-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_6730703-6956209

-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_23-snap.1236-T1
Valid prediction for Augustus_model.g34255.t1
Valid prediction for GlimmerHMM_glimmerT_51216-T1
Couldn't classify 65916, 66290
Sorry, prediction pasa_asmbl_31657.p1 fails validation.
(ATG)	 GC	65916-66290	TA	TGT
Valid prediction for GlimmerHMM_glimmerT_51206-T1
Valid prediction for GlimmerHMM_glimmerT_51201-T1
Valid prediction for Augustus_model.g34251.t1
Valid prediction for GlimmerHMM_glimmerT_51200-T1
Valid prediction for GlimmerHMM_glimmerT_51197-T1
Couldn't classify 46854, 47435
Sorry, prediction pasa_asmbl_31653.p1 fails validation.
(ATG)	 AG	46854-47435	GA	CTG
Valid prediction for snap_scaffold_23-snap.1247-T1
Valid prediction for snap_scaffold_23-snap.1242-T1
Valid prediction for HiQ_model.g34258.t1
Valid prediction for snap_scaffold_23-snap.1229-T1
Valid prediction for snap_scaffold_23-snap.1226-T1
Valid prediction for snap_scaffold_23-snap.1225-T1
Valid prediction for Augustus_model.g34256.t1
Valid prediction for GlimmerHMM_glimmerT_51199-T1
Valid prediction for snap_scaffold_23-snap.1233-T1
Valid prediction for GlimmerHMM_glimmerT_51218-T1
Valid prediction for Augustus_model.g34260.t1
Couldn't classify 83743, 84075
Sorry, prediction pasa_asmbl_31659.p1 fails validation.
(ATG)	 CC	83743-84075	GA	GTG
Valid prediction for snap_scaffold_23-snap.1235-T1
Valid prediction for snap_scaffold_23-snap.1222-T1
Valid prediction for snap_scaffold_23-snap.1218-T1
Valid prediction for GlimmerHMM_glimmerT_51222-T1
Couldn't classify 47655, 48281
Sorry, prediction pasa_asmbl_31654.p1 fails validation.
(CAG)	 TA	47655-48281	GT	CAG
(GCC)	 AG	48330-49157	GC	AAG
-recovered pasa_asmbl_31654.p1, terminal, 48330, 49157
-recovered pasa_asmbl_31654.p1, internal, 48330, 49157
Couldn't classify 32901, 33110
Couldn't classify 33915, 33977
Sorry, prediction pasa_asmbl_31945.p1 fails validation.
(GCC)	 AG	32901-33110	GT	AGG
(TCC)	 AG	33392-33493	GT	TGG
(GAG)	 AG	33915-33977	CA	GCC
-recovered pasa_asmbl_31945.p1, internal, 32901, 33110
-recovered pasa_asmbl_31945.p1, internal, 33392, 33493
Valid prediction for snap_scaffold_23-snap.1232-T1
Valid prediction for snap_scaffold_23-snap.1220-T1
Valid prediction for CodingQuarry_transcript_35697-T1
Valid prediction for GlimmerHMM_glimmerT_51220-T1
Couldn't classify 43822, 44049
Couldn't classify 45042, 45123
Sorry, prediction pasa_asmbl_31651.p1 fails validation.
(GAT)	 CA	43822-44049	GT	GGG
(AAT)	 AG	44168-44290	GT	AGG
(AGT)	 AG	44606-44742	GC	AGG
(GCG)	 AG	45042-45123	TC	GCT
-recovered pasa_asmbl_31651.p1, internal, 44168, 44290
-recovered pasa_asmbl_31651.p1, internal, 44606, 44742
Valid prediction for Augustus_model.g34252.t1
Valid prediction for GlimmerHMM_glimmerT_51198-T1
Couldn't classify 94280, 94373
Couldn't classify 97029, 97113
Sorry, prediction pasa_asmbl_31917.p1 fails validation.
(GTC)	 CA	94280-94373	GT	AGG
(GTC)	 AG	94637-94711	GT	CGG
(ATC)	 AG	94842-94973	GT	AGG
(AAA)	 AG	96316-96517	GT	AGG
(CTG)	 AG	97029-97113	GG	CAG
-recovered pasa_asmbl_31917.p1, internal, 94637, 94711
-recovered pasa_asmbl_31917.p1, internal, 94842, 94973
-recovered pasa_asmbl_31917.p1, internal, 96316, 96517
Valid prediction for GlimmerHMM_glimmerT_51195-T1
Valid prediction for snap_scaffold_23-snap.1246-T1
Valid prediction for GlimmerHMM_glimmerT_51203-T1
Valid prediction for Augustus_model.g34253.t1
Valid prediction for snap_scaffold_23-snap.1253-T1
Valid prediction for snap_scaffold_23-snap.1250-T1
Valid prediction for snap_scaffold_23-snap.1230-T1
Couldn't classify 46074, 46553
Sorry, prediction pasa_asmbl_31652.p1 fails validation.
(CAC)	 GG	46074-46553	CG	CGC
Valid prediction for GlimmerHMM_glimmerT_51212-T1
Valid prediction for snap_scaffold_23-snap.1228-T1
Valid prediction for snap_scaffold_23-snap.1217-T1
Valid prediction for snap_scaffold_23-snap.1252-T1
Valid prediction for Augustus_model.g34254.t1
Valid prediction for pasa_asmbl_31662.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_51210-T1
Valid prediction for pasa_asmbl_30990.p1
Valid prediction for snap_scaffold_23-snap.1251-T1
Valid prediction for snap_scaffold_23-snap.1237-T1
Valid prediction for GlimmerHMM_glimmerT_51204-T1
Valid prediction for CodingQuarry_transcript_35699-T1
Valid prediction for pasa_asmbl_30982.p1
Valid prediction for snap_scaffold_23-snap.1227-T1
Valid prediction for Augustus_model.g34264.t1
Valid prediction for snap_scaffold_23-snap.1224-T1
Valid prediction for GlimmerHMM_glimmerT_51215-T1
Valid prediction for GlimmerHMM_glimmerT_51208-T1
Valid prediction for GlimmerHMM_glimmerT_51214-T1
Valid prediction for snap_scaffold_23-snap.1231-T1
Valid prediction for snap_scaffold_23-snap.1239-T1
Valid prediction for snap_scaffold_23-snap.1248-T1
Valid prediction for GlimmerHMM_glimmerT_51213-T1
Valid prediction for snap_scaffold_23-snap.1243-T1
Valid prediction for GlimmerHMM_glimmerT_51202-T1
Valid prediction for HiQ_model.g34263.t1
Valid prediction for GlimmerHMM_glimmerT_51211-T1
Valid prediction for HiQ_model.g34262.t1
Valid prediction for HiQ_model.g34259.t1
Valid prediction for snap_scaffold_23-snap.1238-T1
Valid prediction for CodingQuarry_transcript_35698-T1
Valid prediction for CodingQuarry_transcript_35701-T1
Valid prediction for Augustus_model.g34257.t1
Valid prediction for snap_scaffold_23-snap.1219-T1
Valid prediction for snap_scaffold_23-snap.1254-T1
Valid prediction for snap_scaffold_23-snap.1244-T1
Valid prediction for snap_scaffold_23-snap.1223-T1
Valid prediction for GlimmerHMM_glimmerT_51217-T1
Valid prediction for GlimmerHMM_glimmerT_51219-T1
Valid prediction for Augustus_model.g34261.t1
Valid prediction for GlimmerHMM_glimmerT_51209-T1
Valid prediction for GlimmerHMM_glimmerT_51207-T1
Valid prediction for GlimmerHMM_glimmerT_51196-T1
Valid prediction for snap_scaffold_23-snap.1249-T1
Valid prediction for snap_scaffold_23-snap.1241-T1
Valid prediction for GlimmerHMM_glimmerT_51205-T1
Valid prediction for GlimmerHMM_glimmerT_51194-T1
Valid prediction for snap_scaffold_23-snap.1245-T1
Couldn't classify 89076, 89967
Sorry, prediction pasa_asmbl_30983.p1 fails validation.
(GTC)	 GC	89076-89967	GT	AGG
(TGT)	 AG	90193-90456	GT	ATG
(ATA)	 AG	90823-90938	GT	CGG
(AAA)	 AG	91502-91655	GT	CAG
(GGA)	 AG	92492-92761	GT	AGG
(ATC)	 AG	92911-93096	GT	TGG
(GAC)	 AG	93374-93463	GT	TGG
(ATC)	 AG	93758-94021	GT	AGG
(AGG)	 AG	96838-97113	GT	AGG
(TGA)	 AG	98696-98968	GT	AGG
(CTG)	 AG	99166-99438	GT	AGG
(AAC)	 AG	99625-99897	GT	AGG
(CTC)	 AG	100313-100609	GT	AGG
(AGG)	 AG	101810-102082	GT	AGG
(GCA)	 AG	102427-102549	GT	AGG
(GCA)	 AG	102734-102877	GT	AGG
(CTC)	 AG	103711-103830	GT	AGG
(GGT)	 AG	103966-104109	GT	GGG
(ATG)	 AG	104413-104543	GT	GGG
(GAG)	 AG	104769-104901	GT	CAG
(TTG)	 AG	105203-105354	GT	TGG
(GTG)	 AG	105536-105632	GT	CGG
(GTC)	 AG	105742-105903	GT	AGG
(GTG)	 AG	106162-106325	GT	AGG
(GGT)	 AG	106522-106632	AT	AAA
add_exon() Sorry, pasa_asmbl_30983.p1 104413-104543-initial-1 is invalid.
-recovered pasa_asmbl_30983.p1, initial, 104413, 104543
-recovered pasa_asmbl_30983.p1, terminal, 106522, 106632
-recovered pasa_asmbl_30983.p1, internal, 90193, 90456
-recovered pasa_asmbl_30983.p1, internal, 90823, 90938
-recovered pasa_asmbl_30983.p1, internal, 91502, 91655
-recovered pasa_asmbl_30983.p1, internal, 92492, 92761
-recovered pasa_asmbl_30983.p1, internal, 92911, 93096
-recovered pasa_asmbl_30983.p1, internal, 93374, 93463
-recovered pasa_asmbl_30983.p1, internal, 93758, 94021
-recovered pasa_asmbl_30983.p1, internal, 96838, 97113
-recovered pasa_asmbl_30983.p1, internal, 98696, 98968
-recovered pasa_asmbl_30983.p1, internal, 99166, 99438
-recovered pasa_asmbl_30983.p1, internal, 99625, 99897
-recovered pasa_asmbl_30983.p1, internal, 100313, 100609
-recovered pasa_asmbl_30983.p1, internal, 101810, 102082
-recovered pasa_asmbl_30983.p1, internal, 102427, 102549
-recovered pasa_asmbl_30983.p1, internal, 102734, 102877
-recovered pasa_asmbl_30983.p1, internal, 103711, 103830
-recovered pasa_asmbl_30983.p1, internal, 103966, 104109
-recovered pasa_asmbl_30983.p1, internal, 104413, 104543
-recovered pasa_asmbl_30983.p1, internal, 104769, 104901
-recovered pasa_asmbl_30983.p1, internal, 105203, 105354
-recovered pasa_asmbl_30983.p1, internal, 105536, 105632
-recovered pasa_asmbl_30983.p1, internal, 105742, 105903
-recovered pasa_asmbl_30983.p1, internal, 106162, 106325
Valid prediction for snap_scaffold_23-snap.1234-T1
Valid prediction for CodingQuarry_transcript_35700-T1
Couldn't classify 17657, 17968
Sorry, prediction pasa_asmbl_31926.p1 fails validation.
(CTC)	 CC	17657-17968	TC	AAT
Valid prediction for GlimmerHMM_glimmerT_51221-T1
Valid prediction for snap_scaffold_23-snap.1240-T1
Valid prediction for snap_scaffold_23-snap.1221-T1
Valid prediction for pasa_asmbl_30994.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8089, rend_intergenic: 6469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14981, rend_intergenic: 12615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17178, rend_intergenic: 15044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28954, rend_intergenic: 27333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49157, rend_intergenic: 34913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86936, rend_intergenic: 85864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97682, rend_intergenic: 94277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100209, rend_intergenic: 98243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202230, rend_intergenic: 197622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215255, rend_intergenic: 203021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225203, rend_intergenic: 215503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 225507
-exon list size: 347


building trellis

0.3    
0.6    
0.9    
1.1    
1.4    
1.7    
2.0    
2.3    
2.6    
2.9    
3.2    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.2    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.5    
13.8    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.8    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.6    
24.9    
25.2    
25.5    
25.8    
26.1    
26.4    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.6    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.2    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.8    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 8089, rend_intergenic: 6469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14981, rend_intergenic: 12615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17178, rend_intergenic: 15044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28954, rend_intergenic: 27333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49157, rend_intergenic: 34913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86936, rend_intergenic: 85864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97682, rend_intergenic: 94277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100209, rend_intergenic: 98243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202230, rend_intergenic: 197622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215255, rend_intergenic: 203021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225203, rend_intergenic: 215503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support