# macsyfinder 20230505.dev
# models : TFF-SF-0.0b2
# /home/bneron/Projects/GEM/MacSyFinder/MacSyFinder/py311/bin/macsyfinder --db-type gembase --models-dir tests/data/models/ --models TFF-SF all -w 5 --sequence-db tests/data/base/gembase_w_slow_genome.fa --timeout 2 --out-dir functional_test_timeout --index-dir .
#
# WARNING: The replicon 'THHY002.0321.00001.C001' has been SKIPPED. Cannot be solved before timeout.
#
# Rejected candidates:

Cluster:
- model = Archaeal-T4P
- replicon = PSAV001.0321.00001.C001
- hits = (PSAV001.0321.00001.C001_02925, Archaeal-T4P_arCOG04148, 2722), (PSAV001.0321.00001.C001_02931, Archaeal-T4P_arCOG05613, 2728)
This candidate has been rejected because:
	- The quorum of mandatory genes required (3) is not reached: 0
	- The quorum of genes required (3) is not reached: 2
============================================================
Cluster:
- model = ComM
- replicon = PSAV001.0321.00001.C001
- hits = (PSAV001.0321.00001.C001_01837, ComM_comEC, 1699)
This candidate has been rejected because:
	- The quorum of mandatory genes required (4) is not reached: 1
	- The quorum of genes required (4) is not reached: 1
============================================================
Cluster:
- model = T2SS
- replicon = PSAV001.0321.00001.C001
- hits = (PSAV001.0321.00001.C001_01018, T4P_pilD, 926)
This candidate has been rejected because:
	- The quorum of mandatory genes required (4) is not reached: 1
	- The quorum of genes required (6) is not reached: 1
============================================================
Cluster:
- model = T4P
- replicon = PSAV001.0321.00001.C001
- hits = (PSAV001.0321.00001.C001_00876, T4P_fimT, 816), (PSAV001.0321.00001.C001_00877, T4P_fimT, 817), (PSAV001.0321.00001.C001_00878, T4P_pilV, 818), (PSAV001.0321.00001.C001_00879, T4P_pilW, 819), (PSAV001.0321.00001.C001_00880, T4P_pilX, 820), (PSAV001.0321.00001.C001_00881, T4P_pilY, 821), (PSAV001.0321.00001.C001_00882, T4P_pilE, 822)
This candidate has been rejected because:
	- The quorum of mandatory genes required (4) is not reached: 1
============================================================
Cluster:
- model = T4P
- replicon = PSAV001.0321.00001.C001
- hits = (PSAV001.0321.00001.C001_00876, T4P_fimT, 816), (PSAV001.0321.00001.C001_00877, T4P_fimT, 817), (PSAV001.0321.00001.C001_00878, T4P_pilV, 818), (PSAV001.0321.00001.C001_00879, T4P_pilW, 819), (PSAV001.0321.00001.C001_00880, T4P_pilX, 820), (PSAV001.0321.00001.C001_00881, T4P_pilY, 821), (PSAV001.0321.00001.C001_00882, T4P_pilE, 822)
Cluster:
- model = T4P
- replicon = PSAV001.0321.00001.C001
- hits = (PSAV001.0321.00001.C001_04959, T4P_pilT, 4643)
This candidate has been rejected because:
	- The quorum of mandatory genes required (4) is not reached: 2
============================================================
Cluster:
- model = T4P
- replicon = PSAV001.0321.00001.C001
- hits = (PSAV001.0321.00001.C001_01018, T4P_pilD, 926), (PSAV001.0321.00001.C001_01019, T4P_pilC, 927), (PSAV001.0321.00001.C001_01020, T4P_pilB, 928), (PSAV001.0321.00001.C001_01021, T4P_pilA, 929)
This candidate has been rejected because:
	- The quorum of mandatory genes required (4) is not reached: 3
	- The quorum of genes required (5) is not reached: 4
============================================================
Cluster:
- model = T4P
- replicon = PSAV001.0321.00001.C001
- hits = (PSAV001.0321.00001.C001_04959, T4P_pilT, 4643)
This candidate has been rejected because:
	- The quorum of mandatory genes required (4) is not reached: 1
	- The quorum of genes required (5) is not reached: 1
============================================================
Cluster:
- model = T4P
- replicon = PSAV001.0321.00001.C001
- hits = (PSAV001.0321.00001.C001_05037, MSH_mshM, 4719), (PSAV001.0321.00001.C001_05040, T4P_pilQ, 4722), (PSAV001.0321.00001.C001_05041, T4P_pilP, 4723), (PSAV001.0321.00001.C001_05042, T4P_pilO, 4724), (PSAV001.0321.00001.C001_05043, T4P_pilN, 4725), (PSAV001.0321.00001.C001_05044, T4P_pilM, 4726)
This candidate has been rejected because:
	- The quorum of mandatory genes required (4) is not reached: 3
============================================================
Cluster:
- model = Tad
- replicon = PSAV001.0321.00001.C001
- hits = (PSAV001.0321.00001.C001_04742, Tad_tadE, 4431), (PSAV001.0321.00001.C001_04743, Tad_tadV, 4432)
This candidate has been rejected because:
	- The quorum of mandatory genes required (4) is not reached: 1
	- The quorum of genes required (6) is not reached: 2
============================================================
Cluster:
- model = Archaeal-T4P
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_00250, Archaeal-T4P_arCOG02900, 7538), (XAOR001.0321.00001.C001_00244, T4P_pilQ, 7534)
This candidate has been rejected because:
	- There is 1 forbidden genes occurrence(s): T4P_pilQ
	- The quorum of mandatory genes required (3) is not reached: 0
	- The quorum of genes required (3) is not reached: 1
============================================================
Cluster:
- model = ComM
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_01504, ComM_comEC, 8557)
This candidate has been rejected because:
	- The quorum of mandatory genes required (4) is not reached: 1
	- The quorum of genes required (4) is not reached: 1
============================================================
Cluster:
- model = T2SS
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_00037, Tad_tadD, 7362), (XAOR001.0321.00001.C001_00040, Tad_tadD, 7365)
This candidate has been rejected because:
	- The quorum of mandatory genes required (4) is not reached: 0
	- The quorum of genes required (6) is not reached: 1
============================================================
Cluster:
- model = T2SS
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_00037, Tad_tadD, 7362), (XAOR001.0321.00001.C001_00040, Tad_tadD, 7365)
Cluster:
- model = T2SS
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_02935, T4P_pilD, 9760)
This candidate has been rejected because:
	- The quorum of mandatory genes required (4) is not reached: 1
	- The quorum of genes required (6) is not reached: 2
============================================================
Cluster:
- model = T2SS
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_02935, T4P_pilD, 9760)
This candidate has been rejected because:
	- The quorum of mandatory genes required (4) is not reached: 1
	- The quorum of genes required (6) is not reached: 1
============================================================
Cluster:
- model = T4P
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_00240, T4P_pilM, 7530), (XAOR001.0321.00001.C001_00241, T4P_pilN, 7531), (XAOR001.0321.00001.C001_00242, T4P_pilO, 7532), (XAOR001.0321.00001.C001_00243, T4P_pilP, 7533), (XAOR001.0321.00001.C001_00244, T4P_pilQ, 7534)
This candidate has been rejected because:
	- The quorum of mandatory genes required (4) is not reached: 3
============================================================
Cluster:
- model = T4P
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_00240, T4P_pilM, 7530), (XAOR001.0321.00001.C001_00241, T4P_pilN, 7531), (XAOR001.0321.00001.C001_00242, T4P_pilO, 7532), (XAOR001.0321.00001.C001_00243, T4P_pilP, 7533), (XAOR001.0321.00001.C001_00244, T4P_pilQ, 7534)
Cluster:
- model = T4P
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_03253, T4P_pilA, 10027)
This candidate has been rejected because:
	- The quorum of mandatory genes required (4) is not reached: 3
============================================================
Cluster:
- model = T4P
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_00601, T4P_pilU, 7819), (XAOR001.0321.00001.C001_00602, T4P_pilT, 7820)
This candidate has been rejected because:
	- The quorum of mandatory genes required (4) is not reached: 1
	- The quorum of genes required (5) is not reached: 2
============================================================
Cluster:
- model = T4P
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_00601, T4P_pilU, 7819), (XAOR001.0321.00001.C001_00602, T4P_pilT, 7820)
Cluster:
- model = T4P
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_00872, T4P_fimT, 8028), (XAOR001.0321.00001.C001_00873, T4P_pilV, 8029), (XAOR001.0321.00001.C001_00874, T4P_pilW, 8030), (XAOR001.0321.00001.C001_00876, T4P_pilY, 8032), (XAOR001.0321.00001.C001_00877, T4P_pilE, 8033), (XAOR001.0321.00001.C001_00879, T4P_fimT, 8034)
This candidate has been rejected because:
	- The quorum of mandatory genes required (4) is not reached: 2
============================================================
Cluster:
- model = T4P
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_00601, T4P_pilU, 7819), (XAOR001.0321.00001.C001_00602, T4P_pilT, 7820)
Cluster:
- model = T4P
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_00872, T4P_fimT, 8028), (XAOR001.0321.00001.C001_00873, T4P_pilV, 8029), (XAOR001.0321.00001.C001_00874, T4P_pilW, 8030), (XAOR001.0321.00001.C001_00876, T4P_pilY, 8032), (XAOR001.0321.00001.C001_00877, T4P_pilE, 8033), (XAOR001.0321.00001.C001_00879, T4P_fimT, 8034)
Cluster:
- model = T4P
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_03253, T4P_pilA, 10027)
This candidate has been rejected because:
	- The quorum of mandatory genes required (4) is not reached: 2
============================================================
Cluster:
- model = T4P
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_00601, T4P_pilU, 7819), (XAOR001.0321.00001.C001_00602, T4P_pilT, 7820)
Cluster:
- model = T4P
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_03253, T4P_pilA, 10027)
This candidate has been rejected because:
	- The quorum of mandatory genes required (4) is not reached: 1
	- The quorum of genes required (5) is not reached: 3
============================================================
Cluster:
- model = T4P
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_00872, T4P_fimT, 8028), (XAOR001.0321.00001.C001_00873, T4P_pilV, 8029), (XAOR001.0321.00001.C001_00874, T4P_pilW, 8030), (XAOR001.0321.00001.C001_00876, T4P_pilY, 8032), (XAOR001.0321.00001.C001_00877, T4P_pilE, 8033), (XAOR001.0321.00001.C001_00879, T4P_fimT, 8034)
This candidate has been rejected because:
	- The quorum of mandatory genes required (4) is not reached: 1
============================================================
Cluster:
- model = T4P
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_00872, T4P_fimT, 8028), (XAOR001.0321.00001.C001_00873, T4P_pilV, 8029), (XAOR001.0321.00001.C001_00874, T4P_pilW, 8030), (XAOR001.0321.00001.C001_00876, T4P_pilY, 8032), (XAOR001.0321.00001.C001_00877, T4P_pilE, 8033), (XAOR001.0321.00001.C001_00879, T4P_fimT, 8034)
Cluster:
- model = T4P
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_03253, T4P_pilA, 10027)
This candidate has been rejected because:
	- The quorum of mandatory genes required (4) is not reached: 1
============================================================
Cluster:
- model = T4P
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_02929, T4P_pilB, 9754), (XAOR001.0321.00001.C001_02933, T4P_pilE, 9758), (XAOR001.0321.00001.C001_02934, T4P_pilC, 9759), (XAOR001.0321.00001.C001_02935, T4P_pilD, 9760)
This candidate has been rejected because:
	- The quorum of genes required (5) is not reached: 4
============================================================
Cluster:
- model = T4P
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_03253, T4P_pilA, 10027)
This candidate has been rejected because:
	- The quorum of mandatory genes required (4) is not reached: 0
	- The quorum of genes required (5) is not reached: 1
============================================================
Cluster:
- model = Tad
- replicon = XAOR001.0321.00001.C001
- hits = (XAOR001.0321.00001.C001_00037, Tad_tadD, 7362), (XAOR001.0321.00001.C001_00040, Tad_tadD, 7365)
This candidate has been rejected because:
	- The quorum of mandatory genes required (4) is not reached: 0
	- The quorum of genes required (6) is not reached: 1
============================================================
