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epi2me-labs / wf-bacterial-genomes

Small variant calling for haploid samples
https://labs.epi2me.io/
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Got "No disjointigs were assembled" error when running denovo #17

Closed bsalehe closed 1 year ago

bsalehe commented 1 year ago

I have tried to run the pipeline with single ONT sample on WSL2 with singularity profile denovo i.e. running with flye assembler. The sample appears to have high coverage. It is from bacteria with 4mb genome size. Further investigation in the .nexflow.log file indicated it is a flye related error which seemed to be the case as reported here.

I manually configured the flye command in the 'main.nf' file by adding the --asm-coverage and --genome-size options which didn't throw that error anymore only threw a memory error.

Would it be convenient to add in the advanced options additional parameters in the pipeline for running flye like it is recommended here in a similar way you hva done for running prokka or medaka which are available in the pipeline usage help (nextflow run epi2me-labs/wf-bacterial-genomes --help)?

Note: The solution given in the flye issue above require to add additional paramter --genome-size <value> as shoen in the current flye usage doc.

Thank you!

cjalder commented 1 year ago

Hi @bsalehe thanks for raising this. We'll try and implement these for a future update.

In regards to the memory issue, you can pass a config file to increase the memory (if your machine has more resources available) by following the instructions in this issue.