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When using the `lineage` command, it would be useful to have an option to specify which ranks should be reported, e.g.:
`taxonkit lineage --show-lineage-ranks --report-ranks "family,genus,species"`.
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Hi Dear Wei,
I was wondering to see if there is a placeholder for clade rank?
I'm using this command and looking to have 8 columns for output (now missing clade rank):
```
./taxonkit reforma…
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### What happened?
When I use the demo data everything works, but when I try to run my own data it keeps failing with errors and also notes that I need to install graphviz however graphviz is already…
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### What happened?
System - Ubuntu 18.04 with Nextflow 22.10.0 and wf-metagenomics v2.0.0 (b2bd2b89da)
Command - nextflow run epi2me-labs/wf-metagenomics --fastq /home/data1/Analyzed_data/metact…
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### What happened?
Hey there,
I’ve seen a similar error in your problems, but it doesn’t really match my personal documents.
I just use your metagenomics workflow for my analyses and I have some…
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Hello and thanks for developing this great tool,
I am currently in the process of preparing a Diamond database from IMG/VR data. I have already prepared the necessary data and successfully created …
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### What happened?
I am trying to use this workflow with `--classifier minimap2` but I am unsure on how to correctly use this option. I try running:
```bash
nextflow run epi2me-labs/wf-metagenomi…
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After having [issues with fastp](#76) I am now able to run hecatomb test data. After a few hours the pipeline crashes:
```console
Error in rule cluster_similar_sequences:
jobid: 29
outpu…
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Hi,
I am currently trying a few data analysis options to detect viral contaminations in my sample. Therefore, I also wanted to test the metagenomics workflow, and also compare the minimap2 and the …
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Hello Team,
This is really a fast genome download. I can download all refseq+genebank assembly in less than 6 hours using 64 threads:
genome_updater.sh -d "refseq,genbank" -g "archaea,bacteria" -f…