-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_5433618-5580321

-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_660-T1
Valid prediction for snap_scaffold_1-snap.851-T1
Valid prediction for snap_scaffold_1-snap.828-T1
Valid prediction for Augustus_model.g518.t1
Valid prediction for snap_scaffold_1-snap.839-T1
Valid prediction for snap_scaffold_1-snap.849-T1
Valid prediction for GlimmerHMM_glimmerT_657-T1
Valid prediction for GlimmerHMM_glimmerT_667-T1
Valid prediction for GlimmerHMM_glimmerT_653-T1
Couldn't classify 107464, 107590
Sorry, prediction pasa_asmbl_1727.p2 fails validation.
(ATC)	 AC	107464-107590	GT	TGG
(GTA)	 AG	107722-107836	GT	AAG
(GAA)	 AG	107950-108086	GT	CGG
(AAT)	 AG	108170-108201	AG	AGA
-recovered pasa_asmbl_1727.p2, terminal, 108170, 108201
-recovered pasa_asmbl_1727.p2, internal, 107722, 107836
-recovered pasa_asmbl_1727.p2, internal, 107950, 108086
Valid prediction for snap_scaffold_1-snap.847-T1
Valid prediction for snap_scaffold_1-snap.841-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_662-T1
Valid prediction for snap_scaffold_1-snap.840-T1
Valid prediction for Augustus_model.g511.t1
Valid prediction for GlimmerHMM_glimmerT_648-T1
Valid prediction for Augustus_model.g517.t1
Valid prediction for snap_scaffold_1-snap.845-T1
Valid prediction for GlimmerHMM_glimmerT_664-T1
Valid prediction for GlimmerHMM_glimmerT_671-T1
Valid prediction for snap_scaffold_1-snap.858-T1
Valid prediction for snap_scaffold_1-snap.833-T1
Valid prediction for snap_scaffold_1-snap.843-T1
Valid prediction for snap_scaffold_1-snap.846-T1
Valid prediction for GlimmerHMM_glimmerT_652-T1
Valid prediction for snap_scaffold_1-snap.835-T1
Valid prediction for GlimmerHMM_glimmerT_651-T1
Valid prediction for Augustus_model.g514.t1
Valid prediction for snap_scaffold_1-snap.850-T1
Valid prediction for Augustus_model.g520.t1
Valid prediction for GlimmerHMM_glimmerT_654-T1
Valid prediction for snap_scaffold_1-snap.837-T1
Valid prediction for snap_scaffold_1-snap.854-T1
Valid prediction for GlimmerHMM_glimmerT_673-T1
Valid prediction for GlimmerHMM_glimmerT_661-T1
Valid prediction for snap_scaffold_1-snap.856-T1
Valid prediction for snap_scaffold_1-snap.829-T1
Couldn't classify 58034, 58792
Sorry, prediction pasa_asmbl_266.p1 fails validation.
(ATG)	 GC	58034-58792	AC	ATA

-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_663-T1
Valid prediction for GlimmerHMM_glimmerT_669-T1
Valid prediction for GlimmerHMM_glimmerT_668-T1
Valid prediction for CodingQuarry_transcript_2608-T1
Valid prediction for snap_scaffold_1-snap.852-T1
Valid prediction for snap_scaffold_1-snap.831-T1
Valid prediction for Augustus_model.g516.t1
Valid prediction for snap_scaffold_1-snap.848-T1
Valid prediction for HiQ_model.g522.t1
Valid prediction for GlimmerHMM_glimmerT_650-T1
Couldn't classify 46273, 46368
Sorry, prediction pasa_asmbl_270.p1 fails validation.
(ATG)	 CC	41498-41616	GT	AAG
(ATA)	 AG	41773-41929	GT	TGG
(GAA)	 AG	42619-42738	GT	AGG
(ACG)	 AG	42863-42945	GT	TGG
(GTG)	 AG	43122-43239	GT	AGG
(GAT)	 AG	43491-43638	GT	AGG
(ACA)	 AG	44993-45080	GT	AAG
(ATT)	 AG	46014-46077	GT	AGG
(TAC)	 AG	46273-46368	GT	CTG
-recovered pasa_asmbl_270.p1, initial, 41498, 41616
-recovered pasa_asmbl_270.p1, internal, 41773, 41929
-recovered pasa_asmbl_270.p1, internal, 42619, 42738
-recovered pasa_asmbl_270.p1, internal, 42863, 42945
-recovered pasa_asmbl_270.p1, internal, 43122, 43239
-recovered pasa_asmbl_270.p1, internal, 43491, 43638
-recovered pasa_asmbl_270.p1, internal, 44993, 45080
-recovered pasa_asmbl_270.p1, internal, 46014, 46077
-recovered pasa_asmbl_270.p1, internal, 46273, 46368
Valid prediction for CodingQuarry_transcript_2609-T1
Valid prediction for GlimmerHMM_glimmerT_670-T1
Valid prediction for snap_scaffold_1-snap.844-T1
Valid prediction for snap_scaffold_1-snap.842-T1
Valid prediction for Augustus_model.g513.t1
Valid prediction for GlimmerHMM_glimmerT_655-T1
Valid prediction for snap_scaffold_1-snap.836-T1
Valid prediction for snap_scaffold_1-snap.830-T1
Valid prediction for snap_scaffold_1-snap.838-T1
Valid prediction for snap_scaffold_1-snap.860-T1
Valid prediction for GlimmerHMM_glimmerT_658-T1
Valid prediction for GlimmerHMM_glimmerT_659-T1
Valid prediction for Augustus_model.g515.t1
Valid prediction for Augustus_model.g512.t1
Valid prediction for GlimmerHMM_glimmerT_666-T1
Valid prediction for snap_scaffold_1-snap.855-T1
Valid prediction for snap_scaffold_1-snap.857-T1
Valid prediction for Augustus_model.g521.t1
Valid prediction for snap_scaffold_1-snap.832-T1
Valid prediction for GlimmerHMM_glimmerT_665-T1
Valid prediction for snap_scaffold_1-snap.859-T1
Valid prediction for GlimmerHMM_glimmerT_672-T1
Valid prediction for GlimmerHMM_glimmerT_656-T1
Valid prediction for Augustus_model.g510.t1
Valid prediction for GlimmerHMM_glimmerT_649-T1
Valid prediction for snap_scaffold_1-snap.834-T1
Valid prediction for pasa_asmbl_274.p1
Valid prediction for snap_scaffold_1-snap.853-T1
Couldn't classify 53897, 54022
Couldn't classify 64397, 64452
Sorry, prediction pasa_asmbl_268.p1 fails validation.
(GTC)	 GG	53897-54022	GT	AGG
(GTG)	 AG	55810-55883	GT	AGG
(CAT)	 AG	56264-56458	GT	TGG
(GTT)	 AG	56598-56684	GT	AGG
(CGA)	 AG	57001-57084	GT	AGG
(GCT)	 AG	58081-58225	GT	AGG
(GAG)	 AG	58717-58837	GT	TGG
(CCT)	 AG	59092-59183	GT	AGG
(GGA)	 AG	59427-59504	GT	TGG
(GCT)	 AG	59723-59844	GT	AGG
(GGA)	 AG	61297-61399	GT	AGG
(TAT)	 AG	61525-61608	GT	AGG
(GAG)	 AG	63315-63489	GT	AGG
(GCT)	 AG	64397-64452	AC	ANA
-recovered pasa_asmbl_268.p1, internal, 55810, 55883
-recovered pasa_asmbl_268.p1, internal, 56264, 56458
-recovered pasa_asmbl_268.p1, internal, 56598, 56684
-recovered pasa_asmbl_268.p1, internal, 57001, 57084
-recovered pasa_asmbl_268.p1, internal, 58081, 58225
-recovered pasa_asmbl_268.p1, internal, 58717, 58837
-recovered pasa_asmbl_268.p1, internal, 59092, 59183
-recovered pasa_asmbl_268.p1, internal, 59427, 59504
-recovered pasa_asmbl_268.p1, internal, 59723, 59844
-recovered pasa_asmbl_268.p1, internal, 61297, 61399
-recovered pasa_asmbl_268.p1, internal, 61525, 61608
-recovered pasa_asmbl_268.p1, internal, 63315, 63489
Couldn't classify 134794, 135024
Sorry, prediction pasa_asmbl_265.p1 fails validation.
(ATG)	 AT	132118-132139	GT	AGG
(TCA)	 AG	133218-133382	GT	AGG
(GTC)	 AG	134300-134514	GT	AGG
(AAA)	 AG	134794-135024	AC	CCA
-recovered pasa_asmbl_265.p1, initial, 132118, 132139
-recovered pasa_asmbl_265.p1, internal, 133218, 133382
-recovered pasa_asmbl_265.p1, internal, 134300, 134514
Valid prediction for Augustus_model.g519.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13633, rend_intergenic: 12213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35355, rend_intergenic: 30589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40411, rend_intergenic: 38729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46719, rend_intergenic: 43771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54387, rend_intergenic: 50934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95445, rend_intergenic: 79045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100811, rend_intergenic: 99209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 146704
-exon list size: 284


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.1    
2.4    
2.8    
3.1    
3.5    
3.8    
4.2    
4.5    
4.9    
5.2    
5.6    
5.9    
6.3    
6.6    
7.0    
7.3    
7.7    
8.0    
8.4    
8.7    
9.1    
9.4    
9.8    
10.1    
10.5    
10.8    
11.2    
11.5    
11.9    
12.2    
12.6    
12.9    
13.3    
13.6    
14.0    
14.3    
14.7    
15.0    
15.4    
15.7    
16.1    
16.4    
16.8    
17.1    
17.5    
17.8    
18.2    
18.5    
18.9    
19.2    
19.6    
19.9    
20.3    
20.6    
21.0    
21.3    
21.7    
22.0    
22.4    
22.7    
23.1    
23.4    
23.8    
24.1    
24.5    
24.8    
25.2    
25.5    
25.9    
26.2    
26.6    
26.9    
27.3    
27.6    
28.0    
28.3    
28.7    
29.0    
29.4    
29.7    
30.1    
30.4    
30.8    
31.1    
31.5    
31.8    
32.2    
32.5    
32.9    
33.2    
33.6    
33.9    
34.3    
34.6    
35.0    
35.3    
35.7    
36.0    
36.4    
36.7    
37.1    
37.4    
37.8    
38.1    
38.5    
38.8    
39.2    
39.5    
39.9    
40.2    
40.6    
40.9    
41.3    
41.6    
42.0    
42.3    
42.7    
43.0    
43.4    
43.7    
44.1    
44.4    
44.8    
45.1    
45.5    
45.8    
46.2    
46.5    
46.9    
47.2    
47.6    
47.9    
48.3    
48.6    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.4    
51.7    
52.1    
52.4    
52.8    
53.1    
53.5    
53.8    
54.2    
54.5    
54.9    
55.2    
55.6    
55.9    
56.3    
56.6    
57.0    
57.3    
57.7    
58.0    
58.4    
58.7    
59.1    
59.4    
59.8    
60.1    
60.5    
60.8    
61.2    
61.5    
61.9    
62.2    
62.6    
62.9    
63.3    
63.6    
64.0    
64.3    
64.7    
65.0    
65.4    
65.7    
66.1    
66.4    
66.8    
67.1    
67.5    
67.8    
68.2    
68.5    
68.9    
69.2    
69.6    
69.9    
70.3    
70.6    
71.0    
71.3    
71.7    
72.0    
72.4    
72.7    
73.1    
73.4    
73.8    
74.1    
74.5    
74.8    
75.2    
75.5    
75.9    
76.2    
76.6    
76.9    
77.3    
77.6    
78.0    
78.3    
78.7    
79.0    
79.4    
79.7    
80.1    
80.4    
80.8    
81.1    
81.5    
81.8    
82.2    
82.5    
82.9    
83.2    
83.6    
83.9    
84.3    
84.6    
85.0    
85.3    
85.7    
86.0    
86.4    
86.7    
87.1    
87.4    
87.8    
88.1    
88.5    
88.8    
89.2    
89.5    
89.9    
90.2    
90.6    
90.9    
91.3    
91.6    
92.0    
92.3    
92.7    
93.0    
93.4    
93.7    
94.1    
94.4    
94.8    
95.1    
95.5    
95.8    
96.2    
96.5    
96.9    
97.2    
97.6    
97.9    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 13633, rend_intergenic: 12213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35355, rend_intergenic: 30589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40411, rend_intergenic: 38729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46719, rend_intergenic: 43771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54387, rend_intergenic: 50934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95445, rend_intergenic: 79045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100811, rend_intergenic: 99209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support