agshumate/Liftoff

how long it takes to finish a job (100 000 features)? I stay at a surface about 2 hours

genewlan opened this issue · 2 comments

extracting features
2022-10-01 21:04:05,628 - INFO - Populating features
2022-10-01 21:04:11,385 - INFO - Populating features table and first-order relations: 105792 features
2022-10-01 21:04:11,385 - INFO - Updating relations
2022-10-01 21:04:11,860 - INFO - Creating relations(parent) index
2022-10-01 21:04:11,878 - INFO - Creating relations(child) index
2022-10-01 21:04:11,896 - INFO - Creating features(featuretype) index
2022-10-01 21:04:11,934 - INFO - Creating features (seqid, start, end) index
2022-10-01 21:04:11,979 - INFO - Creating features (seqid, start, end, strand) index
2022-10-01 21:04:12,028 - INFO - Running ANALYZE features

it`s 2022-10-01 23:15, the same surface

is something wrong in my setting or file?
liftoff -g ref_genomic.gff -o ./out_genomic_3.gff -dir ./out_genomic_3 -a 0.7 -s 0.7 -flank 0.1 -exclude_partial -copies -cds in_genomic_3.fasta ref_genomic.fas

the .gff file download from Genebank
the genome file is processing by ragtag
liftoff version is 1.6.3
OS ubantu

i solved it, the python version is conflict to liftoff requirments. creating new env is work, python =3.8