Hi there,
I have been using the following code to create markers.faa. My goi file is 72k sequences with a size of 27MB, and my reference is the Uniref90 file. The command I used is:
shortbred_identify.py --goi Bacterial.fasta --ref uniref90.fasta --markers Bacterial_markers.faa --tmp tmp
It has been running for over 30 hours, but it still seems to be stuck at the same point. I noticed that it hasn’t generated new output for the past 24 hours, and the process appears to be stuck at the following step:
Making BLAST database for the family consensus sequences...
Making BLAST database for the reference protein sequences...
BLASTing the consensus family sequences against themselves...
BLASTing the consensus family sequences against the reference protein sequences...
Is this normal, or should I be concerned about a potential issue? Any suggestions would be appreciated.
Best