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=$CLASSPATH://path/to/jbzip2-0.9.1.jar ) but it still doesn't work.
The strange thing here is that even though i get this error message the program keeps running and gives me results at the end.
This is the command i run
fastqc /path/to/data/*fastq.bz2 -o QC/ -t 4 -q &
Any ideas??
java.io.IOException: Unexpected end of stream
at org.itadaki.bzip2.BitInputStream.readBits(BitInputStream.java:133)
at org.itadaki.bzip2.BZip2HuffmanStageDecoder.nextSymbol(BZip2HuffmanStageDecoder.java:159)
at org.itadaki.bzip2.BZip2BlockDecompressor.decodeHuffmanData(BZip2BlockDecompressor.java:268)
at org.itadaki.bzip2.BZip2BlockDecompressor.<init>(BZip2BlockDecompressor.java:474)
at org.itadaki.bzip2.BZip2InputStream.initialiseNextBlock(BZip2InputStream.java:231)
at org.itadaki.bzip2.BZip2InputStream.read(BZip2InputStream.java:129)
at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:282)
at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:324)
at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:176)
at java.io.InputStreamReader.read(InputStreamReader.java:184)
at java.io.BufferedReader.fill(BufferedReader.java:153)
at java.io.BufferedReader.readLine(BufferedReader.java:316)
at java.io.BufferedReader.readLine(BufferedReader.java:379)
at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:145)
at uk.ac.babraham.FastQC.Sequence.FastQFile.next(FastQFile.java:105)
at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:76)
at java.lang.Thread.run(Thread.java:701)
I'm trying to run fastqc on my samples and for some samples I get the error below. From what I understand there is a problem with the jbzip2 library. I downloaded the library separately and added it to my CLASSPATH (export CLASSPATH=$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)
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