Closed
Description
Description of the bug
While trying to run KrakenUniq, I noticed the job was taking forever. Turns out it was using 4 CPU by default.
Tried to overwrite this in a config file as follows:
process {
withName: 'KRAKENUNIQ.*' {
cpus = 32
memory = 64.GB
}
}
At run time, it turned out that only the memory requested was correctly updated, not the cpu (from .command.sh):
# Preload the KrakenUniq database into memory.
krakenuniq \
\
--db KrakenUniq_MicrobialDB_2023-08-08 \
--preload \
--preload-size 64G \
--threads 4
# Run the KrakenUniq classification on each sample in the batch.
while IFS=' ' read -r SEQ PREFIX; do
krakenuniq \
--db KrakenUniq_MicrobialDB_2023-08-08 \
--threads 4 \
--report-file "${PREFIX}.krakenuniq.report.txt" \
\
\
\
\
"${SEQ}"
done < .inputs.txt
Possibly related to issue #611 ?
Command used and terminal output
Relevant files
No response
System information
No response