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As per https://docs.python.org/3/library/locale.html#locale.format
> Deprecated since version 3.7: Use [format_string()](https://docs.python.org/3/library/locale.html#locale.format_string) instead.…
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Hi there,
I was trying to run SingleM, but it crashes all time, apparently when it's parsing the DIAMOND output (full debug log further down):
```
[...]
02/07/2024 01:28:14 PM ERROR: Process (DI…
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I was going through results and found this error in the singlem log file.
```
09/15/2023 03:19:36 AM INFO: Using as input 24 different sequence files e.g. bins/final_bins/concoct_bins.tsv.017_sub.…
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Provide the option to export the biodiversity analysis results in BIOM format.
_[Original issue](https://github.ugent.be/unipept/unipept/issues/468) by @pdawyndt on Fri Mar 13 2015 at 15:32._
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When trying to write an `skbio.stats.ordination.OrdinationResults` object to a file, the `.write()` method fails. Seems to be a NumPy deprecation.
# Reproducible example:
```python
import biom
…
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I'm really enjoying Quarto and excited to shift from Rmd to Qmd in my writing and teaching. I use these Lua filters frequently: [scholarly-metadata.lua](https://github.com/pandoc/lua-filters/tree/mast…
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Hi there,
I am trying to use PICRUSt2 to functionally annotate some 16s ASV data. I am using an ASV sequence .fasta and an abundance matrix from DADA2. I have adjusted the ASV abundance table to th…
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`biom convert -i input_hdf5_data_biom.biom -o table_from_hdf5_json.biom --to-json `
Fails with
`TypeError: Object of type int64 is not JSON serializable`
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Dear Sir/Madam,
Sorry to disturb, I followed the sortmerna manual to end with some output, how can I mining them to get a otu table with counts and taxonomy either in biom or tsv format. I noticed …
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Hi,
I have analysed some metagenomic samples using Kraken2 and I would like to visualise my taxonomic profiles using Phinch.
I used the kraken-biom tool (https://github.com/smdabdoub/kraken-biom…