tRNAscan-SE issue on HPC

[Sylvia-li]

parse genome sequences... imported: 1 filtered & revised: 1 contigs: 1

start annotation... predict tRNAs... Traceback (most recent call last): File "/opt/conda/bin/bakta", line 8, in sys.exit(main()) File "/opt/conda/lib/python3.8/site-packages/bakta/main.py", line 155, in main genome['features'][bc.FEATURE_T_RNA] = t_rna.predict_t_rnas(genome, contigs_path) File "/opt/conda/lib/python3.8/site-packages/bakta/features/t_rna.py", line 70, in predict_t_rnas raise Exception(f'tRNAscan-SE error! error code: {proc.returncode}') Exception: tRNAscan-SE error! error code: 2

Bakta container runs fine on the login node, but when I run the image on an HPC node i get tRNAscan-SE error code:2. I checked a previous similar error (error code 2) which had to do with /tmp/ directory - I have tried the option --tmp-dir and set it to different directory but it still outputs Unable to open /local/syl218/932130/tscan861346.fpass for writing. Aborting program. which is not the temporary directory i set in bakta. I do not think the warning about locale matters as running it on the login node is fine and the debug file still has that warning.

tRNAscan-SE by itself is fine, it runs fine on the HPC login node

• Which commands have been executed and what exactly happened Ran salloc --mem=32G singularity run /globalhome/syl218/HPC/bakta.sif sample2.contigs_medaka.fa.gz --min-contig-length 200 --threads 1 --prefix sample1.bakta --db ~/h_somni/nfs/APL_Genomics/db/prod/bakta/db/ --debug

• Detailed logs (execute Bakta with --debug) sample1.bakta.log

• How did you install Bakta: Conda, Pip singularity build bakta.sif docker://oschwengers/bakta:latest

Thank you. I really am not sure what to do

[oschwengers]

Thanks @Sylvia-li for reporting.

1. TMP: tRNAscan-SE does not offer a parameter to specify its temporary directory (or have I missed something?) Hence, we cannot forward the user-provided Bakta tmp to tRNAscan-SE
2. It seems, that there is an issue with your Perl locale setting. Unfortunately, I don't have enough Perl skills to point you to a solution. As this is the first error report of this kind, I tend to conclude that this is more an individual issue with your specific Conda environment and HPC setup. Maybe a local admin can help?

I'm sorry, that I cannot provide more help here.

[fischuu]

I am facing a similar problem and stuggle still with a solution, but in your case @Sylvia-li , have you tried to bind the path of the tmp folder to your singularity call? Like, adding the option -B /locale:/locale to the singularity call, I suppose the problem is that the singularity container cannot access the tmp folder, when it is not mounted/bound to it?

[Sylvia-li]

I am facing a similar problem and stuggle still with a solution, but in your case @Sylvia-li , have you tried to bind the path of the tmp folder to your singularity call? Like, adding the option -B /locale:/locale to the singularity call, I suppose the problem is that the singularity container cannot access the tmp folder, when it is not mounted/bound to it?

@fischuu thank you so much, It works now! Really, thank you! appreciate it.

my HPC has an environmnet variable for the temp folder so i just binded -B $TMPDIR:$TMPDIR

[oschwengers]

Thanks for jumping in @fischuu, just in case you're still struggling with tRNAScan, please do not hesitate to open a new issue describing your case.

Thanks and best regards!