Error using fastqc

[seqador]

I get 8 sra files that was converted to fastq. The first fastq file was successfully analysed with fastqc. But after that all files after 100% get this error:


Approx 90% complete for SRR1503281_1.fastq
Approx 95% complete for SRR1503281_1.fastq
Approx 100% complete for SRR1503281_1.fastq
Exception in thread "Thread-1" java.lang.NullPointerException
at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:141)
at uk.ac.babraham.FastQC.Sequence.FastQFile.next(FastQFile.java:105)
at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:76)
at java.lang.Thread.run(Thread.java:744)




could someone know why this is happening? Thank you.

[Cytosine]

Exception in thread "Thread-1" java.lang.NullPointerException
at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:141)
at uk.ac.babraham.FastQC.Sequence.FastQFile.next(FastQFile.java:105)
at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:76)

This makes me think that FastQC cannot go to the next file simply because it can't find it in memory. Do you call fastqc on all files at once or do it 1 by 1?

Try 1 by 1 if you're feeding all at once to fastqc now.

If that is not the case, maybe try redownloading the sra files and extracting them again.

[seqador]

I try your two suggestions, and try 1 by 1 solve the problem. But i wish to do all files with a single command.

[GenoMax]

You need to run FastQC in non-interactive mode (on command line) to overcome running out of memory.

You could simply do

$ /path_to_/fastqc sequence_file*.fastq

This should produce a self contained folder for each sequence file with all the result you normally see via GUI.