Progressive cactus issue with --slurmArgs

[josh3397]

Hello,

I am trying to run cactus-hal2maf using this command -
cactus-hal2maf ./js /storage/home/hcoda1/7/mjoshi96/scratch/Mukta/Drosophila/drosophila.hal drosophila.maf.gz --chunkSize 100000 --batchCores 20 --batchCount 10 --refGenome D_MELANOGASTER --noAncestors --filterGapCausingDupes --outType single --batchParallelTaf 20 --batchSystem slurm --slurmArgs --account=gts-sanderson353 --logFile drosophila.maf.gz.log --restart

I added --slurmArgs because I kept getting this error -
Errored operation submitJob, code 1: sbatch: error: --account option required
sbatch: error: Batch job submission failed: Invalid account or account/partition combination specified

But after adding --slurmArgs, I still get error saying 'expected one argument'

Could I please get help with this issue? I am running this command as part of batch job get_maf.sbatch

cd /storage/project/r-sanderson353-0/mjoshi96/cactus
source cactus_env/bin/activate

cactus-hal2maf ./js /storage/home/hcoda1/7/mjoshi96/scratch/Mukta/Drosophila/drosophila.hal drosophila.maf.gz --chunkSize 100000 --batchCores 20 --batchCount 10 --refGenome D_MELANOGASTER --noAncestors --filterGapCausingDupes --outType single --batchParallelTaf 20 --batchSystem slurm --slurmArgs --account=gts-sanderson353 -logFile drosophila.maf.gz.log --restart

Best regards,
Mukta

[glennhickey]

Try --slurmArgs=--account=gts-sanderson353 or --slurmArgs " --account=gts-sanderson353" (noting space after first quote).

[josh3397]

Thank you, using --slurmArgs=--account=gts-sanderson353 worked! I am now running into a different issue which I will post in a different ticket.