cannot locate the log file to figure out the problem.

[Indianhedgehog]

Description of the bug

ERROR ~ Error executing process > 'NFCORE_ONCOANALYSER:WGTS:GRIDSS_SVPREP_CALLING:ASSEMBLE (V_H021-2HFQKW)'

Caused by:
  Process `NFCORE_ONCOANALYSER:WGTS:GRIDSS_SVPREP_CALLING:ASSEMBLE (V_H021-2HFQKW)` terminated with an error exit status (1)


Command executed:

  # Create shadow directory with file symlinks of GRIDSS 'working' dir to prevent cache invalidation
  # NOTE(SW): for reasons that elude me, NF doesn't always stage in the workingdir; remove if it is present
  shadow_input_directory() {
      src=${1}
      dst="gridss_assemble/work/${src##*/}"
      for filepath_src in $(find -L ${src} ! -type d); do
          # Get destination location for symlink
          filepath_src_rel=$(sed 's#^'${src}'/*##' <<< ${filepath_src})
          filepath_dst=${dst%/}/${filepath_src_rel}
          # Create directory for symlink
          mkdir -p ${filepath_dst%/*};
          # Get path for symlink source file, then create it
          # NOTE(SW): ideally we would get the relative path using the --relative-to but this is only
          # supported for GNU realpath and fails for others such as BusyBox, which is used in Biocontainers
          symlinkpath=$(realpath ${filepath_src})
          ln -s "${symlinkpath}" ${filepath_dst};
      done
      if [[ -L "${src##*/}" ]]; then
          rm "${src}"
      fi
  }
  for preprocess_dir in V_H021-2HFQKW_N.sv_prep.sorted.bam.gridss.working V_H021-2HFQKW_T.sv_prep.sorted.bam.gridss.working; do
      shadow_input_directory ${preprocess_dir};
  done

  # Symlink indices next to assembly FASTA
  ln -s $(find -L gridss_index_2.13.2 -regex '.*\.\(amb\|ann\|pac\|gridsscache\|sa\|bwt\|img\|alt\)') ./        
 # Run
  gridss_svprep \
       \
      --jvmheap 46922517709 \
      --otherjvmheap 4294967296 \
      --steps assemble \
      --labels V_H021-2HFQKW_N,V_H021-2HFQKW_T \
      --reference hs37d5_PhiX.fa \
      --blacklist gridss_blacklist.37.bed.gz \
      --workingdir gridss_assemble/work \
      --assembly gridss_assemble/sv_assemblies.bam \
      --threads 1 \
      --configuration gridss.properties \
      --bams V_H021-2HFQKW_N.markdups.bam,V_H021-2HFQKW_T.markdups.bam \
      --filtered_bams V_H021-2HFQKW_N.sv_prep.sorted.bam,V_H021-2HFQKW_T.sv_prep.sorted.bam

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_ONCOANALYSER:WGTS:GRIDSS_SVPREP_CALLING:ASSEMBLE":
      gridss: $(CallVariants --version 2>&1 | sed 's/-gridss$//')
      svprep: $(svprep -version | sed 's/^.* //')
  END_VERSIONS

Command exit status:
  1

Command output:
  /usr/bin/time: unrecognized option '--verbose'
  BusyBox v1.36.1 (2023-10-17 11:19:33 UTC) multi-call binary.

  Usage: time [-vpa] [-o FILE] PROG ARGS

  Run PROG, display resource usage when it exits

        -v      Verbose
        -p      POSIX output format
        -f FMT  Custom format
        -o FILE Write result to FILE
        -a      Append (else overwrite)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  Using working directory "gridss_assemble/work"
  Tue Dec 31 13:10:06 CET 2024: Full log file is: gridss_assemble/work/gridss.full.20241231_131006.odcf-cn31u33.191.log
  Tue Dec 31 13:10:06 CET 2024: Found /usr/bin/time
  Tue Dec 31 13:10:06 CET 2024: Using GRIDSS jar /usr/local/share/gridss-2.13.2-3/gridss.jar
 Tue Dec 31 13:10:06 CET 2024: Using reference genome "hs37d5_PhiX.fa"
  Tue Dec 31 13:10:06 CET 2024: Using 1 worker threads.
  Tue Dec 31 13:10:06 CET 2024: Using blacklist gridss_blacklist.37.bed.gz
  Tue Dec 31 13:10:06 CET 2024: Using JVM maximum heap size of 46922517709 for assembly and variant calling.
  Tue Dec 31 13:10:06 CET 2024: Label 0: name=V_H021-2HFQKW_N full-bam=V_H021-2HFQKW_N.markdups.bam filtered-bam=V_H021-2HFQKW_N.sv_prep.sorted.bam
  Tue Dec 31 13:10:06 CET 2024: Label 1: name=V_H021-2HFQKW_T full-bam=V_H021-2HFQKW_T.markdups.bam filtered-bam=V_H021-2HFQKW_T.sv_prep.sorted.bam
  Tue Dec 31 13:10:06 CET 2024: Full BAM args:  INPUT_LABEL=V_H021-2HFQKW_N INPUT_LABEL=V_H021-2HFQKW_T INPUT=V_H021-2HFQKW_N.markdups.bam INPUT=V_H021-2HFQKW_T.markdups.bam
  Tue Dec 31 13:10:06 CET 2024: Filtered BAM args:  INPUT_LABEL=V_H021-2HFQKW_N INPUT_LABEL=V_H021-2HFQKW_T INPUT=V_H021-2HFQKW_N.sv_prep.sorted.bam INPUT=V_H021-2HFQKW_T.sv_prep.sorted.bam
  Tue Dec 31 13:10:06 CET 2024: Found /usr/local/bin/Rscript
  Tue Dec 31 13:10:06 CET 2024: Found /usr/local/bin/samtools
  Tue Dec 31 13:10:06 CET 2024: Found /usr/local/bin/java
  Tue Dec 31 13:10:06 CET 2024: Found /usr/local/bin/bwa
  Tue Dec 31 13:10:06 CET 2024: samtools version: 1.20+htslib-1.20
  Tue Dec 31 13:10:06 CET 2024: bwa Version: 0.7.18-r1243-dirty
  Tue Dec 31 13:10:06 CET 2024: time version: /usr/bin/time: unrecognized option '--version'
  BusyBox v1.36.1 (2023-10-17 11:19:33 UTC) multi-call binary.

  Usage: time [-vpa] [-o FILE] PROG ARGS

  Run PROG, display resource usage when it exits

        -v      Verbose
        -p      POSIX output format
        -f FMT  Custom format
        -o FILE Write result to FILE
        -a      Append (else overwrite)
  Tue Dec 31 13:10:06 CET 2024: bash version: GNU bash, version 5.2.15(1)-release (x86_64-pc-linux-gnu)
  Tue Dec 31 13:10:07 CET 2024: java version: openjdk version "22.0.1-internal" 2024-04-16      OpenJDK Runtime Environment (build 22.0.1-internal-adhoc.conda.src)     OpenJDK 64-Bit Server VM (build 22.0.1-internal-adhoc.conda.src, mixed mode, sharing)
  Tue Dec 31 13:10:07 CET 2024: Max file handles: 131072
  Tue Dec 31 13:10:07 CET 2024: Running GRIDSS steps: assembly
  Tue Dec 31 13:10:07 CET 2024: *** ASSEMBLY ***
  Tue Dec 31 13:10:07 CET 2024: Running AssembleBreakends: writing output to dir gridss_assemble/sv_assemblies.bam
  "$timecmd java -Xmx$jvmheap $jvm_args -Dgridss.output_to_temp_file=true -cp $gridss_jar gridss.AssembleBreakends JOB_INDEX=0 JOB_NODES=1 TMP_DIR=$workingdir WORKING_DIR=$workingdir REFERENCE_SEQUENCE=$reference WORKER_THREADS=$threads $input_filtered_args $blacklist_arg $config_args $readpairing_args O=$assembly" command completed with exit code 1.
  *****
  The underlying error message can be found in gridss_assemble/work/gridss.full.20241231_131006.odcf-cn31u33.191.log
  *****

Work dir:
  /omics/odcf/analysis/evaluation_projects/workflow-validation/workflow_testing/oncoanalyser_test/work/03/40fae213084390c176b5fce2a48d28

Container:
  /omics/odcf/analysis/evaluation_projects/workflow-validation/workflow_testing/oncoanalyser_test/work/singularity/depot.galaxyproject.org-singularity-hmftools-sv-prep-1.2.4--hdfd78af_0.img

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

Command used and terminal output

Relevant files

No response

System information

Nextflow version: version 24.10.2
Hardware: HPC
Executor: local

[scwatts]

Hi @Indianhedgehog, you should be able to find the referenced GRIDSS log under the relevant work directory:

/omics/odcf/analysis/evaluation_projects/workflow-validation/workflow_testing/oncoanalyser_test/work/03/40fae213084390c176b5fce2a48d28/

[Indianhedgehog]

Hi @scwatts , Thanks for getting back.
I searched for the log file with find, but, other than the nextflow log file i don't find any gridss related log file.

[scwatts]

That is unusual! Would you be able to try manually rerunning the stage? Doing this should help us understand what is happening here.

If you can post the .command.sh and .command.run files from that work directory I'll be able to provide some further instructions.

[Indianhedgehog]

hi @scwatts ,

I have figured out the issue. I did not provide the correct path for gridss index files in the configuration file (since i am using different reference genome).

However, I think the issue of no log file still remains. The error message shows the path of the log file in the work directory, but there is none.

Thanks !