problem with Abyss assembler - cma-permission-denied

Question

[macielrodriguez2]

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

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

[Joe]

How did you install Abyss?

[macielrodriguez2]

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

Answer 1

[JC]

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

[macielrodriguez2]

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