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AssertionError: Conflicting values found for "1111886". #186

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liushuqing506 opened this issue Aug 11, 2023 · 3 comments
Open

AssertionError: Conflicting values found for "1111886". #186

liushuqing506 opened this issue Aug 11, 2023 · 3 comments

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@liushuqing506
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liushuqing506 commented Aug 11, 2023

Input directory: align/minimap2/.
Number of alignment files to read: 1.
Demultiplexing: off.
Constructing classification system...
Parsing taxon names file: names.dmp... Done.
Parsing taxon nodes file: nodes.dmp... Done.
Parsing simple map file: taxid.map...Traceback (most recent call last):
File "/home/liusq/miniconda3/bin/woltka", line 8, in
sys.exit(cli())
File "/home/liusq/miniconda3/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/liusq/miniconda3/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/liusq/miniconda3/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/liusq/miniconda3/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/liusq/miniconda3/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return _callback(*args, **kwargs)
File "/home/liusq/miniconda3/lib/python3.10/site-packages/woltka/cli.py", line 187, in classify_cmd
workflow(**kwargs)
File "/home/liusq/miniconda3/lib/python3.10/site-packages/woltka/workflow.py", line 118, in workflow
tree, rankdic, namedic, root = build_hierarchy(
File "/home/liusq/miniconda3/lib/python3.10/site-packages/woltka/workflow.py", line 761, in build_hierarchy
update_dict(tree, map
)
File "/home/liusq/miniconda3/lib/python3.10/site-packages/woltka/util.py", line 75, in update_dict
add_dict(dic, key, value)
File "/home/liusq/miniconda3/lib/python3.10/site-packages/woltka/util.py", line 44, in add_dict
assert dic[key] == value, f'Conflicting values found for "{key}".'
AssertionError: Conflicting values found for "1111886".

@qiyunzhu
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@liushuqing506 It is probably because the TaxID "1111886" have multiple assignments in your taxonomy files. Can you check if that's the case?

@deppworld
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HI
I am facing the same problem with multiple IDs. I checked the reference file "enzyme-to-reaction.txt" which has multiple entries of these IDs. I do not know how to deal with this.

@qiyunzhu
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qiyunzhu commented Mar 6, 2024

@deppworld In this case, you may remove the multiple mapping, or use woltka collapse instead, as detailed here.

Is the reference file enzyme-to-reaction.txt from one of our repositories? i.e., http://ftp.microbio.me/pub/wol2/ or http://ftp.microbio.me/pub/wol-20April2021/ ? I could not find that file.

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