Problem with Prokka to run tbl2asn
3
0
Entering edit mode
3.3 years ago
vmevada102 ▴ 20

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 • 4.9k views
ADD COMMENT
0
Entering edit mode

I had just install today only.

Still getting this error

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

All done but still having the problem to execute

ADD REPLY
1
Entering edit mode
3.3 years ago
aaron.petkau ▴ 10

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 COMMENT
0
Entering edit mode
3.3 years ago
Joe 19k

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 COMMENT
0
Entering edit mode
16 months ago
onestop_data ▴ 280

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

ADD COMMENT

Login before adding your answer.

Traffic: 2192 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6