Issue with using Racon in pipeline-pinfish-analysis

[charlottewright]

I am attempting to use Racon within the pipeline-pinfish-analysis Snakefile but the workflow fails at the point of polishing the transcripts. The sdtout file suggests that the issue is with Racon.

The full error message is:

polish_clusters: 00:02:15 Polishing cluster 31b643a8-a0ec-4b7f-b8fe-a57b4ab35c48 of size 11 polish_clusters: 00:02:15 Failed running command: racon -t 10 -q -1 /tmp/pinfish_31b643a8-a0ec-4b7f-b8fe-a57b4ab35c4$ [Fri Nov 29 00:02:17 2019] Error in rule polish_clusters: jobid: 7 output: results/polished_transcripts.fas shell:

/rds-d4/project/cj107/rds-cj107-jiggins-rds/projects/eratoCortexMapping/Nanopore/20191024_HW_Larva/pipeline-pinfi$

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job polish_clusters since they might be corrupted: results/polished_transcripts.fas

Other people in my group who have previously used racon within this pipeline are also having the same problem with racon, suggesting that this is a bug with racon rather than my installation (I installed Racon from source - github - on November 21st).

Has anything changed with racon to account for why we are now having issues?

Thank you in advance for your help.

[rvaser]

Hi Charlotte, can you please paste the whole Racon command? Which version of Racon did you install (you can get it with racon --version)? I am not much familiar with this pipeline, did you consider raising this issue at the pipeline GitHub page?

Best regards, Robert

[charlottewright]

Hi Robert,

I installed Racon 1.4.3. The command that is executed as part of the pipeline is: racon -t 10 -q -1 /tmp/pinfish_31b643a8-a0ec-4b7f-b8fe-a57b4ab35c4

I have since realised that there is a new Github page with a more updated Racon. I have tried using this with the pipeline and still got the same error messgae.

Best wishes,

Charlotte