I have not been able to run fastqc on any files that were transferred directly from my coworkers directory to mine. I transferred the whole folder from theirs to my directory, I do not have 'w' or 'x' permissions in their directory but all of the files in mine do, I checked.
They were able to successfully run fastqc and multiqc on these files in their directory's but for some reason I can't run it in my directory. It only produces a fastqc.zip file that is empty, no fastqc.html.
I've seen this posted in other forums and here before but my output is a little different than all of the other posts and so I am wondering if this is a problem with Java?
Does anyone have any advice or ideas about what is wrong?
Thank you!
fastqc -o qc_logs -t 8 SB1.fastq.gz
> Started analysis of SB1.fastq.gz
Approx 5% complete for SB1.fastq.gz
Approx 10% complete for SB1.fastq.gz
Approx 15% complete for SB1.fastq.gz
Approx 20% complete for SB1.fastq.gz
Approx 25% complete for SB1.fastq.gz
Approx 30% complete for SB1.fastq.gz
Approx 35% complete for SB1.fastq.gz
Approx 40% complete for SB1.fastq.gz
Approx 45% complete for SB1.fastq.gz
Approx 50% complete for SB1.fastq.gz
Approx 55% complete for SB1.fastq.gz
Approx 60% complete for SB1.fastq.gz
Approx 65% complete for SB1.fastq.gz
Approx 70% complete for SB1.fastq.gz
Approx 75% complete for SB1.fastq.gz
Approx 80% complete for SB1.fastq.gz
Approx 85% complete for SB1.fastq.gz
Approx 90% complete for SB1.fastq.gz
Approx 95% complete for SB1.fastq.gz
Analysis complete for SB1.fastq.gz Failed to process file SB1.fastq.gz
java.lang.IllegalArgumentException: image == null!
at javax.imageio.ImageTypeSpecifier.createFromRenderedImage(ImageTypeSpecifier.java:925)
at javax.imageio.ImageIO.getWriter(ImageIO.java:1592)
at javax.imageio.ImageIO.write(ImageIO.java:1578)
at uk.ac.babraham.FastQC.Utilities.ImageToBase64.imageToBase64(ImageToBase64.java:38)
at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:380)
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)
Are you running into this issue on the same server or a different server?
See the solution posted in this thread. I suggest you download a copy of
fastqc
in your own directory and give it a try.That would make a lot of sense - I am contacting server support to ask to have a reinstallation done since I don't have the permissions to. Thank you!