Comments (3)
@hmontenegro I've updated these scripts in last few days, I'm almost done with a new release with updated taxonomy databases. But it shouldn't have anything to do with the vsearch
version I don't think, but can't guarantee (I'm running v2.7.0 locally at the moment). No surprise, but COI is the hold up. Parsing the bold data isn't very much fun. I think I'm close to something that works better and hope to get it released tonight. I've also had some conda related problems recently, hopefully those get cleared up soon.
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I just tested AMPtk 1.4.0 and bold2utax.py
it worked without errors, thanks for the quick fix.
I am puzzled why I got that error, while apparently other people didn't.
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Not sure if others manually build the databases. You can install the one I created with the amptk install -i COI command. This is a combination of Arthropoda and chordates.
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Related Issues (20)
- Issue installing AMPtk (Mac OS - M1 chip) HOT 2
- getting NoneType vs int error in clustering step
- Error when run quick start HOT 7
- usearch9 not found when generate UTAX database
- VSEARCH error on amptk -filter step
- Support Python 3.8 onwards HOT 3
- SyntaxError in "duplicate ID in mapping file: XXX, exiting"
- Default for -p, --index_bleed documented as 0.005 HOT 1
- Typo "Bjerkandara adusta" --> "Bjerkandera adusta" HOT 1
- Missing species names in amptk_mock1.fa HOT 3
- Missing final new line in amptk_mock1.fa and amptk_synmock.fa HOT 2
- Inconsistent primer trimming sequence in amptk_mock*.fa HOT 5
- Matching MockA, MockB1 and MockB2 to FASTQ filenames HOT 2
- platform.linux_distribution is removed since Python 3.8 HOT 1
- Species names in amptk_mock2.fa and amptk_mock3.fa vs Figure 4
- new users cannot install amptk properly, please help HOT 3
- unoise3 clustering HOT 5
- Problem with TypeError during AMPtk cluster HOT 11
- Saw you started some prelim ONT methods HOT 2
- Problematic unoise3 implementation with VSEARCH HOT 13
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