-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_4832829-4952558

-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_36872-T1
Valid prediction for snap_scaffold_15-snap.1079-T1
Valid prediction for GlimmerHMM_glimmerT_36879-T1
Valid prediction for GeneMark_model.63468_t
Valid prediction for snap_scaffold_15-snap.1071-T1
Valid prediction for GlimmerHMM_glimmerT_36878-T1
Valid prediction for GlimmerHMM_glimmerT_36875-T1
Valid prediction for snap_scaffold_15-snap.1050-T1
Valid prediction for snap_scaffold_15-snap.1072-T1
Valid prediction for GeneMark_model.63466_t
Valid prediction for GeneMark_model.63446_t
Valid prediction for snap_scaffold_15-snap.1062-T1
Valid prediction for GeneMark_model.63445_t
Valid prediction for GlimmerHMM_glimmerT_36882-T1
Valid prediction for GlimmerHMM_glimmerT_36865-T1
Valid prediction for GlimmerHMM_glimmerT_36881-T1
Valid prediction for snap_scaffold_15-snap.1063-T1
Valid prediction for GeneMark_model.63437_t
Valid prediction for GlimmerHMM_glimmerT_36867-T1
Valid prediction for snap_scaffold_15-snap.1068-T1
Valid prediction for GeneMark_model.63455_t
Valid prediction for snap_scaffold_15-snap.1054-T1
Valid prediction for GeneMark_model.63450_t
Valid prediction for GeneMark_model.63464_t
Valid prediction for Augustus_model.g24744.t1
Valid prediction for GeneMark_model.63442_t
Valid prediction for snap_scaffold_15-snap.1069-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_36883-T1
Valid prediction for snap_scaffold_15-snap.1070-T1
Valid prediction for GeneMark_model.63453_t
Valid prediction for GlimmerHMM_glimmerT_36885-T1
Valid prediction for Augustus_model.g24751.t1
Valid prediction for snap_scaffold_15-snap.1084-T1
Valid prediction for Augustus_model.g24746.t1
Valid prediction for GeneMark_model.63457_t
Valid prediction for snap_scaffold_15-snap.1060-T1
Valid prediction for snap_scaffold_15-snap.1058-T1
Valid prediction for snap_scaffold_15-snap.1067-T1
Valid prediction for GeneMark_model.63465_t
Valid prediction for Augustus_model.g24754.t1
Valid prediction for GeneMark_model.63470_t
Valid prediction for GlimmerHMM_glimmerT_36864-T1
Valid prediction for snap_scaffold_15-snap.1065-T1
Valid prediction for snap_scaffold_15-snap.1082-T1
Valid prediction for snap_scaffold_15-snap.1051-T1
Valid prediction for GeneMark_model.63472_t
Valid prediction for GeneMark_model.63440_t
Valid prediction for GeneMark_model.63462_t
Valid prediction for snap_scaffold_15-snap.1078-T1
Valid prediction for GeneMark_model.63460_t
Valid prediction for snap_scaffold_15-snap.1076-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 CodingQuarry_transcript_17949-T1
Valid prediction for GeneMark_model.63454_t
Valid prediction for snap_scaffold_15-snap.1059-T1
Valid prediction for snap_scaffold_15-snap.1075-T1
Valid prediction for Augustus_model.g24752.t1
Valid prediction for snap_scaffold_15-snap.1057-T1
Valid prediction for GeneMark_model.63469_t
Valid prediction for GlimmerHMM_glimmerT_36869-T1
Valid prediction for GeneMark_model.63473_t
Valid prediction for Augustus_model.g24753.t1
Valid prediction for snap_scaffold_15-snap.1066-T1
Valid prediction for snap_scaffold_15-snap.1077-T1
Valid prediction for GlimmerHMM_glimmerT_36868-T1
Valid prediction for GeneMark_model.63471_t
Valid prediction for GeneMark_model.63452_t
Valid prediction for GeneMark_model.63461_t
Valid prediction for GeneMark_model.63443_t
Valid prediction for GeneMark_model.63467_t
Valid prediction for snap_scaffold_15-snap.1080-T1
Valid prediction for GlimmerHMM_glimmerT_36884-T1
Valid prediction for GeneMark_model.63436_t
Valid prediction for snap_scaffold_15-snap.1052-T1
Valid prediction for GlimmerHMM_glimmerT_36880-T1
Valid prediction for snap_scaffold_15-snap.1081-T1
Valid prediction for Augustus_model.g24747.t1
Valid prediction for snap_scaffold_15-snap.1074-T1
Valid prediction for snap_scaffold_15-snap.1083-T1
Couldn't classify 101667, 101682
Couldn't classify 105609, 105735
Sorry, prediction pasa_asmbl_15176.p1 fails validation.
(GAG)	 CC	101667-101682	GT	CGG
(CGA)	 AG	102162-102226	GT	CGG
(GAG)	 AG	102659-102735	GT	AAG
(GAT)	 AG	103438-103519	GT	TGG
(CCG)	 AG	103765-103839	GT	AGG
(TCG)	 AG	104116-104214	GT	AGG
(ATT)	 AG	104318-104379	GT	AGG
(TCT)	 AG	105271-105381	GT	AGG
(TAA)	 AG	105609-105735	TG	GGT
-recovered pasa_asmbl_15176.p1, terminal, 102659, 102735
add_exon() Sorry, pasa_asmbl_15176.p1 105271-105381-terminal-1 is invalid.
-recovered pasa_asmbl_15176.p1, terminal, 105271, 105381
-recovered pasa_asmbl_15176.p1, internal, 102162, 102226
-recovered pasa_asmbl_15176.p1, internal, 102659, 102735
-recovered pasa_asmbl_15176.p1, internal, 103438, 103519
-recovered pasa_asmbl_15176.p1, internal, 103765, 103839
-recovered pasa_asmbl_15176.p1, internal, 104116, 104214
-recovered pasa_asmbl_15176.p1, internal, 104318, 104379
-recovered pasa_asmbl_15176.p1, internal, 105271, 105381
Valid prediction for snap_scaffold_15-snap.1053-T1
Valid prediction for Augustus_model.g24748.t1
Valid prediction for GeneMark_model.63458_t
Valid prediction for GlimmerHMM_glimmerT_36871-T1
Valid prediction for Augustus_model.g24745.t1
Valid prediction for GlimmerHMM_glimmerT_36877-T1
Valid prediction for GeneMark_model.63438_t
Valid prediction for snap_scaffold_15-snap.1055-T1
Valid prediction for snap_scaffold_15-snap.1073-T1
Valid prediction for GlimmerHMM_glimmerT_36876-T1
Valid prediction for Augustus_model.g24750.t1
Valid prediction for GeneMark_model.63448_t
Valid prediction for snap_scaffold_15-snap.1064-T1
Valid prediction for GlimmerHMM_glimmerT_36874-T1
Valid prediction for GlimmerHMM_glimmerT_36873-T1
Valid prediction for GeneMark_model.63456_t
Valid prediction for snap_scaffold_15-snap.1056-T1
Valid prediction for GeneMark_model.63441_t
Valid prediction for Augustus_model.g24749.t1
Valid prediction for CodingQuarry_transcript_17948-T1
Valid prediction for GlimmerHMM_glimmerT_36866-T1
Valid prediction for GeneMark_model.63444_t
Valid prediction for GeneMark_model.63439_t
Valid prediction for GlimmerHMM_glimmerT_36870-T1
Valid prediction for snap_scaffold_15-snap.1061-T1
Valid prediction for GeneMark_model.63463_t
Valid prediction for GeneMark_model.63451_t
Valid prediction for GeneMark_model.63449_t
Valid prediction for GeneMark_model.63447_t
Valid prediction for GeneMark_model.63435_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14110, rend_intergenic: 10471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18436, rend_intergenic: 14565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27454, rend_intergenic: 25732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29906, rend_intergenic: 28438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30865, rend_intergenic: 30223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49332, rend_intergenic: 40424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54649, rend_intergenic: 50463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58673, rend_intergenic: 57640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81146, rend_intergenic: 59532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89153, rend_intergenic: 85848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97885, rend_intergenic: 94284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101521, rend_intergenic: 99087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105892, rend_intergenic: 101754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 119730
-exon list size: 543


building trellis

0.2    
0.4    
0.6    
0.7    
0.9    
1.1    
1.3    
1.5    
1.7    
1.8    
2.0    
2.2    
2.4    
2.6    
2.8    
2.9    
3.1    
3.3    
3.5    
3.7    
3.9    
4.0    
4.2    
4.4    
4.6    
4.8    
5.0    
5.1    
5.3    
5.5    
5.7    
5.9    
6.1    
6.2    
6.4    
6.6    
6.8    
7.0    
7.2    
7.3    
7.5    
7.7    
7.9    
8.1    
8.3    
8.4    
8.6    
8.8    
9.0    
9.2    
9.4    
9.5    
9.7    
9.9    
10.1    
10.3    
10.5    
10.6    
10.8    
11.0    
11.2    
11.4    
11.6    
11.7    
11.9    
12.1    
12.3    
12.5    
12.7    
12.8    
13.0    
13.2    
13.4    
13.6    
13.8    
13.9    
14.1    
14.3    
14.5    
14.7    
14.9    
15.0    
15.2    
15.4    
15.6    
15.8    
16.0    
16.1    
16.3    
16.5    
16.7    
16.9    
17.1    
17.2    
17.4    
17.6    
17.8    
18.0    
18.2    
18.3    
18.5    
18.7    
18.9    
19.1    
19.3    
19.4    
19.6    
19.8    
20.0    
20.2    
20.4    
20.6    
20.7    
20.9    
21.1    
21.3    
21.5    
21.7    
21.8    
22.0    
22.2    
22.4    
22.6    
22.8    
22.9    
23.1    
23.3    
23.5    
23.7    
23.9    
24.0    
24.2    
24.4    
24.6    
24.8    
25.0    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.2    
26.4    
26.6    
26.8    
27.0    
27.2    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.7    
31.9    
32.1    
32.3    
32.5    
32.7    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.4    
39.6    
39.8    
40.0    
40.2    
40.4    
40.6    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.2    
46.4    
46.6    
46.8    
47.0    
47.2    
47.3    
47.5    
47.7    
47.9    
48.1    
48.3    
48.4    
48.6    
48.8    
49.0    
49.2    
49.4    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.6    
50.8    
51.0    
51.2    
51.4    
51.6    
51.7    
51.9    
52.1    
52.3    
52.5    
52.7    
52.8    
53.0    
53.2    
53.4    
53.6    
53.8    
53.9    
54.1    
54.3    
54.5    
54.7    
54.9    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.2    
57.4    
57.6    
57.8    
58.0    
58.2    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.4    
59.6    
59.8    
60.0    
60.2    
60.4    
60.6    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.1    
65.3    
65.5    
65.7    
65.9    
66.1    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.8    
73.0    
73.2    
73.4    
73.6    
73.8    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 14110, rend_intergenic: 10471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18436, rend_intergenic: 14565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27454, rend_intergenic: 25732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29906, rend_intergenic: 28438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30865, rend_intergenic: 30223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49332, rend_intergenic: 40424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54649, rend_intergenic: 50463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58673, rend_intergenic: 57640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81146, rend_intergenic: 59532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89153, rend_intergenic: 85848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97885, rend_intergenic: 94284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101521, rend_intergenic: 99087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105892, rend_intergenic: 101754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support