Test sample

[GiangLeN]

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]

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