----------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~\
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/chipseq v1.2.2
----------------------------------------------------

Run Name: disturbed_mahavira

####################################################
## nf-core/chipseq execution completed unsuccessfully! ##
####################################################
The exit status of the task that caused the workflow execution to fail was: 1.
The full error message was:

Error executing process > 'PHANTOMPEAKQUALTOOLS (Ss2_Input_R1)'

Caused by:
  Process `PHANTOMPEAKQUALTOOLS (Ss2_Input_R1)` terminated with an error exit status (1)

Command executed:

  RUN_SPP=`which run_spp.R`
  Rscript -e "library(caTools); source(\"$RUN_SPP\")" -c="Ss2_Input_R1.mLb.clN.sorted.bam" -savp="Ss2_Input_R1.spp.pdf" -savd="Ss2_Input_R1.spp.Rdata" -out="Ss2_Input_R1.spp.out" -p=6
  cp spp_correlation_header.txt Ss2_Input_R1_spp_correlation_mqc.tsv
  Rscript -e "load('Ss2_Input_R1.spp.Rdata'); write.table(crosscorr\$cross.correlation, file=\"Ss2_Input_R1_spp_correlation_mqc.tsv\", sep=",", quote=FALSE, row.names=FALSE, col.names=FALSE,append=TRUE)"
  
  awk -v OFS='	' '{print "Ss2_Input_R1", $9}' Ss2_Input_R1.spp.out | cat spp_nsc_header.txt - > Ss2_Input_R1_spp_nsc_mqc.tsv
  awk -v OFS='	' '{print "Ss2_Input_R1", $10}' Ss2_Input_R1.spp.out | cat spp_rsc_header.txt - > Ss2_Input_R1_spp_rsc_mqc.tsv

Command exit status:
  1

Command output:
  ################
  ChIP data: Ss2_Input_R1.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: Ss2_Input_R1.spp.Rdata 
  plot pdf filename: Ss2_Input_R1.spp.pdf 
  result filename: Ss2_Input_R1.spp.out 
  Overwrite files?: FALSE
  
  Reading ChIP tagAlign/BAM file Ss2_Input_R1.mLb.clN.sorted.bam 
  opened /tmp/RtmpObgHyb/Ss2_Input_R1.mLb.clN.sorted.tagAlign1f5901cb66
  done. read 2142350 fragments

Command error:
  Loading required package: Rcpp
  Error: protect(): protection stack overflow
  Execution halted

Work dir:
  /external1/PD/nfcore_PD/work/14/16ecaf4e5f071170a3a075c8c46228

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`



The workflow was completed at 2021-07-15T16:24:16.602042+01:00 (duration: 4h 21m 40s)

The command used to launch the workflow was as follows:

  nextflow run nf-core/chipseq --input design_pe.csv --genome AtlanticSalmon -profile docker -c config_Ss --macs_gsize 2700000000 --narrow_peak True --clip_r1 20 --clip_r2 20 --three_prime_clip_r1 10 --three_prime_clip_r2 10 --max_cpus 16



Pipeline Configuration:
-----------------------
 - Run Name: disturbed_mahavira
 - Data Type: Paired-End
 - Design File: design_pe.csv
 - Genome: AtlanticSalmon
 - Fasta File: /external1/PD/genomes/ensembl/Salmo_salar.ICSASG_v2.dna_sm.toplevel.fa
 - GTF File: /external1/PD/genomes/ensembl/Salmo_salar.ICSASG_v2.104.gtf
 - BWA Index: /external1/PD/genomes/ensembl/Salmo_salar.ICSASG_v2.dna_sm.toplevel.fa
 - MACS2 Genome Size: 2700000000
 - Min Consensus Reps: 1
 - MACS2 Narrow Peaks: Yes
 - Trim R1: 20 bp
 - Trim R2: 20 bp
 - Trim 3' R1: 10 bp
 - Trim 3' R2: 10 bp
 - NextSeq Trim: 0 bp
 - Fingerprint Bins: 500000
 - Save Genome Index: No
 - Max Resources: 128 GB memory, 16 cpus, 10d time per job
 - Container: docker - nfcore/chipseq:1.2.2
 - Output Dir: ./results
 - Launch Dir: /external1/PD/nfcore_PD
 - Working Dir: /external1/PD/nfcore_PD/work
 - Script Dir: /root/.nextflow/assets/nf-core/chipseq
 - User: root
 - Config Profile: docker
 - Date Started: 2021-07-15T12:02:36.359610+01:00
 - Date Completed: 2021-07-15T16:24:16.602042+01:00
 - Pipeline script file path: /root/.nextflow/assets/nf-core/chipseq/main.nf
 - Pipeline script hash ID: 39c073c68caf34f6f725e82907fff2bd
 - Pipeline repository Git URL: https://github.com/nf-core/chipseq
 - Pipeline repository Git Commit: 6924b669422215f9021144b251e83fc9929be1fe
 - Pipeline Git branch/tag: master
 - Nextflow Version: 21.04.2
 - Nextflow Build: 5558
 - Nextflow Compile Timestamp: 12-07-2021 07:54 UTC

--
nf-core/chipseq
https://github.com/nf-core/chipseq