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:zap: :aquarius: Rapid prokaryotic genome annotation
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prokka getting stuck on tbl2asn #420

Closed nixon444 closed 5 years ago

nixon444 commented 5 years ago

Hi there,

I have noticed lately that my prokka jobs are getting stuck at the tbl2asn stage of the pipeline. On previous jobs, my large datasets would assemble in a few days at most. Now I have tried to re-annotate after filtering out the majority of contigs (they were too short) and the job was aborted on the university server I use because it was running for 7 days. When I checked the log, it had been stuck at the following point in the process since 2 hours into the job (I removed file paths from the below):

Running: tbl2asn -V b -a r10k -l paired-ends -M b -N 1 -y 'Annotated using prokka 1.14.0 from https://github.com/tseemann/prokka' -Z prokka_G6.err -i prokka_G6.fsa 2> /dev/null

Is this a known issue? Anything suggestions? We have lots of data to analyse and not a huge amount of time...

Cheers!

tseemann commented 5 years ago

How many contigs and what total bases? I assume metagenome. Prokka wasn't designed for them. Filtering all small contigs < 500 is important. Also, you can split your fasta into separate fasta and annotate with separate prokka jobs. If you don't want a .GBK file you can comment out theh tbl2asn line in the prokka script.

Allerdrengen commented 4 years ago

@tseemann Would reducing my contig size fix this issue? I am also running metagenome samples. I am running my jobs on a cluster-service, where all tools (including Prokka) are installed in advance. This also prevents me from altering the script and commenting out tbl2asn, as you suggest. I don't expect there to be a commandline comment that would get the job done?

Zhaoju-Deng commented 1 year ago

hello Allerdrengen, have you solved the problem? I am running into the same issue with metagenomic sequence analysis with prokka and stuck at tbl2asn for days using the university cluster (prokka version 1.14.6, OS: Linux-3.10.0-957.el7.x86_64-x86_64-with-glibc2.17 (linux_64).