Question: fastqc fails only in my directory - not my coworkers
0
gravatar for bioinfo_cat
29 days ago by
bioinfo_cat0 wrote:

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)
rna-seq assembly • 119 views
ADD COMMENTlink written 29 days ago by bioinfo_cat0

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.

ADD REPLYlink written 29 days ago by genomax91k

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!

ADD REPLYlink written 29 days ago by bioinfo_cat0
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