Comments (5)
OK, I see no problem with that code. We'll make some tests to see if we can replicate the problem. If we can, maybe we need to warn users not to use this for Archaea (or not at all)?
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I had a short look, version 2.8.0 has bac & arc files in the config to download:
ampliseq/conf/ref_databases.config
Line 30 in f3c97e1
And this files should be picked up by
ampliseq/bin/taxref_reformat_gtdb.sh
Lines 12 to 16 in f3c97e1
from ampliseq.
So as far as I got that was indeed a bug? For all versions? Or only for the most recent one? Might be good to mention in upcoming release notes...
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Yes, a bug. From r207 and onwards. (GTDB changed the number of markers in r207.)
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Thanks, that info is in the changelog now.
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Related Issues (20)
- Getting ca 50% more ASVs than when using DADA2 on QIIME2 HOT 2
- ampliseq fails during taxonomy assignation when processing ITS sequences HOT 14
- Error No subject alternative DNS name matching zenodo.org found HOT 2
- minor improvement of sort() before denoising with method = "radix HOT 2
- 12S taxonomic classification databases HOT 3
- Remove PhytoRef as it's included in PR2 5.0.0 HOT 1
- Template update 2.13.1 HOT 1
- Barrnap filtration HOT 4
- ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE .........has been broken HOT 3
- ANCOM-BC for differentially abundant taxa HOT 1
- ERROR: R_HOME ('/usr/local/lib/R') not found HOT 5
- Misleading error message when samples are not passing filterandtrim
- Accessing 16S gene identifiers HOT 13
- DADA2 split regions singularity HOT 13
- multi-region analysis: sidle/reconstructed/reconstructed_merged.tsv OCCATIONALLY mis-formatted HOT 1
- Running test error HOT 1
- Abundance plots for qiime2 results without metadata provided HOT 2
- Adding ONT read support for ampliseq
- `overall_summary.tsv` sometimes with misleading numbers in 2.9.0 HOT 7
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