-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_20492426-20652223

-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_2745-T1
Valid prediction for GlimmerHMM_glimmerT_2748-T1
Valid prediction for snap_scaffold_1-snap.3827-T1
Valid prediction for snap_scaffold_1-snap.3806-T1
Valid prediction for snap_scaffold_1-snap.3808-T1
Valid prediction for snap_scaffold_1-snap.3813-T1
Valid prediction for snap_scaffold_1-snap.3831-T1
Valid prediction for snap_scaffold_1-snap.3833-T1
Valid prediction for snap_scaffold_1-snap.3811-T1
Valid prediction for GlimmerHMM_glimmerT_2751-T1
Valid prediction for Augustus_model.g1952.t1
Valid prediction for snap_scaffold_1-snap.3804-T1
Valid prediction for GlimmerHMM_glimmerT_2741-T1
Valid prediction for Augustus_model.g1949.t1
Valid prediction for snap_scaffold_1-snap.3817-T1
Valid prediction for GlimmerHMM_glimmerT_2750-T1
Valid prediction for snap_scaffold_1-snap.3841-T1
Valid prediction for snap_scaffold_1-snap.3840-T1
Couldn't classify 108134, 108297
Sorry, prediction pasa_asmbl_2643.p2 fails validation.
(ATG)	 TC	103738-104023	GT	TGG
(AGC)	 AG	106576-106710	GT	AAG
(CTG)	 AG	108134-108297	GG	TTG
-recovered pasa_asmbl_2643.p2, initial, 103738, 104023
-recovered pasa_asmbl_2643.p2, internal, 106576, 106710
Valid prediction for Augustus_model.g1950.t1
Valid prediction for snap_scaffold_1-snap.3819-T1
Valid prediction for GlimmerHMM_glimmerT_2755-T1
Valid prediction for Augustus_model.g1955.t1
Couldn't classify 111948, 112037
Sorry, prediction pasa_asmbl_2645.p1 fails validation.
(GAA)	 TA	111948-112037	GT	CTG
(GGG)	 AG	112268-112327	GT	AGG
(GTC)	 AG	112663-112798	GT	CGG
(AGC)	 AG	113654-113793	GT	GGG
(GAC)	 AG	114341-114500	GT	AGG
(TGA)	 AG	115212-115348	GT	AGG
(CCT)	 AG	116291-116477	GT	ACG
(AGA)	 AG	117234-117262	AA	AAA
-recovered pasa_asmbl_2645.p1, terminal, 117234, 117262
-recovered pasa_asmbl_2645.p1, internal, 112268, 112327
-recovered pasa_asmbl_2645.p1, internal, 112663, 112798
-recovered pasa_asmbl_2645.p1, internal, 113654, 113793
-recovered pasa_asmbl_2645.p1, internal, 114341, 114500
-recovered pasa_asmbl_2645.p1, internal, 115212, 115348
-recovered pasa_asmbl_2645.p1, internal, 116291, 116477
Valid prediction for snap_scaffold_1-snap.3809-T1
Valid prediction for Augustus_model.g1951.t1
Valid prediction for snap_scaffold_1-snap.3845-T1
Valid prediction for snap_scaffold_1-snap.3829-T1
Valid prediction for GlimmerHMM_glimmerT_2753-T1
Valid prediction for snap_scaffold_1-snap.3832-T1
Valid prediction for snap_scaffold_1-snap.3820-T1
Valid prediction for GlimmerHMM_glimmerT_2749-T1
Valid prediction for GlimmerHMM_glimmerT_2743-T1
Valid prediction for Augustus_model.g1956.t1
Valid prediction for snap_scaffold_1-snap.3815-T1
Valid prediction for snap_scaffold_1-snap.3821-T1
Valid prediction for Augustus_model.g1953.t1
Valid prediction for GlimmerHMM_glimmerT_2757-T1
Valid prediction for GlimmerHMM_glimmerT_2744-T1
Valid prediction for snap_scaffold_1-snap.3816-T1
Valid prediction for GlimmerHMM_glimmerT_2758-T1
Valid prediction for GlimmerHMM_glimmerT_2747-T1
Valid prediction for GlimmerHMM_glimmerT_2742-T1
Valid prediction for snap_scaffold_1-snap.3837-T1
Valid prediction for Augustus_model.g1948.t1
Valid prediction for snap_scaffold_1-snap.3818-T1
Valid prediction for snap_scaffold_1-snap.3825-T1
Valid prediction for snap_scaffold_1-snap.3822-T1
Valid prediction for snap_scaffold_1-snap.3823-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_1-snap.3838-T1
Valid prediction for snap_scaffold_1-snap.3835-T1
Valid prediction for GlimmerHMM_glimmerT_2756-T1
Valid prediction for GlimmerHMM_glimmerT_2754-T1
Valid prediction for snap_scaffold_1-snap.3844-T1
Valid prediction for snap_scaffold_1-snap.3836-T1
Valid prediction for snap_scaffold_1-snap.3830-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 152875, 152909
Sorry, prediction pasa_asmbl_1184.p1 fails validation.
(GAG)	 CA	152875-152909	GT	GGG
(ACC)	 AG	153373-153379	GT	AGG
(AGG)	 AG	153529-153570	GT	AGG
(AGT)	 AG	154203-154334	GT	AGG
(GCG)	 AG	154719-154808	GT	AGG
(ATT)	 AG	154950-155126	GT	AGG
(GAG)	 AG	155590-155694	AC	AGA
-recovered pasa_asmbl_1184.p1, terminal, 155590, 155694
-recovered pasa_asmbl_1184.p1, internal, 153373, 153379
-recovered pasa_asmbl_1184.p1, internal, 153529, 153570
-recovered pasa_asmbl_1184.p1, internal, 154203, 154334
-recovered pasa_asmbl_1184.p1, internal, 154719, 154808
-recovered pasa_asmbl_1184.p1, internal, 154950, 155126
Valid prediction for snap_scaffold_1-snap.3847-T1
Valid prediction for snap_scaffold_1-snap.3824-T1
Valid prediction for snap_scaffold_1-snap.3807-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.3805-T1
Valid prediction for snap_scaffold_1-snap.3834-T1
Valid prediction for snap_scaffold_1-snap.3843-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for HiQ_model.g1947.t1
Valid prediction for GlimmerHMM_glimmerT_2740-T1
Valid prediction for Augustus_model.g1954.t1
Couldn't classify 141110, 141239
Sorry, prediction pasa_asmbl_1185.p1 fails validation.
(AGA)	 TC	141110-141239	GT	CAG
(TGG)	 AG	142217-142385	GT	CAG
(ACC)	 AG	143678-143807	GT	ATG
(TCG)	 AG	145073-145166	GT	AGG
(CGT)	 AG	145344-145420	AG	AGA
-recovered pasa_asmbl_1185.p1, terminal, 145344, 145420
-recovered pasa_asmbl_1185.p1, internal, 142217, 142385
-recovered pasa_asmbl_1185.p1, internal, 143678, 143807
-recovered pasa_asmbl_1185.p1, internal, 145073, 145166
Valid prediction for snap_scaffold_1-snap.3842-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.3810-T1
Valid prediction for GlimmerHMM_glimmerT_2752-T1
Valid prediction for snap_scaffold_1-snap.3826-T1
Valid prediction for GlimmerHMM_glimmerT_2746-T1
Valid prediction for snap_scaffold_1-snap.3812-T1
Valid prediction for snap_scaffold_1-snap.3814-T1
Valid prediction for snap_scaffold_1-snap.3839-T1
Valid prediction for snap_scaffold_1-snap.3828-T1
Valid prediction for Augustus_model.g1946.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13368, rend_intergenic: 7465  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21242, rend_intergenic: 14369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22532, rend_intergenic: 22016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25260, rend_intergenic: 22666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28529, rend_intergenic: 25849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29424, rend_intergenic: 28950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66163, rend_intergenic: 29521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69417, rend_intergenic: 67162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71575, rend_intergenic: 70326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83893, rend_intergenic: 75984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88674, rend_intergenic: 88145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98130, rend_intergenic: 88951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118310, rend_intergenic: 105091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126990, rend_intergenic: 121013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130104, rend_intergenic: 128590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138251, rend_intergenic: 136618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143162, rend_intergenic: 138492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 159798
-exon list size: 313


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.2    
2.5    
2.9    
3.2    
3.5    
3.8    
4.1    
4.4    
4.8    
5.1    
5.4    
5.7    
6.0    
6.3    
6.7    
7.0    
7.3    
7.6    
7.9    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.1    
12.4    
12.7    
13.0    
13.3    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.4    
19.7    
20.0    
20.3    
20.6    
21.0    
21.3    
21.6    
21.9    
22.2    
22.5    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.7    
27.0    
27.3    
27.6    
27.9    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.1    
32.4    
32.7    
33.0    
33.3    
33.7    
34.0    
34.3    
34.6    
34.9    
35.2    
35.6    
35.9    
36.2    
36.5    
36.8    
37.1    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.4    
39.7    
40.0    
40.3    
40.6    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.7    
47.0    
47.3    
47.6    
47.9    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.1    
52.4    
52.7    
53.0    
53.3    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.4    
59.7    
60.0    
60.3    
60.6    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.9    
63.2    
63.5    
63.8    
64.1    
64.4    
64.8    
65.1    
65.4    
65.7    
66.0    
66.3    
66.7    
67.0    
67.3    
67.6    
67.9    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.1    
72.4    
72.7    
73.0    
73.3    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.5    
77.8    
78.1    
78.4    
78.7    
79.0    
79.4    
79.7    
80.0    
80.3    
80.6    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.7    
87.0    
87.3    
87.6    
87.9    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.1    
92.4    
92.7    
93.0    
93.3    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.5    
97.8    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 13368, rend_intergenic: 7465  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21242, rend_intergenic: 14369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22532, rend_intergenic: 22016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25260, rend_intergenic: 22666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28529, rend_intergenic: 25849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29424, rend_intergenic: 28950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66163, rend_intergenic: 29521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69417, rend_intergenic: 67162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71575, rend_intergenic: 70326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83893, rend_intergenic: 75984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88674, rend_intergenic: 88145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98130, rend_intergenic: 88951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118310, rend_intergenic: 105091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126990, rend_intergenic: 121013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130104, rend_intergenic: 128590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138251, rend_intergenic: 136618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143162, rend_intergenic: 138492  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