Description
Hi,
I got around the file-system read only issue running the workflow directly within the container. However now it is complaining about missing files?
roddy@b040c95d83ff:/var/spool/cwl$ perl /roddy/bin/run_workflow.pl --run-id run_id --normal-bam /var/lib/cwl/job699596040_51b50672-7725-4df4-b9c6-e7832ef5de0a/normal-bam --tumor-bam /var/lib/cwl/job699596040_41c2f651-2b2a-4204-9917-f775f6fbb400/tumor-bam --reference-gz /var/lib/cwl/job699596040_8d32d979-dfa1-4c62-89b9-bc825d033d2b/reference-gz
RUNNING CMD: mkdir -p /data/datastore/normal
RUNNING CMD: mkdir -p /data/datastore/tumor/
RUNNING CMD: mkdir -p /data/datastore/delly/
RUNNING CMD: ln -s /var/lib/cwl/job699596040_51b50672-7725-4df4-b9c6-e7832ef5de0a/normal-bam /data/datastore/normal/normal.bam
RUNNING CMD: samtools index /data/datastore/normal/normal.bam
RUNNING CMD: ln -s /var/lib/cwl/job699596040_41c2f651-2b2a-4204-9917-f775f6fbb400/tumor-bam /data/datastore/tumor/tumor.bam
RUNNING CMD: samtools index /data/datastore/tumor/tumor.bam
RUNNING CMD: ln -s /data/datastore/delly/delly.bedpe.txt
RUNNING CMD: mkdir -p /mnt/datastore/workflow_data/
RUNNING CMD: mkdir -p $TMPDIR/reference
RUNNING CMD: cd $TMPDIR/reference && tar zxf /var/lib/cwl/job699596040_8d32d979-dfa1-4c62-89b9-bc825d033d2b/reference-gz
RUNNING CMD: mkdir -p /mnt/datastore/ && ln -s $TMPDIR/reference/bundledFiles /mnt/datastore/
- Restarting Sun Grid Engine Master Scheduler sge_qmaster [ OK ]
/roddy/bin/Roddy/dist/bin/2.2.49/roddy.sh: line 36: /roddy/.roddy/jfxlibInfo: No such file or directory
cat: /roddy/.roddy/jfxlibInfo: No such file or directory
The plugin CopyNumberEstimationWorkflow [ Version: 1.0.189 ] was loaded.
The plugin PluginBase [ Version: 1.0.24 ] was loaded.
The plugin COWorkflows [ Version: 1.1.3 ] was loaded.
The plugin DefaultPlugin [ Version: current ] was loaded.
Found 1 datasets in the in- and output directories.
Selected dataset run_id for processing.
Looking for merged bam files in directory /mnt/datastore/testdata/run_id/alignment
Found merged bam file /mnt/datastore/testdata/run_id/alignment/control_run_id_merged.mdup.bam for sample control
Looking for merged bam files in directory /mnt/datastore/testdata/run_id/alignment
Found merged bam file /mnt/datastore/testdata/run_id/alignment/tumor_run_id_merged.mdup.bam for sample tumor
There were errors for the execution context for dataset run_id
* A path could not be found. WARNING: Output file is missing: /mnt/datastore/testdata/.roddyExecCache.txt
* A path could not be found. WARNING: Output dir is missing: /mnt/datastore/testdata/.roddyExecutionDirectory
* A path could not be found. WARNING: Output file is missing: /mnt/datastore/testdata/.roddyExecutionDirectory/zippedAnalysesMD5.txt
* A path could not be found. WARNING: Output dir is missing: /mnt/datastore/testdata/run_id/roddyExecutionStore
* No input data was found. SEVERE: Delly files were not found in input path.
Creating the following execution directory to store information about this process:
/mnt/datastore/testdata/run_id/roddyExecutionStore/exec_160713_055756785_roddy_copyNumberEstimation
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr1.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr2.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr3.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr4.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr5.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr6.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr7.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr8.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr9.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr10.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr11.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr12.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr13.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr14.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr15.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr16.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr17.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr18.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr19.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr20.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr21.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr22.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chrX.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.CoverageWindowsFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chrY.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/run_id_sex.txt
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr1.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr2.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr3.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr4.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr5.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr6.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr7.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr8.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr9.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr10.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr11.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr12.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr13.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr14.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr15.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr16.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr17.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr18.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr19.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr20.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr21.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr22.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chrX.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chrY.cnv.anno.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/run_id_all.cnv.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr1.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr2.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr3.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr4.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr5.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr6.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr7.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr8.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr9.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr10.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr11.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr12.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr13.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr14.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr15.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr16.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr17.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr18.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr19.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr20.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr21.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chr22.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chrX.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNPPositionFile with path /mnt/datastore/testdata/run_id/ACEseq/cnv_snp/run_id.chrY.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/run_id_sex.txt
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/run_id_all.snp.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr1.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr2.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr3.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr4.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr5.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr6.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr7.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr8.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr9.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr10.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr11.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr12.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr13.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr14.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr15.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr16.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr17.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr18.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr19.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr20.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr21.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr22.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.PhasedGenotypeFile with path /mnt/datastore/testdata/run_id/ACEseq/phasing/phased_chr23.vcf
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/run_id_all.snp.haplo.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/run_id_all.cnv.corrected.tab.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.TextFile with path /mnt/datastore/testdata/run_id/ACEseq/run_id_sex.txt
There were errors for the execution context for dataset run_id
* A path could not be found. WARNING: Output file is missing: /mnt/datastore/testdata/.roddyExecCache.txt
* A path could not be found. WARNING: Output dir is missing: /mnt/datastore/testdata/.roddyExecutionDirectory
* A path could not be found. WARNING: Output file is missing: /mnt/datastore/testdata/.roddyExecutionDirectory/zippedAnalysesMD5.txt
* A path could not be found. WARNING: Output dir is missing: /mnt/datastore/testdata/run_id/roddyExecutionStore
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* No input data was found. SEVERE: Delly files were not found in input path.
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
The user requested to wait for all jobs submitted by this process to finish.
The plugin COWorkflows [ Version: 1.0.132-1 ] was loaded.
The plugin PluginBase [ Version: 1.0.24 ] was loaded.
The plugin DefaultPlugin [ Version: current ] was loaded.
Found 1 datasets in the in- and output directories.
Selected dataset run_id for processing.
Looking for merged bam files in directory /mnt/datastore/testdata/run_id/alignment
Found merged bam file /mnt/datastore/testdata/run_id/alignment/control_run_id_merged.mdup.bam for sample control
Looking for merged bam files in directory /mnt/datastore/testdata/run_id/alignment
Found merged bam file /mnt/datastore/testdata/run_id/alignment/tumor_run_id_merged.mdup.bam for sample tumor
Creating the following execution directory to store information about this process:
/mnt/datastore/testdata/run_id/roddyExecutionStore/exec_160713_060256475_roddy_snvCalling
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNVAnnotationFile with path /mnt/datastore/testdata/run_id/mpileup/snvs_run_id_raw.vcf.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNVAnnotationFile with path /mnt/datastore/testdata/run_id/mpileup/snvs_run_id.vcf.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNVAnnotationFile with path /mnt/datastore/testdata/run_id/mpileup/snvs_run_id.vcf.gz
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.SNVAnnotationFile with path /mnt/datastore/testdata/run_id/mpileup/snvs_run_id_raw.vcf.gz
There were errors for the execution context for dataset run_id
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
The user requested to wait for all jobs submitted by this process to finish.
The plugin COWorkflows [ Version: 1.0.132-1 ] was loaded.
The plugin PluginBase [ Version: 1.0.24 ] was loaded.
The plugin DefaultPlugin [ Version: current ] was loaded.
Found 1 datasets in the in- and output directories.
Selected dataset run_id for processing.
Looking for merged bam files in directory /mnt/datastore/testdata/run_id/alignment
Found merged bam file /mnt/datastore/testdata/run_id/alignment/control_run_id_merged.mdup.bam for sample control
Looking for merged bam files in directory /mnt/datastore/testdata/run_id/alignment
Found merged bam file /mnt/datastore/testdata/run_id/alignment/tumor_run_id_merged.mdup.bam for sample tumor
Creating the following execution directory to store information about this process:
/mnt/datastore/testdata/run_id/roddyExecutionStore/exec_160713_060756435_roddy_indelCalling
Something is wrong for file: BaseFile of type de.dkfz.b080.co.files.VCFFileForIndels with path /mnt/datastore/testdata/run_id/platypus_indel/indel_run_id.vcf.raw.gz
There were errors for the execution context for dataset run_id
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The job submission did not work, aborting job submission. SEVERE: Please check your submission command manually.
Is your access group set properly? [roddy]
Can the submission binary handle your binary?
Is your submission system offline?
* The execution of a job failed. SEVERE: A job execution failed
* The execution of a job failed. SEVERE: A job execution failed
The user requested to wait for all jobs submitted by this process to finish.
Wait for Roddy jobs to finish
Check job state logfiles
No errors found for /mnt/datastore/testdata/run_id/roddyExecutionStore/exec_160713_055756785_roddy_copyNumberEstimation/jobStateLogfile.txt
No errors found for /mnt/datastore/testdata/run_id/roddyExecutionStore/exec_160713_060256475_roddy_snvCalling/jobStateLogfile.txt
No errors found for /mnt/datastore/testdata/run_id/roddyExecutionStore/exec_160713_060756435_roddy_indelCalling/jobStateLogfile.txt
Copying log files
cp: cannot create directory /mnt/datastore/resultdata/run_id_logs': No such file or directory cp: target/mnt/datastore/resultdata/run_id_logs' is not a directory
Filter and / or copy final files
sh: 1: cannot create /mnt/datastore/resultdata/run_id.dkfz-snvCalling_1-0-132-1.20160520.germline.snv_mnv.vcf.gz: Directory nonexistent
sh: 1: cannot create /mnt/datastore/resultdata/run_id.dkfz-snvCalling_1-0-132-1.20160520.somatic.snv_mnv.vcf.gz: Directory nonexistent
gzip: /mnt/datastore/testdata/run_id/mpileup/_pancan.vcf.gz: No such file or directory
sh: 1: cannot create /mnt/datastore/resultdata/run_id.dkfz-indelCalling_1-0-132-1.20160520.germline.indel.vcf.gz: Directory nonexistent
sh: 1: cannot create /mnt/datastore/resultdata/run_id.dkfz-indelCalling_1-0-132-1.20160520.somatic.indel.vcf.gz: Directory nonexistent
gzip: /mnt/datastore/testdata/run_id/platypus_indel/pancan.vcf.gz: No such file or directory
open: No such file or directory
[bgzf_check_bgzf] failed to open the file: /mnt/datastore/resultdata/run_id.dkfz-snvCalling_1-0-132-1.20160520.germline.snv_mnv.vcf.gz
[tabix] was bgzip used to compress this file? /mnt/datastore/resultdata/run_id.dkfz-snvCalling_1-0-132-1.20160520.germline.snv_mnv.vcf.gz
open: No such file or directory
[bgzf_check_bgzf] failed to open the file: /mnt/datastore/resultdata/run_id.dkfz-snvCalling_1-0-132-1.20160520.somatic.snv_mnv.vcf.gz
[tabix] was bgzip used to compress this file? /mnt/datastore/resultdata/run_id.dkfz-snvCalling_1-0-132-1.20160520.somatic.snv_mnv.vcf.gz
open: No such file or directory
[bgzf_check_bgzf] failed to open the file: /mnt/datastore/resultdata/run_id.dkfz-indelCalling_1-0-132-1.20160520.germline.indel.vcf.gz
[tabix] was bgzip used to compress this file? /mnt/datastore/resultdata/run_id.dkfz-indelCalling_1-0-132-1.20160520.germline.indel.vcf.gz
open: No such file or directory
[bgzf_check_bgzf] failed to open the file: /mnt/datastore/resultdata/run_id.dkfz-indelCalling_1-0-132-1.20160520.somatic.indel.vcf.gz
[tabix] was bgzip used to compress this file? /mnt/datastore/resultdata/run_id.dkfz-indelCalling_1-0-132-1.20160520.somatic.indel.vcf.gz
cp: target /mnt/datastore/resultdata/run_id.dkfz-copyNumberEstimation_1-0-189.20160520.somatic.cnv.vcf.gz' is not a directory cp: cannot stat/mnt/datastore/testdata/run_id/ACEseq/plots/.json': No such file or directory
Traceback (most recent call last):
File "/roddy/bin/convertTabToJson.py", line 17, in
args = parser.parse_args()
File "/usr/lib/python2.7/argparse.py", line 1688, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/usr/lib/python2.7/argparse.py", line 1720, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/usr/lib/python2.7/argparse.py", line 1926, in _parse_known_args
start_index = consume_optional(start_index)
File "/usr/lib/python2.7/argparse.py", line 1866, in consume_optional
take_action(action, args, option_string)
File "/usr/lib/python2.7/argparse.py", line 1778, in take_action
argument_values = self._get_values(action, argument_strings)
File "/usr/lib/python2.7/argparse.py", line 2204, in _get_values
value = self._get_value(action, arg_string)
File "/usr/lib/python2.7/argparse.py", line 2233, in _get_value
result = type_func(arg_string)
IOError: [Errno 2] No such file or directory: 'FILE'
Create SNV json file
head: cannot open `/mnt/datastore/testdata/run_id/mpileup/__QC_values.tsv' for reading: No such file or directory
gzip: /mnt/datastore/resultdata/run_id.dkfz-snvCalling_1-0-132-1.20160520.somatic.snv_mnv.vcf.gz: No such file or directory
gzip: /mnt/datastore/resultdata/run_id.dkfz-snvCalling_1-0-132-1.20160520.somatic.snv_mnv.vcf.gz: No such file or directory
gzip: /mnt/datastore/resultdata/run_id.dkfz-snvCalling_1-0-132-1.20160520.germline.snv_mnv.vcf.gz: No such file or directory
/roddy/bin/runwrapper.sh: line 169: /mnt/datastore/resultdata/run_id.dkfz-snvCalling_1-0-132-1.20160520.snv_mnv.json.tab.tmp: No such file or directory
Traceback (most recent call last):
File "/roddy/bin/convertTabToJson.py", line 17, in
args = parser.parse_args()
File "/usr/lib/python2.7/argparse.py", line 1688, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/usr/lib/python2.7/argparse.py", line 1720, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/usr/lib/python2.7/argparse.py", line 1926, in _parse_known_args
start_index = consume_optional(start_index)
File "/usr/lib/python2.7/argparse.py", line 1866, in consume_optional
take_action(action, args, option_string)
File "/usr/lib/python2.7/argparse.py", line 1778, in take_action
argument_values = self._get_values(action, argument_strings)
File "/usr/lib/python2.7/argparse.py", line 2204, in _get_values
value = self._get_value(action, arg_string)
File "/usr/lib/python2.7/argparse.py", line 2233, in _get_value
result = type_func(arg_string)
IOError: [Errno 2] No such file or directory: '/mnt/datastore/resultdata/run_id.dkfz-snvCalling_1-0-132-1.20160520.snv_mnv.json.tab.tmp'
Create INDEL json file
gzip: /mnt/datastore/resultdata/run_id.dkfz-indelCalling_1-0-132-1.20160520.somatic.indel.vcf.gz: No such file or directory
gzip: /mnt/datastore/resultdata/run_id.dkfz-indelCalling_1-0-132-1.20160520.somatic.indel.vcf.gz: No such file or directory
gzip: /mnt/datastore/resultdata/run_id.dkfz-indelCalling_1-0-132-1.20160520.germline.indel.vcf.gz: No such file or directory
/roddy/bin/runwrapper.sh: line 177: /mnt/datastore/resultdata/run_id.dkfz-indelCalling_1-0-132-1.20160520.indel.json.tab.tmp: No such file or directory
Traceback (most recent call last):
File "/roddy/bin/convertTabToJson.py", line 17, in
args = parser.parse_args()
File "/usr/lib/python2.7/argparse.py", line 1688, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/usr/lib/python2.7/argparse.py", line 1720, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/usr/lib/python2.7/argparse.py", line 1926, in _parse_known_args
start_index = consume_optional(start_index)
File "/usr/lib/python2.7/argparse.py", line 1866, in consume_optional
take_action(action, args, option_string)
File "/usr/lib/python2.7/argparse.py", line 1778, in take_action
argument_values = self._get_values(action, argument_strings)
File "/usr/lib/python2.7/argparse.py", line 2204, in _get_values
value = self._get_value(action, arg_string)
File "/usr/lib/python2.7/argparse.py", line 2233, in _get_value
result = type_func(arg_string)
IOError: [Errno 2] No such file or directory: '/mnt/datastore/resultdata/run_id.dkfz-indelCalling_1-0-132-1.20160520.indel.json.tab.tmp'
Traceback (most recent call last):
File "/roddy/bin/combineJsons.py", line 19, in
args = parser.parse_args()
File "/usr/lib/python2.7/argparse.py", line 1688, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/usr/lib/python2.7/argparse.py", line 1720, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/usr/lib/python2.7/argparse.py", line 1926, in _parse_known_args
start_index = consume_optional(start_index)
File "/usr/lib/python2.7/argparse.py", line 1866, in consume_optional
take_action(action, args, option_string)
File "/usr/lib/python2.7/argparse.py", line 1778, in take_action
argument_values = self._get_values(action, argument_strings)
File "/usr/lib/python2.7/argparse.py", line 2204, in _get_values
value = self._get_value(action, arg_string)
File "/usr/lib/python2.7/argparse.py", line 2233, in _get_value
result = type_func(arg_string)
IOError: [Errno 2] No such file or directory: '/mnt/datastore/resultdata/run_id.dkfz-copyNumberEstimation_1-0-189.20160520.cnv.json'
open: No such file or directory
[bgzf_check_bgzf] failed to open the file: /mnt/datastore/resultdata/run_id.dkfz-copyNumberEstimation_1-0-189.20160520.somatic.cnv.vcf.gz
[tabix] was bgzip used to compress this file? /mnt/datastore/resultdata/run_id.dkfz-copyNumberEstimation_1-0-189.20160520.somatic.cnv.vcf.gz
Create tarballs
tar (child): tar (child): /mnt/datastore/resultdata/run_id.dkfz-indelCalling_1-0-132-1.20160520.somatic.indel.tar.gz: Cannot open: No such file or directory/mnt/datastore/resultdata/run_id.dkfz-snvCalling_1-0-132-1.20160520.somatic.snv_mnv.tar.gz: Cannot open
tar (child): : No such file or directoryError is not recoverable: exiting now
tar (child): Error is not recoverable: exiting now
tar (child): /mnt/datastore/resultdata/run_id.dkfz-copyNumberEstimation_1-0-189.20160520.somatic.cnv.tar.gz: Cannot open: No such file or directory
tar (child): Error is not recoverable: exiting now
platypus_indel/
mpileup/
ACEseq/
ACEseq/phasing/
ACEseq/plots/
ACEseq/cnv_snp/
Calculating md5 sums
ls: cannot access /mnt/datastore/resultdata/run_id.dkfz_.tbi: No such file or directory
ls: cannot access /mnt/datastore/resultdata/run_id.dkfz_.gz: No such file or directory
Setup proper access rights
0
mv: cannot stat `/mnt/datastore/resultdata/*': No such file or directory
roddy@b040c95d83ff:/var/spool/cwl$
please advise
thank you