REPOST - GenomeSTRiP error: partition.genotypes.map.dat file missing at Stage 12
NOTE: This question was previously posted to the old forum and was acknowledged as received and under review by support staff.
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 adeshina@plab-node04 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. ------------------------------------------------------------------------------------------
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 adeshina@plab-node04 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. ------------------------------------------------------------------------------------------
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Thank you for your question, ikeoluwao_o. We're working on figuring out your issue and will get back to you soon.
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Thanks for waiting, ikeoluwao_o! This isn't GATK so I'm not sure how much help I can be, but it is clear that there is a file that is not being found due to the error you are receiving here:
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)
So, it may be related to an issue in your directory somewhere. I have asked one of our computational biologists who is knowledgeable in this area and they may have a better solution an I have.
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@ikeoluwao_o I'm not sure why you'd be getting that error. Could you please list the contents of
/mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_6/and the same for:
/mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_12/Did all the other stages of the pipeline (prior to stage 12) complete successfully?
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Hello,
Thank you for your response. Yes, all the other stages prior to stage 12 completed successfully.
I mistakenly overrode the contents of the file you're requesting by re-running the script. The error persists and is now ocurring in seq_21 instead of seq_6. The error now looks like this:
java.io.FileNotFoundException: /mnt/data/ike/projects/Combined_NBU/Analysis6/Data_Files/CNV/cnv_stage10/seq_21/partition.genotypes.map.dat (No such file or directory)Here are the contents of the directory:
-rw-rw-r-- 1 adeshina zfs1fs1 349 Jan 18 22:50 seq_21.adjacent_merged.genotypes.gts.dat
-rw-rw-r-- 1 adeshina zfs1fs1 349 Jan 18 22:50 seq_21.adjacent_merged.genotypes.conf.dat
-rw-rw-r-- 1 adeshina zfs1fs1 28 Jan 18 22:50 seq_21.adjacent_merged.genotypes.map.dat
-rw-rw-r-- 1 adeshina zfs1fs1 307 Jan 18 22:50 seq_21.adjacent_merged.genotypes.counts.dat
-rw-rw-r-- 1 adeshina zfs1fs1 307 Jan 18 22:50 seq_21.adjacent_merged.genotypes.expected.dat
-rw-rw-r-- 1 adeshina zfs1fs1 60 Jan 18 22:50 seq_21.adjacent_merged.genotypes.gmm.dat
-rw-rw-r-- 1 adeshina zfs1fs1 4.0K Jan 18 22:51 seq_21.adjacent_merged.genotypes.vcf.gz
-rw-rw-r-- 1 adeshina zfs1fs1 72 Jan 18 22:51 seq_21.adjacent_merged.genotypes.vcf.gz.tbi
drwxrwsr-x 2 adeshina zfs1fs1 4.0K Jan 18 22:53 eval
drwxrwsr-x 2 adeshina zfs1fs1 306 Jan 18 22:53 logsHere are the contents of the second directory you requested:
-rw-rw-r-- 1 adeshina zfs1fs1 604K Jan 18 21:29 seq_12.adjacent_merged.genotypes.conf.dat
-rw-rw-r-- 1 adeshina zfs1fs1 529K Jan 18 21:29 seq_12.adjacent_merged.genotypes.counts.dat
-rw-rw-r-- 1 adeshina zfs1fs1 1.6M Jan 18 21:29 seq_12.adjacent_merged.genotypes.expected.dat
-rw-rw-r-- 1 adeshina zfs1fs1 687K Jan 18 21:29 seq_12.adjacent_merged.genotypes.gmm.dat
-rw-rw-r-- 1 adeshina zfs1fs1 329K Jan 18 21:29 seq_12.adjacent_merged.genotypes.gts.dat
-rw-rw-r-- 1 adeshina zfs1fs1 128K Jan 18 21:29 partition.genotypes.map.dat
-rw-rw-r-- 1 adeshina zfs1fs1 2.2M Jan 18 21:47 seq_12.adjacent_merged.genotypes.vcf.gz
-rw-rw-r-- 1 adeshina zfs1fs1 22K Jan 18 21:47 seq_12.adjacent_merged.genotypes.vcf.gz.tbi
drwxrwsr-x 2 adeshina zfs1fs1 4.0K Jan 18 21:48 eval
drwxrwsr-x 2 adeshina zfs1fs1 4.0K Jan 18 21:48 logs -
Hi, there,
I'm not sure why the partition.genotypes.map.dat files are no longer there. I can suggest a couple of workarounds.
First, and probably easiest, the code that is trying to access these files is a legacy feature that is no longer needed. In the Genome STRiP distribution, there is a file qscript/discovery/cnv/CNVDiscoveryStage12.q. Lines 76-81 should look like this:
// Temporary:We create a paritition map to the stage10 output directory.
// This is a temporary measure to allow plotting of genotyped sites (via PlotGenotypingResults).
// We should adapt the plotting code to work off of the output VCF directly.
val stage10RunDir = new File(runDirectory.getParent(), "cnv_stage10")
val partitionMap = new File(resultsOutputDir, "partition.genotypes.map.dat")
createPartitionMapFile(stage10RunDir, partitionMap)If you comment the last three lines out, then it should run to completion and no harm done (PlotGenotypingResults has in fact been updated to work off of the vcf directly).
The alternative workaround would be to recreate these files yourself. They are simple tab-delimited files. You could probably get by with stub files containing just a tab delimited header like so:
CNP PARTITION CHR START ENDbecause I believe they are no longer used downstream.
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