-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_20123182-20255732

-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_5761-T1
Valid prediction for GlimmerHMM_glimmerT_5760-T1
Couldn't classify 84303, 84438
Couldn't classify 84589, 84866
Sorry, prediction pasa_asmbl_25305.p1 fails validation.
(CCC)	 TC	84303-84438	GT	AGG
(GCC)	 AG	84589-84866	AC	CCA
Couldn't classify 61777, 62304
Sorry, prediction pasa_asmbl_25303.p1 fails validation.
(CTC)	 AC	61777-62304	TG	CCT
Valid prediction for snap_scaffold_2-snap.3935-T1
Valid prediction for snap_scaffold_2-snap.3936-T1
Valid prediction for GlimmerHMM_glimmerT_5766-T1
Valid prediction for GlimmerHMM_glimmerT_5759-T1
Valid prediction for CodingQuarry_transcript_28878-T1
Couldn't classify 74668, 74754
Sorry, prediction pasa_asmbl_25304.p1 fails validation.
(ATG)	 TC	71803-71946	GT	GCG
(GGA)	 AG	73765-73853	GT	AGG
(GTA)	 AG	73996-74215	GT	TGG
(GTG)	 AG	74376-74477	GT	AGG
(GTC)	 AG	74668-74754	CA	CCC
-recovered pasa_asmbl_25304.p1, initial, 71803, 71946
-recovered pasa_asmbl_25304.p1, internal, 73765, 73853
-recovered pasa_asmbl_25304.p1, internal, 73996, 74215
-recovered pasa_asmbl_25304.p1, internal, 74376, 74477
Couldn't classify 101228, 101288
Couldn't classify 102664, 102734
Sorry, prediction pasa_asmbl_25419.p1 fails validation.
(CAG)	 CT	101228-101288	GT	AGG
(GTC)	 AG	101440-101531	GT	AGG
(GGT)	 AG	101757-101897	GT	AGG
(GGG)	 AG	102008-102146	GT	GGG
(AAA)	 AG	102315-102578	GT	AGG
(GTA)	 AG	102664-102734	TC	ACT
-recovered pasa_asmbl_25419.p1, internal, 101440, 101531
-recovered pasa_asmbl_25419.p1, internal, 101757, 101897
-recovered pasa_asmbl_25419.p1, internal, 102008, 102146
-recovered pasa_asmbl_25419.p1, internal, 102315, 102578
Valid prediction for snap_scaffold_2-snap.3957-T1
Valid prediction for GlimmerHMM_glimmerT_5763-T1
Valid prediction for snap_scaffold_2-snap.3934-T1
Valid prediction for snap_scaffold_2-snap.3922-T1
Couldn't classify 108144, 108194
Couldn't classify 109425, 109687
Sorry, prediction pasa_asmbl_25309.p1 fails validation.
(AGA)	 TC	108144-108194	GT	AGG
(AAC)	 AG	108340-108397	GT	AGG
(GTC)	 AG	108549-108640	GT	AGG
(GGT)	 AG	108867-109007	GT	AGG
(GGG)	 AG	109118-109256	GT	GGG
(AAA)	 AG	109425-109687	GG	CAG
-recovered pasa_asmbl_25309.p1, internal, 108340, 108397
-recovered pasa_asmbl_25309.p1, internal, 108549, 108640
-recovered pasa_asmbl_25309.p1, internal, 108867, 109007
-recovered pasa_asmbl_25309.p1, internal, 109118, 109256
Valid prediction for snap_scaffold_2-snap.3949-T1
Valid prediction for snap_scaffold_2-snap.3952-T1
Valid prediction for GlimmerHMM_glimmerT_5762-T1
Valid prediction for snap_scaffold_2-snap.3939-T1
Valid prediction for snap_scaffold_2-snap.3940-T1
Valid prediction for GlimmerHMM_glimmerT_5753-T1
Valid prediction for snap_scaffold_2-snap.3954-T1
Couldn't classify 15541, 15615
Sorry, prediction pasa_asmbl_25301.p1 fails validation.
(TGG)	 CC	15541-15615	GT	TGG
(GCA)	 AG	15946-16021	GT	AGG
(GTA)	 AG	16160-16327	GT	TGG
(ACA)	 AG	16528-16571	CG	AGC
-recovered pasa_asmbl_25301.p1, terminal, 16528, 16571
-recovered pasa_asmbl_25301.p1, internal, 15946, 16021
-recovered pasa_asmbl_25301.p1, internal, 16160, 16327
Valid prediction for snap_scaffold_2-snap.3956-T1
Valid prediction for snap_scaffold_2-snap.3951-T1
Valid prediction for GlimmerHMM_glimmerT_5769-T1
Couldn't classify 84993, 85925
Sorry, prediction pasa_asmbl_25306.p1 fails validation.
(TCT)	 TA	84993-85925	GT	AGG
(GTG)	 AG	86172-86246	GT	AGG
(GGG)	 AG	86359-86463	GT	AGG
(GTG)	 AG	86583-86883	GT	AGG
(TGA)	 AG	86957-87134	GT	AAG
(ACA)	 AG	87415-87611	GT	AGG
(AAG)	 AG	87729-87878	GT	GGG
(GTT)	 AG	87977-88182	GT	AGG
(ATG)	 AG	88741-89106	CC	AGC
-recovered pasa_asmbl_25306.p1, terminal, 88741, 89106
-recovered pasa_asmbl_25306.p1, internal, 86172, 86246
-recovered pasa_asmbl_25306.p1, internal, 86359, 86463
-recovered pasa_asmbl_25306.p1, internal, 86583, 86883
-recovered pasa_asmbl_25306.p1, internal, 86957, 87134
-recovered pasa_asmbl_25306.p1, internal, 87415, 87611
-recovered pasa_asmbl_25306.p1, internal, 87729, 87878
-recovered pasa_asmbl_25306.p1, internal, 87977, 88182
Valid prediction for snap_scaffold_2-snap.3924-T1
Valid prediction for GlimmerHMM_glimmerT_5767-T1
Valid prediction for snap_scaffold_2-snap.3932-T1
Valid prediction for GlimmerHMM_glimmerT_5754-T1
Valid prediction for snap_scaffold_2-snap.3930-T1
Valid prediction for snap_scaffold_2-snap.3938-T1
Valid prediction for snap_scaffold_2-snap.3926-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 CodingQuarry_transcript_28877-T1
Valid prediction for pasa_asmbl_23971.p1
Valid prediction for GlimmerHMM_glimmerT_5768-T1
Valid prediction for snap_scaffold_2-snap.3941-T1
Valid prediction for GlimmerHMM_glimmerT_5749-T1
Couldn't classify 14596, 14700
Sorry, prediction pasa_asmbl_23889.p1 fails validation.
(ATG)	 AG	11877-12092	GT	AGG
(GTG)	 AG	13841-13978	GT	AAG
(CGC)	 AG	14596-14700	GT	CCG
-recovered pasa_asmbl_23889.p1, initial, 11877, 12092
-recovered pasa_asmbl_23889.p1, internal, 11877, 12092
-recovered pasa_asmbl_23889.p1, internal, 13841, 13978
-recovered pasa_asmbl_23889.p1, internal, 14596, 14700
Valid prediction for snap_scaffold_2-snap.3933-T1
Valid prediction for snap_scaffold_2-snap.3944-T1
Valid prediction for snap_scaffold_2-snap.3948-T1
Valid prediction for GlimmerHMM_glimmerT_5757-T1
Valid prediction for GlimmerHMM_glimmerT_5758-T1
Valid prediction for snap_scaffold_2-snap.3946-T1
Valid prediction for snap_scaffold_2-snap.3931-T1
Valid prediction for snap_scaffold_2-snap.3929-T1
Valid prediction for snap_scaffold_2-snap.3925-T1
Valid prediction for GlimmerHMM_glimmerT_5752-T1
Valid prediction for snap_scaffold_2-snap.3947-T1
Valid prediction for snap_scaffold_2-snap.3937-T1
Valid prediction for GlimmerHMM_glimmerT_5772-T1
Valid prediction for GlimmerHMM_glimmerT_5750-T1
Valid prediction for snap_scaffold_2-snap.3942-T1
Valid prediction for GlimmerHMM_glimmerT_5748-T1
Valid prediction for snap_scaffold_2-snap.3950-T1
Valid prediction for snap_scaffold_2-snap.3945-T1
Valid prediction for pasa_asmbl_23883.p1
Valid prediction for GlimmerHMM_glimmerT_5751-T1
Valid prediction for GlimmerHMM_glimmerT_5773-T1
Valid prediction for snap_scaffold_2-snap.3927-T1
Valid prediction for GlimmerHMM_glimmerT_5764-T1
Valid prediction for snap_scaffold_2-snap.3923-T1
Valid prediction for snap_scaffold_2-snap.3943-T1
Valid prediction for snap_scaffold_2-snap.3928-T1
Valid prediction for GlimmerHMM_glimmerT_5771-T1
Valid prediction for GlimmerHMM_glimmerT_5755-T1
Valid prediction for pasa_asmbl_23887.p1
Valid prediction for GlimmerHMM_glimmerT_5770-T1
Valid prediction for GlimmerHMM_glimmerT_5756-T1
Valid prediction for snap_scaffold_2-snap.3953-T1
Valid prediction for snap_scaffold_2-snap.3955-T1
Valid prediction for GlimmerHMM_glimmerT_5765-T1
Valid prediction for CodingQuarry_transcript_28876-T1
Valid prediction for snap_scaffold_2-snap.3958-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 102908, rend_intergenic: 102905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12291, rend_intergenic: 8530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25933, rend_intergenic: 17742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36099, rend_intergenic: 30198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41794, rend_intergenic: 40911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42647, rend_intergenic: 41821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54519, rend_intergenic: 43373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89106, rend_intergenic: 68340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99195, rend_intergenic: 97161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103331, rend_intergenic: 99647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116121, rend_intergenic: 112286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116757, rend_intergenic: 116434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122166, rend_intergenic: 116912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130586, rend_intergenic: 128334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 132551
-exon list size: 354


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
3.9    
4.2    
4.5    
4.8    
5.1    
5.3    
5.6    
5.9    
6.2    
6.5    
6.7    
7.0    
7.3    
7.6    
7.9    
8.1    
8.4    
8.7    
9.0    
9.3    
9.6    
9.8    
10.1    
10.4    
10.7    
11.0    
11.2    
11.5    
11.8    
12.1    
12.4    
12.6    
12.9    
13.2    
13.5    
13.8    
14.0    
14.3    
14.6    
14.9    
15.2    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.1    
17.4    
17.7    
18.0    
18.3    
18.5    
18.8    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.1    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.0    
23.3    
23.6    
23.9    
24.2    
24.4    
24.7    
25.0    
25.3    
25.6    
25.8    
26.1    
26.4    
26.7    
27.0    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
28.9    
29.2    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.2    
31.5    
31.7    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.8    
35.1    
35.4    
35.7    
36.0    
36.2    
36.5    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.5    
38.8    
39.0    
39.3    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.1    
42.4    
42.7    
43.0    
43.3    
43.5    
43.8    
44.1    
44.4    
44.7    
44.9    
45.2    
45.5    
45.8    
46.1    
46.3    
46.6    
46.9    
47.2    
47.5    
47.8    
48.0    
48.3    
48.6    
48.9    
49.2    
49.4    
49.7    
50.0    
50.3    
50.6    
50.8    
51.1    
51.4    
51.7    
52.0    
52.2    
52.5    
52.8    
53.1    
53.4    
53.7    
53.9    
54.2    
54.5    
54.8    
55.1    
55.3    
55.6    
55.9    
56.2    
56.5    
56.7    
57.0    
57.3    
57.6    
57.9    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.7    
61.0    
61.2    
61.5    
61.8    
62.1    
62.4    
62.6    
62.9    
63.2    
63.5    
63.8    
64.0    
64.3    
64.6    
64.9    
65.2    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.3    
68.5    
68.8    
69.1    
69.4    
69.7    
69.9    
70.2    
70.5    
70.8    
71.1    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.0    
73.3    
73.6    
73.9    
74.2    
74.4    
74.7    
75.0    
75.3    
75.6    
75.8    
76.1    
76.4    
76.7    
77.0    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
78.9    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.2    
81.5    
81.7    
82.0    
82.3    
82.6    
82.9    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.8    
85.1    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.1    
87.4    
87.6    
87.9    
88.2    
88.5    
88.8    
89.0    
89.3    
89.6    
89.9    
90.2    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.1    
92.4    
92.7    
93.0    
93.3    
93.5    
93.8    
94.1    
94.4    
94.7    
94.9    
95.2    
95.5    
95.8    
96.1    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 32 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 102908, rend_intergenic: 102905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12291, rend_intergenic: 8530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25933, rend_intergenic: 17742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36099, rend_intergenic: 30198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41794, rend_intergenic: 40911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42647, rend_intergenic: 41821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54519, rend_intergenic: 43373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89106, rend_intergenic: 68340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99195, rend_intergenic: 97161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103331, rend_intergenic: 99647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116121, rend_intergenic: 112286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116757, rend_intergenic: 116434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122166, rend_intergenic: 116912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130586, rend_intergenic: 128334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support