NFCORE_HIC:HIC:FASTQC error: fastqc tmp dir on HPC

[PaolaD]

Description of the bug

Hello! I'm trying to run the pipeline in a HPC cluster but keep getting the same error

It seems to me like the problem is fastqc, choosing /tmp as default tmpdir.
Is there any way of setting fastqc option --dir so that I can select my tmpdir? Or am I doing something wrong?

Best
Paola

Command used and terminal output

Command used:

export NXF_TEMP='/scratch/XX/nf-hic/'
export TMP='/scratch/XX/nf-hic/'
export TMPDIR='/scratch/XX/nf-hic/'
export SINGULARITY_TMPDIR='/scratch/XX/singularity_folders/tmp/'
export SINGULARITY_LOCALCHACHEDIR='/scratch/XX/singularity_folders/cache'

nextflow run nf-core/hic -profile singularity -r 2.1.0 --input /home/XX/nfcore_pipelines/hic/12dic23/samplesheet.csv --outdir /home/XX/nfcore_pipelines/hic/12dic23/ --digestion "dpnii" --fasta /home/shared/genomics_data/references/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa --bwt2_index /home/shared/genomics_data/references/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/ -c /home/XX/nfcore_pipelines/hic/12dic23/eos.config 

#_________ TERMINAL OUTPUT  ____#

ERROR ~ Error executing process > 'NFCORE_HIC:HIC:FASTQC (18-5390)'

Caused by:
 Missing output file(s) `*.html` expected by process `NFCORE_HIC:HIC:FASTQC (18-5390)`

Command executed:

 printf "%s %s\n" mpimg_L16912-1_18-5390-1_S16_R1_001.fastq.gz 18-5390_1.gz mpimg_L16912-1_18-5390-1_S16_R2_001.fastq.gz 18-5390_2.gz | while read old_name new_nam
e; do
      [ -f "${new_name}" ] || ln -s $old_name $new_name
  done
  fastqc  --threads 2 18-5390_1.gz 18-5390_2.gz
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_HIC:HIC:FASTQC":
      fastqc: $( fastqc --version | sed -e "s/FastQC v//g" )
  END_VERSIONS

Command exit status:
  0

Command output:
  Analysis complete for 18-5390_2.gz
  Analysis complete for 18-5390_1.gz

Command error:
       at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:357)
        ... 6 more
  Failed to process file 18-5390_2.gz
  javax.imageio.IIOException: Can't create cache file!
        at java.desktop/javax.imageio.ImageIO.createImageOutputStream(ImageIO.java:423)
        at java.desktop/javax.imageio.ImageIO.write(ImageIO.java:1589)
        at uk.ac.babraham.FastQC.Modules.AbstractQCModule.writeDefaultImage(AbstractQCModule.java:72)
        at uk.ac.babraham.FastQC.Modules.PerBaseQualityScores.makeReport(PerBaseQualityScores.java:199)
        at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:131)
        at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:185)
        at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
        at java.base/java.lang.Thread.run(Thread.java:834)
  Caused by: java.nio.file.FileSystemException: /tmp/imageio18039410187246626006.tmp: Read-only file system
        at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
        at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
        at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:116)
        at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:215)
        at java.base/java.nio.file.Files.newByteChannel(Files.java:370)
        at java.base/java.nio.file.Files.createFile(Files.java:647)
        at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:137)
        at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:160)
        at java.base/java.nio.file.Files.createTempFile(Files.java:912)
        at java.desktop/javax.imageio.stream.FileCacheImageOutputStream.<init>(FileCacheImageOutputStream.java:88)
        at java.desktop/com.sun.imageio.spi.OutputStreamImageOutputStreamSpi.createOutputStreamInstance(OutputStreamImageOutputStreamSpi.java:68)
        at java.desktop/javax.imageio.ImageIO.createImageOutputStream(ImageIO.java:419)
        ... 7 more

Relevant files

No response

System information

Nextflow version: 23.10.0
Hardware: HPC
Executor: slurm
Container engine: Singularity 3.10.4
OS: Rocky Linux 8.7
Version of nf-core/hic: 2.1.0

[amulyabaral]

Hi, I assume you've managed to fix this since you closed the issue. I'm wondering if you can share how you fixed the bug? I am stuck on it too.

[PaolaD]

Hi @amulyabaral
Just create your own config file and add:

process {
  withName: "NFCORE_HIC:HIC:FASTQC" {
       ext.args = "-d /your_path/to/tmp_folder"
  }
}

For me it worked :)