serka-m / mmlong2 Goto Github PK

Hi

I think it would be great to have an option to use/skip a specified list of binning tools.
e.g.
--use_binners "graphmb,semibin"
--skip_binners "graphmb,semibin"

Best regards
Rasmus

Hey there,

Thanks for this wonderful tool / workflow!

I am wondering if you can elaborate on what format is needed for the coverage CSV file? (e.g. rows = contigs, columns = samples, values = coverage, or something else ?). From the documentation it also sounds like it may possible to provide a path to .fastq files instead of a CSV, which I would assume it then uses for mapping and generating the coverage CSV?

Thanks for the clarification!

~ Ryan

Hello Serka-M, I currently have some bins generated through other methods, but I would like to proceed with the latter part of mmlong2 to evaluate these bins, like to summarize the number of rRNAs and tRNAs. Could you please kindly guide me on how to proceed with this?

Hi Mantas, I really appreciate the work that has gone into the mmlong2 pipeline. This past spring I had it working until my university HPC server went down, and reinstalling mmlong2 is causing some issues. My installation code is below:

mamba create -n mmlong2 -c conda-forge -c bioconda snakemake=7.26.0 singularity=3.8.6 zenodo_get=1.3.4 pv=1.6.6 pigz=2.6 tar=1.34 -y
followed by
mamba activate mmlong2 || source activate mmlong2 && zenodo_get -r 8027235 -o mmlong2/bin
and just as in the readme
pv mmlong2/bin/sing-mmlong2-lite-*.tar.gz | pigz -dc - | tar xf - -C mmlong2/bin/.
pv mmlong2/bin/sing-mmlong2-proc-*.tar.gz | pigz -dc - | tar xf - -C mmlong2/bin/.
chmod +x mmlong2/bin/mmlong2

I then try to run mmlong2 -h and get the error message:
grep: /mnt/home/marshaag/mambaforge/envs/mmlong2/bin/mmlong2-proc-config.yaml: No such file or directory

Leading me to look into my mambaforge bin and it doesn't contain the lite or proc .yaml files or the lite or proc .smk files. I tried cloning the repository and copying those files into my mambaforge mmlong2 bin and that led to the pipeline starting but failing at random steps that did not have issues prior with the same input and arguments. I believe the inconsistent failing at certain steps is just due to my broken installation but you probably know a bit more about those intricacies than I do.

I'm pretty new to snakemake pipelines so any help getting this working again would be greatly appreciated!