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oschwengers / bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
GNU General Public License v3.0
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Issue with trnascan-SE and bakta v1.9.4 #307

Closed rubmc97 closed 2 months ago

rubmc97 commented 2 months ago

bin.1.log

Hi, I keep getting an issue with tRNA-SE... "Traceback (most recent call last): File "/home/comi/ruben.martinez/miniconda3/envs/bakta-env/bin/bakta", line 10, in sys.exit(main()) File "/home/comi/ruben.martinez/miniconda3/envs/bakta-env/lib/python3.10/site-packages/bakta/main.py", line 155, in m$ genome['features'][bc.FEATURE_T_RNA] = t_rna.predict_t_rnas(genome, contigs_path) File "/home/comi/ruben.martinez/miniconda3/envs/bakta-env/lib/python3.10/site-packages/bakta/features/t_rna.py", line$ raise Exception(f'tRNAscan-SE error! error code: {proc.returncode}') Exception: tRNAscan-SE error! error code: 2".

I'm using the bakta version 1.9.4. If I run it alone like trnascan-SE -h and with conda list, it seems to be there and working, but keep getting this error when running bakta.

Thanks!

rubmc97 commented 2 months ago

I think the problem might have been with the TMPDIR that I was using, as trnascan-SE couldn't modify it. Sorry for the inconvenience