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GenomeSTRiP error: partition.genotypes.map.dat file missing at Stage 12

ikeoluwao_oikeoluwao_o Baltimore, MDMember
edited December 2019 in Ask the GATK team

The error below was generated in CNVDiscoveryStage12 of my Snakemake pipeline GenomeSTRiP run on over 100 whole genome samples. I am using JDK/1.8.0_11 and svtoolkit_2.00.1918. How can I solve this?

INFO  13:08:01,285 HelpFormatter - Program Args: -cp /mnt/data/ike/software/svtoolkit/lib/SVToolkit.jar:/mnt/data/ike/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/mnt/data/ike/software/svtoolkit/lib/gatk/Queue.jar -S /mnt/data/ike/software/svtoolkit/qsc
ript/discovery/cnv/CNVDiscoveryStage12.q -S /mnt/data/ike/software/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStageBase.q -S /mnt/data/ike/software/svtoolkit/qscript/discovery/cnv/CNVDiscoveryGenotyper.q -S /mnt/data/ike/software/svtoolkit/qscript/SVQScript
.q -gatk /mnt/data/ike/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -jobLogDir /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage12/logs -memLimit 2.0 -jobRunner Shell -gatkJobRunner Shell -run -runDirectory /mnt/data/ike/projects/Com
bined_NBU/Analysis6/Data_Files/CNV/cnv_stage12 -sentinelFile /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_sentinel_files/stage_12.sent --disableJobReport -configFile /mnt/data/ike/software/svtoolkit/conf/genstrip_parameters.txt -R /cm/sha
red/plab/apps/genome_strip/2.00.1665/svtoolkit/metadata/1000G_phase3/human_g1k_hs37d5.fasta -ploidyMapFile /cm/shared/plab/apps/genome_strip/2.00.1665/svtoolkit/metadata/1000G_phase3/human_g1k_hs37d5.ploidymap.txt -genomeMaskFile /cm/shared/plab/apps/genome_
strip/2.00.1665/svtoolkit/metadata/1000G_phase3/human_g1k_hs37d5.svmask.fasta -genomeMaskFile /cm/shared/plab/apps/genome_strip/2.00.1665/svtoolkit/metadata/1000G_phase3/human_g1k_hs37d5.lcmask.fasta -copyNumberMaskFile /cm/shared/plab/apps/genome_strip/2.00
.1665/svtoolkit/metadata/1000G_phase3/human_g1k_hs37d5.gcmask.fasta -readDepthMaskFile /cm/shared/plab/apps/genome_strip/2.00.1665/svtoolkit/metadata/1000G_phase3/human_g1k_hs37d5.rdmask.bed -genderMaskBedFile /cm/shared/plab/apps/genome_strip/2.00.1665/svto
olkit/metadata/1000G_phase3/human_g1k_hs37d5.gendermask.bed -vdjBedFile /cm/shared/plab/apps/genome_strip/2.00.1665/svtoolkit/metadata/1000G_phase3/human_g1k_hs37d5.vdjregions.bed -genderMapFile /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/tmp/sa
mple_sex.txt -md /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/Strip_Meta -disableGATKTraversal -filteredVcf /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage11/seq_3/seq_3.filtered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/
projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage11/seq_7/seq_7.filtered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage11/seq_18/seq_18.filtered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/projects
/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage11/seq_2/seq_2.filtered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage11/seq_20/seq_20.filtered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/projects/Combine
d_NBU/Analysis6/Data_Files/CNV/cnv_stage11/seq_MT/seq_MT.filtered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage11/seq_14/seq_14.filtered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/projects/Combined_NBU/
Analysis6/Data_Files/CNV/cnv_stage11/seq_17/seq_17.filtered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage11/seq_1/seq_1.filtered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/projects/Combined_NBU/Analysis
6/Data_Files/CNV/cnv_stage11/seq_6/seq_6.filtered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage11/seq_21/seq_21.filtered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_F
iles/CNV/cnv_stage11/seq_10/seq_10.filtered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage11/seq_5/seq_5.filtered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV
/cnv_stage11/seq_16/seq_16.filtered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage11/seq_13/seq_13.filtered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_s
tage11/seq_22/seq_22.filtered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage11/seq_Y/seq_Y.filtered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage11/s
eq_9/seq_9.filtered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage11/seq_11/seq_11.filtered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage11/seq_15/se
q_15.filtered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage11/seq_4/seq_4.filtered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage11/seq_19/seq_19.fil
tered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage11/seq_8/seq_8.filtered.genotypes.vcf.gz -filteredVcf /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage11/seq_12/seq_12.filtered.ge
notypes.vcf.gz -filteredVcf /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage11/seq_X/seq_X.filtered.genotypes.vcf.gz -mergedVcfFile /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage12/gs_cnv.genotypes.vcf.gz -output
Directory /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV -genderGenotypeFilterFile /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/gender_gt_filters/gender_gt_filter.txt -filterDescriptionFile /mnt/data/ike/projects/Combined_NBU/An
alysis6/Data_Files/CNV/gender_gt_filters/gender_gt_filter_descr.txt 
INFO  13:08:01,287 HelpFormatter - Executing as [email protected] on Linux 2.6.32-431.11.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_11-b12. 
INFO  13:08:01,287 HelpFormatter - Date/Time: 2019/12/25 13:08:01 
INFO  13:08:01,287 HelpFormatter - ---------------------------------------------------------------------- 
INFO  13:08:01,287 HelpFormatter - ---------------------------------------------------------------------- 
INFO  13:08:01,292 QCommandLine - Scripting CNVDiscoveryStage12 
INFO  13:08:01,352 QCommandLine - Added 3 functions 
INFO  13:08:01,352 QGraph - Generating graph. 
INFO  13:08:01,361 QGraph - Running jobs. 
INFO  13:08:01,452 FunctionEdge - Starting: CreatePipelineResults: List(/mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage12/eval/GenotypeSiteFilters.summary.dat) > List(/mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/results
/gs_cnv.genotypes.vcf.gz) 
INFO  13:08:01,452 FunctionEdge - Output written to /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage12/logs/CNVDiscoveryStage12-3.out 
#DBG: inFile /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_X/partition.genotypes.map.dat partition /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_X/seq_X.adjacent_merged
#DBG: inFile /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_12/partition.genotypes.map.dat partition /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_12/seq_12.adjacent_merged
#DBG: inFile /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_8/partition.genotypes.map.dat partition /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_8/seq_8.adjacent_merged
#DBG: inFile /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_19/partition.genotypes.map.dat partition /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_19/seq_19.adjacent_merged
#DBG: inFile /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_4/partition.genotypes.map.dat partition /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_4/seq_4.adjacent_merged
#DBG: inFile /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_15/partition.genotypes.map.dat partition /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_15/seq_15.adjacent_merged
#DBG: inFile /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_11/partition.genotypes.map.dat partition /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_11/seq_11.adjacent_merged
#DBG: inFile /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_9/partition.genotypes.map.dat partition /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_9/seq_9.adjacent_merged
#DBG: inFile /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_Y/partition.genotypes.map.dat partition /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_Y/seq_Y.adjacent_merged
#DBG: inFile /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_22/partition.genotypes.map.dat partition /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_22/seq_22.adjacent_merged
#DBG: inFile /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_13/partition.genotypes.map.dat partition /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_13/seq_13.adjacent_merged
#DBG: inFile /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_16/partition.genotypes.map.dat partition /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_16/seq_16.adjacent_merged
#DBG: inFile /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_5/partition.genotypes.map.dat partition /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_5/seq_5.adjacent_merged
#DBG: inFile /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_10/partition.genotypes.map.dat partition /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_10/seq_10.adjacent_merged
#DBG: inFile /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_21/partition.genotypes.map.dat partition /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_21/seq_21.adjacent_merged
#DBG: inFile /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_6/partition.genotypes.map.dat partition /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_6/seq_6.adjacent_merged
ERROR 13:08:07,394 FunctionEdge - Error: CreatePipelineResults: List(/mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage12/eval/GenotypeSiteFilters.summary.dat) > List(/mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/results/gs
_cnv.genotypes.vcf.gz) 
java.io.FileNotFoundException: /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_6/partition.genotypes.map.dat (No such file or directory)
        at java.io.FileInputStream.open(Native Method)
        at java.io.FileInputStream.<init>(FileInputStream.java:131)
        at scala.io.Source$.fromFile(Source.scala:90)
        at scala.io.Source$.fromFile(Source.scala:75)
        at org.broadinstitute.sv.discovery.cnv.CNVDiscoveryStage12$$anonfun$createPartitionMapFile$1.apply(CNVDiscoveryStage12.q:111)
        at org.broadinstitute.sv.discovery.cnv.CNVDiscoveryStage12$$anonfun$createPartitionMapFile$1.apply(CNVDiscoveryStage12.q:106)
        at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
        at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:108)
        at org.broadinstitute.sv.discovery.cnv.CNVDiscoveryStage12.createPartitionMapFile(CNVDiscoveryStage12.q:106)
        at org.broadinstitute.sv.discovery.cnv.CNVDiscoveryStage12$CreatePipelineResults.run(CNVDiscoveryStage12.q:81)
        at org.broadinstitute.gatk.queue.engine.InProcessRunner.start(InProcessRunner.scala:53)
        at org.broadinstitute.gatk.queue.engine.FunctionEdge.start(FunctionEdge.scala:101)
        at org.broadinstitute.gatk.queue.engine.QGraph.startOneJob(QGraph.scala:646)
        at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:507)
        at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:168)
        at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:170)
        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.gatk.queue.QCommandLine$.main(QCommandLine.scala:61)
        at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
INFO  13:08:07,396 QGraph - 0 Pend, 1 Run, 0 Fail, 2 Done 
INFO  13:08:31,442 QGraph - Writing incremental jobs reports... 
INFO  13:08:31,442 QGraph - 0 Pend, 0 Run, 1 Fail, 2 Done 
INFO  13:08:31,443 QCommandLine - Writing final jobs report... 
INFO  13:08:31,444 QCommandLine - Done with errors 
INFO  13:08:31,445 QGraph - ------- 
INFO  13:08:31,445 QGraph - Failed:  CreatePipelineResults: List(/mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage12/eval/GenotypeSiteFilters.summary.dat) > List(/mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/results/gs_cnv
.genotypes.vcf.gz) 
INFO  13:08:31,446 QGraph - Log:     /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage12/logs/CNVDiscoveryStage12-3.out 
INFO  13:08:31,446 QCommandLine - Script failed: 0 Pend, 0 Run, 1 Fail, 2 Done 
------------------------------------------------------------------------------------------
Done. There were no warn messages.
------------------------------------------------------------------------------------------ 
Post edited by ikeoluwao_o on
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