Nextflow workflow report

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 1.

The full error message was:

Error executing process > 'NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (Msd_SD_rep1)'

Caused by:
  Process `NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (Msd_SD_rep1)` terminated with an error exit status (1)


Command executed:

  read_distribution.py \
      -i Msd_SD_rep1.markdup.sorted.bam \
      -r GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.filtered.2.filtered.bed \
      > Msd_SD_rep1.read_distribution.txt
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION":
      rseqc: $(read_distribution.py --version | sed -e "s/read_distribution.py //g")
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  processing GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.filtered.2.filtered.bed ... Traceback (most recent call last):
    File "/home/nspmpego/microbiota_photoperiodism/gut_RNA_seq/ld_sd_rnaseq_analysis/work/conda/env-0e90878ad6b4a0932ac4d3282b759d1e/bin/read_distribution.py", line 302, in 
      main()
    File "/home/nspmpego/microbiota_photoperiodism/gut_RNA_seq/ld_sd_rnaseq_analysis/work/conda/env-0e90878ad6b4a0932ac4d3282b759d1e/bin/read_distribution.py", line 191, in main
      intergenic_down1kb_base,intergenic_down5kb_base,intergenic_down10kb_base) = process_gene_model(options.ref_gene_model)
                                                                                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/home/nspmpego/microbiota_photoperiodism/gut_RNA_seq/ld_sd_rnaseq_analysis/work/conda/env-0e90878ad6b4a0932ac4d3282b759d1e/bin/read_distribution.py", line 81, in process_gene_model
      cds_exon=BED.unionBed3(cds_exon)
               ^^^^^^^^^^^^^^^^^^^^^^^
    File "/home/nspmpego/microbiota_photoperiodism/gut_RNA_seq/ld_sd_rnaseq_analysis/work/conda/env-0e90878ad6b4a0932ac4d3282b759d1e/lib/python3.12/site-packages/qcmodule/BED.py", line 2504, in unionBed3
      bitsets = binned_bitsets_from_list(lst)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/home/nspmpego/microbiota_photoperiodism/gut_RNA_seq/ld_sd_rnaseq_analysis/work/conda/env-0e90878ad6b4a0932ac4d3282b759d1e/lib/python3.12/site-packages/bx/bitset_builders.py", line 155, in binned_bitsets_from_list
      last_bitset.set_range(start, end - start)
    File "lib/bx/bitset.pyx", line 217, in bx.bitset.BinnedBitSet.set_range
    File "lib/bx/bitset.pyx", line 187, in bx.bitset.bb_check_range_count
  IndexError: Count (-456) must be non-negative.

Work dir:
  /home/nspmpego/microbiota_photoperiodism/gut_RNA_seq/ld_sd_rnaseq_analysis/work/a3/506c41cf64e76726cef1f3e30357e9

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