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oschwengers / bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
GNU General Public License v3.0
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Possible issues running bakta in Singularity #286

Closed andreaswallberg closed 6 months ago

andreaswallberg commented 6 months ago

Dear all,

Thanks for providing such a great annotation tool. When I run bakta through Singularity, I can currently only successfully complete the annotation pipeline if I pass --skip-trna to skip using tRNAscan-SE and --skip-plot to skip using Circos, respectively. Otherwise I get these error messages and the process exits prematurely:

ERROR: tRNAscan-SE could not be executed! Please make sure tRNAscan-SE is installed and executable or skip requiring workflow steps via via '--skip-trna'.

ERROR: Circos could not be executed! Please make sure Circos is installed and executable or skip requiring workflow steps via via '--skip-plot'.

Both of these tools are installed and present in the /opt/conda/bin directory of the image.

Any ideas what is going on and how to fix it?

andreaswallberg commented 6 months ago

Dear developers,

Oops! This was a user error.

Both circos and tRNAscan-SE are Perl programs. I have set some specific library paths for Perl in my UNIX environment and these were inherited into the container environment, overriding container paths and creating Perl version mismatches for specific compiled libraries.