-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_4656408-4868883

-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 pasa_asmbl_46896.p1
Valid prediction for GlimmerHMM_glimmerT_14561-T1
Valid prediction for snap_scaffold_6-snap.1121-T1
Valid prediction for CodingQuarry_transcript_55021-T1
Valid prediction for GlimmerHMM_glimmerT_14562-T1
Valid prediction for snap_scaffold_6-snap.1124-T1
Valid prediction for snap_scaffold_6-snap.1130-T1
Valid prediction for snap_scaffold_6-snap.1110-T1
Valid prediction for Augustus_model.g9632.t1
Valid prediction for GlimmerHMM_glimmerT_14540-T1
Valid prediction for Augustus_model.g9636.t1
Valid prediction for snap_scaffold_6-snap.1113-T1
Valid prediction for Augustus_model.g9644.t1
Valid prediction for HiQ_model.g9631.t1
Valid prediction for GlimmerHMM_glimmerT_14558-T1
Valid prediction for snap_scaffold_6-snap.1102-T1
Valid prediction for snap_scaffold_6-snap.1133-T1
Valid prediction for GlimmerHMM_glimmerT_14555-T1
Valid prediction for GlimmerHMM_glimmerT_14553-T1
Valid prediction for snap_scaffold_6-snap.1143-T1
Valid prediction for GlimmerHMM_glimmerT_14567-T1
Valid prediction for GlimmerHMM_glimmerT_14560-T1
Valid prediction for Augustus_model.g9626.t1
Valid prediction for Augustus_model.g9639.t1
Valid prediction for GlimmerHMM_glimmerT_14542-T1
Valid prediction for GlimmerHMM_glimmerT_14563-T1
Valid prediction for GlimmerHMM_glimmerT_14549-T1
Valid prediction for GlimmerHMM_glimmerT_14551-T1
Valid prediction for snap_scaffold_6-snap.1100-T1
Valid prediction for snap_scaffold_6-snap.1117-T1
Valid prediction for GlimmerHMM_glimmerT_14559-T1
Valid prediction for snap_scaffold_6-snap.1136-T1
Valid prediction for snap_scaffold_6-snap.1115-T1
Valid prediction for snap_scaffold_6-snap.1125-T1
Valid prediction for CodingQuarry_transcript_55025-T1
Valid prediction for HiQ_model.g9624.t1
Valid prediction for snap_scaffold_6-snap.1119-T1
Valid prediction for snap_scaffold_6-snap.1122-T1
Valid prediction for snap_scaffold_6-snap.1132-T1
Valid prediction for pasa_asmbl_46899.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 pasa_asmbl_48353.p1
Valid prediction for snap_scaffold_6-snap.1123-T1
Valid prediction for snap_scaffold_6-snap.1126-T1
Valid prediction for snap_scaffold_6-snap.1145-T1
Valid prediction for snap_scaffold_6-snap.1141-T1
Couldn't classify 39737, 39940
Sorry, prediction pasa_asmbl_48359.p1 fails validation.
(ATG)	 GG	39369-39545	GT	AGG
(GTT)	 AG	39737-39940	GG	CAG
-recovered pasa_asmbl_48359.p1, initial, 39369, 39545
Valid prediction for snap_scaffold_6-snap.1106-T1
Couldn't classify 187630, 187722
Sorry, prediction pasa_asmbl_48351.p2 fails validation.
(GTC)	 GA	187630-187722	GT	AGG
(AAA)	 AG	187828-187910	GT	CGG
(GGA)	 AG	188023-188099	GT	CGG
(GTC)	 AG	188213-188307	CA	AAC
-recovered pasa_asmbl_48351.p2, terminal, 188213, 188307
-recovered pasa_asmbl_48351.p2, internal, 187828, 187910
-recovered pasa_asmbl_48351.p2, internal, 188023, 188099
Valid prediction for HiQ_model.g9625.t1
Valid prediction for GlimmerHMM_glimmerT_14565-T1
Valid prediction for snap_scaffold_6-snap.1127-T1
Valid prediction for snap_scaffold_6-snap.1108-T1
Valid prediction for snap_scaffold_6-snap.1134-T1
Valid prediction for GlimmerHMM_glimmerT_14546-T1
Valid prediction for GlimmerHMM_glimmerT_14557-T1
Valid prediction for GlimmerHMM_glimmerT_14539-T1
Valid prediction for GlimmerHMM_glimmerT_14545-T1
Valid prediction for GlimmerHMM_glimmerT_14543-T1
Valid prediction for Augustus_model.g9649.t1
Valid prediction for snap_scaffold_6-snap.1107-T1
Valid prediction for snap_scaffold_6-snap.1105-T1
Valid prediction for Augustus_model.g9634.t1
Couldn't classify 208468, 208510
Couldn't classify 209491, 209565
Sorry, prediction pasa_asmbl_48347.p1 fails validation.
(TAC)	 CA	208468-208510	GT	AGG
(ATC)	 AG	208613-208741	GT	ATG
(TGA)	 AG	208960-209105	GT	CAG
(GAA)	 AG	209491-209565	GA	CAG
-recovered pasa_asmbl_48347.p1, internal, 208613, 208741
-recovered pasa_asmbl_48347.p1, internal, 208960, 209105
Valid prediction for GlimmerHMM_glimmerT_14552-T1
Couldn't classify 27153, 27510
Sorry, prediction pasa_asmbl_48362.p1 fails validation.
(GGT)	 CA	27153-27510	GT	AGG
(CTG)	 AG	28973-29124	GT	CAG
(GAC)	 AG	29807-29929	GT	AGG
(GAA)	 AG	30098-30191	GT	CGG
(CCA)	 AG	30313-30437	CT	AAC
-recovered pasa_asmbl_48362.p1, terminal, 30313, 30437
-recovered pasa_asmbl_48362.p1, internal, 28973, 29124
-recovered pasa_asmbl_48362.p1, internal, 29807, 29929
-recovered pasa_asmbl_48362.p1, internal, 30098, 30191
Valid prediction for HiQ_model.g9630.t1
Valid prediction for snap_scaffold_6-snap.1103-T1
Valid prediction for CodingQuarry_transcript_55022-T1
Valid prediction for Augustus_model.g9646.t1
Valid prediction for GlimmerHMM_glimmerT_14571-T1
Valid prediction for snap_scaffold_6-snap.1120-T1
Valid prediction for Augustus_model.g9629.t1
Valid prediction for GlimmerHMM_glimmerT_14570-T1
Valid prediction for GlimmerHMM_glimmerT_14573-T1
Valid prediction for snap_scaffold_6-snap.1114-T1
Valid prediction for GlimmerHMM_glimmerT_14572-T1
Valid prediction for Augustus_model.g9642.t1
Valid prediction for snap_scaffold_6-snap.1135-T1
Valid prediction for HiQ_model.g9647.t1
Valid prediction for snap_scaffold_6-snap.1112-T1
Valid prediction for HiQ_model.g9648.t1
Valid prediction for snap_scaffold_6-snap.1116-T1
Valid prediction for pasa_asmbl_48349.p1
Valid prediction for snap_scaffold_6-snap.1104-T1
Valid prediction for CodingQuarry_transcript_55024-T1
Valid prediction for Augustus_model.g9633.t1
Valid prediction for snap_scaffold_6-snap.1109-T1
Valid prediction for GlimmerHMM_glimmerT_14568-T1
Valid prediction for Augustus_model.g9637.t1
Valid prediction for GlimmerHMM_glimmerT_14566-T1
Valid prediction for snap_scaffold_6-snap.1144-T1
Valid prediction for snap_scaffold_6-snap.1137-T1
Valid prediction for GlimmerHMM_glimmerT_14554-T1
Valid prediction for GlimmerHMM_glimmerT_14556-T1
Valid prediction for Augustus_model.g9645.t1
Valid prediction for GlimmerHMM_glimmerT_14569-T1
Valid prediction for GlimmerHMM_glimmerT_14550-T1
Valid prediction for snap_scaffold_6-snap.1118-T1
Valid prediction for snap_scaffold_6-snap.1129-T1
Valid prediction for snap_scaffold_6-snap.1142-T1
Valid prediction for GlimmerHMM_glimmerT_14548-T1
Valid prediction for snap_scaffold_6-snap.1101-T1
Valid prediction for Augustus_model.g9641.t1
Valid prediction for GlimmerHMM_glimmerT_14544-T1
Valid prediction for Augustus_model.g9640.t1
Valid prediction for Augustus_model.g9643.t1
Valid prediction for GlimmerHMM_glimmerT_14574-T1
Valid prediction for snap_scaffold_6-snap.1111-T1
Valid prediction for snap_scaffold_6-snap.1140-T1
Valid prediction for Augustus_model.g9638.t1
Couldn't classify 40650, 40709
Sorry, prediction pasa_asmbl_48357.p1 fails validation.
(CTT)	 AG	40650-40709	GT	TGG
(GAT)	 AG	40816-40948	GT	GGG
(GTG)	 AG	41117-41302	GT	GGG
(AGA)	 AG	41460-41710	GT	AGG
(AAC)	 AG	41848-42159	GT	AGG
(ATC)	 AG	42239-42429	GT	CAG
(AAA)	 AG	42551-42644	GC	AGG
(GAA)	 AG	42755-42943	TG	AGT
-recovered pasa_asmbl_48357.p1, terminal, 42755, 42943
-recovered pasa_asmbl_48357.p1, internal, 40650, 40709
-recovered pasa_asmbl_48357.p1, internal, 40816, 40948
-recovered pasa_asmbl_48357.p1, internal, 41117, 41302
-recovered pasa_asmbl_48357.p1, internal, 41460, 41710
-recovered pasa_asmbl_48357.p1, internal, 41848, 42159
-recovered pasa_asmbl_48357.p1, internal, 42239, 42429
-recovered pasa_asmbl_48357.p1, internal, 42551, 42644
Valid prediction for Augustus_model.g9623.t1
Valid prediction for GlimmerHMM_glimmerT_14541-T1
Valid prediction for snap_scaffold_6-snap.1138-T1
Valid prediction for Augustus_model.g9635.t1
Valid prediction for Augustus_model.g9628.t1
Valid prediction for snap_scaffold_6-snap.1139-T1
Valid prediction for snap_scaffold_6-snap.1099-T1
Couldn't classify 34322, 34424
Sorry, prediction pasa_asmbl_48360.p1 fails validation.
(CTG)	 TC	34322-34424	GT	AGG
(TGA)	 AG	34615-34725	GT	AGG
(GAG)	 AG	34824-34960	GT	AGG
(ACG)	 AG	35084-35292	GT	CCG
(GAA)	 AG	35396-35522	GT	AGG
(GGC)	 AG	35645-35755	GT	AGG
(GGT)	 AG	35848-35991	GT	AGG
(ATC)	 AG	36090-36204	GT	TCG
(GAG)	 AG	36304-36340	GT	GGG
(GAA)	 AG	36447-36510	GT	AGG
(ACT)	 AG	36586-36670	GT	CGG
(ACC)	 AG	36826-37019	TT	GAT
-recovered pasa_asmbl_48360.p1, terminal, 36826, 37019
-recovered pasa_asmbl_48360.p1, internal, 34615, 34725
-recovered pasa_asmbl_48360.p1, internal, 34824, 34960
-recovered pasa_asmbl_48360.p1, internal, 35084, 35292
-recovered pasa_asmbl_48360.p1, internal, 35396, 35522
-recovered pasa_asmbl_48360.p1, internal, 35645, 35755
-recovered pasa_asmbl_48360.p1, internal, 35848, 35991
-recovered pasa_asmbl_48360.p1, internal, 36090, 36204
-recovered pasa_asmbl_48360.p1, internal, 36304, 36340
-recovered pasa_asmbl_48360.p1, internal, 36447, 36510
-recovered pasa_asmbl_48360.p1, internal, 36586, 36670
Valid prediction for Augustus_model.g9627.t1
Valid prediction for GlimmerHMM_glimmerT_14564-T1
Valid prediction for Augustus_model.g9650.t1
Valid prediction for pasa_asmbl_48352.p1
Valid prediction for GlimmerHMM_glimmerT_14547-T1
Valid prediction for CodingQuarry_transcript_55023-T1
Valid prediction for snap_scaffold_6-snap.1128-T1
Valid prediction for snap_scaffold_6-snap.1131-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 79049, rend_intergenic: 73573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86649, rend_intergenic: 80177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97354, rend_intergenic: 93257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101563, rend_intergenic: 97551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120012, rend_intergenic: 108557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131177, rend_intergenic: 120076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132088, rend_intergenic: 131715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135654, rend_intergenic: 132119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141886, rend_intergenic: 136341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149651, rend_intergenic: 144007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156286, rend_intergenic: 152741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206398, rend_intergenic: 205076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 212476
-exon list size: 482


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.4    
1.7    
1.9    
2.1    
2.3    
2.5    
2.7    
2.9    
3.1    
3.3    
3.5    
3.7    
3.9    
4.1    
4.3    
4.5    
4.8    
5.0    
5.2    
5.4    
5.6    
5.8    
6.0    
6.2    
6.4    
6.6    
6.8    
7.0    
7.2    
7.4    
7.6    
7.9    
8.1    
8.3    
8.5    
8.7    
8.9    
9.1    
9.3    
9.5    
9.7    
9.9    
10.1    
10.3    
10.5    
10.7    
11.0    
11.2    
11.4    
11.6    
11.8    
12.0    
12.2    
12.4    
12.6    
12.8    
13.0    
13.2    
13.4    
13.6    
13.8    
14.0    
14.3    
14.5    
14.7    
14.9    
15.1    
15.3    
15.5    
15.7    
15.9    
16.1    
16.3    
16.5    
16.7    
16.9    
17.1    
17.4    
17.6    
17.8    
18.0    
18.2    
18.4    
18.6    
18.8    
19.0    
19.2    
19.4    
19.6    
19.8    
20.0    
20.2    
20.5    
20.7    
20.9    
21.1    
21.3    
21.5    
21.7    
21.9    
22.1    
22.3    
22.5    
22.7    
22.9    
23.1    
23.3    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.0    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.4    
26.7    
26.9    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.1    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
47.9    
48.1    
48.3    
48.6    
48.8    
49.0    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.0    
51.2    
51.4    
51.7    
51.9    
52.1    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
61.0    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
63.0    
63.2    
63.4    
63.6    
63.8    
64.0    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.1    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 44 predictions from path traversal
Error with prediction: snap lend_intergenic: 79049, rend_intergenic: 73573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86649, rend_intergenic: 80177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97354, rend_intergenic: 93257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101563, rend_intergenic: 97551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120012, rend_intergenic: 108557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131177, rend_intergenic: 120076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132088, rend_intergenic: 131715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135654, rend_intergenic: 132119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141886, rend_intergenic: 136341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149651, rend_intergenic: 144007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156286, rend_intergenic: 152741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206398, rend_intergenic: 205076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support