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nf-core / genomeqc

Compare the quality of multiple genomes, along with their annotations.
https://nf-co.re/genomeqc
MIT License
1 stars 1 forks source link

BUSCO fails #37

Open FernandoDuarteF opened 2 days ago

FernandoDuarteF commented 2 days ago

When running genomeqc on assests/samplesheet.csv (bees and wasps) BUSCO fails on the SEPP step with this warning message:

Placements failed. Try to rerun increasing the memory or select a lineage manually.

even though 72GB of RAM are being used.

SEPP is being used to automatically infer the lineage database. When the lineage database is explcitly set, BUSCO runs successfully.

Also, check error log file /lustre/home/ucbtfrd/pipelines/genomeqc_subworkflows/work/ff/455472097fece4ccdf81cfdaa15a9b/Osmia_bicornis-auto-busco/Osmia_bicornis.fasta/logs/sepp_err.log for more information.

FernandoDuarteF commented 2 days ago

To further check what's going on see branch subworkflows-agat-longest-isoform

FernandoDuarteF commented 4 hours ago

Seems to be related to agat_sp_keep_longest_isoform.pl filtering. Moving back to excon's GFFREAD solves the issue.