Greetings!
I wanted to check out the redbiom tool to extract the soil data and sort by abundance in order to get the top 50 genera in the data.
From that, I can create an artificial community with known composition. From there, I can proceed with InSilicoSeq to benchmark my parameters in qiime2.
But during the process, I kept getting this error:
Traceback (most recent call last):
File "/home/quan/miniconda3/bin/redbiom", line 10, in
sys.exit(cli())
^^^^^
File "/home/quan/miniconda3/lib/python3.12/site-packages/click/core.py", line 1442, in call
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/quan/miniconda3/lib/python3.12/site-packages/click/core.py", line 1363, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/home/quan/miniconda3/lib/python3.12/site-packages/click/core.py", line 1830, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/quan/miniconda3/lib/python3.12/site-packages/click/core.py", line 1830, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/quan/miniconda3/lib/python3.12/site-packages/click/core.py", line 1226, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/quan/miniconda3/lib/python3.12/site-packages/click/core.py", line 794, in invoke
return callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/quan/miniconda3/lib/python3.12/site-packages/redbiom/commands/fetch.py", line 225, in fetch_samples_from_samples
table, ambig = redbiom.fetch.data_from_samples(context, iterable,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/quan/miniconda3/lib/python3.12/site-packages/redbiom/fetch.py", line 306, in data_from_samples
return _biom_from_samples(context, samples, skip_taxonomy=skip_taxonomy)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/quan/miniconda3/lib/python3.12/site-packages/redbiom/fetch.py", line 399, in _biom_from_samples
table.update_ids(rimap)
File "/home/quan/miniconda3/lib/python3.12/site-packages/biom/table.py", line 1425, in update_ids
max_str_len = max([len(v) for v in id_map.values()])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: max() iterable argument is empty
The command I used was:
export CTX=Deblur_2021.09-Illumina-16S-V3-V4-250nt-8b2bff
redbiom search metadata "where empo_3=='Soil (non-saline)'" > soil_samples.txt
redbiom fetch samples --from soil_samples.txt --context $CTX --output soil_samples.biom
I also tried to change the context:
Deblur_2021.09-Illumina-16S-V3-V4-150nt-ac8c0b
Pick_closed-reference_OTUs-Greengenes-ILLUMINA-16S-V3-V4-150nt-bd7d4d
I also tried the context in the Redbiom github:
export ctx=Pick_closed-reference_OTUs-Greengenes-Illumina-16S-V4-5c6506
redbiom search metadata beer | redbiom fetch samples --context $ctx --output example.biom
The result is also an error: Traceback (most recent call last):
File "/home/quan/miniconda3/bin/redbiom", line 10, in
sys.exit(cli())
^^^^^
File "/home/quan/miniconda3/lib/python3.12/site-packages/click/core.py", line 1442, in call
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/quan/miniconda3/lib/python3.12/site-packages/click/core.py", line 1363, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/home/quan/miniconda3/lib/python3.12/site-packages/click/core.py", line 1830, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/quan/miniconda3/lib/python3.12/site-packages/click/core.py", line 1830, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/quan/miniconda3/lib/python3.12/site-packages/click/core.py", line 1226, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/quan/miniconda3/lib/python3.12/site-packages/click/core.py", line 794, in invoke
return callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/quan/miniconda3/lib/python3.12/site-packages/redbiom/commands/fetch.py", line 225, in fetch_samples_from_samples
table, ambig = redbiom.fetch.data_from_samples(context, iterable,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/quan/miniconda3/lib/python3.12/site-packages/redbiom/fetch.py", line 306, in data_from_samples
return _biom_from_samples(context, samples, skip_taxonomy=skip_taxonomy)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/quan/miniconda3/lib/python3.12/site-packages/redbiom/fetch.py", line 367, in biom_from_samples
data = se(fetch_sample, 0, context, id)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/quan/miniconda3/lib/python3.12/site-packages/redbiom/_requests.py", line 112, in f
return json.loads(req.json()['EVALSHA'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/quan/miniconda3/lib/python3.12/json/init.py", line 339, in loads
raise TypeError(f'the JSON object must be str, bytes or bytearray, '
TypeError: the JSON object must be str, bytes or bytearray, not list
I'm kinda stuck with this. I also don't know if my approach toward my matter is correct or not as well 