You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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.
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
The text was updated successfully, but these errors were encountered: