sarek [BUG] Control-FREEC 'Stack Smashing' error with Mouse SNP file

[BUG] Control-FREEC 'Stack Smashing' error with Mouse SNP file

Open MikeWLloyd opened this issue 2 years ago • 2 comments

Check Documentation

I have checked the following places for your error:

Description of the bug

We are running mouse data with the full pipeline.

The recommended SNP file input: "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.snps_all.dbSNP142.vcf.gz" is causing Control-FREEC to crash.

We have run just FREEC outside of the pipeline, but with pipeline prepared config file to replicate the error:

$ singularity run nfcore-sarek-2.7.1.img freec -conf 846_KB1P_T.config.txt
Control-FREEC v11.6 : a method for automatic detection of copy number alterations, subclones and for accurate estimation of contamination and main ploidy using deep-sequencing data
Multi-threading mode using 8 threads
..consider the sample being female
..Breakpoint threshold for segmentation of copy number profiles is 0.8
..telocenromeric set to 50000
..FREEC is not going to adjust profiles for a possible contamination by normal cells
..Coefficient Of Variation set equal to 0.05
..it will be used to evaluate window size
..Output directory:	.
..Directory with files containing chromosome sequences:	/fastscratch/lloydm/8d7a192defa08d02b633f305e10578/Chromosomes
..Sample file:	/fastscratch/lloydm/8d7a192defa08d02b633f305e10578/846_KB1P_T.pileup
..Sample input format:	pileup
..minimal expected GC-content (general parameter "minExpectedGC") was set to 0.35
..maximal expected GC-content (general parameter "maxExpectedGC") was set to 0.55
..Polynomial degree for "ReadCount ~ GC-content" normalization is 3 or 4: will try both
..Minimal CNA length (in windows) is 1
..File with chromosome lengths:	/fastscratch/lloydm/8d7a192defa08d02b633f305e10578/GRCm38.len
..Using the default minimal mappability value of 0.85
..uniqueMatch = FALSE
..average ploidy set to 2
..break-point type set to 2
..noisyData set to 0
..Control-FREEC will not look for subclones
..will use SNP positions from /fastscratch/lloydm/8d7a192defa08d02b633f305e10578/mgp.v5.merged.snps_all.dbSNP142.vcf.gz to calculate BAF profiles
..Starting reading /fastscratch/lloydm/8d7a192defa08d02b633f305e10578/mgp.v5.merged.snps_all.dbSNP142.vcf.gz to get SNP positions
*** stack smashing detected ***: <unknown> terminated
SIGABRT: abort
PC=0x473c4b m=0 sigcode=0

goroutine 1 [running, locked to thread]:
syscall.RawSyscall(0x3e, 0x1b849, 0x6, 0x0, 0xc000173ef0, 0x49de52, 0x1b849)
	/usr/lib64/go-1.11.1/src/syscall/asm_linux_amd64.s:78 +0x2b fp=0xc000173eb8 sp=0xc000173eb0 pc=0x473c4b
syscall.Kill(0x1b849, 0x6, 0x4388ee, 0xc000173f20)
	/usr/lib64/go-1.11.1/src/syscall/zsyscall_linux_amd64.go:597 +0x4b fp=0xc000173f00 sp=0xc000173eb8 pc=0x4705bb
github.com/sylabs/singularity/internal/app/starter.Master.func2()
	internal/app/starter/master_linux.go:152 +0x3e fp=0xc000173f38 sp=0xc000173f00 pc=0x7395ee
github.com/sylabs/singularity/internal/pkg/util/mainthread.Execute.func1()
	internal/pkg/util/mainthread/mainthread.go:21 +0x2f fp=0xc000173f60 sp=0xc000173f38 pc=0x737dff
main.main()
	cmd/starter/main_linux.go:102 +0x5f fp=0xc000173f98 sp=0xc000173f60 pc=0x91a51f
runtime.main()
	/usr/lib64/go-1.11.1/src/runtime/proc.go:201 +0x207 fp=0xc000173fe0 sp=0xc000173f98 pc=0x430bb7
runtime.goexit()
	/usr/lib64/go-1.11.1/src/runtime/asm_amd64.s:1333 +0x1 fp=0xc000173fe8 sp=0xc000173fe0 pc=0x45c601

goroutine 5 [syscall]:
os/signal.signal_recv(0xaf7ba0)
	/usr/lib64/go-1.11.1/src/runtime/sigqueue.go:139 +0x9c
os/signal.loop()
	/usr/lib64/go-1.11.1/src/os/signal/signal_unix.go:23 +0x22
created by os/signal.init.0
	/usr/lib64/go-1.11.1/src/os/signal/signal_unix.go:29 +0x41

goroutine 7 [chan receive]:
github.com/sylabs/singularity/internal/pkg/util/mainthread.Execute(0xc000242cb0)
	internal/pkg/util/mainthread/mainthread.go:24 +0xb4
github.com/sylabs/singularity/internal/app/starter.Master(0x7, 0x4, 0x1b855, 0xc00000d300)
	internal/app/starter/master_linux.go:151 +0x405
main.startup()
	cmd/starter/main_linux.go:75 +0x4b8
created by main.main
	cmd/starter/main_linux.go:98 +0x35

rax    0x0
rbx    0x0
rcx    0xffffffffffffffff
rdx    0x0
rdi    0x1b849
rsi    0x6
rbp    0xc000173ef0
rsp    0xc000173eb0
r8     0x0
r9     0x0
r10    0x0
r11    0x206
r12    0x24
r13    0x33
r14    0xaeccdc
r15    0x0
rip    0x473c4b
rflags 0x206
cs     0x33
fs     0x0
gs     0x0

As you see, it gets to the SNP parsing step, and crashes.

We raised this with the Control-FREEC development team: https://github.com/BoevaLab/FREEC/issues/92

The reply being to use a cleaned SNP file prepared by their team:

...run with an old SNP file: http://xfer.curie.fr/get/AS9Zncn7yfB/mm10_dbSNP137.ucsc.freec.txt.gz ?

We would like to be able to run mouse data through FREEC as part of the pipeline. Given that you are recommending the use of mgp.v5.merged.snps_all.dbSNP142 as the SNP file, do you have a recommended way to get around this issue?

Sep 17 '21 16:09 MikeWLloyd

As an update, it could be a possible work around to have a FREEC specific input parameter, which would use a different FREEC formatted SNP file. I found a perl script that does the conversion from VCF to FREEC pseduoVCF. The converted file could be used as an input.

Sep 17 '21 18:09 MikeWLloyd

Hi there, I'm running into the same problem. Is there an intermediate solution before 3.0 available? Thanks

Jun 03 '22 11:06 leiendeckerlu

What is the best way to address this if it occurs? I'm using nf-core/sarek v3.3.2-gf034b73 and have the same error.

Nov 08 '23 10:11 oceall-rcsi

What is the best way to address this if it occurs? I'm using nf-core/sarek v3.3.2-gf034b73 and have the same error.

Can you share your .nextflow.log and your samplesheet?

Nov 08 '23 15:11 maxulysse

Hiya

My sample sheet is patient,sex,status,sample,lane,fastq_1,fastq_2 balbc_spont,XX,1,bsample_1,L1,/home/data/wgs_brca_mouse/data/wgs/X204SC23074548-Z01-F001_03/01.RawData/SMT1_N1/SMT1_N1_EKDN230034383-1A_H7MH7DSX7_L1_1.fq.gz,/home/data/wgs_brca_mouse/data/wgs/X204SC23074548-Z01-F001_03/01.RawData/SMT1_N1/SMT1_N1_EKDN230034383-1A_H7MH7DSX7_L1_2.fq.gz balbc_spont,XX,1,bsample_2,L1,/home/data/wgs_brca_mouse/data/wgs/X204SC23074548-Z01-F001_01/01.RawData/SMT1_N2/SMT1_N2_EKDN230034384-1A_H7MH7DSX7_L1_1.fq.gz,/home/data/wgs_brca_mouse/data/wgs/X204SC23074548-Z01-F001_01/01.RawData/SMT1_N2/SMT1_N2_EKDN230034384-1A_H7MH7DSX7_L1_2.fq.gz balbc_spont,XX,1,lsample_1,L2,/home/data/wgs_brca_mouse/data/wgs/X204SC23074548-Z01-F001_02/01.RawData/SMT1_Lung_N1/SMT1_Lung_N1_EKDN230034385-1A_H7MH7DSX7_L2_1.fq.gz,/home/data/wgs_brca_mouse/data/wgs/X204SC23074548-Z01-F001_02/01.RawData/SMT1_Lung_N1/SMT1_Lung_N1_EKDN230034385-1A_H7MH7DSX7_L2_2.fq.gz balbc_spont,XX,1,lsample_2,L2,/home/data/wgs_brca_mouse/data/wgs/X204SC23074548-Z01-F001_03/01.RawData/SMT1_Lung_N2/SMT1_Lung_N2_EKDN230034386-1A_H7MH7DSX7_L2_1.fq.gz,/home/data/wgs_brca_mouse/data/wgs/X204SC23074548-Z01-F001_03/01.RawData/SMT1_Lung_N2/SMT1_Lung_N2_EKDN230034386-1A_H7MH7DSX7_L2_2.fq.gz

and my .nextflow.log is:

`~> TaskHandler[id: 450; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA:MANTA_TUMORONLY (lsample_1); status: NEW; exit: -; error: -; workDir: /home/data/wgs_brca_mouse/work/77/8598fa73a7f4522dcf2f74afb75000]
.. remaining tasks omitted.
Nov-07 13:21:40.934 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 4 -- submitted tasks are shown below
~> TaskHandler[id: 451; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA:MANTA_TUMORONLY (lsample_2); status: RUNNING; exit: -; error: -; workDir: /home/data/wgs_brca_mouse/work/b5/10678bbd005699a6c630aa8aa74fc6]
~> TaskHandler[id: 425; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH (lsample_1); status: RUNNING; exit: -; error: -; workDir: /home/data/wgs_brca_mouse/work/45/193216f7afd3dd0ca174ae517471c5]
~> TaskHandler[id: 420; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH (bsample_1); status: RUNNING; exit: -; error: -; workDir: /home/data/wgs_brca_mouse/work/09/d267a1c455b524fdc19fc1b6deeada]
~> TaskHandler[id: 422; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH (bsample_2); status: RUNNING; exit: -; error: -; workDir: /home/data/wgs_brca_mouse/work/08/56881b94877477ca2596ff07847f70]
Nov-07 13:23:54.438 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 420; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH (bsample_1); status: COMPLETED; exit: 0; error: -; workDir: /home/data/wgs_brca_mouse/work/09/d267a1c455b524fdc19fc1b6deeada]
Nov-07 13:23:54.494 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-07 13:23:54.496 [Task submitter] INFO  nextflow.Session - [33/7f2325] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC_TUMORONLY (bsample_1)
Nov-07 13:23:56.355 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 879; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC_TUMORONLY (bsample_1); status: COMPLETED; exit: 134; error: -; workDir: /home/data/wgs_brca_mouse/work/33/7f2325670b3e9da142a74c1f337502]
Nov-07 13:23:56.356 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC_TUMORONLY (bsample_1); work-dir=/home/data/wgs_brca_mouse/work/33/7f2325670b3e9da142a74c1f337502
  error [nextflow.exception.ProcessFailedException]: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC_TUMORONLY (bsample_1)` terminated with an error exit status (134)
Nov-07 13:23:56.434 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-07 13:23:56.434 [Task submitter] INFO  nextflow.Session - [7e/e8c088] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC_TUMORONLY (bsample_2)
Nov-07 13:23:56.452 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC_TUMORONLY (bsample_1)'

Caused by:
  Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC_TUMORONLY (bsample_1)` terminated with an error exit status (134)

Command executed:

  touch config.txt

  echo "[general]" >> config.txt
  echo BedGraphOutput = TRUE >> config.txt
  echo breakPointThreshold = 0.8 >> config.txt
  echo breakPointType = 2 >> config.txt
  echo chrFiles =${PWD}/Chromosomes >> config.txt
  echo chrLenFile = ${PWD}/genome.fa.fai >> config.txt
  echo coefficientOfVariation = 0.05 >> config.txt
  echo  >> config.txt
  echo  >> config.txt
  echo  >> config.txt
  echo forceGCcontentNormalization = 0 >> config.txt
  echo  >> config.txt
  echo gemMappabilityFile = ${PWD}/GRCm38_68_mm10.gem >> config.txt
  echo  >> config.txt
  echo  >> config.txt
  echo  >> config.txt
  echo  >> config.txt
  echo  >> config.txt
  echo minimalSubclonePresence = 20 >> config.txt
  echo "maxThreads = 4" >> config.txt
  echo noisyData = FALSE >> config.txt
  echo  >> config.txt
  echo ploidy = 2 >> config.txt
  echo printNA = TRUE >> config.txt
  echo readCountThreshold = 10 >> config.txt
  echo sex = XX >> config.txt
  echo  >> config.txt
  echo  >> config.txt
  echo  >> config.txt
  echo  >> config.txt

  echo "[control]" >> config.txt
  echo  >> config.txt
  echo  >> config.txt
  echo  >> config.txt
  echo  >> config.txt
  echo  >> config.txt

  echo "[sample]" >> config.txt
  echo mateFile = ${PWD}/bsample_1.tumor.mpileup.gz >> config.txt
  echo  >> config.txt
  echo  >> config.txt
  echo inputFormat = pileup >> config.txt
  echo mateOrientation = FR >> config.txt

  echo "[BAF]" >> config.txt
  echo  >> config.txt
  echo fastaFile = ${PWD}/genome.fa >> config.txt
  echo  >> config.txt
  echo  >> config.txt
  echo  >> config.txt
  echo SNPfile = $PWD/mgp.v5.merged.snps_all.dbSNP142.vcf.gz >> config.txt

  echo "[target]" >> config.txt
  echo  >> config.txt

  freec -conf config.txt

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC_TUMORONLY":
      controlfreec: $(echo $(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*$//' | sed -e "s/Control-FREEC v//g" )
  END_VERSIONS

Command exit status:
  134

Command output:
  Control-FREEC v11.6 : a method for automatic detection of copy number alterations, subclones and for accurate estimation of contamination and main ploidy using deep-sequencing data
  Multi-threading mode using 4 threads
  ..consider the sample being female
  ..Breakpoint threshold for segmentation of copy number profiles is 0.8
  ..telocenromeric set to 50000
  ..FREEC is not going to adjust profiles for a possible contamination by normal cells
  ..Coefficient Of Variation set equal to 0.05
  ..it will be used to evaluate window size
  ..Output directory:   .
  ..Directory with files containing chromosome sequences:       Chromosomes
  ..Sample file:        bsample_1.tumor.mpileup.gz
  ..Sample input format:        pileup
  ..minimal expected GC-content (general parameter "minExpectedGC") was set to 0.35
  ..maximal expected GC-content (general parameter "maxExpectedGC") was set to 0.55
  ..Polynomial degree for "ReadCount ~ GC-content" normalization is 3 or 4: will try both
  ..Minimal CNA length (in windows) is 1
  ..File with chromosome lengths:       genome.fa.fai
  ..Using the default minimal mappability value of 0.85
  ..uniqueMatch = FALSE
  ..average ploidy set to 2
  ..break-point type set to 2
  ..noisyData set to 0
  ..Control-FREEC will look for subclones present in at least 20% of cell population
  ..will use SNP positions from mgp.v5.merged.snps_all.dbSNP142.vcf.gz to calculate BAF profiles
  ..Starting reading mgp.v5.merged.snps_all.dbSNP142.vcf.gz to get SNP positions

Command error:
  Control-FREEC v11.6 : a method for automatic detection of copy number alterations, subclones and for accurate estimation of contamination and main ploidy using deep-sequencing data
  Multi-threading mode using 4 threads
  ..consider the sample being female
  ..Breakpoint threshold for segmentation of copy number profiles is 0.8
  ..telocenromeric set to 50000
  ..FREEC is not going to adjust profiles for a possible contamination by normal cells
  ..Coefficient Of Variation set equal to 0.05
  ..it will be used to evaluate window size
  ..Output directory:   .
  ..Directory with files containing chromosome sequences:       Chromosomes
  ..Sample file:        bsample_1.tumor.mpileup.gz
  ..Sample input format:        pileup
  ..minimal expected GC-content (general parameter "minExpectedGC") was set to 0.35
  ..maximal expected GC-content (general parameter "maxExpectedGC") was set to 0.55
  ..Polynomial degree for "ReadCount ~ GC-content" normalization is 3 or 4: will try both
  ..Minimal CNA length (in windows) is 1
  ..File with chromosome lengths:       genome.fa.fai
  ..Using the default minimal mappability value of 0.85
  ..uniqueMatch = FALSE
  ..average ploidy set to 2
  ..break-point type set to 2
  ..noisyData set to 0
  ..Control-FREEC will look for subclones present in at least 20% of cell population
  ..will use SNP positions from mgp.v5.merged.snps_all.dbSNP142.vcf.gz to calculate BAF profiles
  ..Starting reading mgp.v5.merged.snps_all.dbSNP142.vcf.gz to get SNP positions
  *** stack smashing detected ***: <unknown> terminated
  .command.sh: line 60:    66 Aborted                 (core dumped) freec -conf config.txt

Work dir:
  /home/data/wgs_brca_mouse/work/33/7f2325670b3e9da142a74c1f337502

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Nov-07 13:23:56.461 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC_TUMORONLY (bsample_1)` terminated with an error exit status (134)
Nov-07 13:23:56.468 [Task monitor] DEBUG nextflow.Session - The following nodes are still active:
[process] NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:ASSESS_SIGNIFICANCE
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC2BED
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC2CIRCOS
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:MAKEGRAPH
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGE_MUTECT2
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: -
  port 2: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGEMUTECTSTATS
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:LEARNREADORIENTATIONMODEL
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:FILTERMUTECTCALLS
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: -
  port 2: (value) bound ; channel: -
  port 3: (value) bound ; channel: -
  port 4: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: -
  port 2: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA_GENOME
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: -
  port 2: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: -
  port 2: (value) bound ; channel: -
  port 3: (value) bound ; channel: -
  port 4: (value) bound ; channel: -
  port 5: (value) bound ; channel: -
  port 6: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: bed
  port 2: (value) bound ; channel: diff_variant_file
  port 3: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: bed
  port 2: (value) bound ; channel: diff_variant_file
  port 3: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: bed
  port 2: (value) bound ; channel: diff_variant_file
  port 3: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: versions
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:MULTIQC
  status=ACTIVE
  port 0: (value) OPEN  ; channel: multiqc_files
  port 1: (value) bound ; channel: multiqc_config
  port 2: (value) bound ; channel: extra_multiqc_config
  port 3: (value) bound ; channel: multiqc_logo
  port 4: (cntrl) -     ; channel: $

Nov-07 13:23:56.471 [main] DEBUG nextflow.Session - Session await > all processes finished
Nov-07 13:23:56.471 [main] DEBUG nextflow.Session - Session await > all barriers passed
Nov-07 13:23:56.478 [Actor Thread 520] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Nov-07 13:23:56.479 [Actor Thread 527] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Nov-07 13:23:56.484 [Actor Thread 325] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 12; slices: 1; internal sort time: 0.007 s; external sort time: 0.001 s; total time: 0.008 s
Nov-07 13:23:56.491 [Actor Thread 325] DEBUG nextflow.file.FileCollector - >> temp file exists? true
Nov-07 13:23:56.505 [Actor Thread 325] DEBUG nextflow.file.FileCollector - Retrieved cached collect-files from: /home/data/wgs_brca_mouse/work/collect-file/d593cc412dd171379cc0de8945db6b41
Nov-07 13:23:56.508 [Actor Thread 325] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /local/scratch/127437/nxf-7871226258441820188
Nov-07 13:23:56.581 [main] INFO  nextflow.Nextflow - -[nf-core/sarek] Pipeline completed with errors-
Nov-07 13:23:56.588 [main] WARN  n.processor.TaskPollingMonitor - Killing running tasks (4)
Nov-07 13:23:56.831 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=1; failedCount=5; ignoredCount=0; cachedCount=611; pendingCount=149; submittedCount=1; runningCount=-1; retriesCount=4; abortedCount=4; succeedDuration=4h 8m 44s; failedDuration=22.7s; cachedDuration=44d 9h 29m 29s;loadCpus=-4; loadMemory=0; peakRunning=5; peakCpus=18; peakMemory=56 GB; ]
Nov-07 13:23:56.831 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Nov-07 13:23:56.860 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Nov-07 13:23:57.171 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
  [{"cpuUsage":{"mean":45.36,"min":44.18,"q1":45.15,"q2":45.56,"q3":45.77,"max":46.13,"minLabel":"NFCORE_SAREK:SAREK:FASTQC (lsample_1-L2)","maxLabel":"NFCORE_SAREK:SAREK:FASTQC (bsample_1-L1)","q1Label":"NFCORE_SAREK:SAREK:FASTQC (lsample_1-L2)","q2Label":"NFCORE_SAREK:SAREK:FASTQC (bsample_2-L1)","q3Label":"NFCORE_SAREK:SAREK:FASTQC (lsample_2-L2)"},"process":"FASTQC","mem":{"mean":1195013120,"min":1184997376,"q1":1188653056,"q2":1195319296,"q3":1201679360,"max":1204416512,"minLabel":"NFCORE_SAREK:SAREK:FASTQC (bsample_2-L1)","maxLabel":"NFCORE_SAREK:SAREK:FASTQC (bsample_1-L1)","q1Label":"NFCORE_SAREK:SAREK:FASTQC (bsample_2-L1)","q2Label":"NFCORE_SAREK:SAREK:FASTQC (lsample_1-L2)","q3Label":"NFCORE_SAREK:SAREK:FASTQC (lsample_2-L2)"},"memUsage":{"mean":27.82,"min":27.59,"q1":27.68,"q2":27.83,"q3":27.98,"max":28.04,"minLabel":"NFCORE_SAREK:SAREK:FASTQC (bsample_2-L1)","maxLabel":"NFCORE_SAREK:SAREK:FASTQC (bsample_1-L1)","q1Label":"NFCORE_SAREK:SAREK:FASTQC 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(lsample_2)"}},{"cpuUsage":{"mean":34.46,"min":32.25,"q1":33.83,"q2":34.5,"q3":35.14,"max":36.6,"minLabel":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_1)","maxLabel":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (bsample_2)","q1Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_1)","q2Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_2)","q3Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (bsample_1)"},"process":"MERGE_FREEBAYES","mem":{"mean":985067520,"min":974270464,"q1":982478848,"q2":986044416,"q3":988633088,"max":993910784,"minLabel":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_2)","maxLabel":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (bsample_1)","q1Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_2)","q2Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (bsample_2)","q3Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_1)"},"memUsage":{"mean":22.94,"min":22.68,"q1":22.88,"q2":22.96,"q3":23.02,"max":23.14,"minLabel":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_2)","maxLabel":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (bsample_1)","q1Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_2)","q2Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (bsample_2)","q3Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_1)"},"timeUsage":{"mean":1.96,"min":1.88,"q1":1.95,"q2":1.98,"q3":1.99,"max":2.02,"minLabel":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (bsample_2)","maxLabel":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_1)","q1Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (bsample_2)","q2Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (bsample_1)","q3Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_2)"},"vmem":{"mean":22336101376,"min":8128450560,"q1":8130788352,"q2":22317000704,"q3":36522313728,"max":36581953536,"minLabel":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_1)","maxLabel":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_2)","q1Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_1)","q2Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (bsample_1)","q3Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (bsample_2)"},"reads":{"mean":1053586026,"min":1043879915,"q1":1049359385.75,"q2":1051916901.5,"q3":1056143541.75,"max":1066630386,"minLabel":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_2)","maxLabel":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (bsample_2)","q1Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_2)","q2Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (bsample_1)","q3Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_1)"},"cpu":{"mean":68.93,"min":64.5,"q1":67.65,"q2":69,"q3":70.28,"max":73.2,"minLabel":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_1)","maxLabel":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (bsample_2)","q1Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_1)","q2Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_2)","q3Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (bsample_1)"},"time":{"mean":565750,"min":542000,"q1":562250,"q2":569000,"q3":572500,"max":583000,"minLabel":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (bsample_2)","maxLabel":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_1)","q1Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (bsample_2)","q2Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (bsample_1)","q3Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_2)"},"writes":{"mean":1479351142.5,"min":1468854169,"q1":1470942318.25,"q2":1474705707,"q3":1483114531.25,"max":1499138987,"minLabel":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_2)","maxLabel":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (bsample_2)","q1Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_2)","q2Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (lsample_1)","q3Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_FREEBAYES:MERGE_FREEBAYES (bsample_1)"}},{"cpuUsage":null,"process":"FREEC_TUMORONLY","mem":null,"memUsage":null,"timeUsage":{"mean":0.01,"min":0,"q1":0.01,"q2":0.01,"q3":0.01,"max":0.02,"minLabel":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC_TUMORONLY (bsample_1)","maxLabel":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC_TUMORONLY (bsample_1)","q1Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC_TUMORONLY (bsample_2)","q2Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC_TUMORONLY (lsample_2)","q3Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC_TUMORONLY (lsample_1)"},"vmem":null,"reads":null,"cpu":null,"time":{"mean":2029.6,"min":1201,"q1":1825,"q2":1932,"q3":2153,"max":3037,"minLabel":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC_TUMORONLY (bsample_1)","maxLabel":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC_TUMORONLY (bsample_1)","q1Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC_TUMORONLY (bsample_2)","q2Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC_TUMORONLY (lsample_2)","q3Label":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC_TUMORONLY (lsample_1)"},"writes":null},{"cpuUsage":null,"process":"MANTA_TUMORONLY","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":null,"writes":null}]
Nov-07 13:23:57.801 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Nov-07 13:23:58.100 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Nov-07 13:23:58.100 [main] INFO  org.pf4j.AbstractPluginManager - Stop plugin '[email protected]'
Nov-07 13:23:58.100 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-amazon
Nov-07 13:23:58.100 [main] INFO  org.pf4j.AbstractPluginManager - Stop plugin '[email protected]'
Nov-07 13:23:58.100 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-prov
Nov-07 13:23:58.100 [main] INFO  org.pf4j.AbstractPluginManager - Stop plugin '[email protected]'
Nov-07 13:23:58.100 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-validation
Nov-07 13:23:58.240 [main] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /local/scratch/127437/nxf-6134086518422222639
Nov-07 13:23:58.242 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
Nov-07 13:23:58.249 [Actor Thread 374] ERROR nextflow.extension.OperatorImpl - @unknown
java.lang.NullPointerException: Cannot invoke "org.iq80.leveldb.impl.Version.retain()" because "this.version" is null
        at org.iq80.leveldb.impl.SnapshotImpl.<init>(SnapshotImpl.java:35)
        at org.iq80.leveldb.impl.DbImpl.getSnapshot(DbImpl.java:805)
        at org.iq80.leveldb.impl.DbImpl.get(DbImpl.java:588)
        at org.iq80.leveldb.impl.DbImpl.get(DbImpl.java:577)
        at nextflow.file.SortFileCollector$IndexSort.getValue(SortFileCollector.groovy:125)
        at nextflow.file.SortFileCollector$IndexSort.compare(SortFileCollector.groovy:110)
        at nextflow.file.SortFileCollector$IndexSort.compare(SortFileCollector.groovy)
        at nextflow.sort.BigSort$SliceComparator.compare(BigSort.java:455)
        at java.base/java.util.TimSort.binarySort(TimSort.java:296)
        at java.base/java.util.TimSort.sort(TimSort.java:239)
        at java.base/java.util.Arrays.sort(Arrays.java:1233)
        at nextflow.sort.BigSort.sliceSort(BigSort.java:280)
        at nextflow.sort.BigSort.sort(BigSort.java:235)
        at nextflow.file.SortFileCollector.makeHash(SortFileCollector.groovy:247)
        at nextflow.file.FileCollector.saveTo(FileCollector.groovy:239)
        at nextflow.file.FileCollector$saveTo$0.call(Unknown Source)
        at nextflow.extension.CollectFileOp.emitItems(CollectFileOp.groovy:187)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:568)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1258)
        at groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1047)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1132)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
        at groovy.lang.Closure.call(Closure.java:412)
        at groovy.lang.Closure.call(Closure.java:428)
        at groovy.lang.Closure$call.call(Unknown Source)
        at nextflow.extension.DataflowHelper$3.afterStop(DataflowHelper.groovy:254)
        at groovyx.gpars.dataflow.operator.DataflowProcessor.fireAfterStop(DataflowProcessor.java:324)
        at groovyx.gpars.dataflow.operator.DataflowProcessorActor.afterStop(DataflowProcessorActor.java:59)
        at jdk.internal.reflect.GeneratedMethodAccessor235.invoke(Unknown Source)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:568)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1258)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
        at org.codehaus.groovy.runtime.InvokerHelper.invokePojoMethod(InvokerHelper.java:1024)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:1015)
        at groovyx.gpars.actor.Actor.callDynamic(Actor.java:369)
        at groovyx.gpars.actor.Actor.handleTermination(Actor.java:320)
        at groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(AbstractLoopingActor.java:86)
        at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
        at java.base/java.lang.Thread.run(Thread.java:833)

Nov 09 '23 10:11 oceall-rcsi

sarek sarek copied to clipboard

[BUG] Control-FREEC 'Stack Smashing' error with Mouse SNP file

Check Documentation

Description of the bug

sarek
sarek copied to clipboard