-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_7335046-7531593

-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 GlimmerHMM_glimmerT_52845-T1
Valid prediction for Augustus_model.g35189.t1
Valid prediction for GlimmerHMM_glimmerT_52836-T1
Valid prediction for Augustus_model.g35195.t1
Valid prediction for snap_scaffold_24-snap.1525-T1
Valid prediction for snap_scaffold_24-snap.1537-T1
Valid prediction for Augustus_model.g35180.t1
Valid prediction for snap_scaffold_24-snap.1518-T1
Valid prediction for snap_scaffold_24-snap.1492-T1
Valid prediction for snap_scaffold_24-snap.1538-T1
Valid prediction for GlimmerHMM_glimmerT_52812-T1
Valid prediction for snap_scaffold_24-snap.1532-T1
Valid prediction for GlimmerHMM_glimmerT_52830-T1
Valid prediction for Augustus_model.g35188.t1
Valid prediction for snap_scaffold_24-snap.1491-T1
Valid prediction for GlimmerHMM_glimmerT_52826-T1
Valid prediction for snap_scaffold_24-snap.1530-T1
Valid prediction for snap_scaffold_24-snap.1533-T1
Valid prediction for GlimmerHMM_glimmerT_52834-T1
Valid prediction for GlimmerHMM_glimmerT_52832-T1
Valid prediction for snap_scaffold_24-snap.1513-T1
Valid prediction for snap_scaffold_24-snap.1502-T1
Valid prediction for Augustus_model.g35190.t1
Valid prediction for snap_scaffold_24-snap.1520-T1
Valid prediction for GlimmerHMM_glimmerT_52811-T1
Valid prediction for GlimmerHMM_glimmerT_52833-T1
Valid prediction for GlimmerHMM_glimmerT_52819-T1
Valid prediction for GlimmerHMM_glimmerT_52841-T1
Valid prediction for Augustus_model.g35193.t1
Valid prediction for snap_scaffold_24-snap.1529-T1
Valid prediction for snap_scaffold_24-snap.1528-T1
Valid prediction for GlimmerHMM_glimmerT_52838-T1
Valid prediction for Augustus_model.g35186.t1
Valid prediction for GlimmerHMM_glimmerT_52817-T1
Valid prediction for GlimmerHMM_glimmerT_52828-T1
Valid prediction for snap_scaffold_24-snap.1539-T1
Valid prediction for Augustus_model.g35194.t1
Valid prediction for snap_scaffold_24-snap.1522-T1
Valid prediction for snap_scaffold_24-snap.1514-T1
Valid prediction for Augustus_model.g35191.t1
Valid prediction for snap_scaffold_24-snap.1516-T1
Valid prediction for snap_scaffold_24-snap.1512-T1
Valid prediction for snap_scaffold_24-snap.1500-T1
Valid prediction for snap_scaffold_24-snap.1524-T1
Valid prediction for snap_scaffold_24-snap.1526-T1
Valid prediction for snap_scaffold_24-snap.1504-T1
Valid prediction for GlimmerHMM_glimmerT_52815-T1
Valid prediction for GlimmerHMM_glimmerT_52822-T1
Valid prediction for GlimmerHMM_glimmerT_52842-T1
Valid prediction for snap_scaffold_24-snap.1534-T1
Valid prediction for Augustus_model.g35179.t1

-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 HiQ_model.g35181.t1
Valid prediction for GlimmerHMM_glimmerT_52839-T1
Valid prediction for snap_scaffold_24-snap.1527-T1
Valid prediction for snap_scaffold_24-snap.1517-T1
Couldn't classify 181178, 181179
Sorry, prediction pasa_asmbl_33028.p1 fails validation.
(ATG)	 GA	181178-181179	GT	ATG
(GAA)	 AG	181466-181764	GT	AGG
(ATG)	 AG	182049-183277	GT	GGG
(CTG)	 AG	183533-183677	GT	TGG
(GGA)	 AG	183824-184029	GT	CAG
(CTT)	 AG	184228-184392	GT	AGG
(GAG)	 AG	184566-184721	GT	GGG
(AAT)	 AG	184829-184902	GT	AAG
(AGA)	 AG	185023-185166	GT	AGG
(GTT)	 AG	185461-185581	TT	GAT
add_exon() Sorry, pasa_asmbl_33028.p1 182049-183277-initial-1 is invalid.
-recovered pasa_asmbl_33028.p1, initial, 182049, 183277
-recovered pasa_asmbl_33028.p1, terminal, 185461, 185581
-recovered pasa_asmbl_33028.p1, internal, 181466, 181764
-recovered pasa_asmbl_33028.p1, internal, 182049, 183277
-recovered pasa_asmbl_33028.p1, internal, 183533, 183677
-recovered pasa_asmbl_33028.p1, internal, 183824, 184029
-recovered pasa_asmbl_33028.p1, internal, 184228, 184392
-recovered pasa_asmbl_33028.p1, internal, 184566, 184721
-recovered pasa_asmbl_33028.p1, internal, 184829, 184902
-recovered pasa_asmbl_33028.p1, internal, 185023, 185166
Valid prediction for Augustus_model.g35183.t1
Valid prediction for Augustus_model.g35192.t1
Valid prediction for snap_scaffold_24-snap.1511-T1
Valid prediction for GlimmerHMM_glimmerT_52837-T1
Valid prediction for GlimmerHMM_glimmerT_52814-T1
Valid prediction for snap_scaffold_24-snap.1536-T1
Valid prediction for Augustus_model.g35196.t1
Valid prediction for GlimmerHMM_glimmerT_52816-T1
Valid prediction for GlimmerHMM_glimmerT_52831-T1
Valid prediction for snap_scaffold_24-snap.1531-T1
Valid prediction for snap_scaffold_24-snap.1515-T1
Valid prediction for snap_scaffold_24-snap.1521-T1
Valid prediction for Augustus_model.g35184.t1
Valid prediction for Augustus_model.g35185.t1
Valid prediction for Augustus_model.g35187.t1
Valid prediction for GlimmerHMM_glimmerT_52821-T1
Couldn't classify 181178, 181179
Sorry, prediction CodingQuarry_transcript_37363-T1 fails validation.
(ATG)	 GA	181178-181179	GT	ATG
(GAA)	 AG	181466-181764	GT	AGG
(ATG)	 AG	182049-183277	GT	GGG
(CTG)	 AG	183533-183677	GT	TGG
(GGA)	 AG	183824-184029	GT	CAG
(CTT)	 AG	184228-184392	GT	AGG
(GAG)	 AG	184566-184721	GT	GGG
(AAT)	 AG	184829-184902	GT	AAG
(AGA)	 AG	185023-185166	GT	AGG
(GTT)	 AG	185461-185581	TT	GAT
add_exon() Sorry, CodingQuarry_transcript_37363-T1 182049-183277-initial-1 is invalid.
-recovered CodingQuarry_transcript_37363-T1, initial, 182049, 183277
-recovered CodingQuarry_transcript_37363-T1, terminal, 185461, 185581
-recovered CodingQuarry_transcript_37363-T1, internal, 181466, 181764
-recovered CodingQuarry_transcript_37363-T1, internal, 182049, 183277
-recovered CodingQuarry_transcript_37363-T1, internal, 183533, 183677
-recovered CodingQuarry_transcript_37363-T1, internal, 183824, 184029
-recovered CodingQuarry_transcript_37363-T1, internal, 184228, 184392
-recovered CodingQuarry_transcript_37363-T1, internal, 184566, 184721
-recovered CodingQuarry_transcript_37363-T1, internal, 184829, 184902
-recovered CodingQuarry_transcript_37363-T1, internal, 185023, 185166
Valid prediction for snap_scaffold_24-snap.1498-T1
Valid prediction for snap_scaffold_24-snap.1508-T1
Valid prediction for snap_scaffold_24-snap.1506-T1
Valid prediction for GlimmerHMM_glimmerT_52823-T1
Valid prediction for GlimmerHMM_glimmerT_52843-T1
Valid prediction for snap_scaffold_24-snap.1507-T1
Valid prediction for Augustus_model.g35182.t1
Valid prediction for snap_scaffold_24-snap.1495-T1
Valid prediction for GlimmerHMM_glimmerT_52813-T1
Valid prediction for snap_scaffold_24-snap.1501-T1
Valid prediction for snap_scaffold_24-snap.1510-T1
Valid prediction for GlimmerHMM_glimmerT_52844-T1
Valid prediction for GlimmerHMM_glimmerT_52824-T1
Valid prediction for snap_scaffold_24-snap.1535-T1
Valid prediction for GlimmerHMM_glimmerT_52827-T1
Valid prediction for snap_scaffold_24-snap.1509-T1
Valid prediction for snap_scaffold_24-snap.1499-T1
Valid prediction for snap_scaffold_24-snap.1493-T1
Valid prediction for snap_scaffold_24-snap.1494-T1
Valid prediction for GlimmerHMM_glimmerT_52825-T1
Valid prediction for GlimmerHMM_glimmerT_52835-T1
Valid prediction for GlimmerHMM_glimmerT_52829-T1
Valid prediction for GlimmerHMM_glimmerT_52818-T1
Valid prediction for GlimmerHMM_glimmerT_52820-T1
Valid prediction for snap_scaffold_24-snap.1505-T1
Valid prediction for snap_scaffold_24-snap.1503-T1
Valid prediction for snap_scaffold_24-snap.1496-T1
Valid prediction for GlimmerHMM_glimmerT_52840-T1
Valid prediction for snap_scaffold_24-snap.1540-T1
Valid prediction for snap_scaffold_24-snap.1523-T1
Valid prediction for snap_scaffold_24-snap.1497-T1
Valid prediction for snap_scaffold_24-snap.1519-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 36837, rend_intergenic: 31454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42912, rend_intergenic: 40637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48944, rend_intergenic: 47898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95070, rend_intergenic: 89530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110276, rend_intergenic: 108163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114716, rend_intergenic: 113424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119021, rend_intergenic: 116629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125568, rend_intergenic: 122398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137732, rend_intergenic: 135980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 196548
-exon list size: 325


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.7    
18.0    
18.3    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
33.9    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.1    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 36837, rend_intergenic: 31454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42912, rend_intergenic: 40637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48944, rend_intergenic: 47898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95070, rend_intergenic: 89530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110276, rend_intergenic: 108163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114716, rend_intergenic: 113424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119021, rend_intergenic: 116629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125568, rend_intergenic: 122398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137732, rend_intergenic: 135980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support