Problem with Prokka to run tbl2asn

Question

[vmevada102]

I am having problem with running the Prokka in Galaxy Tools.

I am here by submitting the detaills of the log file available in that,

Fatal error: Exit code 2 () [tbl2asn] This copy of tbl2asn is more than a year old. Please download the current version. [14:31:23] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.12 from https://github.com/tseemann/prokka' -Z outdir\/prokka.err -i outdir\/prokka.fsa 2> /dev/null

I have tested changing the files from several sources, but it is not working properl.

I have received same error.

[vmevada102]

I had just install today only.

Still getting this error

[WouterDeCoster]

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your reaction but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

[Joe]

And you redownloaded the latest version?

This is definitely the cause of the error (and the error explicitly tells you so!) so there is a problem with your configuration. I don't use Galaxy, so I can't offer any input on how to configure this specifically, but if it's just a case of installing it as you would in a usual *Nix environment, you'll need to make sure the new version of tbl2asn is the one that's taking preference in your $PATH.

Try checking the version of whatever the default tbl2asn is pointing to.

[vmevada102]

All done but still having the problem to execute

Answer 1

[aaron.petkau]

As others have mentioned, tbl2asn, which is used by prokka, expires every 6-12 months and you need to re-download from NCBI (ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/) and install in the appropriate location in Galaxy.

Galaxy installs separate tools into there own conda environment named __tool@version. The default location for Prokka will be galaxy/database/dependencies/_conda/envs/__prokka@1.12, so you can check the version of tbl2asn used by Prokka with:

./galaxy/database/dependencies/_conda/envs/__prokka@1.12/bin/tbl2asn --version

You can replace tbl2asn with:

wget -O tbl2asn.gz ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz
gunzip tbl2asn.gz
chmod +x tbl2asn
cp tbl2asn ./galaxy/database/dependencies/_conda/envs/__prokka@1.12/bin/tbl2asn

If your instance of Galaxy uses conda from a different location you may have to check the file galaxy.ini to figure out this location (https://github.com/galaxyproject/galaxy/blob/v17.09/config/galaxy.ini.sample#L205). And/or you may have to use find (e.g., find galaxy/ -iname 'tbl2asn').

Answer 2

[Joe]

This is a known issue with tbl2asn and prokka. The software expires every 6-12 months unfortunately. For now the only option is to reinstall it with the latest version.

Answer 3

[onestop_data]

Someone just posted on twitter a hack so tbl2asn never expires - Enjoy it