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hoelzer-lab / hypro

Extend hypothetical prokka protein annotations using additional homology searches against larger databases
GNU General Public License v3.0
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FileNotFoundError: [Errno 2] No such file or directory: 'run/prokka/testrun.gbk' #10

Closed hoelzer closed 4 years ago

hoelzer commented 4 years ago

The extension command seems to look for a *.gbk file in the prokka output folder. In my case this does not exist.

Also my prokka command finished with an error and I think this is why no gbk file is produced:

[14:45:46] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14.0 from https://github.com/tseemann/prokka' -Z run\/prokka\/testrun\.err -i run\/prokka\/testrun\.fsa 2> /dev/null

I thought we should update the environment to 

prokka-1.14.5

but I still got the same error... You don't have problems executing the pipeline in your conda env @CoffeeMA2go ?

hoelzer commented 4 years ago

wow... this really seems to be a problem of the NCBI executable that expires after some months. How shit is that?

https://discourse.climb.ac.uk/t/prokka-keeps-on-crashing-when-it-gets-to-tge-tbl2asn-stage/1136

hoelzer commented 4 years ago

I downloaded the executable from here

ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/

and replaced the own in my conda env. After chmod +x prokka was working fine again.

phhhhh