aMeta
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NBISweden
Ancient microbiome snakemake workflow
fastqc uses everything up to the fastq suffix as sample name. Unless the prefix matches the sample name, the fastqc rules will fail with a missing output file exception. Unfortunately,...
Currently the workflow report consists of the workflow rulegraph and the default content (statistics, configuration). Things to add could be: - krakenuniq summary - authentication results - ...
Hi, I installed aMeta after reading "Remote providers have been replaced" in the issues folder. Also, the test run worked without any errors. Right now, I am trying to run...
@percyfal looks like something has happened to the latest snakemake release. Currently the aMeta testrun fails with strange error, it was not the case two weeks ago: ``` (aMeta) nikolay@dell:~/WABI/A_Gotherstrom/aMeta/.test$...
Hi everyone, I've been running the aMeta pipeline for over a week (I have many samples) but it got stuck in a step for days. I cancelled the run and...
For the rule breadth of coverage to work, MaltExtract first has to run in order to generate the results/AUTHENTICATION/{wildcards.sample}/{wildcards.taxid}/MaltExtract_output/default/readDist/{wildcards.sample}.trimmed.rma6_additionalNodeEntries.txt file. This file is then used by the function get_ref_id in...
Hi, I was running aMeta on microbial and full databases, and in both cases pipeline was running generally smoothly. However, I noticed that MapDamage is not generating all expected files...
Hi aMeta team! Thanks for providing such a great ancient metagenome pipe. I found a very minor issue when downloading the krakendb from https://doi.org/10.17044/scilifelab.20518251. After wget, there was a 'taxDB.'...
Hi, I got the following error Error in rule Plot_Authentication_Score: jobid: 15 input: results/AUTHENTICATION/.30012ssL12c.collapsed_done output: results/overview_heatmap_scores.pdf log: logs/PLOT_AUTHENTICATION_SCORE/plot_authentication_score.log (check log file(s) for error details) conda-env: /aMeta/.snakemake/conda/55e1a8bf92c9925034725aa9b149b81b_ shell: Rscript /aMeta/workflow/scripts/plot_score.R results/AUTHENTICATION...
