Panaroo error

[varunshamanna]

Hi,
I was trying to extract the cps loci for which seroba has identified as untypable.
I am getting this error in the PANAROO_REF_COMPARISON step.

RuntimeError: Nearly all clusters have been trimmed! Try reducing your clustering sequence identity thresholds and/or running Panaroo in sensitive mode.

I have attached log files for your reference.
command.log

[Oliver-Lorenz-dev]

Hello,

This is most likely because the tool has only found a small sequence that matches with the CPS reference database (1 or 2 genes) which is not enough for panaroo to run on. If you look in the GFF3 file created by the tool, how many genes do you see?

Cheers,
Oli

[varunshamanna]

Hi Oliver,
Yes as you said there are only 3 genes in the GFF3 files of the samples. What do you suggest as an alternative in this scenario?

Even if the panaroo step fails. The pipeline says it was completed successfully. You have to introduce some checkpoints to check if the step got completed properly and fail the pipeline if the step has failed.

These samples are part of GPS2. I can send you the files also if needed. Alternatively, we can meet sometime and discuss this.

Let me know your thoughts.

Regards
Varun

[Oliver-Lorenz-dev]

Hi Varun,

Ok, yes this suggests there isn't much of a CPS sequence there as predicted by SeroBA.

I think it would be helpful to have a meeting about this. This software is still under development, so it is helpful for me to have feedback.

At the moment, the pipeline ignores panaroo errors because if this one sample fails it will terminate all other samples running through the pipeline which is a bit irritating for users.

My email is [email protected] - if you contact me there we can arrange a meeting.

Best,
Oli