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SamStudio8 / reticulatus

A snakemake-based pipeline for assembling and polishing long genomes from long nanopore reads
MIT License
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Test sample #56

Open GiangLeN opened 2 years ago

GiangLeN commented 2 years ago

Hi, I am interest in using reticulatus for nanopore metagenome samples. However, I could not get the pipeline to run. Here is what I tried. Downloaded the Zymo-GridION .fastq.gz (12GB) from LomanLab mockcommunity Edit the read.cfg as follow gigasci-zymo-even ../test/Zymo-GridION-EVEN-BB-SN-PCR-R10HC-flipflop.fq.gz - - - * hoot meow

The other files: configs.yaml and manifest.cfg were not changed.

Upon running snakemake I am getting the error: Missing input files for rule polish_pilon

How could I solve this issue. Do you have any tutorial regarding this pipeline.

Thank you Giang

cinnetcrash commented 1 year ago

I faced the same issue and skipped that and it's working. I will do the polishing manually.