Unable to run vsearch cluster-features-de-novo

[leila (LE)]

Hi,

I am trying to run vsearch cluster-features-de-novo using qiime2-2020.8. Here is the code I have been trying to run:

qiime vsearch cluster-features-de-novo
--i-table nc_merged_table.qza
--i-sequences nc_merged_seqs.qza
--p-perc-identity 0.97
--o-clustered-table 97_otu_table_nc.qza
--o-clustered-sequences 97_rep-seqs_nc.qza
--verbose

It seems to work well until I encountered the following error:

Reading file /tmp/tmpo6cy75_r 100%
335415543 nt in 816440 seqs, min 195, max 451, avg 411
Sorting by abundance 100%
Counting k-mers 100%
Clustering 100%
Sorting clusters 100%
Writing clusters 100%
Clusters: 245334 Size min 1, max 730, avg 3.3
Singletons: 150055, 18.4% of seqs, 61.2% of clusters
File "/home/user/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in cluster_features_de_novo
File "/home/luser/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/home/user/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/action.py", line 418, in callable_executor
spec.qiime_type, output_view, spec.view_type, prov)
File "/home/user/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/result.py", line 273, in _from_view
provenance_capture=provenance_capture)
File "/home/user/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/core/archive/archiver.py", line 316, in from_data
Format.write(rec, type, format, data_initializer, provenance_capture)
File "/home/user/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/core/archive/format/v5.py", line 21, in write
provenance_capture)
File "/home/user/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/core/archive/format/v1.py", line 26, in write
prov_dir, [root / cls.METADATA_FILE, archive_record.version_fp])
File "/home/user/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/core/archive/provenance.py", line 318, in finalize
self.write_citations_bib()
File "/home/user/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/core/archive/provenance.py", line 309, in write_citations_bib
self.citations.save(str(self.path / self.CITATION_FILE))
File "/home/user/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/core/cite.py", line 71, in save
bp.dump(db, f, writer=writer)
File "/home/user/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/bibtexparser/init.py", line 111, in dump
bibtex_file.write(writer.write(bib_database))
UnicodeEncodeError: 'latin-1' codec can't encode character '\u0161' in position 3969: ordinal not in range(256)

Plugin error from vsearch:

'latin-1' codec can't encode character '\u0161' in position 3969: ordinal not in range(256)

See above for debug info.

We tried to fix the error using the following method:

1. activating qiime2
2. typing the following in the terminal export PYTHONNOUSERSITE=True
3. typing the following: export LC_ALL=en_US
4. run the analysis

However it still does not work. Does anyone have any idea to fix this issue?
Thank you very much in advance

[ChrisKeefe]

Hi @leila, I suspect you're on the right track here (looking at locale environment variables). You're probably looking for a locale that specifies .utf-8 or .UTF-8. The formatting (caps) depends on your system, and must be a perfect match.

I did a quick search for your error message, and there are a bunch of good topics troubleshooting this already. Start here, see if you can figure out what's going on, and let us know if it keeps giving you trouble!

[leila (LE)]

Thank you very much for your quick reply and advice!! I therefore typed the following command : LC_ALL=en_US.UTF-8 and it worked