fastQC bzip2 error

[Matina]

Hi everyone,

I'm trying to run fastqc on my samples and for some samples I get the error below. From what I understand there is a problem with the jbzip2 library. I downloaded the library separately and added it to my CLASSPATH (export CLASSPATH=$CLASSPATH://path/to/jbzip2-0.9.1.jar ) but it still doesn't work.

The strange thing here is that even though i get this error message the program keeps running and gives me results at the end.

This is the command i run

fastqc /path/to/data/*fastq.bz2 -o QC/ -t 4 -q &

Any ideas??

java.io.IOException: Unexpected end of stream
at org.itadaki.bzip2.BitInputStream.readBits(BitInputStream.java:133)
at org.itadaki.bzip2.BZip2HuffmanStageDecoder.nextSymbol(BZip2HuffmanStageDecoder.java:159)
at org.itadaki.bzip2.BZip2BlockDecompressor.decodeHuffmanData(BZip2BlockDecompressor.java:268)
at org.itadaki.bzip2.BZip2BlockDecompressor.<init>(BZip2BlockDecompressor.java:474)
at org.itadaki.bzip2.BZip2InputStream.initialiseNextBlock(BZip2InputStream.java:231)
at org.itadaki.bzip2.BZip2InputStream.read(BZip2InputStream.java:129)
at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:282)
at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:324)
at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:176)
at java.io.InputStreamReader.read(InputStreamReader.java:184)
at java.io.BufferedReader.fill(BufferedReader.java:153)
at java.io.BufferedReader.readLine(BufferedReader.java:316)
at java.io.BufferedReader.readLine(BufferedReader.java:379)
at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:145)
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:701)

[TiborNagy]

Adding jar files to the CLASSPATH won't help, because the launch script (fastqc) overwrite it. You can edit it inside fastqc. But my guess is the problem not this library, but the input file. Can you decompress it with command line utilities?