No Space left on device error
Shashankti opened this issue · comments
Shashank Tiwari commented
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
Shashank Tiwari commented
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