Nextflow chipseq error: Prevent PHANTOMPEAKQUALTOOLS from running out of disk space

Question

[gdeniz]

Hi,

I was hoping someone could help me understand the reason for the error message below. I ran the nextflow pipeline for chipseq (https://nf-co.re/chipseq/) using default settings. The message suggests not enough disk space but at least the output directory has multiple TBs of free space and thus should not be the issue. I am wondering whether "." could possible referring to a different location and if so how one could change the location of this directory? Thanks for any insights.

Error executing process > 'PHANTOMPEAKQUALTOOLS (F3_22_BirA_R2)'

Caused by:
  Process `PHANTOMPEAKQUALTOOLS (F3_22_BirA_R2)` terminated with an error exit status (1)

Command executed:

  RUN_SPP=`which run_spp.R`
  Rscript -e "library(caTools); source(\"$RUN_SPP\")" -c="F3_22_BirA_R2.mLb.clN.sorted.bam" -savp="F3_22_BirA_R2.spp.pdf" -savd="F3_22_BirA_R2.spp.Rdata" -out="F3_22_BirA_R2.spp.out" -p=6
  cp spp_correlation_header.txt F3_22_BirA_R2_spp_correlation_mqc.tsv
  Rscript -e "load('F3_22_BirA_R2.spp.Rdata'); write.table(crosscorr\$cross.correlation, file=\"F3_22_BirA_R2_spp_correlation_mqc.tsv\", sep=",", quote=FALSE, row.names=FALSE, col.names=FALSE,append=TRUE)"

  awk -v OFS='  ' '{print "F3_22_BirA_R2", $9}' F3_22_BirA_R2.spp.out | cat spp_nsc_header.txt - > F3_22_BirA_R2_spp_nsc_mqc.tsv
  awk -v OFS='  ' '{print "F3_22_BirA_R2", $10}' F3_22_BirA_R2.spp.out | cat spp_rsc_header.txt - > F3_22_BirA_R2_spp_rsc_mqc.tsv

Command exit status:
  1

Command output:
  ################
  ChIP data: F3_22_BirA_R2.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: F3_22_BirA_R2.spp.Rdata 
  plot pdf filename: F3_22_BirA_R2.spp.pdf 
  result filename: F3_22_BirA_R2.spp.out 
  Overwrite files?: FALSE

  Reading ChIP tagAlign/BAM file F3_22_BirA_R2.mLb.clN.sorted.bam 

Command error:
  Warning message:
  package ‘caTools’ was built under R version 3.6.3 
  Loading required package: Rcpp
  awk: cmd. line:1: (FILENAME=- FNR=20697793) fatal: print to "standard output" failed: No space left on device
  Error converting BAM to tagalign file: /tmp/RtmpmKSnv5/F3_22_BirA_R2.mLb.clN.sorted.bamdedb1b3a0bb7
  Warning message:
  package ‘Rcpp’ was built under R version 3.6.3 

Work dir:
  /blellochlab/data1/deniz/dgrb010208/work/78/fcf62876fd06eec0311e49b00a3afc

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

[Sam]

Maybe you ran out of space in the tmp space? Does setting NXF_WORK or NXF_TEMP to current directory help?

[gdeniz]

Thanks for your suggestion, Sam. I added:

env {
  NXF_WORK = "/lab/data1/deniz/dgrb010208/temp"
  NXF_TEMP = "/lab/data1/deniz/dgrb010208/temp"
}

To the custom config file and fed it in via the -c option but keep getting the same error. Any other ideas?

[Sam]

Maybe this is relevant??

https://groups.google.com/g/nextflow/c/XxfaS26RCh4/m/iipzlU7eAAAJ

Basically, instead of settingenv {}, do

workDir = "/lab/data1/deniz/dgrb010208/temp"