-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_18461060-18687760

-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 snap_scaffold_3-snap.3663-T1
Valid prediction for snap_scaffold_3-snap.3634-T1
Valid prediction for GlimmerHMM_glimmerT_8359-T1
Valid prediction for Augustus_model.g5510.t1
Valid prediction for snap_scaffold_3-snap.3638-T1
Valid prediction for GlimmerHMM_glimmerT_8362-T1
Valid prediction for snap_scaffold_3-snap.3635-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8388-T1
Valid prediction for CodingQuarry_transcript_46474-T1
Valid prediction for GlimmerHMM_glimmerT_8365-T1
Valid prediction for GlimmerHMM_glimmerT_8363-T1
Valid prediction for snap_scaffold_3-snap.3658-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.3653-T1
Valid prediction for snap_scaffold_3-snap.3641-T1
Valid prediction for Augustus_model.g5503.t1
Valid prediction for snap_scaffold_3-snap.3667-T1
Valid prediction for snap_scaffold_3-snap.3643-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.3645-T1
Valid prediction for GlimmerHMM_glimmerT_8360-T1
Valid prediction for Augustus_model.g5504.t1
Valid prediction for GlimmerHMM_glimmerT_8374-T1
Valid prediction for snap_scaffold_3-snap.3650-T1
Valid prediction for snap_scaffold_3-snap.3620-T1
Valid prediction for snap_scaffold_3-snap.3621-T1
Valid prediction for snap_scaffold_3-snap.3625-T1
Valid prediction for Augustus_model.g5508.t1
Valid prediction for snap_scaffold_3-snap.3664-T1
Valid prediction for Augustus_model.g5515.t1
Valid prediction for snap_scaffold_3-snap.3656-T1
Valid prediction for GlimmerHMM_glimmerT_8379-T1
Valid prediction for snap_scaffold_3-snap.3632-T1
Valid prediction for Augustus_model.g5518.t1
Valid prediction for snap_scaffold_3-snap.3626-T1
Valid prediction for snap_scaffold_3-snap.3651-T1
Valid prediction for snap_scaffold_3-snap.3670-T1
Valid prediction for GlimmerHMM_glimmerT_8361-T1
Valid prediction for snap_scaffold_3-snap.3637-T1
Valid prediction for GlimmerHMM_glimmerT_8370-T1
Valid prediction for Augustus_model.g5509.t1
Valid prediction for Augustus_model.g5502.t1
Valid prediction for snap_scaffold_3-snap.3629-T1
Valid prediction for Augustus_model.g5519.t1
Valid prediction for snap_scaffold_3-snap.3619-T1
Valid prediction for snap_scaffold_3-snap.3630-T1
Valid prediction for GlimmerHMM_glimmerT_8386-T1
Valid prediction for snap_scaffold_3-snap.3623-T1
Valid prediction for pasa_asmbl_40739.p1
Valid prediction for GlimmerHMM_glimmerT_8373-T1
Valid prediction for GlimmerHMM_glimmerT_8381-T1
Valid prediction for snap_scaffold_3-snap.3646-T1
Valid prediction for GlimmerHMM_glimmerT_8376-T1
Valid prediction for GlimmerHMM_glimmerT_8368-T1
Valid prediction for snap_scaffold_3-snap.3652-T1
Valid prediction for snap_scaffold_3-snap.3648-T1
Valid prediction for GlimmerHMM_glimmerT_8371-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_8366-T1
Valid prediction for snap_scaffold_3-snap.3628-T1
Valid prediction for GlimmerHMM_glimmerT_8382-T1
Valid prediction for GlimmerHMM_glimmerT_8384-T1
Valid prediction for snap_scaffold_3-snap.3633-T1
Valid prediction for Augustus_model.g5520.t1
Valid prediction for snap_scaffold_3-snap.3655-T1
Valid prediction for GlimmerHMM_glimmerT_8378-T1
Valid prediction for snap_scaffold_3-snap.3668-T1
Valid prediction for snap_scaffold_3-snap.3631-T1
Valid prediction for GlimmerHMM_glimmerT_8369-T1
Couldn't classify 30891, 30975
Sorry, prediction pasa_asmbl_39634.p1 fails validation.
(CAG)	 CT	30891-30975	GT	AGG
(ACA)	 AG	31124-31274	GT	TGG
(GTA)	 AG	31370-31531	GT	GGG
(GAA)	 AG	31655-31850	GT	AGG
(AAA)	 AG	32925-33149	GT	AGG
(TCC)	 AG	33353-33473	GT	AGG
(GTT)	 AG	33615-33682	GT	AGG
(GTT)	 AG	34083-34160	TG	AAT
add_exon() Sorry, pasa_asmbl_39634.p1 33353-33473-terminal-3 is invalid.
-recovered pasa_asmbl_39634.p1, terminal, 33353, 33473
-recovered pasa_asmbl_39634.p1, terminal, 34083, 34160
-recovered pasa_asmbl_39634.p1, internal, 31124, 31274
-recovered pasa_asmbl_39634.p1, internal, 31370, 31531
-recovered pasa_asmbl_39634.p1, internal, 31655, 31850
-recovered pasa_asmbl_39634.p1, internal, 32925, 33149
-recovered pasa_asmbl_39634.p1, internal, 33353, 33473
-recovered pasa_asmbl_39634.p1, internal, 33615, 33682
Valid prediction for snap_scaffold_3-snap.3640-T1
Couldn't classify 94953, 102309
Couldn't classify 102355, 104585
Sorry, prediction CodingQuarry_transcript_46477-T1 fails validation.
(ATG)	 TC	92738-92863	GT	AGG
(GAA)	 AG	94192-94281	GT	TGG
(GTC)	 AG	94445-94502	GT	AGG
(AGG)	 AG	94614-94702	GT	AGG
(ATG)	 AG	94953-102309	CA	GGC
(AAG)	 GG	102355-104585	TG	GAT
-recovered CodingQuarry_transcript_46477-T1, initial, 92738, 92863
-recovered CodingQuarry_transcript_46477-T1, internal, 94192, 94281
-recovered CodingQuarry_transcript_46477-T1, internal, 94445, 94502
-recovered CodingQuarry_transcript_46477-T1, internal, 94614, 94702
Valid prediction for Augustus_model.g5514.t1
Valid prediction for snap_scaffold_3-snap.3618-T1
Valid prediction for snap_scaffold_3-snap.3661-T1
Valid prediction for snap_scaffold_3-snap.3659-T1
Couldn't classify 179556, 179687
Sorry, prediction pasa_asmbl_39629.p2 fails validation.
(ATG)	 AG	177339-177508	GT	AGG
(GTT)	 AG	179033-179138	GT	AGG
(CAC)	 AG	179556-179687	TA	TGT
-recovered pasa_asmbl_39629.p2, initial, 177339, 177508
-recovered pasa_asmbl_39629.p2, internal, 177339, 177508
-recovered pasa_asmbl_39629.p2, internal, 179033, 179138
Valid prediction for Augustus_model.g5506.t1
Valid prediction for snap_scaffold_3-snap.3665-T1
Valid prediction for GlimmerHMM_glimmerT_8380-T1
Valid prediction for Augustus_model.g5512.t1
Valid prediction for snap_scaffold_3-snap.3666-T1
Valid prediction for GlimmerHMM_glimmerT_8387-T1
Valid prediction for GlimmerHMM_glimmerT_8367-T1
Couldn't classify 191384, 191539
Sorry, prediction pasa_asmbl_39628.p2 fails validation.
(ATT)	 GG	191384-191539	GT	AGG
(GCA)	 AG	191862-191885	GT	ACG
(GTG)	 AG	193072-193239	CC	GAC
-recovered pasa_asmbl_39628.p2, terminal, 193072, 193239
-recovered pasa_asmbl_39628.p2, internal, 191862, 191885
Valid prediction for Augustus_model.g5516.t1
Valid prediction for snap_scaffold_3-snap.3647-T1
Valid prediction for GlimmerHMM_glimmerT_8383-T1
Valid prediction for snap_scaffold_3-snap.3639-T1
Valid prediction for snap_scaffold_3-snap.3642-T1
Valid prediction for snap_scaffold_3-snap.3660-T1
Valid prediction for Augustus_model.g5521.t1
Valid prediction for snap_scaffold_3-snap.3622-T1
Valid prediction for GlimmerHMM_glimmerT_8372-T1
Valid prediction for snap_scaffold_3-snap.3627-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.3624-T1
Valid prediction for GlimmerHMM_glimmerT_8385-T1
Valid prediction for snap_scaffold_3-snap.3662-T1
Couldn't classify 94953, 102309
Couldn't classify 102355, 104568
Sorry, prediction CodingQuarry_transcript_46476-T1 fails validation.
(ATG)	 AC	94279-94281	GT	TGG
(GTC)	 AG	94445-94502	GT	AGG
(AGG)	 AG	94614-94702	GT	AGG
(ATG)	 AG	94953-102309	CA	GGC
(AAG)	 GG	102355-104568	GT	CGG
(GTT)	 AG	104978-105069	AT	AAA
-recovered CodingQuarry_transcript_46476-T1, initial, 94279, 94281
-recovered CodingQuarry_transcript_46476-T1, terminal, 104978, 105069
-recovered CodingQuarry_transcript_46476-T1, internal, 94445, 94502
-recovered CodingQuarry_transcript_46476-T1, internal, 94614, 94702
Valid prediction for snap_scaffold_3-snap.3644-T1
Valid prediction for CodingQuarry_transcript_46475-T1
Valid prediction for Augustus_model.g5507.t1
Valid prediction for Augustus_model.g5513.t1
Valid prediction for snap_scaffold_3-snap.3649-T1
Valid prediction for snap_scaffold_3-snap.3654-T1
Valid prediction for Augustus_model.g5505.t1
Valid prediction for Augustus_model.g5511.t1
Valid prediction for GlimmerHMM_glimmerT_8375-T1
Valid prediction for snap_scaffold_3-snap.3657-T1
Valid prediction for HiQ_model.g5501.t1
Valid prediction for CodingQuarry_transcript_46473-T1
Valid prediction for snap_scaffold_3-snap.3636-T1
Valid prediction for Augustus_model.g5517.t1
Valid prediction for GlimmerHMM_glimmerT_8358-T1
Valid prediction for pasa_asmbl_39625.p1
Valid prediction for snap_scaffold_3-snap.3617-T1
Valid prediction for GlimmerHMM_glimmerT_8364-T1
Valid prediction for GlimmerHMM_glimmerT_8377-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 37796, rend_intergenic: 33463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40063, rend_intergenic: 38220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43680, rend_intergenic: 41291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59764, rend_intergenic: 55548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69692, rend_intergenic: 59924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70293, rend_intergenic: 70077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74010, rend_intergenic: 71087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108041, rend_intergenic: 106130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123173, rend_intergenic: 122117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135804, rend_intergenic: 132439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141834, rend_intergenic: 137979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151267, rend_intergenic: 147087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169614, rend_intergenic: 166348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177677, rend_intergenic: 173056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185053, rend_intergenic: 183437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188816, rend_intergenic: 185069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203836, rend_intergenic: 196247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 226701
-exon list size: 446


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    
3.3    
3.6    
3.8    
4.0    
4.2    
4.5    
4.7    
4.9    
5.1    
5.4    
5.6    
5.8    
6.0    
6.2    
6.5    
6.7    
6.9    
7.1    
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7.6    
7.8    
8.0    
8.3    
8.5    
8.7    
8.9    
9.2    
9.4    
9.6    
9.8    
10.0    
10.3    
10.5    
10.7    
10.9    
11.2    
11.4    
11.6    
11.8    
12.1    
12.3    
12.5    
12.7    
12.9    
13.2    
13.4    
13.6    
13.8    
14.1    
14.3    
14.5    
14.7    
15.0    
15.2    
15.4    
15.6    
15.8    
16.1    
16.3    
16.5    
16.7    
17.0    
17.2    
17.4    
17.6    
17.9    
18.1    
18.3    
18.5    
18.8    
19.0    
19.2    
19.4    
19.6    
19.9    
20.1    
20.3    
20.5    
20.8    
21.0    
21.2    
21.4    
21.7    
21.9    
22.1    
22.3    
22.5    
22.8    
23.0    
23.2    
23.4    
23.7    
23.9    
24.1    
24.3    
24.6    
24.8    
25.0    
25.2    
25.4    
25.7    
25.9    
26.1    
26.3    
26.6    
26.8    
27.0    
27.2    
27.5    
27.7    
27.9    
28.1    
28.3    
28.6    
28.8    
29.0    
29.2    
29.5    
29.7    
29.9    
30.1    
30.4    
30.6    
30.8    
31.0    
31.2    
31.5    
31.7    
31.9    
32.1    
32.4    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.2    
34.4    
34.6    
34.8    
35.0    
35.3    
35.5    
35.7    
35.9    
36.2    
36.4    
36.6    
36.8    
37.1    
37.3    
37.5    
37.7    
37.9    
38.2    
38.4    
38.6    
38.8    
39.1    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.8    
41.1    
41.3    
41.5    
41.7    
42.0    
42.2    
42.4    
42.6    
42.9    
43.1    
43.3    
43.5    
43.8    
44.0    
44.2    
44.4    
44.6    
44.9    
45.1    
45.3    
45.5    
45.8    
46.0    
46.2    
46.4    
46.7    
46.9    
47.1    
47.3    
47.5    
47.8    
48.0    
48.2    
48.4    
48.7    
48.9    
49.1    
49.3    
49.6    
49.8    
50.0    
50.2    
50.4    
50.7    
50.9    
51.1    
51.3    
51.6    
51.8    
52.0    
52.2    
52.5    
52.7    
52.9    
53.1    
53.3    
53.6    
53.8    
54.0    
54.2    
54.5    
54.7    
54.9    
55.1    
55.4    
55.6    
55.8    
56.0    
56.2    
56.5    
56.7    
56.9    
57.1    
57.4    
57.6    
57.8    
58.0    
58.3    
58.5    
58.7    
58.9    
59.2    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
60.7    
60.9    
61.2    
61.4    
61.6    
61.8    
62.1    
62.3    
62.5    
62.7    
62.9    
63.2    
63.4    
63.6    
63.8    
64.1    
64.3    
64.5    
64.7    
65.0    
65.2    
65.4    
65.6    
65.8    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.6    
67.9    
68.1    
68.3    
68.5    
68.8    
69.0    
69.2    
69.4    
69.6    
69.9    
70.1    
70.3    
70.5    
70.8    
71.0    
71.2    
71.4    
71.7    
71.9    
72.1    
72.3    
72.5    
72.8    
73.0    
73.2    
73.4    
73.7    
73.9    
74.1    
74.3    
74.6    
74.8    
75.0    
75.2    
75.4    
75.7    
75.9    
76.1    
76.3    
76.6    
76.8    
77.0    
77.2    
77.5    
77.7    
77.9    
78.1    
78.3    
78.6    
78.8    
79.0    
79.2    
79.5    
79.7    
79.9    
80.1    
80.4    
80.6    
80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.1    
82.4    
82.6    
82.8    
83.0    
83.3    
83.5    
83.7    
83.9    
84.2    
84.4    
84.6    
84.8    
85.0    
85.3    
85.5    
85.7    
85.9    
86.2    
86.4    
86.6    
86.8    
87.1    
87.3    
87.5    
87.7    
87.9    
88.2    
88.4    
88.6    
88.8    
89.1    
89.3    
89.5    
89.7    
90.0    
90.2    
90.4    
90.6    
90.8    
91.1    
91.3    
91.5    
91.7    
92.0    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.4    
94.6    
94.9    
95.1    
95.3    
95.5    
95.8    
96.0    
96.2    
96.4    
96.7    
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 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 37796, rend_intergenic: 33463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40063, rend_intergenic: 38220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43680, rend_intergenic: 41291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59764, rend_intergenic: 55548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69692, rend_intergenic: 59924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70293, rend_intergenic: 70077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74010, rend_intergenic: 71087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108041, rend_intergenic: 106130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123173, rend_intergenic: 122117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135804, rend_intergenic: 132439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141834, rend_intergenic: 137979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151267, rend_intergenic: 147087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169614, rend_intergenic: 166348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177677, rend_intergenic: 173056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185053, rend_intergenic: 183437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188816, rend_intergenic: 185069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203836, rend_intergenic: 196247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support