-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_2347914-2567159

-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_22-snap.420-T1
Valid prediction for snap_scaffold_22-snap.419-T1
Valid prediction for GlimmerHMM_glimmerT_49030-T1
Valid prediction for GlimmerHMM_glimmerT_49039-T1
Couldn't classify 27488, 27571
Couldn't classify 30016, 30063
Sorry, prediction pasa_asmbl_29937.p1 fails validation.
(AGG)	 CC	27488-27571	GT	CTG
(GCG)	 AG	28174-28302	GT	AGG
(GAT)	 AG	29254-29439	GT	AGG
(GGC)	 AG	30016-30063	AA	AGA
-recovered pasa_asmbl_29937.p1, internal, 28174, 28302
-recovered pasa_asmbl_29937.p1, internal, 29254, 29439
Valid prediction for snap_scaffold_22-snap.421-T1
Valid prediction for snap_scaffold_22-snap.406-T1
Valid prediction for pasa_asmbl_29944.p1
Valid prediction for snap_scaffold_22-snap.401-T1
Valid prediction for snap_scaffold_22-snap.399-T1
Valid prediction for GlimmerHMM_glimmerT_49043-T1
Valid prediction for GlimmerHMM_glimmerT_49035-T1
Valid prediction for snap_scaffold_22-snap.407-T1
Valid prediction for Augustus_model.g32749.t1
Couldn't classify 31690, 31717
Sorry, prediction pasa_asmbl_29938.p1 fails validation.
(GAG)	 TG	31690-31717	GT	AGG
(AAG)	 AG	32344-32418	GT	CGG
(GAG)	 AG	32660-32739	GT	TTG
(GTG)	 AG	32940-33086	GT	AGG
(GTC)	 AG	33385-33555	GT	AGG
(ATA)	 AG	34293-34490	GT	AGG
(GAC)	 AG	35251-35460	GT	CAG
(ATT)	 AG	36951-37112	GT	AGG
(GGA)	 AG	38871-38982	GT	TGG
(GGA)	 AG	39369-39567	GT	GGG
(ATC)	 AG	40202-40243	GT	GTG
(CAT)	 AG	41821-41916	GT	AGG
(GAG)	 AG	42162-42263	GT	AAG
(AGT)	 AG	42531-42708	GT	AGG
(GTG)	 AG	43489-43599	GT	GAG
(TCA)	 AG	45503-45565	GT	AGG
(ATC)	 AG	46684-46852	GT	GAG
(AGA)	 AG	48245-48441	GT	AGG
(ATC)	 AG	48646-48737	GT	AGG
(GAA)	 AG	49345-49420	GT	AGG
(GTG)	 AG	50566-50658	GT	AGG
(GAT)	 AG	50775-50849	GT	CGG
(GTC)	 AG	50989-51172	GT	CAG
(GTT)	 AG	51469-51614	GT	TGG
(GGT)	 AG	53461-53544	GT	AGG
(GTG)	 AG	54362-54555	GT	AGG
(GAG)	 AG	55767-55914	GT	AGG
(TGC)	 AG	56133-56219	GT	AGG
(ATG)	 AG	56445-56541	GT	CTG
(CAC)	 AG	56627-56667	GT	AGG
(GGT)	 AG	56756-56878	GT	AGG
(ATA)	 AG	57741-57845	GT	AGG
(GTG)	 AG	58072-58181	GT	GGG
(CCC)	 AG	58627-58750	GT	AGG
(GGG)	 AG	59193-59339	AC	AGA
-recovered pasa_asmbl_29938.p1, initial, 56445, 56541
-recovered pasa_asmbl_29938.p1, terminal, 59193, 59339
-recovered pasa_asmbl_29938.p1, internal, 32344, 32418
-recovered pasa_asmbl_29938.p1, internal, 32660, 32739
-recovered pasa_asmbl_29938.p1, internal, 32940, 33086
-recovered pasa_asmbl_29938.p1, internal, 33385, 33555
-recovered pasa_asmbl_29938.p1, internal, 34293, 34490
-recovered pasa_asmbl_29938.p1, internal, 35251, 35460
-recovered pasa_asmbl_29938.p1, internal, 36951, 37112
-recovered pasa_asmbl_29938.p1, internal, 38871, 38982
-recovered pasa_asmbl_29938.p1, internal, 39369, 39567
-recovered pasa_asmbl_29938.p1, internal, 40202, 40243
-recovered pasa_asmbl_29938.p1, internal, 41821, 41916
-recovered pasa_asmbl_29938.p1, internal, 42162, 42263
-recovered pasa_asmbl_29938.p1, internal, 42531, 42708
-recovered pasa_asmbl_29938.p1, internal, 43489, 43599
-recovered pasa_asmbl_29938.p1, internal, 45503, 45565
-recovered pasa_asmbl_29938.p1, internal, 46684, 46852
-recovered pasa_asmbl_29938.p1, internal, 48245, 48441
-recovered pasa_asmbl_29938.p1, internal, 48646, 48737
-recovered pasa_asmbl_29938.p1, internal, 49345, 49420
-recovered pasa_asmbl_29938.p1, internal, 50566, 50658
-recovered pasa_asmbl_29938.p1, internal, 50775, 50849
-recovered pasa_asmbl_29938.p1, internal, 50989, 51172
-recovered pasa_asmbl_29938.p1, internal, 51469, 51614
-recovered pasa_asmbl_29938.p1, internal, 53461, 53544
-recovered pasa_asmbl_29938.p1, internal, 54362, 54555
-recovered pasa_asmbl_29938.p1, internal, 55767, 55914
-recovered pasa_asmbl_29938.p1, internal, 56133, 56219
-recovered pasa_asmbl_29938.p1, internal, 56445, 56541
-recovered pasa_asmbl_29938.p1, internal, 56627, 56667
-recovered pasa_asmbl_29938.p1, internal, 56756, 56878
-recovered pasa_asmbl_29938.p1, internal, 57741, 57845
-recovered pasa_asmbl_29938.p1, internal, 58072, 58181
-recovered pasa_asmbl_29938.p1, internal, 58627, 58750
Valid prediction for snap_scaffold_22-snap.395-T1
Valid prediction for GlimmerHMM_glimmerT_49048-T1
Valid prediction for snap_scaffold_22-snap.397-T1
Valid prediction for snap_scaffold_22-snap.409-T1
Valid prediction for snap_scaffold_22-snap.422-T1
Valid prediction for snap_scaffold_22-snap.398-T1
Valid prediction for snap_scaffold_22-snap.418-T1
Valid prediction for snap_scaffold_22-snap.415-T1
Valid prediction for GlimmerHMM_glimmerT_49045-T1
Valid prediction for Augustus_model.g32745.t1
Valid prediction for GlimmerHMM_glimmerT_49034-T1
Valid prediction for snap_scaffold_22-snap.417-T1
Couldn't classify 26796, 26882
Sorry, prediction pasa_asmbl_30507.p1 fails validation.
(ATG)	 AG	22492-22507	GT	GGG
(ATA)	 AG	23816-23982	GT	AGG
(GGA)	 AG	26074-26232	GT	AGG
(GGC)	 AG	26796-26882	GG	GGG
-recovered pasa_asmbl_30507.p1, initial, 22492, 22507
-recovered pasa_asmbl_30507.p1, internal, 22492, 22507
-recovered pasa_asmbl_30507.p1, internal, 23816, 23982
-recovered pasa_asmbl_30507.p1, internal, 26074, 26232
Valid prediction for Augustus_model.g32750.t1
Valid prediction for CodingQuarry_transcript_34114-T1
Valid prediction for snap_scaffold_22-snap.416-T1
Valid prediction for snap_scaffold_22-snap.410-T1
Valid prediction for GlimmerHMM_glimmerT_49040-T1
Valid prediction for GlimmerHMM_glimmerT_49028-T1
Valid prediction for snap_scaffold_22-snap.394-T1
Valid prediction for snap_scaffold_22-snap.393-T1
Valid prediction for GlimmerHMM_glimmerT_49044-T1
Valid prediction for GlimmerHMM_glimmerT_49033-T1
Valid prediction for snap_scaffold_22-snap.396-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 pasa_asmbl_29155.p1
Valid prediction for GlimmerHMM_glimmerT_49037-T1
Valid prediction for CodingQuarry_transcript_34115-T1
Valid prediction for GlimmerHMM_glimmerT_49038-T1
Valid prediction for Augustus_model.g32747.t1
Valid prediction for snap_scaffold_22-snap.391-T1
Valid prediction for snap_scaffold_22-snap.414-T1
Valid prediction for GlimmerHMM_glimmerT_49042-T1
Valid prediction for GlimmerHMM_glimmerT_49032-T1
Couldn't classify 135158, 135215
Sorry, prediction pasa_asmbl_29156.p1 fails validation.
(TTC)	 CC	135158-135215	GT	GGG
(GCT)	 AG	135484-135663	GT	GGG
(ATT)	 AG	135932-136078	GT	ATG
(CTC)	 AG	136436-136620	GA	AAG
-recovered pasa_asmbl_29156.p1, terminal, 136436, 136620
-recovered pasa_asmbl_29156.p1, internal, 135484, 135663
-recovered pasa_asmbl_29156.p1, internal, 135932, 136078
Valid prediction for GlimmerHMM_glimmerT_49046-T1
Valid prediction for snap_scaffold_22-snap.402-T1
Valid prediction for snap_scaffold_22-snap.412-T1
Valid prediction for CodingQuarry_transcript_34116-T1
Valid prediction for Augustus_model.g32744.t1
Valid prediction for GlimmerHMM_glimmerT_49047-T1
Valid prediction for GlimmerHMM_glimmerT_49041-T1
Valid prediction for snap_scaffold_22-snap.408-T1
Valid prediction for GlimmerHMM_glimmerT_49031-T1
Valid prediction for snap_scaffold_22-snap.405-T1
Valid prediction for snap_scaffold_22-snap.413-T1
Valid prediction for snap_scaffold_22-snap.411-T1
Valid prediction for snap_scaffold_22-snap.423-T1
Valid prediction for snap_scaffold_22-snap.392-T1
Valid prediction for snap_scaffold_22-snap.404-T1
Valid prediction for GlimmerHMM_glimmerT_49029-T1
Valid prediction for HiQ_model.g32746.t1
Valid prediction for snap_scaffold_22-snap.403-T1
Valid prediction for Augustus_model.g32748.t1
Valid prediction for snap_scaffold_22-snap.400-T1
Valid prediction for GlimmerHMM_glimmerT_49036-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 55925, rend_intergenic: 52759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187638, rend_intergenic: 173202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212857, rend_intergenic: 211389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 219246
-exon list size: 251


building trellis

0.4    
0.8    
1.2    
1.6    
2.0    
2.4    
2.8    
3.2    
3.6    
4.0    
4.3    
4.7    
5.1    
5.5    
5.9    
6.3    
6.7    
7.1    
7.5    
7.9    
8.3    
8.7    
9.1    
9.5    
9.9    
10.3    
10.7    
11.1    
11.5    
11.9    
12.3    
12.6    
13.0    
13.4    
13.8    
14.2    
14.6    
15.0    
15.4    
15.8    
16.2    
16.6    
17.0    
17.4    
17.8    
18.2    
18.6    
19.0    
19.4    
19.8    
20.2    
20.6    
20.9    
21.3    
21.7    
22.1    
22.5    
22.9    
23.3    
23.7    
24.1    
24.5    
24.9    
25.3    
25.7    
26.1    
26.5    
26.9    
27.3    
27.7    
28.1    
28.5    
28.9    
29.2    
29.6    
30.0    
30.4    
30.8    
31.2    
31.6    
32.0    
32.4    
32.8    
33.2    
33.6    
34.0    
34.4    
34.8    
35.2    
35.6    
36.0    
36.4    
36.8    
37.2    
37.5    
37.9    
38.3    
38.7    
39.1    
39.5    
39.9    
40.3    
40.7    
41.1    
41.5    
41.9    
42.3    
42.7    
43.1    
43.5    
43.9    
44.3    
44.7    
45.1    
45.5    
45.8    
46.2    
46.6    
47.0    
47.4    
47.8    
48.2    
48.6    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.4    
51.8    
52.2    
52.6    
53.0    
53.4    
53.8    
54.2    
54.5    
54.9    
55.3    
55.7    
56.1    
56.5    
56.9    
57.3    
57.7    
58.1    
58.5    
58.9    
59.3    
59.7    
60.1    
60.5    
60.9    
61.3    
61.7    
62.1    
62.5    
62.8    
63.2    
63.6    
64.0    
64.4    
64.8    
65.2    
65.6    
66.0    
66.4    
66.8    
67.2    
67.6    
68.0    
68.4    
68.8    
69.2    
69.6    
70.0    
70.4    
70.8    
71.1    
71.5    
71.9    
72.3    
72.7    
73.1    
73.5    
73.9    
74.3    
74.7    
75.1    
75.5    
75.9    
76.3    
76.7    
77.1    
77.5    
77.9    
78.3    
78.7    
79.1    
79.4    
79.8    
80.2    
80.6    
81.0    
81.4    
81.8    
82.2    
82.6    
83.0    
83.4    
83.8    
84.2    
84.6    
85.0    
85.4    
85.8    
86.2    
86.6    
87.0    
87.4    
87.7    
88.1    
88.5    
88.9    
89.3    
89.7    
90.1    
90.5    
90.9    
91.3    
91.7    
92.1    
92.5    
92.9    
93.3    
93.7    
94.1    
94.5    
94.9    
95.3    
95.7    
96.0    
96.4    
96.8    
97.2    
97.6    
98.0    
98.4    
98.8    
99.2    
99.6    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 55925, rend_intergenic: 52759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187638, rend_intergenic: 173202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212857, rend_intergenic: 211389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support