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nf-core / atacseq

ATAC-seq peak-calling and QC analysis pipeline
https://nf-co.re/atacseq
MIT License
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Error executing process > 'MERGED_LIB_BAM_REMOVE_ORPHAN (control_R2)' #151

Closed zhumengyan closed 1 year ago

zhumengyan commented 3 years ago

I come across a problem when apply this pipeline to mu ATAC-Seq data. The error is:

[7c/09c5ba] process > CHECK_DESIGN (design_pe.csv)                [100%] 1 of 1 ✔
[b4/ee799a] process > MAKE_TSS_BED (genes.bed)                    [100%] 1 of 1 ✔
[13/faeee3] process > MAKE_GENOME_FILTER (genome.fa)              [100%] 1 of 1 ✔
[2f/d479cc] process > FASTQC (control_R1_T1)                      [100%] 6 of 6 ✔
[1a/e63261] process > TRIMGALORE (control_R1_T1)                  [100%] 6 of 6 ✔
[33/26fa1d] process > BWA_MEM (control_R1_T1)                     [100%] 6 of 6 ✔
[61/91e2c7] process > SORT_BAM (control_R1_T1)                    [100%] 6 of 6 ✔
[92/184f6a] process > MERGED_LIB_BAM (control_R1)                 [100%] 6 of 6 ✔
[ba/aa1a62] process > MERGED_LIB_BAM_FILTER (control_R1)          [100%] 6 of 6, failed: 1 ✘
[b3/673a59] process > MERGED_LIB_BAM_REMOVE_ORPHAN (treatment_R2) [100%] 5 of 5, failed: 3
[9c/8925dc] process > MERGED_LIB_PRESEQ (control_R1)              [100%] 6 of 6 ✔
[01/7ed5bf] process > MERGED_LIB_PICARD_METRICS (treatment_R3)    [100%] 1 of 1
[24/988e66] process > MERGED_LIB_BIGWIG (treatment_R3)            [100%] 1 of 1, failed: 1
[-        ] process > MERGED_LIB_PLOTPROFILE                      -
[a2/7e963d] process > MERGED_LIB_PLOTFINGERPRINT (treatment_R3)   [100%] 1 of 1
[72/a435fe] process > MERGED_LIB_MACS2 (treatment_R3)             [100%] 1 of 1
[-        ] process > MERGED_LIB_MACS2_ANNOTATE                   -
[-        ] process > MERGED_LIB_MACS2_QC                         -
[-        ] process > MERGED_LIB_CONSENSUS                        -
[-        ] process > MERGED_LIB_CONSENSUS_ANNOTATE               -
[-        ] process > MERGED_LIB_CONSENSUS_COUNTS                 -
[-        ] process > MERGED_LIB_CONSENSUS_DESEQ2                 -
[-        ] process > MERGED_LIB_ATAQV                            -
[-        ] process > MERGED_LIB_ATAQV_MKARV                      -
[-        ] process > MERGED_REP_BAM                              -
[-        ] process > MERGED_REP_BIGWIG                           -
[-        ] process > MERGED_REP_MACS2                            -
[-        ] process > MERGED_REP_MACS2_ANNOTATE                   -
[-        ] process > MERGED_REP_MACS2_QC                         -
[-        ] process > MERGED_REP_CONSENSUS                        -
[-        ] process > MERGED_REP_CONSENSUS_ANNOTATE               -
[-        ] process > MERGED_REP_CONSENSUS_COUNTS                 -
[-        ] process > MERGED_REP_CONSENSUS_DESEQ2                 -
[-        ] process > IGV                                         -
[cb/5b2c2c] process > get_software_versions                       [100%] 1 of 1 ✔
[-        ] process > MULTIQC                                     -
[d7/ac8744] process > output_documentation                        [100%] 1 of 1 ✔

-[nf-core/atacseq] Pipeline completed with errors-
Error executing process > 'MERGED_LIB_BAM_REMOVE_ORPHAN (control_R2)'

Caused by:
  Process `MERGED_LIB_BAM_REMOVE_ORPHAN (control_R2)` terminated with an error exit status (120)

Command executed:

  bampe_rm_orphan.py control_R2.mLb.flT.bam control_R2.mLb.clN.bam --only_fr_pairs

  samtools sort -@ 6 -o control_R2.mLb.clN.sorted.bam -T control_R2.mLb.clN control_R2.mLb.clN.bam
  samtools index control_R2.mLb.clN.sorted.bam
  samtools flagstat control_R2.mLb.clN.sorted.bam > control_R2.mLb.clN.sorted.bam.flagstat
  samtools idxstats control_R2.mLb.clN.sorted.bam > control_R2.mLb.clN.sorted.bam.idxstats
  samtools stats control_R2.mLb.clN.sorted.bam > control_R2.mLb.clN.sorted.bam.stats

Command exit status:
  120
drpatelh commented 1 year ago

Hi @zhumengyan ! Thanks for reporting and apologies for the delay in responding! We are about to release a much updated version of the pipeline that has been completely refactored to be written in Nextflow DSL2. When this is released, it would be great if you can let us know if the problem still persists. I will close this issue for now.

For faster, real-time help for these sorts of things please join the #atacseq channel on the nf-core Slack workspace. You can join via the link below: https://nf-co.re/join