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uclahs-cds / metapipeline-DNA

Nextflow pipeline to convert BAM to FASTQ, align, perform QC, assess targeted coverage, call gSNP, call sSNV, call mtSNV, call SVs, call sCNA, and perform subclonal reconstruction
GNU General Public License v2.0
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Cannot remove convert-BAM2FASTQ work directroy: Directory not empty #186

Open zhuchcn opened 7 months ago

zhuchcn commented 7 months ago

This is a repeated issue: /hot/project/process/MissingPeptides/MISP-000132-MissingPeptidesPanCanP1/CPTAC_PAAD/WXS/work/d6/18e638e93144f211ed12a14280164c/slurm.out

convert-BAM2FASTQ failed.

[13/11e8f9] process > convert_BAM2FASTQ:extract_r... [100%] 4 of 4 ✔
[a2/9ec20a] process > convert_BAM2FASTQ:create_CS... [100%] 4 of 4 ✔
[0a/fe75c5] process > convert_BAM2FASTQ:call_conv... [100%] 1 of 1, failed: 1
[-        ] process > align_DNA:create_CSV_align_DNA -
[-        ] process > align_DNA:call_align_DNA       -
[-        ] process > recalibrate_BAM:create_YAML... -
[-        ] process > recalibrate_BAM:run_recalib... -
[-        ] process > recalibrate_BAM:run_recalib... -
[-        ] process > generate_SQC_BAM:create_YAM... -
[-        ] process > generate_SQC_BAM:run_genera... -
[-        ] process > call_gSNP:create_YAML_call_... -
[-        ] process > call_gSNP:run_call_gSNP        -
[-        ] process > call_sSNV:create_YAML_call_... -
[-        ] process > call_sSNV:run_call_sSNV        -
[-        ] process > call_mtSNV:create_YAML_call... -
[-        ] process > call_mtSNV:run_call_mtSNV      -
ERROR ~ Error executing process > 'convert_BAM2FASTQ:call_convert_BAM2FASTQ (1)'

But the pipeline actually finished successfully, except that the working directory cannot be removed.

executor >  local (245)
  [e6/34a10b] process > run_validate_PipeVal (1)       [100%] 1 of 1 ✔
  [fb/1d9d94] process > get_bam_stats_SAMtools (1)     [100%] 1 of 1 ✔
  [d8/1bd1c2] process > get_readcount_BAM (1)          [100%] 1 of 1 ✔
  [73/0f8264] process > revert_alignment_Picard_Too... [100%] 1 of 1 ✔
  [35/b5e26f] process > collate_bam_SAMtools (35)      [100%] 48 of 48 ✔
  [76/9f8f37] process > remove_intermediate_files (48) [100%] 48 of 48 ✔
  [34/b966b1] process > create_fastqs_SAMtools (48)    [100%] 48 of 48 ✔
  [b9/6fdfbd] process > get_readcount_FASTQ (96)       [100%] 96 of 96 ✔
  [dd/edb8d1] process > compare_readcounts (1)         [100%] 1 of 1 ✔
  Completed at: 03-Apr-2024 10:39:59
  Duration    : 58m 9s
  CPU hours   : 55.8
  Succeeded   : 245

  rm: cannot remove ‘/hot/project/process/MissingPeptides/MISP-000132-MissingPeptidesPanCanP1/CPTAC_PAAD/WXS/work/d6/18e638e93144f211ed12a14280164c/work/work-bam2fastq-C3L-00017-02/97/55aacf56446fb98c3cd9f14bd61d1e’: Directory not empty

I'm guessing maybe this is because Ln 55 exceuted too early, before the publishDir finishes moving files to the destination directory, because the working directory that it failed to remove is indeed empty now.

https://github.com/uclahs-cds/metapipeline-DNA/blob/59b96630180f0dca2cb9963478fc8cf507a10a57/module/convert_BAM2FASTQ/call_convert_BAM2FASTQ.nf#L41-L55

zhuchcn commented 7 months ago

What I don't understand is rm -r should remove the directory even if it is not empty. So why does it complain that the directoy isn't empty? Maybe the files were being used (for example being moved by publishDir)?

yashpatel6 commented 7 months ago

The publishDir rules shouldn't have any race conditions since the L55 doesn't run until the nextflow run finishes and that only finished after all publishDir have finished; I'm not sure why the complaint is there about rm -r