Error in ConsensusPeakSet process #134
Description
Hi there,
I am running the pipeline on some yeast ChIP-seq data and it is giving an error in the ConsensusPeakSet. I am running it in local and with singularity:
nextflow run nf-core/chipseq --input design.csv --genome 'R64-1-1' -profile singularity -r 1.1.0 --save_reference --max_memory '30.GB' --max_cpus 5 -resume
The pipeline gives the following error:
Error executing process > 'ConsensusPeakSet'
Caused by:
Process `ConsensusPeakSet` terminated with an error exit status (1)
Command executed:
sort -k1,1 -k2,2n ab_0_R1_peaks.broadPeak ab_0_R2_peaks.broadPeak ab_0_R3_peaks.broadPeak ab_5_R1_peaks.broadPeak ab_5_R2_peaks.broadPeak ab_5_R3_peaks.broadPeak \
| mergeBed -c 2,3,4,5,6,7,8,9 -o collapse,collapse,collapse,collapse,collapse,collapse,collapse,collapse > ab.consensus_peaks.txt
macs2_merged_expand.py ab.consensus_peaks.txt \
ab_0_R1,ab_0_R2,ab_0_R3,ab_5_R1,ab_5_R2,ab_5_R3 \
ab.consensus_peaks.boolean.txt \
--min_replicates 1 \
awk -v FS=' ' -v OFS=' ' 'FNR > 1 { print $1, $2, $3, $4, "0", "+" }' ab.consensus_peaks.boolean.txt > ab.consensus_peaks.bed
echo -e "GeneIDprojectChrranscStarton_Endess_yStrand" > ab.consensus_peaks.saf
awk -v FS=' ' -v OFS=' ' 'FNR > 1 { print $4, $1, $2, $3, "+" }' ab.consensus_peaks.boolean.txt >> ab.consensus_peaks.saf
plot_peak_intersect.r -i ab.consensus_peaks.boolean.intersect.txt -o ab.consensus_peaks.boolean.intersect.plot.pdf
find * -type f -name "ab.consensus_peaks.bed" -exec echo -e "bwa/mergedLibrary/macs/broadPeak/consensus/ab/"{}"\t0,0,0" \; > ab.consensus_peaks.bed.igv.txt
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Not mounting requested bind point (already mounted in container): /home/platorre
Error: package or namespace load failed for ‘UpSetR’:
.onLoad failed in loadNamespace() for 'pillar', details:
call: loadNamespace(name)
error: there is no package called ‘crayon’
Execution halted
Any idea about why is this behaviour happening?
Thanks,
Pablo