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lbcb-sci / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
MIT License
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Issue with using Racon in pipeline-pinfish-analysis #14

Closed charlottewright closed 3 years ago

charlottewright commented 4 years ago

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: 16:17:30 Polishing cluster be37aa9e-8202-4afd-8c18-ebde5ef7c6fa of size 10 polish_clusters: 16:17:30 Failed running command: racon -t 20 -q -1 /tmp/pinfish_be37aa9e-8202-4afd-8c18-ebde5ef7c6fa_713003653/reads.fq /tmp/pinfish_be37aa9e-8202-4afd-8c18-ebde5ef7c6fa_713003653/alignments.s$ [Fri Dec 6 16:17:31 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-pinfish-analysis-fast-v4/pinfish/polish_clusters/polish_clusters -t 20 -a results/cluster_membersh$

    (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 am using racon v1.4.10

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

Thank you in advance for your help.

rvaser commented 4 years ago

Hi Charlotte, by the pipeline github page i meant https://github.com/nanoporetech/pipeline-pinfish-analysis. This racon repository is the same as isovic/racon but with newer updates.

Best regards, Robert