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  • Bowtie2 with no output

    Dear all:

    I recently run Bowtie/2.2.0 on Linux

    I used the command:

    bowtie2 -x myindex -u ./myfastqfile --un ./161.fq -S 161_RNA.sam

    I wants to store the unmapped reads in 161.fq and I got this error message:

    Error: Encountered internal Bowtie 2 exception (#1)
    Command: /opt/software/bowtie/2.2.0--GCC-4.4.5/bin/bowtie2-align --wrapper basic-0 -x rRNA_56 -U ./myfile --passthrough

    Has anyone seen this before?

    I am sure that the bowtie2 is run successfully and .sam file is generated, but no output file for unmapped reads, which I specified as 161.fq. Should I generate the empty file before I run this or it will automatically generate a file?

    Thanks very much!

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