Open i-artjom opened 1 year ago
how much RAM do you have?
you can pass nextflow run ... --maxram 8 ...
to limit this, see
https://github.com/phiweger/uv/blob/main/workflows/processes/uv.nf#L21
the protein search is the (brute force and) most computationally intensive step; on my laptop (16 GB RAM) it completes in about 20 mins for the two test genomes.
I let it run overnight and it finished, but I can't say exactly how long it took (maybe when I run it next time). Also running on 16GB RAM.
doesn't nextflow give you the time it took to run?
Unfortunately I can't see it but maybe it's because I'm still getting an error at annotate:collect_hmms
(even though it finishes the process annotate:search_tails
):
Error executing process > 'annotate:collect_hmms (1)'
Caused by:
Process `annotate:collect_hmms (1)` terminated with an error exit status (127)
Command executed:
cat *.bed > all
bedtools sort -i all > sorted
/uv/bin/deduplicate_and_rename.py -i sorted -o annotation.bed --names 43b63e6b-323d-473a-8d19-d2d9238d965c.contig_names.txt
Command exit status:
127
Command output:
(empty)
Command error:
.command.sh: line 3: bedtools: command not found
https://github.com/phiweger/uv/blob/main/workflows/processes/uv.nf#L243
bedtools is missing from env.yml
, my bad. thanks for spotting. can you add and rerun?
runs smoothly now with the test genomes and finishes in 5mins 🤌
haha, now I still need to fix that
Hi :)
After installing and downloading the test data and databases the workflow seems to freeze at uv:search_protein_db (stops for hours, several times tried).