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taxid #137

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duxi190914 opened this issue Aug 21, 2024 · 9 comments
Open

taxid #137

duxi190914 opened this issue Aug 21, 2024 · 9 comments

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@duxi190914
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Homology search started at 2024-08-21 08:40:06.163220.
Settings:
Search method: diamond.
Self-alignment method: native.
Remote fetch enabled: no.
Reading input proteins...
Sulfurospirillum_multivorans: 3224 proteins.
Done. Read 3224 proteins from 1 samples.
Dropping sequences shorter than 30 aa... done.
Reading local taxonomy database... done.
Read 2597948 taxa.
Batch homology search of Sulfurospirillum_multivorans started at 2024-08-21 08:40:16.227200.
Number of queries: 3223.
WARNING: Cannot obtain taxIds for 470074 sequences. These hits will be dropped.
There are so many taxIds that have not been obtained, will it affect the results

@qiyunzhu
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It will. Could there be some issues with the database? If it was automatically generated from NCBI, all sequences should have taxIDs.

@duxi190914
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duxi190914 commented Aug 27, 2024 via email

@qiyunzhu
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Hi @duxi190914 It could be that NCBI has updated its database structure such that the existing HGTector pulls more than expected. It is totally fine to use the 50G database.

@duxi190914
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duxi190914 commented Aug 28, 2024 via email

@duxi190914
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duxi190914 commented Sep 7, 2024 via email

@qiyunzhu
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Hello @duxi190914 It you disable remote fetch, it may resolve the problem. Remote fetch could introduce instability of the taxonomy structure.

@duxi190914
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duxi190914 commented Sep 25, 2024 via email

@qiyunzhu
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Hi @duxi190914 it could be 20% of the genome, but usually one should be critical if that's the output. Adjusting the parameters, especially the definition of self / close / distal groups, can help to refine your results. Under the default mode, the program will automatically define the three groups based on the taxonomy tree, which may or may not be what you want.

@duxi190914
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duxi190914 commented Oct 17, 2024 via email

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