Error while running hal2maf

[josh3397]

Hello,

I am running hal2maf using this command -

cactus-hal2maf ./js /storage/home/hcoda1/7/mjoshi96/scratch/Mukta/Drosophila/drosophila.hal drosophila.maf.gz --workDir /storage/home/hcoda1/7/mjoshi96/scratch/Mukta/Drosophila/cactus --chunkSize 10000 --batchCores 20 --batchCount 10 --refGenome D_MELANOGASTER --noAncestors --filterGapCausingDupes --outType single --batchSystem slurm --slurmArgs=--account=gts-sanderson353 --logFile drosophila.maf.gz.log --restart
#cactus-hal2maf ./js /storage/home/hcoda1/7/mjoshi96/scratch/Mukta/Drosophila/drosophila.hal drosophila.maf.gz --refGenome D_MELANOGASTER --logFile drosophila.maf.gz.log --restart

And getting this error -
RuntimeError: Command /usr/bin/time -f "CACTUS-LOGGED-MEMORY-IN-KB: %M" bash -c 'set -eo pipefail && cat /storage/home/hcoda1/7/mjoshi96/scratch/Mukta/Drosophila/cactus/toilwf-66dba8c74e675f20b3f74d1463c3670d/868b/job/tmpc6dhazil/hal2maf_cmds.txt | parallel -j 20 '"'"'{}'"'"'' exited 127: stderr=bash: line 1: parallel: command not found
Command exited with non-zero status 127

I removed --batchParallelTaf option thinking it caused the error, but that doesn't seem to be the case.

Best regards,
Mukta

[glennhickey]

parallel has been included in the cactus binary release since v2.4.1. How did you install cactus? what happens when you type which parallel or parallel directly from the cactus virtualenv?

[josh3397]

Hi, here is what it prints -

/usr/bin/which: no parallel in (/storage/project/r-sanderson353-0/mjoshi96/cactus/bin:/storage/project/r-sanderson353-0/mjoshi96/cactus/cactus_env/bin:/usr/local/pace-apps/manual/packages/xalt/xalt/bin:/usr/local/pace-apps/spack/packages/linux-rhel9-x86_64_v3/gcc-12.3.0/mvapich2-2.3.7-1-qv3gjagtbx5e3rlbdy6iy2sfczryftyt/bin:/opt/slurm/current/bin:/opt/pmix/4.2.6/bin:/usr/local/pace-apps/spack/packages/linux-rhel9-x86_64_v3/gcc-11.3.1/gcc-12.3.0-ukkkutsxfl5kpnnaxflpkq2jtliwthfz/bin:/opt/pace-common/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/mellanox/doca/tools:/opt/iozone/bin:/storage/home/hcoda1/7/mjoshi96/bin)

[glennhickey]

If you're building cactus yourself, you need to install parallel yourself. otherwise use the cactus release binaries or docker.