Error executing process > 'MACS2_QC'

[Rohit-Satyam]

Hi. I have a Single End MiSeq Chipseq runs(single replicate). My design.csv is as follows

group,replicate,fastq_1,fastq_2,antibody,control
A1_IP,1,A1_S1_L001_R1_001.fastq.gz,,,
C1_TF_Ab,1,C1_S2_L001_R1_001.fastq.gz,,TF,A1_IP
E1_IgG_control,1,E1_S3_L001_R1_001.fastq.gz,,IgG,A1_IP
G1_H3K27Ac_Ab,1,G1_S4_L001_R1_001.fastq.gz,,H3K27Ac,A1_IP

I tried running peak-calling using your nf-core pipeline using the following command:

nextflow run nf-core/chipseq -profile docker --input design.csv --single_end --macs_gsize 2.7e9 --genome GRCh38 --save_trimmed --save_align_intermeds --narrow_peak --save_macs_pileup --outdir sulu_results --publish_dir_mode copy --email [email protected] 

But after running MACS2, I get the following error:

-[nf-core/chipseq] Pipeline completed with errors-
Error executing process > 'MACS2_QC'

Caused by:
  Process `MACS2_QC` terminated with an error exit status (1)

Command executed:

  plot_macs_qc.r \
      -i C1_TF_Ab_R1_peaks.narrowPeak,E1_IgG_control_R1_peaks.narrowPeak,G1_H3K27Ac_Ab_R1_peaks.narrowPeak \
      -s C1_TF_Ab_R1,E1_IgG_control_R1,G1_H3K27Ac_Ab_R1 \
      -o ./ \
      -p macs_peak
  
  plot_homer_annotatepeaks.r \
      -i C1_TF_Ab_R1_peaks.annotatePeaks.txt,E1_IgG_control_R1_peaks.annotatePeaks.txt,G1_H3K27Ac_Ab_R1_peaks.annotatePeaks.txt \
      -s C1_TF_Ab_R1,E1_IgG_control_R1,G1_H3K27Ac_Ab_R1 \
      -o ./ \
      -p macs_annotatePeaks
  
  cat peak_annotation_header.txt macs_annotatePeaks.summary.txt > macs_annotatePeaks.summary_mqc.tsv

Command exit status:
  1

Command output:
  (empty)

Command error:
  WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
  Error in read.table(PeakFiles[idx], sep = "\t", header = FALSE) : 
    no lines available in input
  Execution halted

Work dir:
  /home/subudhak/Documents/sulu/data/work/2d/b329b9a6038069c9e5b06322128cc9

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

[JoseEspinosa]

This could be an error related to the lack of called peaks on one of the samples no lines athinvailable in input.
I think this should be fixed in version 2.0.0 of the pipeline that was launched yesterday. Maybe worth a try and let us know if you keep finding the same issue.

[JoseEspinosa]

Will close it now as it has not had activity for long time