-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_6723367-6920541

-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_14868-T1
Valid prediction for snap_scaffold_6-snap.1530-T1
Valid prediction for Augustus_model.g9840.t1
Valid prediction for CodingQuarry_transcript_55078-T1
Valid prediction for GlimmerHMM_glimmerT_14873-T1
Valid prediction for snap_scaffold_6-snap.1538-T1
Couldn't classify 182745, 184884
Sorry, prediction pasa_asmbl_47020.p1 fails validation.
(AAC)	 GT	182745-184884	GT	AAG
(GCT)	 AG	186545-186784	GT	TGG
(GAG)	 AG	186951-187105	GT	AGG
(ATG)	 AG	187274-187351	GT	CTG
(AGA)	 AG	187448-187499	GT	AGG
(GGA)	 AG	187715-187842	GT	AGG
(AAT)	 AG	188850-188981	GT	AGG
(GTC)	 AG	189094-189231	GT	AGG
(CGT)	 AG	189496-189588	GT	AGG
(GGT)	 AG	189697-189868	GT	AGG
(GCT)	 AG	189987-190118	GT	TGG
(GTG)	 AG	190200-190373	GT	AGG
(AGT)	 AG	190495-190635	GT	TGG
(GGC)	 AG	190831-190938	GT	AGG
(CCA)	 AG	191169-191375	GT	CGG
(GGT)	 AG	191483-191559	GT	AGG
(ATT)	 AG	191673-191812	GT	ATG
(GTG)	 AG	191928-192288	AT	GAA
-recovered pasa_asmbl_47020.p1, initial, 187274, 187351
add_exon() Sorry, pasa_asmbl_47020.p1 189697-189868-terminal-3 is invalid.
-recovered pasa_asmbl_47020.p1, terminal, 189697, 189868
-recovered pasa_asmbl_47020.p1, terminal, 191928, 192288
-recovered pasa_asmbl_47020.p1, internal, 186545, 186784
-recovered pasa_asmbl_47020.p1, internal, 186951, 187105
-recovered pasa_asmbl_47020.p1, internal, 187274, 187351
-recovered pasa_asmbl_47020.p1, internal, 187448, 187499
-recovered pasa_asmbl_47020.p1, internal, 187715, 187842
-recovered pasa_asmbl_47020.p1, internal, 188850, 188981
-recovered pasa_asmbl_47020.p1, internal, 189094, 189231
-recovered pasa_asmbl_47020.p1, internal, 189496, 189588
-recovered pasa_asmbl_47020.p1, internal, 189697, 189868
-recovered pasa_asmbl_47020.p1, internal, 189987, 190118
-recovered pasa_asmbl_47020.p1, internal, 190200, 190373
-recovered pasa_asmbl_47020.p1, internal, 190495, 190635
-recovered pasa_asmbl_47020.p1, internal, 190831, 190938
-recovered pasa_asmbl_47020.p1, internal, 191169, 191375
-recovered pasa_asmbl_47020.p1, internal, 191483, 191559
-recovered pasa_asmbl_47020.p1, internal, 191673, 191812
Valid prediction for CodingQuarry_transcript_55080-T1
Valid prediction for GlimmerHMM_glimmerT_14875-T1
Valid prediction for Augustus_model.g9839.t1
Valid prediction for Augustus_model.g9831.t1
Valid prediction for GlimmerHMM_glimmerT_14874-T1
Valid prediction for Augustus_model.g9835.t1
Valid prediction for CodingQuarry_transcript_55079-T1
Valid prediction for Augustus_model.g9837.t1
Valid prediction for snap_scaffold_6-snap.1528-T1
Valid prediction for snap_scaffold_6-snap.1557-T1
Valid prediction for snap_scaffold_6-snap.1559-T1
Valid prediction for GlimmerHMM_glimmerT_14872-T1
Valid prediction for pasa_asmbl_47017.p1
Valid prediction for snap_scaffold_6-snap.1533-T1
Valid prediction for snap_scaffold_6-snap.1539-T1
Valid prediction for snap_scaffold_6-snap.1537-T1
Valid prediction for pasa_asmbl_47007.p1
Couldn't classify 182176, 182669
Sorry, prediction pasa_asmbl_47019.p1 fails validation.
(ATG)	 GC	181093-181138	GT	AGG
(GTT)	 AG	182176-182669	TG	CCT
-recovered pasa_asmbl_47019.p1, initial, 181093, 181138
Valid prediction for snap_scaffold_6-snap.1532-T1
Valid prediction for Augustus_model.g9828.t1
Valid prediction for GlimmerHMM_glimmerT_14870-T1
Valid prediction for snap_scaffold_6-snap.1563-T1
Valid prediction for pasa_asmbl_47012.p1
Valid prediction for snap_scaffold_6-snap.1548-T1
Couldn't classify 150923, 151011
Couldn't classify 152674, 152733
Sorry, prediction pasa_asmbl_47016.p1 fails validation.
(CGC)	 CT	150923-151011	GT	GCG
(TGA)	 AG	151155-151327	GT	CTG
(GTA)	 AG	151748-151851	GT	AGG
(GCA)	 AG	152010-152326	GT	AAG
(AGA)	 AG	152467-152545	GT	CGG
(GGT)	 AG	152674-152733	GG	CAG
-recovered pasa_asmbl_47016.p1, internal, 151155, 151327
-recovered pasa_asmbl_47016.p1, internal, 151748, 151851
-recovered pasa_asmbl_47016.p1, internal, 152010, 152326
-recovered pasa_asmbl_47016.p1, internal, 152467, 152545
Valid prediction for GlimmerHMM_glimmerT_14878-T1
Valid prediction for Augustus_model.g9836.t1
Valid prediction for Augustus_model.g9833.t1
Valid prediction for snap_scaffold_6-snap.1531-T1
Valid prediction for GlimmerHMM_glimmerT_14876-T1
Valid prediction for snap_scaffold_6-snap.1551-T1
Valid prediction for snap_scaffold_6-snap.1544-T1
Valid prediction for GlimmerHMM_glimmerT_14877-T1
Valid prediction for snap_scaffold_6-snap.1552-T1
Valid prediction for Augustus_model.g9829.t1
Valid prediction for snap_scaffold_6-snap.1555-T1
Valid prediction for pasa_asmbl_47006.p1
Valid prediction for GlimmerHMM_glimmerT_14880-T1
Valid prediction for snap_scaffold_6-snap.1536-T1
Valid prediction for snap_scaffold_6-snap.1541-T1
Valid prediction for Augustus_model.g9834.t1
Valid prediction for Augustus_model.g9838.t1
Valid prediction for CodingQuarry_transcript_55076-T1
Valid prediction for GlimmerHMM_glimmerT_14881-T1
Valid prediction for Augustus_model.g9842.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_6-snap.1561-T1
Valid prediction for Augustus_model.g9830.t1
Valid prediction for GlimmerHMM_glimmerT_14871-T1
Valid prediction for Augustus_model.g9841.t1
Valid prediction for snap_scaffold_6-snap.1560-T1
Valid prediction for snap_scaffold_6-snap.1554-T1
Valid prediction for snap_scaffold_6-snap.1534-T1
Valid prediction for snap_scaffold_6-snap.1547-T1
Valid prediction for GlimmerHMM_glimmerT_14867-T1
Valid prediction for CodingQuarry_transcript_55081-T1
Valid prediction for snap_scaffold_6-snap.1565-T1
Valid prediction for snap_scaffold_6-snap.1543-T1
Valid prediction for snap_scaffold_6-snap.1553-T1
Valid prediction for snap_scaffold_6-snap.1546-T1
Valid prediction for GlimmerHMM_glimmerT_14869-T1
Valid prediction for snap_scaffold_6-snap.1549-T1
Valid prediction for snap_scaffold_6-snap.1529-T1
Valid prediction for snap_scaffold_6-snap.1556-T1
Valid prediction for snap_scaffold_6-snap.1564-T1
Valid prediction for snap_scaffold_6-snap.1535-T1
Valid prediction for snap_scaffold_6-snap.1540-T1
Valid prediction for snap_scaffold_6-snap.1558-T1
Valid prediction for GlimmerHMM_glimmerT_14879-T1
Valid prediction for snap_scaffold_6-snap.1542-T1
Valid prediction for snap_scaffold_6-snap.1545-T1
Valid prediction for Augustus_model.g9832.t1
Valid prediction for Augustus_model.g9827.t1
Valid prediction for snap_scaffold_6-snap.1562-T1
Valid prediction for snap_scaffold_6-snap.1550-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8043, rend_intergenic: 4844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52623, rend_intergenic: 37038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72080, rend_intergenic: 65654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74287, rend_intergenic: 72205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91091, rend_intergenic: 76917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113977, rend_intergenic: 92035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121378, rend_intergenic: 118006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130023, rend_intergenic: 123333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135842, rend_intergenic: 130135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144903, rend_intergenic: 138875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158444, rend_intergenic: 149820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171923, rend_intergenic: 160372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192288, rend_intergenic: 183559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 197175
-exon list size: 417


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.4    
1.7    
1.9    
2.1    
2.4    
2.6    
2.9    
3.1    
3.3    
3.6    
3.8    
4.1    
4.3    
4.5    
4.8    
5.0    
5.3    
5.5    
5.7    
6.0    
6.2    
6.4    
6.7    
6.9    
7.2    
7.4    
7.6    
7.9    
8.1    
8.4    
8.6    
8.8    
9.1    
9.3    
9.5    
9.8    
10.0    
10.3    
10.5    
10.7    
11.0    
11.2    
11.5    
11.7    
11.9    
12.2    
12.4    
12.6    
12.9    
13.1    
13.4    
13.6    
13.8    
14.1    
14.3    
14.6    
14.8    
15.0    
15.3    
15.5    
15.8    
16.0    
16.2    
16.5    
16.7    
16.9    
17.2    
17.4    
17.7    
17.9    
18.1    
18.4    
18.6    
18.9    
19.1    
19.3    
19.6    
19.8    
20.0    
20.3    
20.5    
20.8    
21.0    
21.2    
21.5    
21.7    
22.0    
22.2    
22.4    
22.7    
22.9    
23.2    
23.4    
23.6    
23.9    
24.1    
24.3    
24.6    
24.8    
25.1    
25.3    
25.5    
25.8    
26.0    
26.3    
26.5    
26.7    
27.0    
27.2    
27.4    
27.7    
27.9    
28.2    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.8    
30.1    
30.3    
30.5    
30.8    
31.0    
31.3    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.1    
34.4    
34.6    
34.8    
35.1    
35.3    
35.6    
35.8    
36.0    
36.3    
36.5    
36.8    
37.0    
37.2    
37.5    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.1    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
42.5    
42.7    
43.0    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.6    
44.9    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.5    
46.8    
47.0    
47.3    
47.5    
47.7    
48.0    
48.2    
48.4    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.8    
51.1    
51.3    
51.6    
51.8    
52.0    
52.3    
52.5    
52.7    
53.0    
53.2    
53.5    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.1    
55.4    
55.6    
55.8    
56.1    
56.3    
56.6    
56.8    
57.0    
57.3    
57.5    
57.8    
58.0    
58.2    
58.5    
58.7    
58.9    
59.2    
59.4    
59.7    
59.9    
60.1    
60.4    
60.6    
60.9    
61.1    
61.3    
61.6    
61.8    
62.1    
62.3    
62.5    
62.8    
63.0    
63.2    
63.5    
63.7    
64.0    
64.2    
64.4    
64.7    
64.9    
65.2    
65.4    
65.6    
65.9    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.5    
67.8    
68.0    
68.3    
68.5    
68.7    
69.0    
69.2    
69.5    
69.7    
69.9    
70.2    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.8    
72.1    
72.3    
72.6    
72.8    
73.0    
73.3    
73.5    
73.7    
74.0    
74.2    
74.5    
74.7    
74.9    
75.2    
75.4    
75.7    
75.9    
76.1    
76.4    
76.6    
76.8    
77.1    
77.3    
77.6    
77.8    
78.0    
78.3    
78.5    
78.8    
79.0    
79.2    
79.5    
79.7    
80.0    
80.2    
80.4    
80.7    
80.9    
81.1    
81.4    
81.6    
81.9    
82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.5    
83.8    
84.0    
84.2    
84.5    
84.7    
85.0    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.6    
86.9    
87.1    
87.4    
87.6    
87.8    
88.1    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.7    
90.0    
90.2    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
92.8    
93.1    
93.3    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
95.0    
95.2    
95.5    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.1    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 8043, rend_intergenic: 4844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52623, rend_intergenic: 37038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72080, rend_intergenic: 65654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74287, rend_intergenic: 72205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91091, rend_intergenic: 76917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113977, rend_intergenic: 92035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121378, rend_intergenic: 118006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130023, rend_intergenic: 123333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135842, rend_intergenic: 130135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144903, rend_intergenic: 138875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158444, rend_intergenic: 149820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171923, rend_intergenic: 160372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192288, rend_intergenic: 183559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support