run_preCluster.py --cpus=30 CalledProcessError(retcode, cmd)

[bijendrabio]

Hello All, I am receiving following error while running the Family finding step of Cogent for a large dataset. Kindly suggest.

input file: isoseq_flnc.fasta

command: python /path/to/cDNA_Cupcake/cupcake2/tofu2/run_preCluster.py --cpus=30

raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '/usr/bin/time -v minimap2 -H -f 0.00001 -N 2000000 -m 20 -t 20 seed0.fasta seed0.fasta > seed0.fasta.seed0.fasta.f00001.minimap 2> seed0.fasta.seed0.fasta.f00001.minimap.log' returned non-zero exit status 127

[LionOfComarre]

Hey, this script seems to have been removed in v29 of cupcake, but for anyone attempting to run cogent with v28, this issue is caused by the default time program on macos being different from the linux one. To fix it, you can run

brew install gnu-time

if you have brew installed and then going into the script AlignerRunners.py mentioned further up in the error message and changing /usr/bin/time to gtime. Though that's a bit of a hack and I would recommend running Cogent on a linix platform if possible.