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Old 10-12-2014, 09:33 PM   #5
Nanu
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Location: New Delhi

Join Date: Sep 2014
Posts: 30
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When I use the command reformat.sh in bbtools package I am getting the following error::
java -ea -Xmx200m -cp /home/himanshu/Downloads/me2/bbmap/current/ jgi.ReformatReads -in=reads.fna qfin=reads.qual out=reads.fasta
Executing jgi.ReformatReads [-in=reads.fna, qfin=reads.qual, out=reads.fasta]

Input is being processed as unpaired
Exception in thread "Thread-1" java.lang.AssertionError
at stream.FastaQualReadInputStream3.makeRead(FastaQualReadInputStream3.java:257)
at stream.FastaQualReadInputStream3.toReadList(FastaQualReadInputStream3.java:147)
at stream.FastaQualReadInputStream3.toReads(FastaQualReadInputStream3.java:113)
at stream.FastaQualReadInputStream3.fillBuffer(FastaQualReadInputStream3.java:97)
at stream.FastaQualReadInputStream3.hasMore(FastaQualReadInputStream3.java:56)
at stream.ConcurrentGenericReadInputStream$ReadThread.readLists(ConcurrentGenericReadInputStream.java:745)
at stream.ConcurrentGenericReadInputStream$ReadThread.run(ConcurrentGenericReadInputStream.java:737)

Please help me
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