-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_3361599-3519719

-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_10-snap.734-T1
Valid prediction for GlimmerHMM_glimmerT_24421-T1
Valid prediction for Augustus_model.g16265.t1
Valid prediction for Augustus_model.g16279.t1
Valid prediction for pasa_asmbl_3042.p1
Couldn't classify 131273, 131578
Sorry, prediction pasa_asmbl_3048.p2 fails validation.
(AGC)	 CC	131273-131578	TC	AGT
Valid prediction for snap_scaffold_10-snap.749-T1
Couldn't classify 77128, 77586
Sorry, prediction pasa_asmbl_4210.p1 fails validation.
(GTA)	 GG	77128-77586	GT	GAG
Valid prediction for snap_scaffold_10-snap.763-T1
Valid prediction for GlimmerHMM_glimmerT_24433-T1
Valid prediction for Augustus_model.g16278.t1
Valid prediction for snap_scaffold_10-snap.747-T1
Valid prediction for snap_scaffold_10-snap.736-T1
Valid prediction for snap_scaffold_10-snap.731-T1
Couldn't classify 119366, 119478
Couldn't classify 123456, 123582
Sorry, prediction pasa_asmbl_3047.p1 fails validation.
(AGT)	 GC	119366-119478	GT	AGG
(GTG)	 AG	119986-120052	GT	TGG
(GAG)	 AG	120364-120466	GT	AGG
(ATA)	 AG	120568-120737	GT	AGG
(ATG)	 AG	121092-121254	GT	AGG
(ACA)	 AG	121857-121950	GT	TGG
(GCA)	 AG	123456-123582	GA	AGG
-recovered pasa_asmbl_3047.p1, initial, 121092, 121254
-recovered pasa_asmbl_3047.p1, internal, 119986, 120052
-recovered pasa_asmbl_3047.p1, internal, 120364, 120466
-recovered pasa_asmbl_3047.p1, internal, 120568, 120737
-recovered pasa_asmbl_3047.p1, internal, 121092, 121254
-recovered pasa_asmbl_3047.p1, internal, 121857, 121950
Valid prediction for GlimmerHMM_glimmerT_24428-T1
Valid prediction for pasa_asmbl_3040.p1
Valid prediction for HiQ_model.g16268.t1
Valid prediction for CodingQuarry_transcript_5333-T1
Valid prediction for GlimmerHMM_glimmerT_24426-T1
Valid prediction for snap_scaffold_10-snap.746-T1
Valid prediction for Augustus_model.g16277.t1
Valid prediction for Augustus_model.g16280.t1
Valid prediction for GlimmerHMM_glimmerT_24429-T1
Couldn't classify 115232, 115380
Sorry, prediction pasa_asmbl_3046.p1 fails validation.
(ATG)	 TC	110916-111068	GT	AGG
(GTG)	 AG	114012-114041	GT	AGG
(ATC)	 AG	114842-115169	GT	AGG
(GAG)	 AG	115232-115380	GG	GGG
-recovered pasa_asmbl_3046.p1, initial, 110916, 111068
-recovered pasa_asmbl_3046.p1, internal, 114012, 114041
-recovered pasa_asmbl_3046.p1, internal, 114842, 115169
Valid prediction for snap_scaffold_10-snap.754-T1
Valid prediction for GlimmerHMM_glimmerT_24442-T1
Valid prediction for GlimmerHMM_glimmerT_24440-T1
Valid prediction for Augustus_model.g16263.t1
Valid prediction for GlimmerHMM_glimmerT_24420-T1
Valid prediction for snap_scaffold_10-snap.745-T1
Couldn't classify 138815, 138928
Couldn't classify 144385, 144495
Sorry, prediction pasa_asmbl_3052.p1 fails validation.
(GAG)	 AG	138815-138928	GT	AGG
(GCC)	 AG	139814-139888	GT	ATG
(ATG)	 AG	140058-140183	GT	AGG
(GAG)	 AG	140419-140562	GT	AGG
(GGC)	 AG	140676-140717	GT	GGG
(ACC)	 AG	140993-141121	GT	AGG
(ATC)	 AG	143859-143951	GT	AGG
(AGG)	 AG	144385-144495	GT	ACG
-recovered pasa_asmbl_3052.p1, initial, 140058, 140183
-recovered pasa_asmbl_3052.p1, internal, 138815, 138928
-recovered pasa_asmbl_3052.p1, internal, 139814, 139888
-recovered pasa_asmbl_3052.p1, internal, 140058, 140183
-recovered pasa_asmbl_3052.p1, internal, 140419, 140562
-recovered pasa_asmbl_3052.p1, internal, 140676, 140717
-recovered pasa_asmbl_3052.p1, internal, 140993, 141121
-recovered pasa_asmbl_3052.p1, internal, 143859, 143951
-recovered pasa_asmbl_3052.p1, internal, 144385, 144495
Valid prediction for CodingQuarry_transcript_5334-T1
Valid prediction for GlimmerHMM_glimmerT_24441-T1
Valid prediction for snap_scaffold_10-snap.732-T1
Valid prediction for pasa_asmbl_3039.p1
Valid prediction for snap_scaffold_10-snap.738-T1
Couldn't classify 145307, 145393
Sorry, prediction pasa_asmbl_3053.p2 fails validation.
(CAG)	 CA	145307-145393	GC	AGG
(ATC)	 AG	146282-146353	GT	GGG
(CTG)	 AG	147074-147271	GT	AGG
(GAT)	 AG	147369-147491	GC	AAG
-recovered pasa_asmbl_3053.p2, terminal, 147369, 147491
-recovered pasa_asmbl_3053.p2, internal, 146282, 146353
-recovered pasa_asmbl_3053.p2, internal, 147074, 147271
-recovered pasa_asmbl_3053.p2, internal, 147369, 147491
Valid prediction for snap_scaffold_10-snap.743-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.759-T1
Valid prediction for GlimmerHMM_glimmerT_24431-T1
Valid prediction for HiQ_model.g16267.t1
Valid prediction for snap_scaffold_10-snap.737-T1
Valid prediction for snap_scaffold_10-snap.752-T1
Valid prediction for snap_scaffold_10-snap.742-T1
Valid prediction for snap_scaffold_10-snap.740-T1
Valid prediction for CodingQuarry_transcript_5332-T1
Valid prediction for HiQ_model.g16270.t1
Valid prediction for GlimmerHMM_glimmerT_24425-T1
Valid prediction for pasa_asmbl_3037.p1

-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_24432-T1
Valid prediction for snap_scaffold_10-snap.756-T1
Valid prediction for GlimmerHMM_glimmerT_24430-T1
Valid prediction for Augustus_model.g16276.t1
Valid prediction for snap_scaffold_10-snap.739-T1
Valid prediction for CodingQuarry_transcript_5335-T1
Valid prediction for Augustus_model.g16273.t1
Valid prediction for snap_scaffold_10-snap.751-T1
Valid prediction for GlimmerHMM_glimmerT_24434-T1
Valid prediction for GlimmerHMM_glimmerT_24424-T1
Valid prediction for snap_scaffold_10-snap.741-T1
Couldn't classify 76999, 77097
Couldn't classify 77864, 78003
Sorry, prediction pasa_asmbl_4212.p1 fails validation.
(GCG)	 AG	76999-77097	GT	TGG
(ATC)	 AG	77327-77468	GT	AAG
(ACG)	 AG	77864-78003	CA	GCC
-recovered pasa_asmbl_4212.p1, internal, 76999, 77097
-recovered pasa_asmbl_4212.p1, internal, 77327, 77468
Valid prediction for snap_scaffold_10-snap.744-T1
Valid prediction for snap_scaffold_10-snap.735-T1
Valid prediction for GlimmerHMM_glimmerT_24419-T1
Valid prediction for snap_scaffold_10-snap.733-T1
Valid prediction for GlimmerHMM_glimmerT_24435-T1
Valid prediction for Augustus_model.g16264.t1
Valid prediction for snap_scaffold_10-snap.729-T1
Valid prediction for GlimmerHMM_glimmerT_24436-T1
Valid prediction for GlimmerHMM_glimmerT_24423-T1
Valid prediction for snap_scaffold_10-snap.750-T1
Valid prediction for snap_scaffold_10-snap.748-T1
Valid prediction for snap_scaffold_10-snap.730-T1
Valid prediction for snap_scaffold_10-snap.761-T1
Valid prediction for snap_scaffold_10-snap.753-T1
Valid prediction for GlimmerHMM_glimmerT_24439-T1
Valid prediction for Augustus_model.g16275.t1
Valid prediction for GlimmerHMM_glimmerT_24437-T1
Valid prediction for snap_scaffold_10-snap.760-T1
Valid prediction for Augustus_model.g16274.t1
Valid prediction for GlimmerHMM_glimmerT_24427-T1
Valid prediction for Augustus_model.g16271.t1
Valid prediction for snap_scaffold_10-snap.757-T1
Valid prediction for snap_scaffold_10-snap.755-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.758-T1
Valid prediction for Augustus_model.g16262.t1
Valid prediction for pasa_asmbl_4199.p1
Valid prediction for snap_scaffold_10-snap.762-T1
Valid prediction for GlimmerHMM_glimmerT_24443-T1
Valid prediction for HiQ_model.g16269.t1
Couldn't classify 116739, 116911
Sorry, prediction pasa_asmbl_4202.p1 fails validation.
(GAG)	 CA	116739-116911	GT	CTG
(GAA)	 AG	117608-117745	GT	AAG
(ATC)	 AG	117869-117988	GT	ATG
(GCT)	 AG	118152-118274	GT	GAG
(TGC)	 AG	119101-119290	GT	TGG
(GAG)	 AG	120428-120517	GT	CGG
(TTC)	 AG	120697-120900	GT	ATG
(AAT)	 AG	121040-121162	GT	AGG
(GAC)	 AG	121723-121779	GT	AGG
(GGG)	 AG	122197-122312	GT	AGG
(GAT)	 AG	123030-123124	GT	AGG
(GAG)	 AG	123269-123392	GT	AGG
(AGA)	 AG	124723-124877	GT	TGG
(GGA)	 AG	125091-125213	GT	AGG
(GGT)	 AG	125387-125523	CC	AAC
add_exon() Sorry, pasa_asmbl_4202.p1 118152-118274-terminal-1 is invalid.
-recovered pasa_asmbl_4202.p1, terminal, 118152, 118274
-recovered pasa_asmbl_4202.p1, terminal, 125387, 125523
-recovered pasa_asmbl_4202.p1, internal, 117608, 117745
-recovered pasa_asmbl_4202.p1, internal, 117869, 117988
-recovered pasa_asmbl_4202.p1, internal, 118152, 118274
-recovered pasa_asmbl_4202.p1, internal, 119101, 119290
-recovered pasa_asmbl_4202.p1, internal, 120428, 120517
-recovered pasa_asmbl_4202.p1, internal, 120697, 120900
-recovered pasa_asmbl_4202.p1, internal, 121040, 121162
-recovered pasa_asmbl_4202.p1, internal, 121723, 121779
-recovered pasa_asmbl_4202.p1, internal, 122197, 122312
-recovered pasa_asmbl_4202.p1, internal, 123030, 123124
-recovered pasa_asmbl_4202.p1, internal, 123269, 123392
-recovered pasa_asmbl_4202.p1, internal, 124723, 124877
-recovered pasa_asmbl_4202.p1, internal, 125091, 125213
Valid prediction for GlimmerHMM_glimmerT_24422-T1
Valid prediction for GlimmerHMM_glimmerT_24444-T1
Valid prediction for Augustus_model.g16266.t1
Valid prediction for GlimmerHMM_glimmerT_24438-T1
Valid prediction for Augustus_model.g16272.t1
Valid prediction for GlimmerHMM_glimmerT_24418-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 45592, rend_intergenic: 43933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66169, rend_intergenic: 65560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72442, rend_intergenic: 66173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78047, rend_intergenic: 75766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88332, rend_intergenic: 78980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90989, rend_intergenic: 89647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95165, rend_intergenic: 92526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111161, rend_intergenic: 108032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131578, rend_intergenic: 115042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134061, rend_intergenic: 132832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147491, rend_intergenic: 134078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157479, rend_intergenic: 152856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 158121
-exon list size: 385


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.3    
2.6    
2.8    
3.1    
3.4    
3.6    
3.9    
4.1    
4.4    
4.7    
4.9    
5.2    
5.4    
5.7    
5.9    
6.2    
6.5    
6.7    
7.0    
7.2    
7.5    
7.8    
8.0    
8.3    
8.5    
8.8    
9.0    
9.3    
9.6    
9.8    
10.1    
10.3    
10.6    
10.9    
11.1    
11.4    
11.6    
11.9    
12.1    
12.4    
12.7    
12.9    
13.2    
13.4    
13.7    
14.0    
14.2    
14.5    
14.7    
15.0    
15.2    
15.5    
15.8    
16.0    
16.3    
16.5    
16.8    
17.1    
17.3    
17.6    
17.8    
18.1    
18.3    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.2    
20.4    
20.7    
20.9    
21.2    
21.4    
21.7    
22.0    
22.2    
22.5    
22.7    
23.0    
23.3    
23.5    
23.8    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.4    
26.6    
26.9    
27.1    
27.4    
27.6    
27.9    
28.2    
28.4    
28.7    
28.9    
29.2    
29.5    
29.7    
30.0    
30.2    
30.5    
30.7    
31.0    
31.3    
31.5    
31.8    
32.0    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.7    
35.9    
36.2    
36.4    
36.7    
37.0    
37.2    
37.5    
37.7    
38.0    
38.2    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
45.0    
45.2    
45.5    
45.7    
46.0    
46.3    
46.5    
46.8    
47.0    
47.3    
47.5    
47.8    
48.1    
48.3    
48.6    
48.8    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.2    
51.4    
51.7    
51.9    
52.2    
52.5    
52.7    
53.0    
53.2    
53.5    
53.7    
54.0    
54.3    
54.5    
54.8    
55.0    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.8    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.7    
58.9    
59.2    
59.4    
59.7    
59.9    
60.2    
60.5    
60.7    
61.0    
61.2    
61.5    
61.8    
62.0    
62.3    
62.5    
62.8    
63.0    
63.3    
63.6    
63.8    
64.1    
64.3    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
68.0    
68.2    
68.5    
68.7    
69.0    
69.3    
69.5    
69.8    
70.0    
70.3    
70.5    
70.8    
71.1    
71.3    
71.6    
71.8    
72.1    
72.4    
72.6    
72.9    
73.1    
73.4    
73.6    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.2    
76.5    
76.7    
77.0    
77.3    
77.5    
77.8    
78.0    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.7    
81.9    
82.2    
82.4    
82.7    
82.9    
83.2    
83.5    
83.7    
84.0    
84.2    
84.5    
84.8    
85.0    
85.3    
85.5    
85.8    
86.0    
86.3    
86.6    
86.8    
87.1    
87.3    
87.6    
87.9    
88.1    
88.4    
88.6    
88.9    
89.1    
89.4    
89.7    
89.9    
90.2    
90.4    
90.7    
91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.5    
92.8    
93.0    
93.3    
93.5    
93.8    
94.1    
94.3    
94.6    
94.8    
95.1    
95.3    
95.6    
95.9    
96.1    
96.4    
96.6    
96.9    
97.2    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 45592, rend_intergenic: 43933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66169, rend_intergenic: 65560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72442, rend_intergenic: 66173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78047, rend_intergenic: 75766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88332, rend_intergenic: 78980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90989, rend_intergenic: 89647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95165, rend_intergenic: 92526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111161, rend_intergenic: 108032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131578, rend_intergenic: 115042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134061, rend_intergenic: 132832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147491, rend_intergenic: 134078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157479, rend_intergenic: 152856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support