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NBISweden / aMeta

Ancient microbiome snakemake workflow
MIT License
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added ANI filter, vignettes, pathogens to list, fixed a few bugs, tuned fontsize for heatmaps #134

Closed LeandroRitter closed 11 months ago

LeandroRitter commented 11 months ago

This PR addresses a number of issues, for example #121, #124, #127, #128, #132, #133

ZoePochon commented 11 months ago

There is a small typo that comes up twice in the readme as well :

KarkenUniq abundance matrix

Instead of KrakenUniq

Le mer. 9 août 2023, 16:58, Nikolay Oskolkov @.***> a écrit :

@.**** commented on this pull request.

In workflow/rules/authentic.smk https://github.com/NBISweden/aMeta/pull/134#discussion_r1288665107:

@@ -89,7 +92,7 @@ checkpoint Malt_Extract: message: "Malt_Extract: RUNNING MALT EXTRACT FOR SAMPLE {input.rma6}" shell:

  • "time MaltExtract -i {input.rma6} -f def_anc -o {params.extract} --reads --threads {threads} --matches --minPI 85.0 --maxReadLength 0 --minComp 0.0 --meganSummary -t {input.node_list} -v 2> {log}"
  • "time MaltExtract -Xmx32G -i {input.rma6} -f def_anc -o {params.extract} -r {params.ncbi_db} --reads --threads {threads} --matches --minPI 85.0 --maxReadLength 0 --minComp 0.0 --meganSummary -t {input.node_list} -v 2> {log}"

I believe, the -r flag should be there by default because we have a rule NCBIMapTre that downloads ncbi.map and ncbi.tre and places them to ncbi_db. In case, the downloading fails, when there is not internet connection as TJ noticed, there should be at least a chance to point MaltExtract to ncbi_db where one could manually upload the ncbi.map and ncbi.tre files. I ran aMeta with the -r flag a few times on my laptop and Uppmax, i.e. with internet connection, and it always worked

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