Hello! I'm trying to run the chipseq pipeline on 6...
# chipseq
a
Hello! I'm trying to run the chipseq pipeline on 6 samples, with the following script
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#!/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:
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-[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!