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.