Comments (6)
Hello @Midnighter and thank you for providing Taxpasta. I did a fresh install of Taxpasta 0.6.0 last week and came across this error as well, thinking my own custom Taxonkit taxdump was to blame. But actually, the How-to Add Taxa Names to Output tutorial produces the exact same error. I saw in the commits there has been refactoring of the sample ETL service, so I figured this could be a regression induced by the latest commits.
Workaround: git checkout 7f43707
I had to wind back this far because the commit just after, cd6fe48
still produced the error. Hope this helps and keep up the good work.
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Awesome, thank you for the detective work 🕵🏼. I'll try to fix it soon.
from taxpasta.
Alright, I found the problem. I will try to release a fix tomorrow.
from taxpasta.
Thanks for the report!
from taxpasta.
Awesome, thank you for the detective work 🕵🏼. I'll try to fix it soon.
Great, because although that version supports merge to BIOM, it does not write the lineage to it.
from taxpasta.
from taxpasta.
Related Issues (20)
- [Feature] Add support for ganon 'tre' report
- [BUG] CRITICAL error when parsing MetaPhlAn4's output HOT 2
- Should we support the OPAL format as output? HOT 10
- [Feature] Add support for Sourmash HOT 5
- [BUG] Problem with kraken-type reports (from KrakenUniq) HOT 2
- [Feature] Add `--add-rank-lineage` to `taxpasta merge` and `taxpasta standardise` HOT 2
- [Refactor] Provide an internal error hierarchy to simplify exception handling
- [Feature] Add support for kmcp profiler
- [Feature] Reverse the order of the current lineages
- [Feature] Add a taxonomy table to the BIOM output
- Allow ignoring profile errors when merging
- [BUG] (I think): "Unrecognized file type extension '.biom'" HOT 10
- [BUG] MetaPhlAn 4 output with duplicate clade tax id is not supported HOT 16
- [BUG] tax entries with `no rank` failed `--add-lineage`, `--add-id-lineage` or `--add-rank-lineage` HOT 2
- [Feature] add an option to let taxpasta report relative abundance as fractions instead of only counts HOT 1
- [BUG] Metaphlan4 run error in Microba datasets HOT 8
- Error with Biom format output from kraken2 report HOT 4
- [Feature] Changing/adding taxonomies on standardized profile tables HOT 1
- [Feature] Adding metabarcoding/amplicon support HOT 1
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