'ascii' codec

[yl030]

Hello ppanggolin team,
I installed ppanggolin through manual and when I run % ppanggolin all --anno genomes.gff.list

100%|██████████| 2675/2675 [17:46<00:00, 2.51file/s]

0%| | 0/2675 [00:00<?, ?genome/s]
0%| | 0/2675 [00:00<?, ?genome/s]
Traceback (most recent call last):
File "/gss1/App_os7/miniconda3/envs/ppanggolin/bin/ppanggolin", line 10, in
sys.exit(main())
^^^^^^
File "/gss1/App_os7/miniconda3/envs/ppanggolin/lib/python3.12/site-packages/ppanggolin/main.py", line 222, in main
ppanggolin.workflow.all.launch(args)
File "/gss1/App_os7/miniconda3/envs/ppanggolin/lib/python3.12/site-packages/ppanggolin/workflow/all.py", line 295, in launch
launch_workflow(args, panrgp=True, panmodule=True)
File "/gss1/App_os7/miniconda3/envs/ppanggolin/lib/python3.12/site-packages/ppanggolin/workflow/all.py", line 62, in launch_workflow
write_pangenome(pangenome, filename, args.force, disable_bar=args.disable_prog_bar)
File "/gss1/App_os7/miniconda3/envs/ppanggolin/lib/python3.12/site-packages/ppanggolin/formats/writeBinaries.py", line 709, in write_pangenome
write_annotations(pangenome, h5f, disable_bar=disable_bar)
File "/gss1/App_os7/miniconda3/envs/ppanggolin/lib/python3.12/site-packages/ppanggolin/formats/writeAnnotations.py", line 390, in write_annotations
write_organisms(pangenome, h5f, annotation, desc, disable_bar)
File "/gss1/App_os7/miniconda3/envs/ppanggolin/lib/python3.12/site-packages/ppanggolin/formats/writeAnnotations.py", line 74, in write_organisms
organism_row["name"] = org.name
~~~~~~~~~~~~^^^^^^^^
File "tables/tableextension.pyx", line 1673, in tables.tableextension.Row.setitem
UnicodeEncodeError: 'ascii' codec can't encode character '\ufeff' in position 0: ordinal not in range(128)
/gss1/App_os7/miniconda3/envs/ppanggolin/lib/python3.12/site-packages/tables/file.py:113: UnclosedFileWarning:

Closing remaining open file: ppanggolin_output_DATE2024-07-16_HOUR08.10.22_PID12964/pangenome.h5

[jpjarnoux]

Hi !

Could I know the source of the annotation files ?
It looks like there is an unknown field in your GFF.
Related issue that could help #222 #232 #233

Also if none of that help you. Could you share your files or a sample that reproduce the error ?

Regards

[CedricMidoux]

I had the same problem with \u2019 (’ in /product="ATPase/5’-3’ helicase helicase subunit RecD)

[Tsingsjeen]

Does this issue solved? I also tried with output files, .gff3 and gbff from bakta, neither of them worked and same report errors, "UnicodeEncodeError: 'ascii' codec...". I then back to .fna files, it works, but the annotation became less clear.

[Tsingsjeen]

Sorry for the spam, now worked following the solution above!

[JeanMainguy]

Hello,

Great to hear.

We have addressed this issue in PR #291 which will be in the next release.
So this problem should no longer occur.

[JeanMainguy]

With version 2.2.0, non-ASCII characters are now filtered out, which should prevent the error reported above.

Please don’t hesitate to reopen this issue or create a new one if the error reappears.

Thanks!