-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_4510414-4787543

-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 77787, 77858
Couldn't classify 81564, 81617
Sorry, prediction pasa_asmbl_16793.p2 fails validation.
(ATT)	 AC	77787-77858	GT	AGG
(CTG)	 AG	79053-79212	GT	TGG
(AGC)	 AG	81169-81290	GT	AGG
(AAC)	 AG	81564-81617	GA	GAG
-recovered pasa_asmbl_16793.p2, internal, 79053, 79212
-recovered pasa_asmbl_16793.p2, internal, 81169, 81290
Valid prediction for snap_scaffold_16-snap.899-T1
Valid prediction for pasa_asmbl_16199.p1
Valid prediction for GlimmerHMM_glimmerT_38262-T1
Valid prediction for snap_scaffold_16-snap.918-T1
Valid prediction for snap_scaffold_16-snap.925-T1
Valid prediction for GlimmerHMM_glimmerT_38263-T1
Valid prediction for CodingQuarry_transcript_19956-T1
Valid prediction for snap_scaffold_16-snap.886-T1
Valid prediction for GlimmerHMM_glimmerT_38252-T1
Valid prediction for GlimmerHMM_glimmerT_38254-T1
Valid prediction for CodingQuarry_transcript_19955-T1
Valid prediction for Augustus_model.g25532.t1
Valid prediction for GlimmerHMM_glimmerT_38269-T1
Valid prediction for HiQ_model.g25540.t1
Valid prediction for CodingQuarry_transcript_19952-T1
Valid prediction for snap_scaffold_16-snap.907-T1
Valid prediction for snap_scaffold_16-snap.894-T1
Sorry, intron length (5) is less than minimum required (10)
Couldn't classify 128027, 128093
Sorry, prediction pasa_asmbl_16191.p1 fails validation.
(GTA)	 AT	128027-128093	GT	TGG
(GTT)	 AG	128421-128552	GT	CGG
(GTT)	 AG	128925-129045	GT	TGG
(GGA)	 AG	129660-129732	GT	TTG
(ATC)	 AG	129948-130065	GT	AGG
(GAT)	 AG	130591-130818	GT	AGG
(ACC)	 AG	130919-131128	GT	AGG
(ATC)	 AG	131728-131822	GT	AGG
(GGC)	 AG	131924-132170	GT	GGG
(GTT)	 AG	132348-132547	GT	AGG
(GCA)	 AG	132775-132834	GT	AGG
(AAA)	 AG	133048-133157	GT	AGG
(ACG)	 AG	133271-133283	GA	GAG
-recovered pasa_asmbl_16191.p1, terminal, 133271, 133283
-recovered pasa_asmbl_16191.p1, internal, 128421, 128552
-recovered pasa_asmbl_16191.p1, internal, 128925, 129045
-recovered pasa_asmbl_16191.p1, internal, 129660, 129732
-recovered pasa_asmbl_16191.p1, internal, 129948, 130065
-recovered pasa_asmbl_16191.p1, internal, 130591, 130818
-recovered pasa_asmbl_16191.p1, internal, 130919, 131128
-recovered pasa_asmbl_16191.p1, internal, 131728, 131822
-recovered pasa_asmbl_16191.p1, internal, 131924, 132170
-recovered pasa_asmbl_16191.p1, internal, 132348, 132547
-recovered pasa_asmbl_16191.p1, internal, 132775, 132834
-recovered pasa_asmbl_16191.p1, internal, 133048, 133157
Valid prediction for snap_scaffold_16-snap.911-T1
Valid prediction for snap_scaffold_16-snap.909-T1
Valid prediction for GlimmerHMM_glimmerT_38272-T1
Valid prediction for Augustus_model.g25523.t1
Valid prediction for GlimmerHMM_glimmerT_38274-T1
Valid prediction for snap_scaffold_16-snap.913-T1
Valid prediction for snap_scaffold_16-snap.898-T1
Valid prediction for snap_scaffold_16-snap.928-T1
Valid prediction for snap_scaffold_16-snap.912-T1
Valid prediction for Augustus_model.g25526.t1
Valid prediction for GlimmerHMM_glimmerT_38250-T1
Valid prediction for snap_scaffold_16-snap.897-T1
Valid prediction for pasa_asmbl_16194.p1
Valid prediction for snap_scaffold_16-snap.891-T1
Valid prediction for snap_scaffold_16-snap.904-T1
Valid prediction for Augustus_model.g25535.t1
Valid prediction for Augustus_model.g25522.t1
Couldn't classify 81852, 81884
Couldn't classify 84524, 84531
Sorry, prediction pasa_asmbl_16186.p1 fails validation.
(GGG)	 CT	81852-81884	GT	AGG
(ACA)	 AG	82143-82253	GT	AGG
(CAC)	 AG	83973-84071	GT	AGG
(TAT)	 AG	84289-84403	GT	GGG
(CTA)	 AG	84524-84531	TC	CCT
-recovered pasa_asmbl_16186.p1, internal, 82143, 82253
-recovered pasa_asmbl_16186.p1, internal, 83973, 84071
-recovered pasa_asmbl_16186.p1, internal, 84289, 84403
Valid prediction for HiQ_model.g25534.t1
Valid prediction for snap_scaffold_16-snap.888-T1
Valid prediction for GlimmerHMM_glimmerT_38246-T1
Valid prediction for GlimmerHMM_glimmerT_38248-T1
Valid prediction for snap_scaffold_16-snap.921-T1
Valid prediction for Augustus_model.g25524.t1
Valid prediction for snap_scaffold_16-snap.884-T1
Valid prediction for pasa_asmbl_16188.p1
Valid prediction for snap_scaffold_16-snap.890-T1
Valid prediction for snap_scaffold_16-snap.896-T1
Valid prediction for snap_scaffold_16-snap.901-T1
Valid prediction for GlimmerHMM_glimmerT_38264-T1
Valid prediction for GlimmerHMM_glimmerT_38259-T1
Valid prediction for snap_scaffold_16-snap.889-T1
Valid prediction for snap_scaffold_16-snap.893-T1
Valid prediction for HiQ_model.g25528.t1
Valid prediction for GlimmerHMM_glimmerT_38249-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_16-snap.926-T1
Valid prediction for snap_scaffold_16-snap.923-T1
Valid prediction for snap_scaffold_16-snap.915-T1
Valid prediction for snap_scaffold_16-snap.900-T1
Valid prediction for GlimmerHMM_glimmerT_38270-T1
Valid prediction for Augustus_model.g25531.t1
Valid prediction for GlimmerHMM_glimmerT_38267-T1
Valid prediction for HiQ_model.g25529.t1
Valid prediction for HiQ_model.g25539.t1
Couldn't classify 186941, 186950
Sorry, prediction pasa_asmbl_17063.p1 fails validation.
(AGA)	 CA	186941-186950	GT	TGG
(AGG)	 AG	187046-187164	GT	AGG
(GAT)	 AG	187279-187407	GT	AGG
(TTT)	 AG	187535-187599	GC	AGG
(TAA)	 AG	187694-187750	GT	AGG
(GTC)	 AG	187874-187972	GT	AGG
(CCT)	 AG	188179-188246	GT	AGG
(GTG)	 AG	188360-188447	GT	AGG
(GAA)	 AG	188557-188626	GT	TGG
(GGG)	 AG	188780-188852	GT	TGG
(GAG)	 AG	188953-189036	GT	AAG
(ATT)	 AG	189121-189250	GT	AGG
(AGC)	 AG	189397-189441	GT	AGG
(GTT)	 AG	189618-189699	GT	AGG
(CTG)	 AG	189815-189907	GT	AGG
(GCC)	 AG	190061-190140	GT	AGG
(ACA)	 AG	190235-190278	GT	AAG
(GCG)	 AG	190463-190542	GT	AGG
(GTG)	 AG	190629-190751	CT	GAC
-recovered pasa_asmbl_17063.p1, terminal, 190629, 190751
-recovered pasa_asmbl_17063.p1, internal, 187046, 187164
-recovered pasa_asmbl_17063.p1, internal, 187279, 187407
-recovered pasa_asmbl_17063.p1, internal, 187535, 187599
-recovered pasa_asmbl_17063.p1, internal, 187694, 187750
-recovered pasa_asmbl_17063.p1, internal, 187874, 187972
-recovered pasa_asmbl_17063.p1, internal, 188179, 188246
-recovered pasa_asmbl_17063.p1, internal, 188360, 188447
-recovered pasa_asmbl_17063.p1, internal, 188557, 188626
-recovered pasa_asmbl_17063.p1, internal, 188780, 188852
-recovered pasa_asmbl_17063.p1, internal, 188953, 189036
-recovered pasa_asmbl_17063.p1, internal, 189121, 189250
-recovered pasa_asmbl_17063.p1, internal, 189397, 189441
-recovered pasa_asmbl_17063.p1, internal, 189618, 189699
-recovered pasa_asmbl_17063.p1, internal, 189815, 189907
-recovered pasa_asmbl_17063.p1, internal, 190061, 190140
-recovered pasa_asmbl_17063.p1, internal, 190235, 190278
-recovered pasa_asmbl_17063.p1, internal, 190463, 190542
Valid prediction for Augustus_model.g25537.t1
Valid prediction for GlimmerHMM_glimmerT_38275-T1
Valid prediction for GlimmerHMM_glimmerT_38255-T1
Valid prediction for GlimmerHMM_glimmerT_38251-T1
Valid prediction for snap_scaffold_16-snap.920-T1
Valid prediction for snap_scaffold_16-snap.914-T1
Valid prediction for snap_scaffold_16-snap.906-T1
Valid prediction for GlimmerHMM_glimmerT_38271-T1
Valid prediction for GlimmerHMM_glimmerT_38253-T1
Valid prediction for snap_scaffold_16-snap.927-T1
Valid prediction for GlimmerHMM_glimmerT_38266-T1
Valid prediction for snap_scaffold_16-snap.922-T1
Valid prediction for GlimmerHMM_glimmerT_38265-T1
Valid prediction for Augustus_model.g25525.t1
Valid prediction for snap_scaffold_16-snap.902-T1
Valid prediction for pasa_asmbl_17068.p1
Valid prediction for GlimmerHMM_glimmerT_38273-T1
Couldn't classify 141125, 141179
Sorry, prediction pasa_asmbl_17067.p1 fails validation.
(ATC)	 CG	141125-141179	GT	TGG
(ACT)	 AG	141351-141464	GT	AGG
(ACA)	 AG	141550-141651	GC	AGG
(GAC)	 AG	141801-141958	GT	AGG
-recovered pasa_asmbl_17067.p1, terminal, 141801, 141958
-recovered pasa_asmbl_17067.p1, internal, 141351, 141464
-recovered pasa_asmbl_17067.p1, internal, 141550, 141651
-recovered pasa_asmbl_17067.p1, internal, 141801, 141958
Valid prediction for snap_scaffold_16-snap.887-T1
Valid prediction for snap_scaffold_16-snap.903-T1
Valid prediction for Augustus_model.g25530.t1
Valid prediction for snap_scaffold_16-snap.924-T1
Valid prediction for Augustus_model.g25541.t1
Valid prediction for HiQ_model.g25527.t1
Valid prediction for snap_scaffold_16-snap.910-T1
Valid prediction for GlimmerHMM_glimmerT_38261-T1
Valid prediction for GlimmerHMM_glimmerT_38258-T1
Couldn't classify 169280, 169359
Couldn't classify 178803, 178822
Sorry, prediction pasa_asmbl_17538.p1 fails validation.
(GGA)	 GA	169280-169359	GT	GGG
(CCG)	 AG	170324-170464	GT	AGG
(TGG)	 AG	173037-173137	GT	AGG
(CGG)	 AG	175136-175441	GT	AAG
(TGT)	 AG	177255-177341	GT	CAG
(TCG)	 AG	178803-178822	CC	CCC
-recovered pasa_asmbl_17538.p1, internal, 170324, 170464
-recovered pasa_asmbl_17538.p1, internal, 173037, 173137
-recovered pasa_asmbl_17538.p1, internal, 175136, 175441
-recovered pasa_asmbl_17538.p1, internal, 177255, 177341
Valid prediction for snap_scaffold_16-snap.917-T1
Valid prediction for snap_scaffold_16-snap.885-T1
Valid prediction for Augustus_model.g25536.t1
Valid prediction for snap_scaffold_16-snap.919-T1
Valid prediction for GlimmerHMM_glimmerT_38257-T1
Valid prediction for Augustus_model.g25533.t1
Valid prediction for CodingQuarry_transcript_19951-T1
Valid prediction for GlimmerHMM_glimmerT_38247-T1
Valid prediction for snap_scaffold_16-snap.916-T1
Valid prediction for CodingQuarry_transcript_19950-T1
Valid prediction for snap_scaffold_16-snap.892-T1
Valid prediction for CodingQuarry_transcript_19953-T1
Valid prediction for snap_scaffold_16-snap.908-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_38268-T1
Valid prediction for pasa_asmbl_17070.p1
Valid prediction for snap_scaffold_16-snap.895-T1
Valid prediction for snap_scaffold_16-snap.905-T1
Valid prediction for Augustus_model.g25543.t1
Valid prediction for HiQ_model.g25538.t1
Valid prediction for GlimmerHMM_glimmerT_38256-T1
Valid prediction for Augustus_model.g25542.t1
Valid prediction for GlimmerHMM_glimmerT_38260-T1
Valid prediction for CodingQuarry_transcript_19954-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15292, rend_intergenic: 12942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20150, rend_intergenic: 16208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40072, rend_intergenic: 37860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108855, rend_intergenic: 99553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121181, rend_intergenic: 116595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233076, rend_intergenic: 231891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 277130
-exon list size: 454


building trellis

0.2    
0.4    
0.7    
0.9    
1.1    
1.3    
1.5    
1.8    
2.0    
2.2    
2.4    
2.6    
2.9    
3.1    
3.3    
3.5    
3.7    
3.9    
4.2    
4.4    
4.6    
4.8    
5.0    
5.3    
5.5    
5.7    
5.9    
6.1    
6.4    
6.6    
6.8    
7.0    
7.2    
7.5    
7.7    
7.9    
8.1    
8.3    
8.6    
8.8    
9.0    
9.2    
9.4    
9.6    
9.9    
10.1    
10.3    
10.5    
10.7    
11.0    
11.2    
11.4    
11.6    
11.8    
12.1    
12.3    
12.5    
12.7    
12.9    
13.2    
13.4    
13.6    
13.8    
14.0    
14.3    
14.5    
14.7    
14.9    
15.1    
15.4    
15.6    
15.8    
16.0    
16.2    
16.4    
16.7    
16.9    
17.1    
17.3    
17.5    
17.8    
18.0    
18.2    
18.4    
18.6    
18.9    
19.1    
19.3    
19.5    
19.7    
20.0    
20.2    
20.4    
20.6    
20.8    
21.1    
21.3    
21.5    
21.7    
21.9    
22.1    
22.4    
22.6    
22.8    
23.0    
23.2    
23.5    
23.7    
23.9    
24.1    
24.3    
24.6    
24.8    
25.0    
25.2    
25.4    
25.7    
25.9    
26.1    
26.3    
26.5    
26.8    
27.0    
27.2    
27.4    
27.6    
27.9    
28.1    
28.3    
28.5    
28.7    
28.9    
29.2    
29.4    
29.6    
29.8    
30.0    
30.3    
30.5    
30.7    
30.9    
31.1    
31.4    
31.6    
31.8    
32.0    
32.2    
32.5    
32.7    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.9    
35.1    
35.3    
35.5    
35.7    
36.0    
36.2    
36.4    
36.6    
36.8    
37.1    
37.3    
37.5    
37.7    
37.9    
38.2    
38.4    
38.6    
38.8    
39.0    
39.3    
39.5    
39.7    
39.9    
40.1    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
41.7    
41.9    
42.1    
42.3    
42.5    
42.8    
43.0    
43.2    
43.4    
43.6    
43.9    
44.1    
44.3    
44.5    
44.7    
45.0    
45.2    
45.4    
45.6    
45.8    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.4    
47.6    
47.8    
48.0    
48.2    
48.5    
48.7    
48.9    
49.1    
49.3    
49.6    
49.8    
50.0    
50.2    
50.4    
50.7    
50.9    
51.1    
51.3    
51.5    
51.8    
52.0    
52.2    
52.4    
52.6    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.2    
54.4    
54.6    
54.8    
55.0    
55.3    
55.5    
55.7    
55.9    
56.1    
56.4    
56.6    
56.8    
57.0    
57.2    
57.5    
57.7    
57.9    
58.1    
58.3    
58.6    
58.8    
59.0    
59.2    
59.4    
59.6    
59.9    
60.1    
60.3    
60.5    
60.7    
61.0    
61.2    
61.4    
61.6    
61.8    
62.1    
62.3    
62.5    
62.7    
62.9    
63.2    
63.4    
63.6    
63.8    
64.0    
64.3    
64.5    
64.7    
64.9    
65.1    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.3    
67.5    
67.8    
68.0    
68.2    
68.4    
68.6    
68.9    
69.1    
69.3    
69.5    
69.7    
70.0    
70.2    
70.4    
70.6    
70.8    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.4    
72.6    
72.8    
73.0    
73.2    
73.5    
73.7    
73.9    
74.1    
74.3    
74.6    
74.8    
75.0    
75.2    
75.4    
75.7    
75.9    
76.1    
76.3    
76.5    
76.8    
77.0    
77.2    
77.4    
77.6    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.2    
79.4    
79.6    
79.8    
80.0    
80.3    
80.5    
80.7    
80.9    
81.1    
81.4    
81.6    
81.8    
82.0    
82.2    
82.5    
82.7    
82.9    
83.1    
83.3    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.9    
85.1    
85.3    
85.5    
85.7    
86.0    
86.2    
86.4    
86.6    
86.8    
87.1    
87.3    
87.5    
87.7    
87.9    
88.2    
88.4    
88.6    
88.8    
89.0    
89.3    
89.5    
89.7    
89.9    
90.1    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.7    
91.9    
92.1    
92.3    
92.5    
92.8    
93.0    
93.2    
93.4    
93.6    
93.9    
94.1    
94.3    
94.5    
94.7    
95.0    
95.2    
95.4    
95.6    
95.8    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.0    
98.2    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 15292, rend_intergenic: 12942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20150, rend_intergenic: 16208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40072, rend_intergenic: 37860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108855, rend_intergenic: 99553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121181, rend_intergenic: 116595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233076, rend_intergenic: 231891  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