-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_8287156-8505681

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for GeneMark_model.1610_t
Valid prediction for GlimmerHMM_glimmerT_1201-T1
Valid prediction for GeneMark_model.1596_t
Valid prediction for GeneMark_model.1599_t
Valid prediction for Augustus_model.g880.t1
Valid prediction for snap_scaffold_1-snap.1517-T1
Valid prediction for GeneMark_model.1578_t
Valid prediction for Augustus_model.g876.t1
Valid prediction for snap_scaffold_1-snap.1535-T1
Valid prediction for Augustus_model.g869.t1
Valid prediction for GeneMark_model.1606_t
Valid prediction for GeneMark_model.1598_t
Valid prediction for GeneMark_model.1614_t
Valid prediction for snap_scaffold_1-snap.1512-T1
Valid prediction for snap_scaffold_1-snap.1508-T1
Valid prediction for Augustus_model.g879.t1
Valid prediction for snap_scaffold_1-snap.1503-T1
Valid prediction for GlimmerHMM_glimmerT_1210-T1
Valid prediction for GeneMark_model.1586_t
Valid prediction for snap_scaffold_1-snap.1519-T1
Valid prediction for snap_scaffold_1-snap.1525-T1
Valid prediction for GeneMark_model.1602_t
Valid prediction for snap_scaffold_1-snap.1533-T1
Valid prediction for GlimmerHMM_glimmerT_1212-T1
Valid prediction for snap_scaffold_1-snap.1518-T1
Valid prediction for pasa_asmbl_1926.p1
Valid prediction for GeneMark_model.1617_t
Valid prediction for GeneMark_model.1583_t
Valid prediction for GeneMark_model.1571_t
Valid prediction for snap_scaffold_1-snap.1492-T1
Valid prediction for snap_scaffold_1-snap.1531-T1
Valid prediction for GeneMark_model.1620_t
Valid prediction for GeneMark_model.1612_t
Valid prediction for GlimmerHMM_glimmerT_1221-T1
Couldn't classify 158521, 158619
Couldn't classify 163598, 163630
Sorry, prediction pasa_asmbl_2794.p1 fails validation.
(ATT)	 GA	158521-158619	GT	GCG
(GTA)	 AG	161026-161193	GT	GGG
(TCA)	 AG	162799-162891	GT	CGG
(TTC)	 AG	163598-163630	GT	AGG
-recovered pasa_asmbl_2794.p1, internal, 161026, 161193
-recovered pasa_asmbl_2794.p1, internal, 162799, 162891
-recovered pasa_asmbl_2794.p1, internal, 163598, 163630
Valid prediction for Augustus_model.g872.t1
Valid prediction for HiQ_model.g875.t1
Valid prediction for GlimmerHMM_glimmerT_1222-T1
Valid prediction for GeneMark_model.1568_t
Valid prediction for GeneMark_model.1613_t
Valid prediction for GlimmerHMM_glimmerT_1206-T1
Valid prediction for Augustus_model.g868.t1
Valid prediction for snap_scaffold_1-snap.1513-T1
Valid prediction for snap_scaffold_1-snap.1500-T1
Valid prediction for snap_scaffold_1-snap.1498-T1
Valid prediction for GlimmerHMM_glimmerT_1207-T1
Valid prediction for GeneMark_model.1588_t
Valid prediction for GeneMark_model.1580_t
Valid prediction for snap_scaffold_1-snap.1514-T1
Valid prediction for GeneMark_model.1582_t
Valid prediction for GeneMark_model.1604_t
Valid prediction for GlimmerHMM_glimmerT_1220-T1
Couldn't classify 183191, 183301
Couldn't classify 185746, 185861
Sorry, prediction pasa_asmbl_2742.p1 fails validation.
(CCA)	 CT	183191-183301	GT	AGG
(CCT)	 AG	184661-184751	GT	AGG
(AGT)	 AG	184918-185065	GT	AGG
(TCG)	 AG	185235-185452	GT	TGG
(TGA)	 AG	185746-185861	GT	AGG
-recovered pasa_asmbl_2742.p1, internal, 184661, 184751
-recovered pasa_asmbl_2742.p1, internal, 184918, 185065
-recovered pasa_asmbl_2742.p1, internal, 185235, 185452
-recovered pasa_asmbl_2742.p1, internal, 185746, 185861
Valid prediction for GeneMark_model.1591_t
Valid prediction for GlimmerHMM_glimmerT_1214-T1
Valid prediction for GlimmerHMM_glimmerT_1217-T1
Valid prediction for GlimmerHMM_glimmerT_1215-T1
Valid prediction for Augustus_model.g878.t1
Valid prediction for GeneMark_model.1576_t
Valid prediction for GlimmerHMM_glimmerT_1211-T1
Valid prediction for snap_scaffold_1-snap.1501-T1
Valid prediction for snap_scaffold_1-snap.1491-T1
Valid prediction for snap_scaffold_1-snap.1522-T1
Valid prediction for GeneMark_model.1573_t
Valid prediction for Augustus_model.g871.t1
Valid prediction for snap_scaffold_1-snap.1507-T1
Valid prediction for snap_scaffold_1-snap.1510-T1
Valid prediction for GlimmerHMM_glimmerT_1208-T1
Valid prediction for GeneMark_model.1589_t
Valid prediction for GlimmerHMM_glimmerT_1216-T1
Couldn't classify 186628, 186752
Sorry, prediction pasa_asmbl_2735.p1 fails validation.
(TTT)	 GG	186628-186752	GT	AGG
(TGA)	 AG	187399-187480	GT	TGG
(AGC)	 AG	187736-187834	GT	AGG
(AAG)	 AG	188220-188366	GT	AGG
(GCT)	 AG	188581-188662	GT	AGG
(ATG)	 AG	188959-189105	GT	CAG
(ACC)	 AG	189611-189792	CA	GAC
add_exon() Sorry, pasa_asmbl_2735.p1 188959-189105-initial-1 is invalid.
-recovered pasa_asmbl_2735.p1, initial, 188959, 189105
-recovered pasa_asmbl_2735.p1, terminal, 189611, 189792
-recovered pasa_asmbl_2735.p1, internal, 187399, 187480
-recovered pasa_asmbl_2735.p1, internal, 187736, 187834
-recovered pasa_asmbl_2735.p1, internal, 188220, 188366
-recovered pasa_asmbl_2735.p1, internal, 188581, 188662
-recovered pasa_asmbl_2735.p1, internal, 188959, 189105
Valid prediction for snap_scaffold_1-snap.1496-T1
Valid prediction for GeneMark_model.1608_t
Valid prediction for GeneMark_model.1593_t
Valid prediction for GeneMark_model.1619_t
Valid prediction for GlimmerHMM_glimmerT_1224-T1
Valid prediction for GlimmerHMM_glimmerT_1209-T1
Valid prediction for snap_scaffold_1-snap.1493-T1
Valid prediction for GeneMark_model.1615_t
Valid prediction for GlimmerHMM_glimmerT_1205-T1
Valid prediction for GeneMark_model.1574_t

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for Augustus_model.g866.t1
Valid prediction for GeneMark_model.1572_t
Valid prediction for snap_scaffold_1-snap.1516-T1
Valid prediction for GeneMark_model.1587_t
Valid prediction for Augustus_model.g883.t1
Valid prediction for GlimmerHMM_glimmerT_1223-T1
Valid prediction for GlimmerHMM_glimmerT_1199-T1
Valid prediction for GeneMark_model.1595_t
Valid prediction for Augustus_model.g865.t1
Valid prediction for GeneMark_model.1609_t
Valid prediction for GeneMark_model.1601_t
Valid prediction for GeneMark_model.1581_t
Valid prediction for GlimmerHMM_glimmerT_1203-T1
Valid prediction for Augustus_model.g867.t1
Valid prediction for GlimmerHMM_glimmerT_1202-T1
Valid prediction for GeneMark_model.1597_t
Valid prediction for snap_scaffold_1-snap.1526-T1
Valid prediction for snap_scaffold_1-snap.1521-T1
Valid prediction for Augustus_model.g873.t1
Valid prediction for snap_scaffold_1-snap.1505-T1
Valid prediction for snap_scaffold_1-snap.1494-T1
Valid prediction for snap_scaffold_1-snap.1537-T1
Valid prediction for GeneMark_model.1575_t
Valid prediction for snap_scaffold_1-snap.1528-T1
Valid prediction for snap_scaffold_1-snap.1532-T1
Valid prediction for GeneMark_model.1616_t
Valid prediction for GlimmerHMM_glimmerT_1200-T1
Valid prediction for GeneMark_model.1603_t
Valid prediction for snap_scaffold_1-snap.1524-T1
Couldn't classify 496, 1029
Sorry, prediction pasa_asmbl_456.p1 fails validation.
(GAT)	 CC	496-1029	GC	TGG
Valid prediction for GeneMark_model.1567_t
Valid prediction for GeneMark_model.1566_t
Valid prediction for Augustus_model.g882.t1
Valid prediction for GeneMark_model.1605_t
Valid prediction for snap_scaffold_1-snap.1499-T1
Valid prediction for GeneMark_model.1607_t
Valid prediction for snap_scaffold_1-snap.1520-T1
Valid prediction for GeneMark_model.1570_t
Valid prediction for Augustus_model.g874.t1
Valid prediction for Augustus_model.g864.t1
Valid prediction for snap_scaffold_1-snap.1504-T1
Valid prediction for GeneMark_model.1618_t
Valid prediction for GeneMark_model.1577_t
Valid prediction for snap_scaffold_1-snap.1515-T1
Valid prediction for snap_scaffold_1-snap.1534-T1
Valid prediction for snap_scaffold_1-snap.1530-T1
Valid prediction for snap_scaffold_1-snap.1511-T1
Valid prediction for Augustus_model.g870.t1
Valid prediction for GlimmerHMM_glimmerT_1213-T1
Valid prediction for GeneMark_model.1569_t
Valid prediction for snap_scaffold_1-snap.1497-T1
Valid prediction for GlimmerHMM_glimmerT_1225-T1
Valid prediction for GeneMark_model.1621_t
Valid prediction for GeneMark_model.1579_t
Valid prediction for snap_scaffold_1-snap.1529-T1
Valid prediction for GeneMark_model.1592_t
Valid prediction for GlimmerHMM_glimmerT_1218-T1
Valid prediction for GeneMark_model.1594_t
Valid prediction for GeneMark_model.1611_t
Valid prediction for Augustus_model.g877.t1
Valid prediction for snap_scaffold_1-snap.1506-T1
Valid prediction for snap_scaffold_1-snap.1536-T1
Valid prediction for GlimmerHMM_glimmerT_1219-T1
Couldn't classify 11751, 11796
Sorry, prediction pasa_asmbl_455.p1 fails validation.
(AAC)	 CT	11751-11796	GT	CGG
(GCG)	 AG	11899-12033	GT	CAG
(GTG)	 AG	12135-12283	GT	AGG
(GTG)	 AG	12469-12654	AC	AGA
-recovered pasa_asmbl_455.p1, terminal, 12469, 12654
-recovered pasa_asmbl_455.p1, internal, 11899, 12033
-recovered pasa_asmbl_455.p1, internal, 12135, 12283
Valid prediction for snap_scaffold_1-snap.1509-T1
Valid prediction for GlimmerHMM_glimmerT_1204-T1
Valid prediction for GeneMark_model.1600_t
Valid prediction for snap_scaffold_1-snap.1502-T1
Valid prediction for snap_scaffold_1-snap.1527-T1
Valid prediction for snap_scaffold_1-snap.1523-T1
Valid prediction for snap_scaffold_1-snap.1495-T1
Valid prediction for Augustus_model.g881.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18549, rend_intergenic: 11565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20801, rend_intergenic: 19133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33004, rend_intergenic: 26401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37638, rend_intergenic: 33171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57753, rend_intergenic: 55241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59816, rend_intergenic: 57990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105665, rend_intergenic: 102220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158128, rend_intergenic: 152304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159728, rend_intergenic: 158533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167190, rend_intergenic: 160138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171555, rend_intergenic: 168568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189792, rend_intergenic: 171718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199913, rend_intergenic: 198044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202678, rend_intergenic: 200227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208411, rend_intergenic: 208020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213283, rend_intergenic: 208597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 218526
-exon list size: 792


building trellis

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73.8    
73.9    
74.1    
74.2    
74.3    
74.4    
74.6    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.4    
75.6    
75.7    
75.8    
75.9    
76.1    
76.2    
76.3    
76.4    
76.6    
76.7    
76.8    
77.0    
77.1    
77.2    
77.3    
77.5    
77.6    
77.7    
77.8    
78.0    
78.1    
78.2    
78.3    
78.5    
78.6    
78.7    
78.8    
79.0    
79.1    
79.2    
79.3    
79.5    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.4    
80.5    
80.6    
80.7    
80.9    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.7    
81.9    
82.0    
82.1    
82.2    
82.4    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.1    
84.3    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.1    
86.3    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
92.9    
93.1    
93.2    
93.3    
93.5    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.3    
95.5    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.7    
98.9    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 18549, rend_intergenic: 11565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20801, rend_intergenic: 19133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33004, rend_intergenic: 26401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37638, rend_intergenic: 33171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57753, rend_intergenic: 55241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59816, rend_intergenic: 57990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105665, rend_intergenic: 102220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158128, rend_intergenic: 152304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159728, rend_intergenic: 158533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167190, rend_intergenic: 160138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171555, rend_intergenic: 168568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189792, rend_intergenic: 171718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199913, rend_intergenic: 198044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202678, rend_intergenic: 200227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208411, rend_intergenic: 208020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213283, rend_intergenic: 208597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support