I am trying to use BUSCO to assess the quality of a transcriptome assembled with Trinity. My run fails after ~2h running, when the HMMER phase begins. I couldn't find any support options for BUSCO.
Is there any way to get support for BUSCO? I couldn't find anything on line or on the documentation.
This is my command and programs versions:
module load Python/3.2.1 module load BLAST+/2.2.31 module load HMMER/3.1b2 module load EMBOSS/6.5.7 python3 ~/MyPrograms/BUSCO_v1.1b1/BUSCO_v1.1b1.py -in ../Trinity-GG.fasta -o GG \ -l ~/MyPrograms/BUSCO_v1.1b1/vertebrata -m trans -c 4 -f
After ~2 hours running, this is the error I get:
*** Running HMMER to confirm transcript orthology *** Traceback (most recent call last): File "/.../MyPrograms/BUSCO_v1.1b1/BUSCO_v1.1b1.py", line 594, in <module> name=i[:-7];group=transdic[name] KeyError: 'TRINITY_'
Any help would be appreciated
Just curious, but did you try with the version 1.1 instead of beta? I had problems with busco but it was usually due to using latest Augustus release (species model config was missing) instead of an older one. Also, probably it has to do with the sequence names in your trinity assembly, did you check that?