MACS2 steps did not carried out

[wook2014]

Description of the bug

I have run chipseq workflow and I can not find the MACS2 result. I have checked the log file and it seemed that the steps after deeptools did not executed.

Command used and terminal output

nextflow run ~/chipseq/nf-core-chipseq-2.0.0/workflow/ -profile singularity --input ~/chipseq/data/chipseq.csv --outdir ~/chipseq/res --fasta ~/GRCh38/GRCh38_genomic.fna --gff ~/GRCh38/GRCh38_genomic.gff --bowtie2_index ~/GRCh38/bowtie2 --gtf ~/GRCh38/GRCh38_genomic.gtf --read_length 150 --macs_gsize 2875000000 --aligner bowtie2

Relevant files

nextflow.log

System information

Nextflow version ( 22.10.6 build 5843 ) Hardware ( HPC ) Executor ( pbs ) Container engine: ( Singularity ) OS ( Linux 3.10.0-862.el7.x86_64 ) Version of nf-core/chipseq ( 2.0.0)

[lesidon]

I have the same issue as the author of the reported bug. wook2014, did you find the solution?

[wook2014]

I have the same issue as the author of the reported bug. wook2014, did you find the solution?

No, I run it in HPC and I don't have many permissions to debug it. I run it manually by different softwares myself later. but it still helps a lot, I don't need to set a lot of parameters in bwa and samtools to mapping.

[JoseEspinosa]

First, sorry for the late reply. I would say (although I would need to see the samplesheet to be sure) that the problem is related to the fact that a few processes (MACS2_CONSENSUS, HOMER_ANNOTATEPEAKS_CONSENSUS, ANNOTATE_BOOLEAN_PEAKS, SUBREAD_FEATURECOUNTS or DESEQ2_QC) are skipped when either replicates or multiple groups do not exist e.g. here.

[JoseEspinosa]

I will close this issue now for lack of activity, if you have any further questions please feel free to re-open it.