Alice Rossi
04/02/2024, 11:11 AM#!/bin/sh
export NXF_SINGULARITY_CACHEDIR="/camp/home/rossia/working/alice_r/nfcache/sing_images"
## LOAD REQUIRED MODULES
ml purge
ml Nextflow/23.10.0
ml Singularity/3.6.4
ml Graphviz
## UPDATE PIPELINE
nextflow pull nf-core/chipseq
## RUN PIPELINE
nextflow run nf-core/chipseq \
-resume \
-r dev \
-profile crick \
--input samplesheet.csv \
--read_length 200 \
--outdir results_narrow \
--genome mm10 \
--aligner bowtie2 \
--narrow_peak true \
--skip_consensus_peak true \
But I get this error:
-[nf-core/chipseq] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_CHIPSEQ:CHIPSEQ:PHANTOMPEAKQUALTOOLS (aNSC_p300_REP1)'
Caused by:
Process `NFCORE_CHIPSEQ:CHIPSEQ:PHANTOMPEAKQUALTOOLS (aNSC_p300_REP1)` terminated with an error exit status (1)
Command executed:
RUN_SPP=`which run_spp.R`
Rscript --max-ppsize=500000 -e "library(caTools); source(\"$RUN_SPP\")" -c="aNSC_p300_REP1.mLb.clN.sorted.bam" -savp="aNSC_p300_REP1.spp.pdf" -savd="aNSC_p300_REP1.spp.Rdata" -out="aNSC_p300_REP1.spp.out" -p=6
cat <<-END_VERSIONS > versions.yml
"NFCORE_CHIPSEQ:CHIPSEQ:PHANTOMPEAKQUALTOOLS":
phantompeakqualtools: 1.2.2
END_VERSIONS
Command exit status:
1
Command output:
################
ChIP data: aNSC_p300_REP1.mLb.clN.sorted.bam
Control data: NA
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift NA
exclusion(min): 10
exclusion(max): NaN
num parallel nodes: 6
FDR threshold: 0.01
NumPeaks Threshold: NA
Output Directory: .
narrowPeak output file name: NA
regionPeak output file name: NA
Rdata filename: aNSC_p300_REP1.spp.Rdata
plot pdf filename: aNSC_p300_REP1.spp.pdf
result filename: aNSC_p300_REP1.spp.out
Overwrite files?: FALSE
Reading ChIP tagAlign/BAM file aNSC_p300_REP1.mLb.clN.sorted.bam
opened /tmp/RtmpzIL53s/aNSC_p300_REP1.mLb.clN.sorted.tagAlign2f4bdff2a6
done. read 0 fragments
Command error:
WARNING: Skipping mount /flask/apps/eb/software/Singularity/3.6.4/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
Loading required package: Rcpp
[E::hts_open_format] Failed to open file "/tmp/RtmpzIL53s/aNSC_p300_REP1.mLb.clN.sorted.bam2f4bdff2a6" : Permission denied
samtools view: failed to open "/tmp/RtmpzIL53s/aNSC_p300_REP1.mLb.clN.sorted.bam2f4bdff2a6" for reading: Permission denied
Error in read.table(bam2align.filename, nrows = 500) :
no lines available in input
Calls: source ... withVisible -> eval -> eval -> read.align -> read.table
Execution halted
Work dir:
/nemo/lab/guillemotf/working/alice_r/nfcache/Martinyoga_2013/work/3c/2e272f275a564e14f7adef86acd0d2
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '.nextflow.log' file for details
Note, I'm using the -r dev version as the pipeline was getting stuck while marking duplicates with the latest release.
Can anyone please help me solving this?
Thank you in advance!