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hsgweon / pipits

Automated pipeline for analyses of fungal ITS from the Illumina
GNU General Public License v3.0
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Error: None zero returncode - biom.exception.TableException: Unsupported matrix data type. #33

Closed ckeuschn closed 5 years ago

ckeuschn commented 5 years ago

Hi

I installed pipits on macOS mojave as well as on a linux cluster, but I run into a similar problem, when testing on the included test files, as reportet here #20. Changing the local to en_US.UTF-8 could not solve the problem...

2019-05-26 18:17:44 Converting classic tabular OTU into a BIOM format [BIOM] Traceback (most recent call last): File "/home/ampere/ckeuschn/anaconda3/envs/pipits_env/bin/biom", line 11, in sys.exit(cli()) File "/home/ampere/ckeuschn/anaconda3/envs/pipits_env/lib/python3.6/site-packages/click/core.py", line 764, in call return self.main(args, kwargs) File "/home/ampere/ckeuschn/anaconda3/envs/pipits_env/lib/python3.6/site-packages/click/core.py", line 717, in main rv = self.invoke(ctx) File "/home/ampere/ckeuschn/anaconda3/envs/pipits_env/lib/python3.6/site-packages/click/core.py", line 1137, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/ampere/ckeuschn/anaconda3/envs/pipits_env/lib/python3.6/site-packages/click/core.py", line 956, in invoke return ctx.invoke(self.callback, ctx.params) File "/home/ampere/ckeuschn/anaconda3/envs/pipits_env/lib/python3.6/site-packages/click/core.py", line 555, in invoke return callback(args, **kwargs) File "/home/ampere/ckeuschn/anaconda3/envs/pipits_env/lib/python3.6/site-packages/biom/cli/table_converter.py", line 129, in convert table_type, process_obs_metadata, tsv_metadata_formatter) File "/home/ampere/ckeuschn/anaconda3/envs/pipits_env/lib/python3.6/site-packages/biom/cli/table_converter.py", line 207, in _convert write_biom_table(result, fmt, output_filepath) File "/home/ampere/ckeuschn/anaconda3/envs/pipits_env/lib/python3.6/site-packages/biom/cli/util.py", line 26, in write_biom_table f.write(table.to_json(biom.parse.generatedby())) File "/home/ampere/ckeuschn/anaconda3/envs/pipits_env/lib/python3.6/site-packages/biom/table.py", line 4278, in to_json raise TableException("Unsupported matrix data type.") biom.exception.TableException: Unsupported matrix data type. 2019-05-26 18:18:01 Error: None zero returncode: biom convert -i out_process/intermediate/otu_table_prelim.txt -o out_process/intermediate/otu_table_prelim.biom --table-type="OTU table" --to-json

Any help is appreciated Thanks

hsgweon commented 5 years ago

Sorry @ckeuschn Thanks for letting me know about this. I'm resolving it at the moment (it's mostly done actually). I will let you know when this has been fixed and conda package has been updated.

ckeuschn commented 5 years ago

Great thanks a lot!

hsgweon commented 5 years ago

All done. Can you please remove pipits_env and try all again? You can remove the previous env by: conda remove --name pipits_env --all Please do let me know how it goes?

ckeuschn commented 5 years ago

I uninstalled and installed pipits as you told and after setting locale to en_US.utf8 everything worked without problems in the test directory. Thanks for the quick support!

hsgweon commented 5 years ago

Perfect. Good luck with your analyses and if you need any help regarding PIPITS, do let me know.