Question: Problem with Prokka to run tbl2asn
0
gravatar for vmevada102
13 months ago by
vmevada10220
vmevada10220 wrote:

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.

prokka galaxy • 1.6k views
ADD COMMENTlink modified 13 months ago by aaron.petkau0 • written 13 months ago by vmevada10220

I had just install today only.

Still getting this error

ADD REPLYlink written 13 months ago by vmevada10220

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.

ADD REPLYlink written 13 months ago by WouterDeCoster38k

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.

ADD REPLYlink written 13 months ago by jrj.healey12k

All done but still having the problem to execute

ADD REPLYlink written 13 months ago by vmevada10220
0
gravatar for jrj.healey
13 months ago by
jrj.healey12k
United Kingdom
jrj.healey12k wrote:

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.

ADD COMMENTlink modified 13 months ago • written 13 months ago by jrj.healey12k
0
gravatar for aaron.petkau
13 months ago by
aaron.petkau0 wrote:

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').

ADD COMMENTlink written 13 months ago by aaron.petkau0
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