terminated for an unknown reason -- Likely it has been terminated by the external system

[fan040]

Description of the bug

i don not know why there are such errors

Command used and terminal output

Caused by:
  Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (AK58_C_1)` terminated for an unknown reason -- Likely it has been terminated by the external system

Command executed:

  gatk --java-options "-Xmx163840M -XX:-UsePerfData" \
      HaplotypeCaller \
      --input AK58_C_1.md.cram \
      --output AK58_C_1.haplotypecaller.chr2A_part1_1-384157900.g.vcf.gz \
      --reference wheat_AK58v4MP.genome_part.fa \
       \
      --intervals chr2A_part1_1-384157900.bed \
       \
       \
      --tmp-dir . \
      -ERC GVCF
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER":
      gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*$//')
  END_VERSIONS

Command exit status:
  -

Command output:
  (empty)

Work dir:
  /public/home/fanrong/work_lei/01_htt/01_240927_well_bse_bsr/01_bsr/02_sarek/02_vcf/work/bd/a8da3f055c7df258c4271504de32d7

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details

Relevant files

No response

System information

No response

[FriederikeHanssen]

this happens when the scheduler kills your job, typically because you either run out of memory or time. To investigate, can you take a look at the .command.log file of the failing task? You can find it in the work directory: /public/home/fanrong/work_lei/01_htt/01_240927_well_bse_bsr/01_bsr/02_sarek/02_vcf/work/bd/a8da3f055c7df258c4271504de32d7

[fan040]

no .command.log in file,just have .command.run and .command.sh.