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  • Bowtie2 refusing to parallelize job

    Hi guys, today I had a problem that I never heard of before.
    I am aligning some transcriptome samples agains different references (mammals).
    At first I tried to run these alignments in a Mac pro (2012), running Linux Mint 18.2 (kernel 4.10.0-33-generic), and bowtie2 (2.2.6) piping the output to samtools (1.5) for converting to bam on the fly.
    I did the references normally (bowtie2-build etc etc...) for all the ten mammals downloaded from NCBI (https://www.ncbi.nlm.nih.gov/genome/browse/) using the same Linux machine.
    I wrote the scripts in order to use all the cores available. At first, it was running correctly, using as many cores as I told to, but today it was using ony one... I did some tests and I realized that this only happens with a specific reference, not with others.
    Thinking that perhaps it was a problem with the machine, I shared the data through NFS to a Centos 7 machine (kernel 3.10.0-514.16.1.el7.x86_64) and bowtie2 (2.2.9) piping the output to samtools (1.3.1) for converting to bam on the fly. Same problem here...

    Now I am rebuilding the referenses using this second machine.

    Basically bowtie is refusing to parallelize.

    Any clue?

    Thank you!

  • #2
    Solved

    Guys, problem solved when I rebuild the references. I do not know what caused this, but now is everything ok with both systems.

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