-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_12307294-12497908

-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_41230-T1
Valid prediction for snap_scaffold_17-snap.2543-T1
Valid prediction for snap_scaffold_17-snap.2546-T1
Valid prediction for GlimmerHMM_glimmerT_41210-T1
Valid prediction for snap_scaffold_17-snap.2509-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_41217-T1
Valid prediction for GlimmerHMM_glimmerT_41226-T1
Valid prediction for GlimmerHMM_glimmerT_41213-T1
Valid prediction for CodingQuarry_transcript_22214-T1
Valid prediction for snap_scaffold_17-snap.2527-T1
Valid prediction for GlimmerHMM_glimmerT_41215-T1
Valid prediction for snap_scaffold_17-snap.2525-T1
Valid prediction for snap_scaffold_17-snap.2518-T1
Valid prediction for snap_scaffold_17-snap.2533-T1
Valid prediction for CodingQuarry_transcript_22215-T1
Valid prediction for GlimmerHMM_glimmerT_41206-T1
Valid prediction for Augustus_model.g27479.t1
Valid prediction for GlimmerHMM_glimmerT_41207-T1
Valid prediction for Augustus_model.g27486.t1
Valid prediction for Augustus_model.g27485.t1
Valid prediction for snap_scaffold_17-snap.2550-T1
Valid prediction for GlimmerHMM_glimmerT_41211-T1
Valid prediction for snap_scaffold_17-snap.2507-T1
Valid prediction for snap_scaffold_17-snap.2542-T1
Valid prediction for snap_scaffold_17-snap.2515-T1
Valid prediction for GlimmerHMM_glimmerT_41212-T1
Valid prediction for snap_scaffold_17-snap.2516-T1
Valid prediction for snap_scaffold_17-snap.2522-T1
Valid prediction for snap_scaffold_17-snap.2535-T1
Valid prediction for snap_scaffold_17-snap.2514-T1
Valid prediction for snap_scaffold_17-snap.2520-T1
Valid prediction for GlimmerHMM_glimmerT_41221-T1
Valid prediction for HiQ_model.g27480.t1
Valid prediction for snap_scaffold_17-snap.2513-T1
Valid prediction for snap_scaffold_17-snap.2526-T1
Valid prediction for snap_scaffold_17-snap.2547-T1
Valid prediction for GlimmerHMM_glimmerT_41209-T1
Valid prediction for snap_scaffold_17-snap.2540-T1
Valid prediction for snap_scaffold_17-snap.2511-T1
Valid prediction for GlimmerHMM_glimmerT_41219-T1
Valid prediction for GlimmerHMM_glimmerT_41208-T1
Valid prediction for snap_scaffold_17-snap.2524-T1
Valid prediction for snap_scaffold_17-snap.2538-T1
Valid prediction for Augustus_model.g27487.t1
Valid prediction for GlimmerHMM_glimmerT_41223-T1
Couldn't classify 52686, 52687
Sorry, prediction pasa_asmbl_19285.p1 fails validation.
(ATG)	 GT	52686-52687	GT	ATG
(GTG)	 AG	53264-53537	GT	CTG
(AGC)	 AG	54711-54788	GT	AGG
(CAT)	 AG	55351-55467	GT	CCG
(ATT)	 AG	55641-55771	GT	GGG
(CTA)	 AG	56096-56236	GT	TAG
(CCA)	 AG	56495-56791	GT	CTG
(GCA)	 AG	57322-57433	GT	TGG
(GAG)	 AG	57803-57973	AC	AAA
-recovered pasa_asmbl_19285.p1, terminal, 57803, 57973
-recovered pasa_asmbl_19285.p1, internal, 53264, 53537
-recovered pasa_asmbl_19285.p1, internal, 54711, 54788
-recovered pasa_asmbl_19285.p1, internal, 55351, 55467
-recovered pasa_asmbl_19285.p1, internal, 55641, 55771
-recovered pasa_asmbl_19285.p1, internal, 56096, 56236
-recovered pasa_asmbl_19285.p1, internal, 56495, 56791
-recovered pasa_asmbl_19285.p1, internal, 57322, 57433

-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_41224-T1
Valid prediction for GlimmerHMM_glimmerT_41227-T1
Valid prediction for snap_scaffold_17-snap.2537-T1
Valid prediction for snap_scaffold_17-snap.2517-T1
Valid prediction for snap_scaffold_17-snap.2528-T1
Valid prediction for GlimmerHMM_glimmerT_41225-T1
Valid prediction for GlimmerHMM_glimmerT_41218-T1
Couldn't classify 99651, 99768
Sorry, prediction pasa_asmbl_18335.p2 fails validation.
(CAT)	 TC	99651-99768	GT	TGG
(ACA)	 AG	100938-101076	GT	AGG
(GTG)	 AG	101340-101500	GT	AGG
(TGT)	 AG	102230-102267	GT	GAG
-recovered pasa_asmbl_18335.p2, terminal, 102230, 102267
-recovered pasa_asmbl_18335.p2, internal, 100938, 101076
-recovered pasa_asmbl_18335.p2, internal, 101340, 101500
-recovered pasa_asmbl_18335.p2, internal, 102230, 102267
Valid prediction for snap_scaffold_17-snap.2532-T1
Valid prediction for snap_scaffold_17-snap.2512-T1
Valid prediction for snap_scaffold_17-snap.2510-T1
Couldn't classify 114680, 114754
Sorry, prediction pasa_asmbl_18326.p1 fails validation.
(TCT)	 GA	114680-114754	GT	GTG
(GTG)	 AG	115521-115678	GT	AGG
(GTT)	 AG	116073-116160	GT	AGG
(ATC)	 AG	116300-116446	GT	AGG
(ATG)	 AG	116883-116989	GT	CGG
(GAT)	 AG	119683-119857	GT	TAG
(AGT)	 AG	120206-120339	GT	AAG
(AGA)	 AG	120575-120820	GT	TCG
(GTG)	 AG	121241-121346	GT	CGG
(ATG)	 AG	121662-121823	GT	AGG
(GTG)	 AG	122139-122252	GT	AGG
(CCC)	 AG	123280-123441	GT	AGG
(AAA)	 AG	124096-124347	GT	AGG
(TTC)	 AG	124767-124835	GT	AGG
(TTC)	 AG	124962-125135	GT	TGG
(GTG)	 AG	125994-126131	GT	TGG
(GAG)	 AG	126693-126793	GT	AGG
(ATC)	 AG	127349-127400	GT	GAG
(TCA)	 AG	129435-129458	GG	AGG
-recovered pasa_asmbl_18326.p1, initial, 116883, 116989
-recovered pasa_asmbl_18326.p1, initial, 121662, 121823
-recovered pasa_asmbl_18326.p1, terminal, 129435, 129458
-recovered pasa_asmbl_18326.p1, internal, 115521, 115678
-recovered pasa_asmbl_18326.p1, internal, 116073, 116160
-recovered pasa_asmbl_18326.p1, internal, 116300, 116446
-recovered pasa_asmbl_18326.p1, internal, 116883, 116989
-recovered pasa_asmbl_18326.p1, internal, 119683, 119857
-recovered pasa_asmbl_18326.p1, internal, 120206, 120339
-recovered pasa_asmbl_18326.p1, internal, 120575, 120820
-recovered pasa_asmbl_18326.p1, internal, 121241, 121346
-recovered pasa_asmbl_18326.p1, internal, 121662, 121823
-recovered pasa_asmbl_18326.p1, internal, 122139, 122252
-recovered pasa_asmbl_18326.p1, internal, 123280, 123441
-recovered pasa_asmbl_18326.p1, internal, 124096, 124347
-recovered pasa_asmbl_18326.p1, internal, 124767, 124835
-recovered pasa_asmbl_18326.p1, internal, 124962, 125135
-recovered pasa_asmbl_18326.p1, internal, 125994, 126131
-recovered pasa_asmbl_18326.p1, internal, 126693, 126793
-recovered pasa_asmbl_18326.p1, internal, 127349, 127400
Valid prediction for GlimmerHMM_glimmerT_41214-T1
Valid prediction for CodingQuarry_transcript_22216-T1
Valid prediction for snap_scaffold_17-snap.2539-T1
Valid prediction for GlimmerHMM_glimmerT_41229-T1
Valid prediction for Augustus_model.g27483.t1
Valid prediction for snap_scaffold_17-snap.2544-T1
Valid prediction for Augustus_model.g27482.t1
Valid prediction for Augustus_model.g27484.t1
Valid prediction for GlimmerHMM_glimmerT_41216-T1
Valid prediction for snap_scaffold_17-snap.2534-T1
Valid prediction for snap_scaffold_17-snap.2529-T1
Valid prediction for snap_scaffold_17-snap.2519-T1
Valid prediction for snap_scaffold_17-snap.2548-T1
Valid prediction for snap_scaffold_17-snap.2521-T1
Valid prediction for snap_scaffold_17-snap.2541-T1
Valid prediction for GlimmerHMM_glimmerT_41220-T1
Valid prediction for snap_scaffold_17-snap.2545-T1
Valid prediction for GlimmerHMM_glimmerT_41228-T1
Valid prediction for snap_scaffold_17-snap.2531-T1
Valid prediction for snap_scaffold_17-snap.2536-T1
Valid prediction for CodingQuarry_transcript_22217-T1
Valid prediction for snap_scaffold_17-snap.2549-T1
Valid prediction for snap_scaffold_17-snap.2523-T1
Valid prediction for snap_scaffold_17-snap.2508-T1
Valid prediction for GlimmerHMM_glimmerT_41222-T1
Valid prediction for snap_scaffold_17-snap.2530-T1
Valid prediction for CodingQuarry_transcript_22218-T1
Valid prediction for HiQ_model.g27481.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28073, rend_intergenic: 25866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30846, rend_intergenic: 28304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40442, rend_intergenic: 32333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47989, rend_intergenic: 44277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57973, rend_intergenic: 56051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70974, rend_intergenic: 61100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73837, rend_intergenic: 71231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96937, rend_intergenic: 74204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104257, rend_intergenic: 98224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132319, rend_intergenic: 128471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136212, rend_intergenic: 133545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141125, rend_intergenic: 138853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144074, rend_intergenic: 142709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149520, rend_intergenic: 148039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151975, rend_intergenic: 149539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158654, rend_intergenic: 152013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172281, rend_intergenic: 160610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180508, rend_intergenic: 172637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187516, rend_intergenic: 183483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190615
-exon list size: 348


building trellis

0.3    
0.6    
0.9    
1.1    
1.4    
1.7    
2.0    
2.3    
2.6    
2.9    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.1    
9.4    
9.7    
10.0    
10.3    
10.6    
10.9    
11.1    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.1    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.1    
19.4    
19.7    
20.0    
20.3    
20.6    
20.9    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.9    
39.1    
39.4    
39.7    
40.0    
40.3    
40.6    
40.9    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.1    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.1    
59.4    
59.7    
60.0    
60.3    
60.6    
60.9    
61.1    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
64.9    
65.1    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.1    
79.4    
79.7    
80.0    
80.3    
80.6    
80.9    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
82.9    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 28073, rend_intergenic: 25866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30846, rend_intergenic: 28304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40442, rend_intergenic: 32333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47989, rend_intergenic: 44277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57973, rend_intergenic: 56051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70974, rend_intergenic: 61100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73837, rend_intergenic: 71231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96937, rend_intergenic: 74204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104257, rend_intergenic: 98224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132319, rend_intergenic: 128471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136212, rend_intergenic: 133545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141125, rend_intergenic: 138853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144074, rend_intergenic: 142709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149520, rend_intergenic: 148039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151975, rend_intergenic: 149539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158654, rend_intergenic: 152013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172281, rend_intergenic: 160610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180508, rend_intergenic: 172637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187516, rend_intergenic: 183483  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