npcarter
commented
2 years ago Hello,
This patch seems to be doing the right thing in terms of letting one restrict the set of HMMs searched, but I have a question about the output the pipeline statistics that are returned. In my tests, when I run a search against an HMM database with --hmmdb-ranges, I can tell from the worker node output that a subset of the database is being searched, but the output from hmmc2 shows that the number of models is the full size of the database. Is what what you want to happen for this?
Example output from two searches via hmmc2, one without --hmmdb_ranges, one with, showing that the Target Models line of the output is the same in both cases:
Enter next sequence: @--hmmdb 1
test YLGPWVQAEY /// Sending data 32: Internal pipeline statistics summary:
Query sequence(s): 1 (0 residues searched) Target model(s): 19632 (0 nodes) Passed MSV filter: 62 (0.00315811); expected 392.6 (0.02) Passed bias filter: 53 (0.00269967); expected 392.6 (0.02) Passed Vit filter: 0 (0); expected 19.6 (0.001) Passed Fwd filter: 0 (0); expected 0.2 (1e-05) Initial search space (Z): 19632 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold]
CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.03
Mc/sec: 0.00
// Total bytes received 122
Enter next sequence: @--hmmdb 1 --hmmdb_ranges 1..10
test YLGPWVQAEY // Sending data 52: Internal pipeline statistics summary:
Query sequence(s): 1 (0 residues searched) Target model(s): 19632 (0 nodes) Passed MSV filter: 0 (0); expected 392.6 (0.02) Passed bias filter: 0 (0); expected 392.6 (0.02) Passed Vit filter: 0 (0); expected 19.6 (0.001) Passed Fwd filter: 0 (0); expected 0.2 (1e-05) Initial search space (Z): 19632 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold]
CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.04
Mc/sec: 0.00
// Total bytes received 122
Implements hmmdb_ranges option much like seqdb_ranges one.