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hello,when using any taxonkit commond, got following errors.
`
$taxonkit list --ids 9606 --indent ""
panic: runtime error: index out of range [4] with length 4
goroutine 17 [running]:
github.c…
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### What happened?
I'm trying to run the workflow in command line, but I have an issue with docker permissions. I ran the following command:
`nextflow run epi2me-labs/wf-metagenomics --fastq test_…
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Hi there!
I try to classify my ASV after 16S/18S gene sequncing with kraken and get lineage for each taxid.
here is my pipe:
```
cat kraken2_console_out.tsv \
| csvtk cut -Ht -f 2,3 \
| ta…
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### Prerequisites
- [x] make sure you're are using the latest version by `taxonkit version`: I'm using `taxonkit v0.14.1` (installed via conda)
- [x] read the [usage](http://bioinf.shenwei.me/tax…
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It's a small change to https://github.com/shenwei356/taxonkit/blob/master/taxonkit/cmd/taxid-changelog.go#L326-L341
1. check if plain files exist. if yes, load as usual.
2. if not, load the gzip …
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### Prerequisites
- [x] make sure you're are using the latest version by `taxonkit version`
- [x] read the [usage](http://bioinf.shenwei.me/taxonkit/usage/)
### Describe your issue
I've had …
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### What happened?
We've just hit the error below. After some diagnosing we've noticed that aggregate_lineages_bracken.py is hitting a line in `lineages.txt` that contains only one string: `Lu`. This…
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Hi, when i run:
> `nextflow run epi2me-labs/wf-metagenomics/ --fastq /mnt/lustre/scratch/nlsas/home/csic/nmy/vgc/dataANDanalysis/analysis/16s/16s_initial_5samples/16s_quality_length_filter.fastq -…
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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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I cannot successfully run the pipeline on my own or the test data. Both kraken2 and minimap2 fail to classify any sequences.
I downloaded the test data and confirmed that it contains 1000 reads. Th…