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  • laramaktub
    Junior Member
    • Aug 2017
    • 1
    #1

    Bowtie2 gets stuck

    Hi!

    i am trying to run this command on bowtie 2.3.2 in Ubuntu 16.04

    time bowtie2 -x bowtie2/index/myindex -1 bowtie2/hmgz/reads_left_hmgz.fq -2 bowtie2/hmgz/reads_right_hmgz.fq -U bowtie2/hmgz/reads_left_lonely.fq -S bowtie2/aligned_reads.sam -p 16 --maxins 500 --minins 0 --end-to-end --sensitive 2

    It just gets stuck and does nothing (also it gives no error). Trying this same command with bowtie2 2.0.2 it works without any problem.

    Someone is experiencing a similar issue?

    Thanks!


    Lara
    Last edited by laramaktub; 08-02-2017, 08:00 AM.
    Tags: None
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