Closed the-eon-flux closed 9 months ago
By excluding you mean deleting the line from the sample.tsv, isn't it?
What you probably need to do is to delete all files in Intermediate/cobinning And in Binning/
And Restart. Check with dryrun that you don't execute steps from assembly in or before.
Also there is I think a monor update to atlas
Yes, I am deleting the sample rows.
I made another file excluded_samples.tsv
and moved the sample rows there to keep a track.
Thank you for your help. I deleted all the files, and I am running binning now. It didn't show any assembly run jobs with --dry-run.
Will keep you posted if I get the same error.
Hey, thank you for your help!
It worked and I am running atlas genomes
now.
It is interesting how without co-binning, 37 samples had failed earlier after binning. And now, only 20 samples failed binning. So I ended up removing fewer samples.
I have some bins with the co-binning group (Healthy or Pneumonia) as a suffix name.
Just a quick question. Are those 17 samples (that are not failing to be binned now), retained now because there are some bins in those samples with more coverage or something?
Vamb get more bins in general. I think it also gets more bins from low quality samples.
I suggest you to quantify all samples once you have a final set of mags.
E.g. add the samples vack and run 'atlas run quantify_genomes'
Chack that binning is not triggered again.
Sorry for the late reply. You were right. Some bins are of lower quality but they are good enough. Thanks for your help!
Error in rule parse_vamb_output
Here is the relevant log output:
Atlas, version 2.18.0
Additional context
The error is for a sample that I excluded from the analysis after there were no Bins for the same. It seems like this rule in the workflow is not updated to the removed sample. or maybe I am doing something wrong.
I tried the following things:
I was actually doing single-sample binning first and then I switched to co-binning by updating the BinGroup in samples.tsv file. Some of the samples failed in the initial binning step so I removed them later. But then the error that I am getting is for samples which I have excluded now.
localrule parse_vamb_output: input: Intermediate/cobinning/healthy/vamb_output, Intermediate/cobinning/Pneumonia/vamb_output'
I got the same error.Is there a quick fix to this? Or do I have to run ATLAS again from the beginning?
I think I made it too complicated with the binning and co-binning back to back. Any help from your side would be appreciated.