Ubuntu: rbcl fasta file run error

[Canxis]

Hi, I'm using the BOLDigger v1.5.6 with Python 3.8 and there was an error:

Traceback (most recent call last): File "/home/yao/.local/bin/boldigger", line 8, in sys.exit(main()) File "/home/yao/.local/lib/python3.8/site-packages/boldigger/main.py", line 108, in main boldblast_rbcl.main(session, values['fasta_path'], values['output_folder'], values['batch_size']) File "/home/yao/.local/lib/python3.8/site-packages/boldigger/boldblast_rbcl.py", line 70, in main tables = asyncio.run(as_session(links)) File "/usr/lib/python3.8/asyncio/runners.py", line 44, in run return loop.run_until_complete(main) File "/usr/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete return future.result() File "/home/yao/.local/lib/python3.8/site-packages/boldigger/boldblast_its.py", line 70, in as_session return await asyncio.gather(*tasks) File "/home/yao/.local/lib/python3.8/site-packages/boldigger/boldblast_its.py", line 46, in as_request table = pd.DataFrame([[0], ['No Match'] * 7 + [np.nan] * 3 + [''] * 2] * 20, File "/home/yao/.local/lib/python3.8/site-packages/pandas/core/frame.py", line 721, in init arrays, columns, index = nested_data_to_arrays( File "/home/yao/.local/lib/python3.8/site-packages/pandas/core/internals/construction.py", line 519, in nested_data_to_arrays arrays, columns = to_arrays(data, columns, dtype=dtype) File "/home/yao/.local/lib/python3.8/site-packages/pandas/core/internals/construction.py", line 883, in to_arrays content, columns = _finalize_columns_and_data(arr, columns, dtype) File "/home/yao/.local/lib/python3.8/site-packages/pandas/core/internals/construction.py", line 985, in _finalize_columns_and_data raise ValueError(err) from err ValueError: 13 columns passed, passed data had 12 columns

My input file is .fas file and contains 100 sequences, the batch size was set as 5. DO anyone know how to fix it ? Thanks a lot !!

[DominikBuchner]

Hi Canxis,

I rarely work with rbcl as a marker. If you can provide me with the file, I'll fix this issue.

[Canxis]

Hi Canxis,

I rarely work with rbcl as a marker. If you can provide me with the file, I'll fix this issue.

Thank you sooooo much! I have provided a txt file, since the upload interface can not recognize files in fas format. Thanks again for this powerful tool! ALIQC_100.txt

[filipamsmartins]

Hi @DominikBuchner , I am getting the same error. Any plans in place to address this issue? thanks a lot

[DominikBuchner]

I will tackle this in July!

filipamsmartins @.***> schrieb am Do., 29. Juni 2023, 17:50:

Hi @DominikBuchner https://github.com/DominikBuchner , I am getting the same error. Any plans in place to address this issue? thanks a lot

— Reply to this email directly, view it on GitHub https://github.com/DominikBuchner/BOLDigger/issues/11#issuecomment-1613445571, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJH6ILHYG7WGV4QBTTTF3RLXNWP3DANCNFSM5WWOU6TA . You are receiving this because you were mentioned.Message ID: @.***>

[DominikBuchner]

On the TODO for BOLDigger2, but I think rbcl and ITS are rarely used.