
INFO 15:13:55,429 GenomeAnalysisEngine - Done preparing for traversal
INFO 15:13:55,429 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 15:13:55,429 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 15:13:55,429 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime
INFO 15:13:55,430 MetaData - Opening metadata ...
INFO 15:13:55,430 MetaData - Adding metadata directory test1/metadata ...
INFO 15:13:55,432 MetaData - Opened metadata.
INFO 15:13:55,481 MetaData - Loading insert size distributions ...
INFO 15:13:55,493 ComputeReadDepthCoverageWalker - Using genome mask /share/apps/genomics/reference/masks/human_g1k_v37.mask.100.fasta
INFO 15:13:56,811 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.RuntimeException: Interval X:2699521-154931043 has gender-independent ploidy of NaN
at org.broadinstitute.sv.metadata.depth.ComputeReadDepthCoverageWalker.validateReadDepthIntervalList(ComputeReadDepthCoverageWalker.java:210)
at org.broadinstitute.sv.metadata.depth.ComputeReadDepthCoverageWalker.initialize(ComputeReadDepthCoverageWalker.java:143)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:125)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:79)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:59)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version ):
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 http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Interval X:2699521-154931043 has gender-independent ploidy of NaN
ERROR ------------------------------------------------------------------------------------------

I use the ploidy map available here:
ftp://ftp.broadinstitute.org/pub/svtoolkit/ploidymaps/

I can't work out what the error means nor how to fix it, any help appreciated

Tagged:

Best Answer

  • skashinskashin Member
    Accepted Answer

    Hi,

    ComputeReadDepthCoverageWalker is not meant to pick up this interval on chrX, so it seems like a bug. I will fix it, but in the meantime you should be able to work around this problem by supplying the explicit list of the intervals over which read depth will be computed. To do that, download the attached file human_g1k_v37.rdmask.txt
    somewhere on the network and supply an additional argument in your Queue script pointing to this file:

    -readDepthMaskFile ${dir}/human_g1k_v37.rdmask.txt

    Then just rerun your Queue script

    Seva

    P.S. As a clarification, in our reference metadata we actually call this intervals file human_g1k_v37.rdmask.bed, but I had to rename it to *.txt to be able to upload it to the forum page.

Answers

  • skashinskashin Member
    Accepted Answer

    Hi,

    ComputeReadDepthCoverageWalker is not meant to pick up this interval on chrX, so it seems like a bug. I will fix it, but in the meantime you should be able to work around this problem by supplying the explicit list of the intervals over which read depth will be computed. To do that, download the attached file human_g1k_v37.rdmask.txt
    somewhere on the network and supply an additional argument in your Queue script pointing to this file:

    -readDepthMaskFile ${dir}/human_g1k_v37.rdmask.txt

    Then just rerun your Queue script

    Seva

    P.S. As a clarification, in our reference metadata we actually call this intervals file human_g1k_v37.rdmask.bed, but I had to rename it to *.txt to be able to upload it to the forum page.

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