xargs can be used to run iqtree bootsraps, each bootstrap as individual process in a cluster environment

[Vigneshwaran Renganathan]

I have installed a non MPI version of iqtree in KNL environment, I couldn't able to install a MPI version since my compiler was not recognized by cmake , I used the below command to replicate the bootstrap process 64 times using xargs system command which helped me out change the output filename and input filename stored as a list in a file.

#!/bin/sh

#PBS -l select=1

#PBS -l accelerator_type=Intel

#PBS -l walltime=24:00:00

#PBS -l place=scatter

#PBS -S /bin/sh@sdb -V

. /opt/modules/default/init/sh

cd /XXX/iqtree/bin

aprun -j 1 -n 64 -N 64 xargs --arg-file=list.txt -P 64 -I AA iqtree -s protein_AA.msa -m JTT+G4 -bo 2 -pre boots_AA

Note ( list.txt: contains the number list from 1..64 separated by new line)

input file was copied 64 times using the same xargs and seq command (seq 64 | xargs -I AA  file.msa file_AA.msa )

Thanks

Vignesh

[Minh Bui]

Cool, thanks for the information!

Minh

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