search

SysBioChalmers / HGTphyloDetect

HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.
MIT License
30 stars 5 forks source link

Problem with running HGTphyloDetect #12

Closed mainakbioinfo closed 5 months ago

mainakbioinfo commented 7 months ago

I have retrieved a protein sequence for the gene with Genbank acc.id AAK99679.1 (its a prokaryotic gene) and run the blastp in the 'main' directory of the tool by using the command **_python blastp.py input.fasta_ and the blastp file was successfully generated in the designated folder. In the next step, for Horizontally transferred gene dectection, I run the command _python HGT_workflowclose.py input.fasta (for prokaryote to prokaryote). Unfortunately, the following error message popped up: This is gene 1------------------ AAK99679.1 Yes, blast file already exists, nice! `Attention:` please check the gene accession id!** I have tried the same multiple times but the same error continued to occur. Please help! I need my analysis to be done at the earliest! Waiting for your positive response!

cslamo commented 6 months ago

same here. tried different proteins that were obtained from ncbi/protein and I get the 'not found' error.

le-yuan commented 5 months ago

Sorry for the late reply! I am recently super busy in working on my new projects. For a few proteins that does not have specific subphylum (taxonomy id), HGTphyloDetect can not give the HGT identification result. This is defined by the workflow of HGTphyloDetect. But we will consider your feedback for the improvement of our computational toolbox.

Thanks for your attention! Best, Le