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problem with Abyss assembler - cma-permission-denied
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11 months ago

Hi everyone! I'm new in the process of assembling a genome so, please, forgive my mistakes.

I was trying to find the optimal k parameter with the Abyss assembler. For that I followed the manual and wrote this bash script:

    #!/bin/bash

for k in `seq 20 8 90`; do
        mkdir k$k
        abyss-pe np=4 -C k$k k=$k name=cloroplast lib='pea' \
        pea='../../../ZM1/ZM1_R1.fastq ../../../ZM1/ZM1_R2.fastq'
done
abyss-fac k*/cloroplast-contigs.fa

enter image description here Can someone tell me what did I do wrong? Thank you in advance :)

assembly • 220 views
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How did you install Abyss?

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I installed it in an Anaconda environment, with this conda installers: https://anaconda.org/bioconda/abyss

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11 months ago
JC 7.9k
Mexico

Your bash script is fine, but your MPI installation is restricting memory access as the WARNING correctly describes.

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Thank you for your answer :) Is there a way to change this MPI installation that is restrincting memory access?

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