Issue/Error in tRNAscan-SE running

[hackerzone85]

I have installed bakta using the following command:

mamba create -n bakta -c conda-forge -c bioconda bakta

And the database was downloaded using the following command:

bakta_db download --type full

While running bakta for a metagenome assembly (2009015 Contigs, 135329 Contigs >1000 bp), it stuck at "predict tRNAs..." step though it is generating file trna.fasta and trna.tsv of 0 size.

(bakta) ddalab@DP7820-WS:ASMs$ bakta --min-contig-length 1000 --prefix C1_ASM --output ASMs_ORF/BAKTA --locus C1_ASM --meta --verbose --threads 70 Renamed_ASM/C1_ASM_Renamed.fa --force --tmp-dir ASMs_ORF/BAKTA/tmp
Bakta v1.9.4
Options and arguments:
    input: /mnt/MyBackup/MAHENDRA/PRAGYA/ASMs/Renamed_ASM/C1_ASM_Renamed.fa
    db: /mnt/MyBackup/DDALAB/BAKTA_DATA/db, version 5.1, full
    output: /mnt/MyBackup/MAHENDRA/PRAGYA/ASMs/ASMs_ORF/BAKTA
    force: True
    tmp directory: /mnt/MyBackup/MAHENDRA/PRAGYA/ASMs/ASMs_ORF/BAKTA/tmp/tmp9kdyf_ti
    prefix: C1_ASM
    threads: 70
    meta mode: True
    translation table: 11
    locus prefix: C1_ASM

parse genome sequences...
    imported: 2009015
    filtered & revised: 135329
    contigs: 135329

start annotation...
predict tRNAs...

Here is the version and build of few installed pkg in bakta env bakta=1.9.4=pyhdfd78af_0 aragorn=1.2.41=h031d066_3 blast=2.16.0=hc155240_2 diamond=2.1.8=h43eeafb_0 infernal=1.1.5=pl5321h031d066_2 pyrodigal=3.5.1=py310h7c593f9_1 python=3.10.14=hd12c33a_0_cpython trnascan-se=2.0.12=pl5321h031d066_0

[DingJingZhi]

If I add --replicons _tryc.tsv, time suspending in predict tRNAs ... then I have tried many ,found del --replicons ,it passed

[DingJingZhi]

If I add --replicons _tryc.tsv, time suspending in predict tRNAs ... then I have tried many ,found del --replicons ,it passed

[DingJingZhi]

oh I change the tsv to csv, --replicons _tryc.csv predict tRNAs... pass!

[oschwengers]

Hi @hackerzone85 , I guess tRNAscan-SE just got stuck while reading/processing all these files? Maybe we need to parallelize tRNAscan-SE as also suggested in other issues. I'll put this on my list, but this might take a while hence, won't make it into the upcoming v1.10.0.