picard mark duplicates error command exit status 140

[natpeckett]

Description of the bug

I'm using the nextflow cut&run pipeline which I used last year for cut&run analysis. I'm now getting an error from the mark duplicates step citing 'handling an unexpected condition' and giving the exit status 140. I can't seem to find anything online regarding similar issues.

Command used and terminal output

Apr-30 12:38:04.698 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_CUTANDRUN:CUTANDRUN:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (AKP_NT_Igg_H_PC_R2); work-dir=/exports/eddie/scratch/s1804715/cutandrun/work/5d/fb64d790e2eac4cb8df9b14d6d6f30
  error [nextflow.exception.ProcessFailedException]: Process `NFCORE_CUTANDRUN:CUTANDRUN:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (AKP_NT_Igg_H_PC_R2)` terminated with an error exit status (140)
Apr-30 12:38:04.744 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_CUTANDRUN:CUTANDRUN:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (AKP_NT_Igg_H_PC_R2)'

Caused by:
  Process `NFCORE_CUTANDRUN:CUTANDRUN:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (AKP_NT_Igg_H_PC_R2)` terminated with an error exit status (140)

Command executed:

  picard \
      -Xmx64g \
      MarkDuplicates \
      --ASSUME_SORT_ORDER coordinate --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp \
      --INPUT AKP_NT_Igg_H_PC_R2.target.filtered.sorted.bam \
      --OUTPUT AKP_NT_Igg_H_PC_R2.target.markdup.bam \
      --REFERENCE_SEQUENCE genome.fa \
      --METRICS_FILE AKP_NT_Igg_H_PC_R2.target.markdup.MarkDuplicates.metrics.txt

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_CUTANDRUN:CUTANDRUN:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES":
      picard: $(echo $(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
  END_VERSIONS

Command exit status:
  140

Command output:
  (empty)

Command error:
  ^[[34mINFO:   ^[[0m Convert SIF file to sandbox...
  /usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
  11:38:01.799 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-2.27.4-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
  [Tue Apr 30 11:38:01 GMT 2024] MarkDuplicates --INPUT AKP_NT_Igg_H_PC_R2.target.filtered.sorted.bam --OUTPUT AKP_NT_Igg_H_PC_R2.target.markdup.bam --METRICS_FILE AKP_NT_Igg_H_PC_R2.target.markdup.MarkDuplicates.metrics.txt --REMOVE_DUPLICATES false --ASSUME_SORT_ORDER coordi$
  [Tue Apr 30 11:38:01 GMT 2024] Executing as [email protected] on Linux 3.10.0-1160.108.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 11.0.15-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.27.4-SN$
  INFO  2024-04-30 11:38:01     MarkDuplicates  Start of doWork freeMemory: 108826936; totalMemory: 117440512; maxMemory: 68719476736
  INFO  2024-04-30 11:38:01     MarkDuplicates  Reading input file and constructing read end information.
  INFO  2024-04-30 11:38:01     MarkDuplicates  Will retain up to 248983611 data points before spilling to disk.

Relevant files

No response

System information

No response

[chris-cheshire]

Hey, is this still an issue? Sorry for the delay, its best to post on the nf-core slack channels for a faster response