-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_2232458-2481317

-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: +)Couldn't classify 195806, 195903
Sorry, prediction pasa_asmbl_7493.p1 fails validation.
(ATG)	 AC	193136-193164	GT	AGG
(GTC)	 AG	195275-195498	GT	CTG
(TGC)	 AG	195806-195903	GC	AGG
-recovered pasa_asmbl_7493.p1, initial, 193136, 193164
-recovered pasa_asmbl_7493.p1, internal, 195275, 195498
-recovered pasa_asmbl_7493.p1, internal, 195806, 195903
Valid prediction for snap_scaffold_12-snap.475-T1
Valid prediction for GlimmerHMM_glimmerT_28948-T1
Valid prediction for snap_scaffold_12-snap.468-T1
Valid prediction for GlimmerHMM_glimmerT_28954-T1
Valid prediction for GlimmerHMM_glimmerT_28951-T1
Valid prediction for GlimmerHMM_glimmerT_28959-T1
Couldn't classify 190004, 190167
Couldn't classify 192262, 192337
Sorry, prediction pasa_asmbl_7492.p1 fails validation.
(GCC)	 CG	190004-190167	GT	AGG
(GTA)	 AG	190540-190923	GT	AGG
(CGG)	 AG	192262-192337	GG	TTG
-recovered pasa_asmbl_7492.p1, internal, 190540, 190923
Valid prediction for snap_scaffold_12-snap.498-T1
Valid prediction for snap_scaffold_12-snap.464-T1
Valid prediction for Augustus_model.g19107.t1
Couldn't classify 200714, 200889
Couldn't classify 202336, 202975
Sorry, prediction pasa_asmbl_7495.p1 fails validation.
(CCA)	 TC	200714-200889	GT	GGG
(AGG)	 AG	202336-202975	TT	GGT
Couldn't classify 188322, 188478
Sorry, prediction pasa_asmbl_7490.p1 fails validation.
(ATG)	 AC	182404-182496	GT	AGG
(CTG)	 AG	183900-184058	GT	AGG
(TTT)	 AG	184439-184591	GT	AGG
(GGG)	 AG	184735-184899	GT	AGG
(GTT)	 AG	185491-185598	GT	AGG
(AAA)	 AG	185870-186073	GT	AGG
(ATC)	 AG	187220-187328	GT	AGG
(TGT)	 AG	187791-188064	GT	AAG
(CGA)	 AG	188322-188478	GG	CAG
-recovered pasa_asmbl_7490.p1, initial, 182404, 182496
add_exon() Sorry, pasa_asmbl_7490.p1 187220-187328-terminal-3 is invalid.
-recovered pasa_asmbl_7490.p1, terminal, 187220, 187328
-recovered pasa_asmbl_7490.p1, internal, 183900, 184058
-recovered pasa_asmbl_7490.p1, internal, 184439, 184591
-recovered pasa_asmbl_7490.p1, internal, 184735, 184899
-recovered pasa_asmbl_7490.p1, internal, 185491, 185598
-recovered pasa_asmbl_7490.p1, internal, 185870, 186073
-recovered pasa_asmbl_7490.p1, internal, 187220, 187328
-recovered pasa_asmbl_7490.p1, internal, 187791, 188064
Valid prediction for HiQ_model.g19100.t1
Valid prediction for snap_scaffold_12-snap.489-T1
Valid prediction for Augustus_model.g19106.t1
Valid prediction for snap_scaffold_12-snap.491-T1
Valid prediction for snap_scaffold_12-snap.476-T1
Valid prediction for snap_scaffold_12-snap.492-T1
Valid prediction for HiQ_model.g19099.t1
Couldn't classify 101444, 101647
Couldn't classify 101678, 101679
Sorry, prediction CodingQuarry_transcript_10138-T1 fails validation.
(ATG)	 CA	97830-97839	GT	AGG
(GTC)	 AG	97987-98105	GT	AGG
(GTA)	 AG	98716-98793	GT	AGG
(GAC)	 AG	99069-99215	GT	AGG
(CTA)	 AG	99499-99639	GT	TGG
(GTG)	 AG	100240-100383	GT	AGG
(TGC)	 AG	100941-101109	GT	AGG
(GAC)	 AG	101444-101647	AG	TTA
(AGA)	 TA	101678-101679	AG	AGA
-recovered CodingQuarry_transcript_10138-T1, initial, 97830, 97839
-recovered CodingQuarry_transcript_10138-T1, internal, 97987, 98105
-recovered CodingQuarry_transcript_10138-T1, internal, 98716, 98793
-recovered CodingQuarry_transcript_10138-T1, internal, 99069, 99215
-recovered CodingQuarry_transcript_10138-T1, internal, 99499, 99639
-recovered CodingQuarry_transcript_10138-T1, internal, 100240, 100383
-recovered CodingQuarry_transcript_10138-T1, internal, 100941, 101109
Valid prediction for snap_scaffold_12-snap.470-T1
Valid prediction for snap_scaffold_12-snap.474-T1
Valid prediction for Augustus_model.g19103.t1
Valid prediction for GlimmerHMM_glimmerT_28957-T1
Valid prediction for snap_scaffold_12-snap.469-T1
Valid prediction for Augustus_model.g19098.t1
Valid prediction for GlimmerHMM_glimmerT_28963-T1
Couldn't classify 97797, 97839
Sorry, prediction pasa_asmbl_7489.p1 fails validation.
(ATT)	 CG	97797-97839	GT	AGG
(GTC)	 AG	97987-98105	GT	AGG
(GTA)	 AG	98716-98793	GT	AGG
(GAC)	 AG	99069-99215	GT	AGG
(CTA)	 AG	99499-99639	GT	TGG
(GTG)	 AG	100240-100383	GT	AGG
(TGC)	 AG	100941-101109	GT	AGG
(GAC)	 AG	101444-101626	GT	AGG
(GCT)	 AG	102290-102511	GT	AGG
(GTG)	 AG	103031-103194	GT	GAG
-recovered pasa_asmbl_7489.p1, terminal, 103031, 103194
-recovered pasa_asmbl_7489.p1, internal, 97987, 98105
-recovered pasa_asmbl_7489.p1, internal, 98716, 98793
-recovered pasa_asmbl_7489.p1, internal, 99069, 99215
-recovered pasa_asmbl_7489.p1, internal, 99499, 99639
-recovered pasa_asmbl_7489.p1, internal, 100240, 100383
-recovered pasa_asmbl_7489.p1, internal, 100941, 101109
-recovered pasa_asmbl_7489.p1, internal, 101444, 101626
-recovered pasa_asmbl_7489.p1, internal, 102290, 102511
-recovered pasa_asmbl_7489.p1, internal, 103031, 103194
Valid prediction for snap_scaffold_12-snap.496-T1
Valid prediction for GlimmerHMM_glimmerT_28956-T1
Valid prediction for Augustus_model.g19110.t1
Valid prediction for Augustus_model.g19104.t1
Valid prediction for snap_scaffold_12-snap.477-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_10137-T1
Valid prediction for snap_scaffold_12-snap.483-T1
Valid prediction for GlimmerHMM_glimmerT_28942-T1
Valid prediction for GlimmerHMM_glimmerT_28945-T1
Valid prediction for GlimmerHMM_glimmerT_28962-T1
Valid prediction for Augustus_model.g19109.t1
Valid prediction for Augustus_model.g19108.t1
Valid prediction for snap_scaffold_12-snap.480-T1
Valid prediction for GlimmerHMM_glimmerT_28960-T1
Valid prediction for GlimmerHMM_glimmerT_28946-T1
Valid prediction for snap_scaffold_12-snap.486-T1
Valid prediction for snap_scaffold_12-snap.457-T1
Valid prediction for Augustus_model.g19105.t1
Valid prediction for GlimmerHMM_glimmerT_28953-T1
Valid prediction for snap_scaffold_12-snap.487-T1
Couldn't classify 97394, 97623
Sorry, prediction pasa_asmbl_7487.p1 fails validation.
(ATG)	 AA	95721-95760	GT	AGG
(CTA)	 AG	96811-96963	GT	AGG
(GTG)	 AG	97394-97623	GT	GGG
-recovered pasa_asmbl_7487.p1, initial, 95721, 95760
-recovered pasa_asmbl_7487.p1, internal, 96811, 96963
-recovered pasa_asmbl_7487.p1, internal, 97394, 97623
Valid prediction for snap_scaffold_12-snap.465-T1
Valid prediction for snap_scaffold_12-snap.459-T1
Valid prediction for GlimmerHMM_glimmerT_28949-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_12-snap.488-T1
Valid prediction for snap_scaffold_12-snap.467-T1
Valid prediction for snap_scaffold_12-snap.462-T1
Valid prediction for pasa_asmbl_8324.p1
Valid prediction for snap_scaffold_12-snap.471-T1
Valid prediction for snap_scaffold_12-snap.461-T1
Valid prediction for GlimmerHMM_glimmerT_28941-T1
Valid prediction for snap_scaffold_12-snap.463-T1
Valid prediction for snap_scaffold_12-snap.500-T1
Valid prediction for snap_scaffold_12-snap.481-T1
Valid prediction for HiQ_model.g19097.t1
Valid prediction for snap_scaffold_12-snap.458-T1
Valid prediction for CodingQuarry_transcript_10136-T1
Valid prediction for snap_scaffold_12-snap.485-T1
Valid prediction for snap_scaffold_12-snap.493-T1
Valid prediction for snap_scaffold_12-snap.494-T1
Valid prediction for GlimmerHMM_glimmerT_28940-T1
Valid prediction for snap_scaffold_12-snap.497-T1
Valid prediction for GlimmerHMM_glimmerT_28961-T1
Valid prediction for HiQ_model.g19096.t1
Valid prediction for GlimmerHMM_glimmerT_28943-T1
Valid prediction for snap_scaffold_12-snap.478-T1
Valid prediction for snap_scaffold_12-snap.473-T1
Valid prediction for GlimmerHMM_glimmerT_28952-T1
Valid prediction for snap_scaffold_12-snap.482-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g19102.t1
Valid prediction for snap_scaffold_12-snap.499-T1
Valid prediction for snap_scaffold_12-snap.455-T1
Valid prediction for Augustus_model.g19095.t1
Valid prediction for snap_scaffold_12-snap.466-T1
Valid prediction for snap_scaffold_12-snap.484-T1
Valid prediction for snap_scaffold_12-snap.456-T1
Valid prediction for snap_scaffold_12-snap.501-T1
Valid prediction for snap_scaffold_12-snap.495-T1
Sorry, intron length (5) is less than minimum required (10)
Couldn't classify 207409, 207547
Sorry, prediction pasa_asmbl_8322.p1 fails validation.
(AAT)	 AA	207409-207547	GT	AGG
(ATG)	 AG	208030-208247	GT	AGG
(ATT)	 AG	208565-208795	GT	GGG
(ACT)	 AG	210585-210659	CC	GAC
add_exon() Sorry, pasa_asmbl_8322.p1 208030-208247-initial-1 is invalid.
-recovered pasa_asmbl_8322.p1, initial, 208030, 208247
-recovered pasa_asmbl_8322.p1, terminal, 210585, 210659
-recovered pasa_asmbl_8322.p1, internal, 208030, 208247
-recovered pasa_asmbl_8322.p1, internal, 208565, 208795
Valid prediction for snap_scaffold_12-snap.472-T1
Valid prediction for GlimmerHMM_glimmerT_28950-T1
Valid prediction for snap_scaffold_12-snap.479-T1
Valid prediction for pasa_asmbl_8319.p1
Valid prediction for snap_scaffold_12-snap.490-T1
Valid prediction for GlimmerHMM_glimmerT_28958-T1
Valid prediction for GlimmerHMM_glimmerT_28955-T1
Valid prediction for GlimmerHMM_glimmerT_28944-T1
Valid prediction for CodingQuarry_transcript_10139-T1
Valid prediction for snap_scaffold_12-snap.502-T1
Valid prediction for HiQ_model.g19101.t1
Valid prediction for GlimmerHMM_glimmerT_28947-T1
Valid prediction for snap_scaffold_12-snap.460-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12023, rend_intergenic: 8949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29997, rend_intergenic: 23728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40877, rend_intergenic: 38163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103194, rend_intergenic: 96755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152345, rend_intergenic: 133238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167914, rend_intergenic: 157690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172802, rend_intergenic: 170098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178938, rend_intergenic: 174753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182902, rend_intergenic: 179176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186118, rend_intergenic: 183860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186351, rend_intergenic: 186145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199102, rend_intergenic: 192258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201751, rend_intergenic: 199414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 248860
-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 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 12023, rend_intergenic: 8949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29997, rend_intergenic: 23728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40877, rend_intergenic: 38163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103194, rend_intergenic: 96755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152345, rend_intergenic: 133238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167914, rend_intergenic: 157690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172802, rend_intergenic: 170098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178938, rend_intergenic: 174753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182902, rend_intergenic: 179176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186118, rend_intergenic: 183860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186351, rend_intergenic: 186145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199102, rend_intergenic: 192258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201751, rend_intergenic: 199414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support