FastQC on HPC system doesn't work

Question

[Sbrillo]

Hi!

I'm trying to run fastQC on an HPC system but i'm having this error:

It seems that something is wrong with java.

Started analysis of raw_f.fastq

Approx 5% complete for raw_f.fastq

Approx 10% complete for raw_f.fastq

Approx 15% complete for raw_f.fastq

Approx 20% complete for raw_f.fastq

Approx 25% complete for raw_f.fastq

Approx 30% complete for raw_f.fastq

Approx 35% complete for raw_f.fastq

Approx 40% complete for raw_f.fastq

Approx 45% complete for raw_f.fastq

Approx 50% complete for raw_f.fastq

Approx 55% complete for raw_f.fastq

Approx 60% complete for raw_f.fastq

Approx 65% complete for raw_f.fastq

Approx 70% complete for raw_f.fastq

ecc...

javax.imageio.IIOException: Can't create cache file!
    at javax.imageio.ImageIO.createImageInputStream(ImageIO.java:361)
    at javax.imageio.ImageIO.read(ImageIO.java:1397)
    at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:379)
    at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:303)
    at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
    at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:185)
    at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
    at java.lang.Thread.run(Thread.java:745)
Caused by: java.nio.file.AccessDeniedException: /tmp/imageio6327552574161602354.tmp
    at sun.nio.fs.UnixException.translateToIOException(UnixException.java:84)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
    at sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:214)
    at java.nio.file.Files.newByteChannel(Files.java:361)
    at java.nio.file.Files.createFile(Files.java:632)
    at java.nio.file.TempFileHelper.create(TempFileHelper.java:138)
    at java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:161)
    at java.nio.file.Files.createTempFile(Files.java:897)
    at javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
    at com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)

I installed the latest fastQC version inside the HPC on my personal conda environment but I'm still getting the same error. Fastqc creates the report.txt file but the HTML file is missed and i can't see any plot in the zipped file generated.

Any suggestion?

Answer 1

[Pierre Lindenbaum]

your problem is here:

Caused by: java.nio.file.AccessDeniedException: /tmp/imageio6327552574161602354.tmp

use option -d

   -d --dir         Selects a directory to be used for temporary files written when
                    generating report images. Defaults to system temp directory if
                    not specified.

[Sbrillo]

Amazing!

Problem solved!