Describe the bug
I noticed specific hit in the hmmer out file is neither present in the best_solution nor in the rejected list.
To Reproduce
Steps to reproduce the behavior:
- macsyfinder --db-type gembase -w 0 --sequence-db proteins.fasta --models CONJScan/Plasmids all -o CONJScan/result
- $ls -lh 1.8G Dec 1 15:20 proteins.fasta
- proteins are named after >plasmidID_proteinID
Expected behavior
All the proteins fullfill the GA score in each profile will be reported either in best_solution or rejected list.
Please complete the following information):
OS:
MacSyFinder Version:
2.1.4, I am testing 2.1.6 but I think should be the same
Additional context
This param i-evalue-sel default=0.001 and the coverage-profile are independent, given one large gembase file, E-value in the hmmer result increases, the proteins barely have a score above the GA cutoff will not be picked up by MSF. They should be disabled when there is a GA score available in the hmm profile and not GA 0 0.
Describe the bug
I noticed specific hit in the hmmer out file is neither present in the best_solution nor in the rejected list.
To Reproduce
Steps to reproduce the behavior:
Expected behavior
All the proteins fullfill the GA score in each profile will be reported either in best_solution or rejected list.
Please complete the following information):
OS:
MacSyFinder Version:
2.1.4, I am testing 2.1.6 but I think should be the same
Additional context
This param i-evalue-sel default=0.001 and the coverage-profile are independent, given one large gembase file, E-value in the hmmer result increases, the proteins barely have a score above the GA cutoff will not be picked up by MSF. They should be disabled when there is a GA score available in the hmm profile and not GA 0 0.