No Space left on device error

[Shashankti]

Description of the bug

While running the PHANTOMPEAKQUALTOOLS part of the pipeline, I get the error about No space left on device. I am running the pipeline on the scratch directory of an HPC. I tried to specify a different folder to store the temporary files to overcome the error, but the issue persists.

Here is the detailed output:

WARNING: Skipping mount /local/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in $
Loading required package: Rcpp
################
ChIP data: SW5_Input.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: SW5_Input.spp.Rdata
plot pdf filename: SW5_Input.spp.pdf
result filename: SW5_Input.spp.out
Overwrite files?: FALSE

Reading ChIP tagAlign/BAM file SW5_Input.mLb.clN.sorted.bam
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
awk: cmd. line:1: (FILENAME=- FNR=159) fatal: print to "standard output" failed (No space left on device)
Error converting BAM to tagalign file: /tmp/RtmprOqx4p/SW5_Input.mLb.clN.sorted.bam276873b65a
Warning message:
In file.append(to[okay], from[okay]) : write error during file append

Command used and terminal output

nextflow run nf-core/chip-seq --outdir ./ --genome GRCh38 -profile singularity --macs_gsize 2701495761 --input samplesheet_se.csv --narrow_peak

ERROR ~ Error executing process > 'NFCORE_CHIPSEQ:CHIPSEQ:PHANTOMPEAKQUALTOOLS (SW5_Input)'

Caused by:
  Process `NFCORE_CHIPSEQ:CHIPSEQ:PHANTOMPEAKQUALTOOLS (SW5_Input)` terminated with an error exit status (1)

Command executed:

  RUN_SPP=`which run_spp.R`

  Rscript  -e "library(caTools); source(\"$RUN_SPP\")" -c="SW5_Input.mLb.clN.sorted.bam" -savp="SW5_Input.spp.pdf" -savd="SW5_Input.spp.Rdata" -out="SW5_Input.spp.out" -p=6

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_CHIPSEQ:CHIPSEQ:PHANTOMPEAKQUALTOOLS":
      phantompeakqualtools: 1.2.2
  END_VERSIONS

Command exit status:
  1

Relevant files

No response

System information

Nextflow version 23.04.2.5870 Running on GWDG HPC -profile Singularity nf-core/chipseq_2.0.0

[Shashankti]

Fixed the issue by providing a custom config file as specified here.

singularity {
  enabled = true
  autoMounts = true
  runOptions = '-B /scratch1/users/shashank.tiwari/tmp/'
}

env {
  TMPDIR="/scratch1/users/shashank.tiwari/tmp/"
}

The issue was due to not using quotes when defining $TMPDIR. Thank you to the nf-core slack channel for the help

[fperezcobos]

Hi! I'm having exactly the same problem as Shashankti, but I'm running nextflow with the -profile docker option. I tried to run nextflox with a config file just including:

env { TMPDIR = "/path/to/tmp/" }

but it didn't work. I suppose I have to set some docker variables as well, but I'm not an expert and I don't know how to do it.

Can someone help me to fix the problem please? Thank you very much!

[Shashankti]

Were you able to fix the issue @fperezcobos ? You can try running with singularity or change the options for the docker profile, similar to what I had to do for the singularity profile