tbl2asn hung

[chienchi]

Hi all,

I know it is not prokka's issue but does anyone have the issue that tbl2asn hung there for many days. The prokka version is 1.9 and tbl2asn (23.6) is not expired yet.

The last few lines in the log file are

[19:10:34] Assigned 916938 locus_tags to CDS and RNA features.
[19:10:34] Writing outputs to /data/edge_v1.0/edge_ui/EDGE_output/JSA12/AssemblyBasedAnalysis/Annotation/
[19:23:13] Generating annotation statistics file
[19:23:28] Generating Genbank and Sequin files
[19:23:28] Running: tbl2asn -V b -a s -N 1 -y 'Annotated using prokka 1.9 from http://www.vicbioinformatics.com' -Z /data/edge_v1.0/edge_ui/EDGE_output/JSA12/AssemblyBasedAnalysis/Annotation/JSA12.err -i /data/edge_v1.0/edge_ui/EDGE_output/JSA12/AssemblyBasedAnalysis/Annotation/JSA12.fsa 2> /dev/null

Note: No .err file generated.

Thanks,
Chienchi

[tseemann]

I notice you have about 1 million CDS features!
I assume this is a metagenome.
I wonder if tbl2asn can't cope with that?
Can you contact NCBI about it?

[chienchi]

We have a workaround to split the contig and tbl file and run through tbl2asn by GNU parallel and concatenate genbank files. However, this workaround can not get the .sqn file properly.

From: Torsten Seemann <[email protected]mailto:[email protected]>
Reply-To: Victorian-Bioinformatics-Consortium/prokka <[email protected]mailto:[email protected]>
Date: Friday, February 13, 2015 at 6:19 PM
To: Victorian-Bioinformatics-Consortium/prokka <[email protected]mailto:[email protected]>
Cc: Chien-Chi Lo <[email protected]mailto:[email protected]>
Subject: Re: [prokka] tbl2asn hung (#65)

I notice you have about 1 million CDS features!

I assume this is a metagenome.
I wonder if tbl2asn can't cope with that?
Can you contact NCBI about it?

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/65#issuecomment-74354308.

[ayshwaryas]

Same issue as @chienchi. @tseemann : Is it possible to add a flag option for turning this step off? Atleast I don't need it for my purpose (and assume there are other users too) and this step causes the jobs to hang for many days.

[aclum]

An option to turn off tbl2asn would be useful for my purposes as well, primarily for in-house benchmarking of different assemblers. I end up just commenting out the code in the perl script but it would be useful if this was a command line option.