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qiyunzhu / woltka

Woltka: a versatile meta'omic data classifier
BSD 3-Clause "New" or "Revised" License
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AssertionError: Conflicting values found for "1111886". #186

Open liushuqing506 opened 1 year ago

liushuqing506 commented 1 year ago

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 updatedict(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 commented 1 year ago

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

deppworld commented 8 months ago

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 commented 8 months ago

@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.