-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_14/scaffold_14_1616777-1884013

-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_15567-T1
Valid prediction for snap_scaffold_14-snap.296-T1
Couldn't classify 234208, 234346
Couldn't classify 238957, 239028
Sorry, prediction pasa_asmbl_12701.p1 fails validation.
(CTA)	 GG	234208-234346	GT	AGG
(GTC)	 AG	235926-236051	GT	AGG
(GCG)	 AG	236187-236311	GT	AGG
(AAC)	 AG	238416-238514	GT	AGG
(GTC)	 AG	238957-239028	TG	ACT
-recovered pasa_asmbl_12701.p1, internal, 235926, 236051
-recovered pasa_asmbl_12701.p1, internal, 236187, 236311
-recovered pasa_asmbl_12701.p1, internal, 238416, 238514
Valid prediction for snap_scaffold_14-snap.273-T1
Valid prediction for snap_scaffold_14-snap.292-T1
Valid prediction for Augustus_model.g22270.t1
Valid prediction for snap_scaffold_14-snap.257-T1
Valid prediction for pasa_asmbl_11834.p1
Valid prediction for CodingQuarry_transcript_15568-T1
Valid prediction for Augustus_model.g22271.t1
Valid prediction for GlimmerHMM_glimmerT_33324-T1
Valid prediction for GlimmerHMM_glimmerT_33327-T1
Valid prediction for snap_scaffold_14-snap.298-T1
Valid prediction for snap_scaffold_14-snap.285-T1
Valid prediction for snap_scaffold_14-snap.291-T1
Valid prediction for Augustus_model.g22285.t1
Valid prediction for snap_scaffold_14-snap.280-T1
Valid prediction for snap_scaffold_14-snap.267-T1
Valid prediction for snap_scaffold_14-snap.266-T1
Valid prediction for snap_scaffold_14-snap.282-T1
Valid prediction for GlimmerHMM_glimmerT_33310-T1
Valid prediction for GlimmerHMM_glimmerT_33309-T1
Valid prediction for snap_scaffold_14-snap.263-T1
Valid prediction for HiQ_model.g22275.t1
Valid prediction for GlimmerHMM_glimmerT_33313-T1
Valid prediction for snap_scaffold_14-snap.290-T1
Valid prediction for GlimmerHMM_glimmerT_33325-T1
Valid prediction for HiQ_model.g22284.t1
Valid prediction for snap_scaffold_14-snap.294-T1
Valid prediction for snap_scaffold_14-snap.300-T1
Valid prediction for GlimmerHMM_glimmerT_33304-T1
Couldn't classify 222635, 222692
Couldn't classify 230618, 230691
Sorry, prediction pasa_asmbl_11836.p1 fails validation.
(GAC)	 GT	222635-222692	GT	AGG
(GCT)	 AG	223048-223088	GT	AAG
(GGC)	 AG	223467-223522	GT	GGG
(GCA)	 AG	224181-224277	GT	TAG
(GGG)	 AG	224829-224977	GT	AAG
(GTA)	 AG	226367-226502	GT	GGG
(TCG)	 AG	228103-228260	GT	AGG
(TGA)	 AG	228443-228524	GT	CGG
(GAC)	 AG	229073-229208	GT	AGG
(TAA)	 AG	230618-230691	TG	CGT
-recovered pasa_asmbl_11836.p1, internal, 223048, 223088
-recovered pasa_asmbl_11836.p1, internal, 223467, 223522
-recovered pasa_asmbl_11836.p1, internal, 224181, 224277
-recovered pasa_asmbl_11836.p1, internal, 224829, 224977
-recovered pasa_asmbl_11836.p1, internal, 226367, 226502
-recovered pasa_asmbl_11836.p1, internal, 228103, 228260
-recovered pasa_asmbl_11836.p1, internal, 228443, 228524
-recovered pasa_asmbl_11836.p1, internal, 229073, 229208
Valid prediction for GlimmerHMM_glimmerT_33307-T1
Valid prediction for snap_scaffold_14-snap.286-T1
Couldn't classify 257219, 257275
Sorry, prediction pasa_asmbl_11837.p2 fails validation.
(ATG)	 TC	250586-250639	GT	TGG
(GTG)	 AG	251781-251881	GT	ACG
(GAA)	 AG	252185-252313	GT	CAG
(GCT)	 AG	254486-254594	GT	AGG
(GGC)	 AG	257219-257275	CC	ATC
-recovered pasa_asmbl_11837.p2, initial, 250586, 250639
-recovered pasa_asmbl_11837.p2, internal, 251781, 251881
-recovered pasa_asmbl_11837.p2, internal, 252185, 252313
-recovered pasa_asmbl_11837.p2, internal, 254486, 254594
Valid prediction for snap_scaffold_14-snap.276-T1
Valid prediction for GlimmerHMM_glimmerT_33323-T1
Valid prediction for snap_scaffold_14-snap.260-T1
Valid prediction for snap_scaffold_14-snap.271-T1
Valid prediction for snap_scaffold_14-snap.281-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 snap_scaffold_14-snap.265-T1
Couldn't classify 170501, 171112
Sorry, prediction pasa_asmbl_12911.p1 fails validation.
(ATG)	 AG	170501-171112	GA	GTG
Valid prediction for GlimmerHMM_glimmerT_33326-T1
Valid prediction for snap_scaffold_14-snap.297-T1
Valid prediction for snap_scaffold_14-snap.293-T1
Valid prediction for snap_scaffold_14-snap.288-T1
Valid prediction for snap_scaffold_14-snap.264-T1
Valid prediction for snap_scaffold_14-snap.274-T1
Valid prediction for snap_scaffold_14-snap.278-T1
Valid prediction for snap_scaffold_14-snap.272-T1
Valid prediction for Augustus_model.g22273.t1
Valid prediction for snap_scaffold_14-snap.268-T1
Valid prediction for snap_scaffold_14-snap.279-T1
Valid prediction for GlimmerHMM_glimmerT_33321-T1
Valid prediction for snap_scaffold_14-snap.269-T1
Valid prediction for snap_scaffold_14-snap.284-T1
Valid prediction for snap_scaffold_14-snap.275-T1
Valid prediction for GlimmerHMM_glimmerT_33319-T1
Valid prediction for snap_scaffold_14-snap.295-T1
Valid prediction for Augustus_model.g22283.t1
Valid prediction for Augustus_model.g22278.t1
Valid prediction for snap_scaffold_14-snap.283-T1
Valid prediction for Augustus_model.g22272.t1
Valid prediction for snap_scaffold_14-snap.287-T1
Valid prediction for GlimmerHMM_glimmerT_33306-T1
Couldn't classify 171344, 171415
Sorry, prediction pasa_asmbl_12910.p1 fails validation.
(GGG)	 TA	171344-171415	GT	AAG
(GTT)	 AG	171718-171859	GT	TGG
(GTG)	 AG	172004-172261	GT	AGG
(GTA)	 AG	172368-172540	GT	ATG
(GTG)	 AG	172816-173121	GT	GAG
-recovered pasa_asmbl_12910.p1, terminal, 172816, 173121
-recovered pasa_asmbl_12910.p1, internal, 171718, 171859
-recovered pasa_asmbl_12910.p1, internal, 172004, 172261
-recovered pasa_asmbl_12910.p1, internal, 172368, 172540
-recovered pasa_asmbl_12910.p1, internal, 172816, 173121
Valid prediction for Augustus_model.g22282.t1
Valid prediction for Augustus_model.g22280.t1
Valid prediction for GlimmerHMM_glimmerT_33303-T1
Valid prediction for Augustus_model.g22279.t1
Valid prediction for snap_scaffold_14-snap.262-T1
Valid prediction for GlimmerHMM_glimmerT_33316-T1
Valid prediction for GlimmerHMM_glimmerT_33311-T1
Valid prediction for GlimmerHMM_glimmerT_33317-T1
Valid prediction for GlimmerHMM_glimmerT_33312-T1
Valid prediction for pasa_asmbl_12913.p1
Valid prediction for Augustus_model.g22269.t1
Valid prediction for snap_scaffold_14-snap.259-T1
Valid prediction for GlimmerHMM_glimmerT_33320-T1
Couldn't classify 136157, 136265
Couldn't classify 136720, 136771
Sorry, prediction pasa_asmbl_13789.p1 fails validation.
(GTG)	 AG	136157-136265	GT	AGG
(ACC)	 AG	136427-136562	GT	CGG
(GTC)	 AG	136720-136771	CA	CCC
-recovered pasa_asmbl_13789.p1, internal, 136157, 136265
-recovered pasa_asmbl_13789.p1, internal, 136427, 136562
Valid prediction for GlimmerHMM_glimmerT_33308-T1
Valid prediction for Augustus_model.g22276.t1
Valid prediction for CodingQuarry_transcript_15565-T1
Valid prediction for snap_scaffold_14-snap.289-T1
Valid prediction for GlimmerHMM_glimmerT_33314-T1
Valid prediction for GlimmerHMM_glimmerT_33315-T1
Valid prediction for snap_scaffold_14-snap.258-T1
Valid prediction for GlimmerHMM_glimmerT_33322-T1
Valid prediction for CodingQuarry_transcript_15566-T1
Valid prediction for GlimmerHMM_glimmerT_33305-T1
Valid prediction for snap_scaffold_14-snap.299-T1
Valid prediction for Augustus_model.g22277.t1
Valid prediction for snap_scaffold_14-snap.270-T1
Valid prediction for HiQ_model.g22267.t1
Valid prediction for Augustus_model.g22274.t1
Valid prediction for Augustus_model.g22268.t1
Valid prediction for Augustus_model.g22281.t1
Valid prediction for snap_scaffold_14-snap.277-T1
Valid prediction for snap_scaffold_14-snap.261-T1
Valid prediction for GlimmerHMM_glimmerT_33318-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8692, rend_intergenic: 1786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14968, rend_intergenic: 13760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21295, rend_intergenic: 15104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22421, rend_intergenic: 21621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42369, rend_intergenic: 40045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45164, rend_intergenic: 43689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234369, rend_intergenic: 223413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244342, rend_intergenic: 240849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 252317, rend_intergenic: 244811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260183, rend_intergenic: 258183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 267237
-exon list size: 350


building trellis

0.3    
0.6    
0.9    
1.1    
1.4    
1.7    
2.0    
2.3    
2.6    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.5    
4.8    
5.1    
5.4    
5.7    
6.0    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.2    
8.5    
8.8    
9.1    
9.4    
9.7    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.0    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.1    
26.4    
26.7    
27.0    
27.3    
27.6    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.3    
40.6    
40.9    
41.2    
41.5    
41.8    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
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    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.2    
58.5    
58.8    
59.1    
59.4    
59.7    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.4    
72.7    
73.0    
73.3    
73.6    
73.9    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.0    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
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: 8692, rend_intergenic: 1786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14968, rend_intergenic: 13760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21295, rend_intergenic: 15104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22421, rend_intergenic: 21621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42369, rend_intergenic: 40045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45164, rend_intergenic: 43689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234369, rend_intergenic: 223413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244342, rend_intergenic: 240849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 252317, rend_intergenic: 244811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260183, rend_intergenic: 258183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support