-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_4494141-4695334

-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 CodingQuarry_transcript_41878-T1
Valid prediction for Augustus_model.g37928.t1
Valid prediction for snap_scaffold_27-snap.1073-T1
Valid prediction for snap_scaffold_27-snap.1089-T1
Valid prediction for GlimmerHMM_glimmerT_57215-T1
Valid prediction for GlimmerHMM_glimmerT_57231-T1
Valid prediction for GlimmerHMM_glimmerT_57221-T1
Valid prediction for GlimmerHMM_glimmerT_57214-T1
Valid prediction for GlimmerHMM_glimmerT_57227-T1
Valid prediction for snap_scaffold_27-snap.1067-T1
Valid prediction for snap_scaffold_27-snap.1094-T1
Valid prediction for GlimmerHMM_glimmerT_57210-T1
Valid prediction for snap_scaffold_27-snap.1077-T1
Valid prediction for snap_scaffold_27-snap.1082-T1
Valid prediction for snap_scaffold_27-snap.1085-T1
Valid prediction for GlimmerHMM_glimmerT_57209-T1
Valid prediction for snap_scaffold_27-snap.1070-T1
Valid prediction for GlimmerHMM_glimmerT_57228-T1
Couldn't classify 18545, 18668
Sorry, prediction pasa_asmbl_36297.p1 fails validation.
(ATG)	 TC	16240-16278	GT	AGG
(ATC)	 AG	16427-16555	GT	TGG
(GGC)	 AG	16657-16703	GT	GGG
(GGT)	 AG	16914-17060	GT	AAG
(GAA)	 AG	17289-17489	GT	AGG
(TAA)	 AG	18545-18668	GG	AGG
-recovered pasa_asmbl_36297.p1, initial, 16240, 16278
-recovered pasa_asmbl_36297.p1, internal, 16427, 16555
-recovered pasa_asmbl_36297.p1, internal, 16657, 16703
-recovered pasa_asmbl_36297.p1, internal, 16914, 17060
-recovered pasa_asmbl_36297.p1, internal, 17289, 17489
Valid prediction for GlimmerHMM_glimmerT_57224-T1
Valid prediction for GlimmerHMM_glimmerT_57211-T1
Valid prediction for Augustus_model.g37931.t1
Valid prediction for GlimmerHMM_glimmerT_57203-T1
Valid prediction for Augustus_model.g37925.t1
Valid prediction for snap_scaffold_27-snap.1092-T1
Valid prediction for GlimmerHMM_glimmerT_57206-T1
Valid prediction for snap_scaffold_27-snap.1068-T1
Valid prediction for snap_scaffold_27-snap.1075-T1
Valid prediction for snap_scaffold_27-snap.1086-T1
Valid prediction for GlimmerHMM_glimmerT_57229-T1
Valid prediction for Augustus_model.g37927.t1
Valid prediction for Augustus_model.g37937.t1
Valid prediction for snap_scaffold_27-snap.1091-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.1072-T1
Valid prediction for GlimmerHMM_glimmerT_57218-T1
Valid prediction for GlimmerHMM_glimmerT_57207-T1
Valid prediction for GlimmerHMM_glimmerT_57225-T1
Valid prediction for snap_scaffold_27-snap.1078-T1
Valid prediction for CodingQuarry_transcript_41879-T1
Valid prediction for snap_scaffold_27-snap.1084-T1
Valid prediction for snap_scaffold_27-snap.1063-T1
Valid prediction for CodingQuarry_transcript_41880-T1
Valid prediction for snap_scaffold_27-snap.1057-T1
Valid prediction for Augustus_model.g37938.t1
Valid prediction for snap_scaffold_27-snap.1095-T1
Valid prediction for HiQ_model.g37926.t1
Couldn't classify 20029, 20052
Couldn't classify 20293, 20637
Sorry, prediction pasa_asmbl_36564.p1 fails validation.
(GAG)	 GT	20029-20052	GT	AGG
(GAG)	 AG	20293-20637	CC	CGC
Couldn't classify 13516, 13561
Sorry, prediction pasa_asmbl_36295.p1 fails validation.
(CCT)	 CC	13516-13561	GT	AGG
(GTG)	 AG	14391-14455	GT	TGG
(GCG)	 AG	14690-14811	GT	AGG
(CTC)	 AG	14965-15030	GT	GGG
(GGG)	 AG	15207-15272	GT	TGG
(GTC)	 AG	15385-15583	GT	GAG
-recovered pasa_asmbl_36295.p1, terminal, 15385, 15583
-recovered pasa_asmbl_36295.p1, internal, 14391, 14455
-recovered pasa_asmbl_36295.p1, internal, 14690, 14811
-recovered pasa_asmbl_36295.p1, internal, 14965, 15030
-recovered pasa_asmbl_36295.p1, internal, 15207, 15272
-recovered pasa_asmbl_36295.p1, internal, 15385, 15583
Valid prediction for pasa_asmbl_36303.p1
Valid prediction for GlimmerHMM_glimmerT_57208-T1
Valid prediction for snap_scaffold_27-snap.1061-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 GlimmerHMM_glimmerT_57220-T1
Valid prediction for snap_scaffold_27-snap.1058-T1
Valid prediction for Augustus_model.g37932.t1
Valid prediction for snap_scaffold_27-snap.1074-T1
Valid prediction for snap_scaffold_27-snap.1088-T1
Valid prediction for GlimmerHMM_glimmerT_57212-T1
Valid prediction for snap_scaffold_27-snap.1081-T1
Valid prediction for snap_scaffold_27-snap.1066-T1
Valid prediction for GlimmerHMM_glimmerT_57204-T1
Valid prediction for snap_scaffold_27-snap.1083-T1
Valid prediction for GlimmerHMM_glimmerT_57232-T1
Valid prediction for Augustus_model.g37935.t1
Valid prediction for GlimmerHMM_glimmerT_57230-T1
Valid prediction for snap_scaffold_27-snap.1059-T1
Valid prediction for snap_scaffold_27-snap.1064-T1
Valid prediction for Augustus_model.g37929.t1
Valid prediction for GlimmerHMM_glimmerT_57213-T1
Valid prediction for GlimmerHMM_glimmerT_57216-T1
Valid prediction for snap_scaffold_27-snap.1071-T1
Valid prediction for snap_scaffold_27-snap.1079-T1
Valid prediction for snap_scaffold_27-snap.1093-T1
Valid prediction for Augustus_model.g37930.t1
Valid prediction for Augustus_model.g37934.t1
Valid prediction for Augustus_model.g37940.t1
Valid prediction for snap_scaffold_27-snap.1069-T1
Valid prediction for snap_scaffold_27-snap.1060-T1
Valid prediction for snap_scaffold_27-snap.1062-T1
Valid prediction for snap_scaffold_27-snap.1076-T1
Valid prediction for GlimmerHMM_glimmerT_57223-T1
Valid prediction for Augustus_model.g37939.t1
Valid prediction for GlimmerHMM_glimmerT_57217-T1
Valid prediction for snap_scaffold_27-snap.1090-T1
Valid prediction for GlimmerHMM_glimmerT_57222-T1
Valid prediction for GlimmerHMM_glimmerT_57219-T1
Valid prediction for snap_scaffold_27-snap.1087-T1
Valid prediction for GlimmerHMM_glimmerT_57226-T1
Couldn't classify 179074, 179391
Sorry, prediction pasa_asmbl_36573.p1 fails validation.
(CAC)	 CA	179074-179391	TT	GAT
Valid prediction for GlimmerHMM_glimmerT_57205-T1
Valid prediction for snap_scaffold_27-snap.1080-T1
Valid prediction for Augustus_model.g37936.t1
Valid prediction for snap_scaffold_27-snap.1065-T1
Valid prediction for Augustus_model.g37933.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23022, rend_intergenic: 4780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27554, rend_intergenic: 26421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33449, rend_intergenic: 28077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35497, rend_intergenic: 34230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54062, rend_intergenic: 45967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59391, rend_intergenic: 57867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60903, rend_intergenic: 60170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63429, rend_intergenic: 61090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72514, rend_intergenic: 63595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74967, rend_intergenic: 72514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75268, rend_intergenic: 75045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77296, rend_intergenic: 75408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82834, rend_intergenic: 77766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90093, rend_intergenic: 83964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120339, rend_intergenic: 104597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128273, rend_intergenic: 120585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147308, rend_intergenic: 128275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161173, rend_intergenic: 153478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167269, rend_intergenic: 162060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195510, rend_intergenic: 167301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 201194
-exon list size: 445


building trellis

0.2    
0.4    
0.7    
0.9    
1.1    
1.3    
1.6    
1.8    
2.0    
2.2    
2.5    
2.7    
2.9    
3.1    
3.4    
3.6    
3.8    
4.0    
4.3    
4.5    
4.7    
4.9    
5.1    
5.4    
5.6    
5.8    
6.0    
6.3    
6.5    
6.7    
6.9    
7.2    
7.4    
7.6    
7.8    
8.1    
8.3    
8.5    
8.7    
8.9    
9.2    
9.4    
9.6    
9.8    
10.1    
10.3    
10.5    
10.7    
11.0    
11.2    
11.4    
11.6    
11.9    
12.1    
12.3    
12.5    
12.8    
13.0    
13.2    
13.4    
13.6    
13.9    
14.1    
14.3    
14.5    
14.8    
15.0    
15.2    
15.4    
15.7    
15.9    
16.1    
16.3    
16.6    
16.8    
17.0    
17.2    
17.4    
17.7    
17.9    
18.1    
18.3    
18.6    
18.8    
19.0    
19.2    
19.5    
19.7    
19.9    
20.1    
20.4    
20.6    
20.8    
21.0    
21.3    
21.5    
21.7    
21.9    
22.1    
22.4    
22.6    
22.8    
23.0    
23.3    
23.5    
23.7    
23.9    
24.2    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.7    
26.0    
26.2    
26.4    
26.6    
26.8    
27.1    
27.3    
27.5    
27.7    
28.0    
28.2    
28.4    
28.6    
28.9    
29.1    
29.3    
29.5    
29.8    
30.0    
30.2    
30.4    
30.6    
30.9    
31.1    
31.3    
31.5    
31.8    
32.0    
32.2    
32.4    
32.7    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.5    
34.7    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.2    
36.5    
36.7    
36.9    
37.1    
37.4    
37.6    
37.8    
38.0    
38.3    
38.5    
38.7    
38.9    
39.1    
39.4    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
40.9    
41.2    
41.4    
41.6    
41.8    
42.1    
42.3    
42.5    
42.7    
43.0    
43.2    
43.4    
43.6    
43.8    
44.1    
44.3    
44.5    
44.7    
45.0    
45.2    
45.4    
45.6    
45.9    
46.1    
46.3    
46.5    
46.8    
47.0    
47.2    
47.4    
47.7    
47.9    
48.1    
48.3    
48.5    
48.8    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.2    
51.5    
51.7    
51.9    
52.1    
52.3    
52.6    
52.8    
53.0    
53.2    
53.5    
53.7    
53.9    
54.1    
54.4    
54.6    
54.8    
55.0    
55.3    
55.5    
55.7    
55.9    
56.2    
56.4    
56.6    
56.8    
57.0    
57.3    
57.5    
57.7    
57.9    
58.2    
58.4    
58.6    
58.8    
59.1    
59.3    
59.5    
59.7    
60.0    
60.2    
60.4    
60.6    
60.9    
61.1    
61.3    
61.5    
61.7    
62.0    
62.2    
62.4    
62.6    
62.9    
63.1    
63.3    
63.5    
63.8    
64.0    
64.2    
64.4    
64.7    
64.9    
65.1    
65.3    
65.5    
65.8    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.3    
67.6    
67.8    
68.0    
68.2    
68.5    
68.7    
68.9    
69.1    
69.4    
69.6    
69.8    
70.0    
70.2    
70.5    
70.7    
70.9    
71.1    
71.4    
71.6    
71.8    
72.0    
72.3    
72.5    
72.7    
72.9    
73.2    
73.4    
73.6    
73.8    
74.0    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.1    
76.3    
76.5    
76.7    
77.0    
77.2    
77.4    
77.6    
77.9    
78.1    
78.3    
78.5    
78.7    
79.0    
79.2    
79.4    
79.6    
79.9    
80.1    
80.3    
80.5    
80.8    
81.0    
81.2    
81.4    
81.7    
81.9    
82.1    
82.3    
82.6    
82.8    
83.0    
83.2    
83.4    
83.7    
83.9    
84.1    
84.3    
84.6    
84.8    
85.0    
85.2    
85.5    
85.7    
85.9    
86.1    
86.4    
86.6    
86.8    
87.0    
87.2    
87.5    
87.7    
87.9    
88.1    
88.4    
88.6    
88.8    
89.0    
89.3    
89.5    
89.7    
89.9    
90.2    
90.4    
90.6    
90.8    
91.1    
91.3    
91.5    
91.7    
91.9    
92.2    
92.4    
92.6    
92.8    
93.1    
93.3    
93.5    
93.7    
94.0    
94.2    
94.4    
94.6    
94.9    
95.1    
95.3    
95.5    
95.7    
96.0    
96.2    
96.4    
96.6    
96.9    
97.1    
97.3    
97.5    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 23022, rend_intergenic: 4780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27554, rend_intergenic: 26421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33449, rend_intergenic: 28077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35497, rend_intergenic: 34230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54062, rend_intergenic: 45967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59391, rend_intergenic: 57867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60903, rend_intergenic: 60170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63429, rend_intergenic: 61090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72514, rend_intergenic: 63595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74967, rend_intergenic: 72514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75268, rend_intergenic: 75045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77296, rend_intergenic: 75408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82834, rend_intergenic: 77766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90093, rend_intergenic: 83964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120339, rend_intergenic: 104597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128273, rend_intergenic: 120585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147308, rend_intergenic: 128275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161173, rend_intergenic: 153478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167269, rend_intergenic: 162060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195510, rend_intergenic: 167301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support