NC bins

[LorrieMacc]

Hello Jakob,

I am using Vamb 1.4.3 and I have generated clusters using models vae and aae as:
vamb --outdir 06_VAMB_bam -o C --fasta 03_Concat/catalogue.fna.gz --bamfiles 04_BAM/*sorted.bam --minfasta 10000 --model vae-aae --cuda
Just like Joseph in #280 , I am trying now to manually dereplicate the bins checking your snakemake workflow from avamb.
and could successfully create the cluster scores, run the manual derep, create the ripped bins.

Now i cannot run mv_bins_from_mdrep_clusters.py because it appears that I am missing the NC_bins.
I must have missed an obvious step, but could you please help me to understand when the Non contaminated bins are generated and how ?

Thank you very much in advance.
lorrie

[jakobnissen]

Cc @Paupiera

[Paupiera]

Hi Lorrie,

The snakemake workflow is a bit convoluted, not always following the same snakemake graph, so it might be a bit difficult to help without more information. Could you share the current directory structure of the generated files, including the tmp and log directories? I just would like to have an idea of what rules were executed and which files were created.

Best,
Pau