You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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
The text was updated successfully, but these errors were encountered:
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!
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/HGT/HGTphyloDetect/main/HGT_workflow_distant.py", line 196, in mainmain()
File "
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/HGT/HGTphyloDetect/main/HGT_workflow_distant.py", line 196, in mainmain()
File "
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
The text was updated successfully, but these errors were encountered: