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Is that a Bug? #17

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wsh-1046 opened this issue Oct 14, 2024 · 1 comment
Open

Is that a Bug? #17

wsh-1046 opened this issue Oct 14, 2024 · 1 comment

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@wsh-1046
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Hi le-yuan:
When I was operating the step
"python HGT_workflow_distant.py Nanorana_parkeri_SimID.faa",
I got a problem,which show below:
Taxid by BLAST: 7917
Taxid by BLAST: 13616
Alien index: 299.19
This is a HGT event
Accession_id: AAP36269.1
Evalue: 1.16e-130
Traceback (most recent call last):
File "/HGT/HGTphyloDetect/main/HGT_workflow_distant.py", line 222, in
main()
File "
/HGT/HGTphyloDetect/main/HGT_workflow_distant.py", line 196, in main
taxid2name = ncbi.get_taxid_translator([ranks2lineage['phylum'], ranks2lineage['class'], ranks2lineage['superkingdom']])
~~~~~~~~~~~~~^^^^^^^^^^
Traceback (most recent call last):
File "/HGT/HGTphyloDetect/main/HGT_workflow_distant.py", line 222, in
main()
File "
/HGT/HGTphyloDetect/main/HGT_workflow_distant.py", line 196, in main
taxid2name = ncbi.get_taxid_translator([ranks2lineage['phylum'], ranks2lineage['class'], ranks2lineage['superkingdom']])
~~~~~~~~~~~~~^^^^^^^^^^
KeyError: 'phylum'

Please tell me how to deal this problem. THANK YOU VERY MUCH!
BEST WISHES

@wsh-1046
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After I changed the script in HGT_workflow_distant.py in order to ignore the problem "KeyError:'phylum'",I have found that when I got into the next step,it would be interrupted often by the problem like this"This is gene 3------------------
XP_018426332.1
Yes, blast file already exists, nice!
Attention: please check the gene accession id!"
Please tell me how to deal with it.Thanks!

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