chipqc Error in ChIPseq snakePipe

[skhassafi]

While running SnakePipes, ChIP-seq workflow, the ChIPQC step fails with the following error in rule chipqc

Rscript --vanilla chipqc.R

Error in names(b) <- sub("[0-9]$", "", names(b)) : 
  attempt to set an attribute on NULL
Execution halted

RuleException:
CalledProcessError in file "/package/conda/py312_24.5.0-0/envs/snakePipes-3.2.0/lib/python3.12/site-packages/snakePipes/shared/rules/ChIP_peak_calling.snakefile", line 246:
Command 'source /localenv/khassafi/anaconda/bin/activate '/package/conda/py312_24.5.0-0/envs/snakePipes-3.2.0_envs/083aac90ceef8d42ece6ec42716ef3fb'; set -euo pipefail;  
Rscript --vanilla /.snakemake/scripts/tmpcx1pphmt.chipqc.R' returned non-zero exit status 1.

[Tue Jun  3 13:43:31 2025]
Error in rule chipqc:
    message: None

Environment details:

• snakePipes version: 3.2.0
• Conda environment: Python 3.12
• Execution type: cluster FORK, MulticoreParam
• Relevant Snakemake rule: chipqc (in ChIP_peak_calling.snakefile, line 246)

The MACS2_chipqc folder is empty as a result

Here are a few of the MACS2_peaks output:

1014 MACS2/MOF_WT_t1_Rep1_366.filtered.BAM_peaks.narrowPeak
    5651 MACS2/MOF_WT_t1_Rep1_366.filtered.BAMPE_peaks.narrowPeak
     170 MACS2/MOF_WT_t1_Rep2_370.filtered.BAM_peaks.narrowPeak
     734 MACS2/MOF_WT_t1_Rep2_370.filtered.BAMPE_peaks.narrowPeak
   20219 MACS2/MOF_WT_t2_Rep1_99.filtered.BAM_peaks.narrowPeak
   21487 MACS2/MOF_WT_t2_Rep1_99.filtered.BAMPE_peaks.narrowPeak
    1183 MACS2/MOF_WT_t2_Rep2_379.filtered.BAM_peaks.narrowPeak
    1622 MACS2/MOF_WT_t2_Rep2_379.filtered.BAMPE_peaks.narrowPeak

[skhassafi]

When I run the pipeline for another ChIP sample set, the other part of the chipqc histoneHMM_chipqc rule fails with a similar error message from chipqc.R:

[1] broad
<0 rows> (or 0-length row.names)
Error in names(b) <- sub("[0-9]$", "", names(b)) : 
  attempt to set an attribute on NULL
Execution halted

RuleException:
CalledProcessError in file "/package/conda/py312_24.5.0-0/envs/snakePipes-3.2.0/lib/python3.12/site-packages/snakePipes/shared/rules/histoneHMM.snakefile", line 91:
Command 'source /localenv/khassafi/anaconda/bin/activate '/package/conda/py312_24.5.0-0/envs/snakePipes-3.2.0_envs/083aac90ceef8d42ece6ec42716ef3fb'; set -euo pipefail;  
Rscript --vanilla /.snakemake/scripts/tmpt0v4ff7t.chipqc.R' returned non-zero exit status 1.

Error in rule histoneHMM_chipqc:
    message: None

Input file:
chip_samples.yaml

This error happens regardless of whether the rule chipqc goes through or not. A folder called histoneHMM_chipqc is made and left empty in both cases. Even though in both scenarios the peaks are called as narrow. However, if only this error occurs, the MACS2_chipqc has the results. opposite to the original issue.

MACS2_peaks output of this run for records:

21833 MACS2/BMAL1_KO_t1_Rep1_559.filtered.BAM_peaks.narrowPeak
   19207 MACS2/BMAL1_KO_t1_Rep1_559.filtered.BAMPE_peaks.narrowPeak
    9794 MACS2/BMAL1_KO_t1_Rep2_554.filtered.BAM_peaks.narrowPeak
    9719 MACS2/BMAL1_KO_t1_Rep2_554.filtered.BAMPE_peaks.narrowPeak
    2616 MACS2/BMAL1_KO_t2_Rep1_567.filtered.BAM_peaks.narrowPeak
   10918 MACS2/BMAL1_KO_t2_Rep1_567.filtered.BAMPE_peaks.narrowPeak
    9756 MACS2/BMAL1_KO_t2_Rep2_575.filtered.BAM_peaks.narrowPeak
    8923 MACS2/BMAL1_KO_t2_Rep2_575.filtered.BAMPE_peaks.narrowPeak