-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_3193565-3393932

-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_35847-T1
Couldn't classify 178350, 178559
Sorry, prediction pasa_asmbl_15097.p1 fails validation.
(CAC)	 TC	178350-178559	GT	AGG
(AGG)	 AG	179689-179809	GT	CGG
(GGC)	 AG	180516-180706	AC	AGA
-recovered pasa_asmbl_15097.p1, terminal, 180516, 180706
-recovered pasa_asmbl_15097.p1, internal, 179689, 179809
Valid prediction for GlimmerHMM_glimmerT_35846-T1
Valid prediction for snap_scaffold_15-snap.685-T1
Valid prediction for GlimmerHMM_glimmerT_35844-T1
Valid prediction for snap_scaffold_15-snap.702-T1
Valid prediction for snap_scaffold_15-snap.705-T1
Valid prediction for snap_scaffold_15-snap.715-T1
Valid prediction for snap_scaffold_15-snap.687-T1
Valid prediction for GlimmerHMM_glimmerT_35861-T1
Valid prediction for GlimmerHMM_glimmerT_35866-T1
Valid prediction for GlimmerHMM_glimmerT_35855-T1
Valid prediction for Augustus_model.g23911.t1
Valid prediction for GlimmerHMM_glimmerT_35865-T1
Valid prediction for snap_scaffold_15-snap.688-T1
Valid prediction for snap_scaffold_15-snap.712-T1
Valid prediction for CodingQuarry_transcript_17956-T1
Valid prediction for GlimmerHMM_glimmerT_35856-T1
Valid prediction for GlimmerHMM_glimmerT_35858-T1
Valid prediction for snap_scaffold_15-snap.684-T1
Valid prediction for snap_scaffold_15-snap.700-T1
Valid prediction for snap_scaffold_15-snap.691-T1
Valid prediction for snap_scaffold_15-snap.694-T1
Valid prediction for HiQ_model.g23916.t1
Valid prediction for Augustus_model.g23907.t1
Valid prediction for GlimmerHMM_glimmerT_35859-T1
Valid prediction for snap_scaffold_15-snap.690-T1
Valid prediction for Augustus_model.g23912.t1
Valid prediction for snap_scaffold_15-snap.697-T1
Valid prediction for GlimmerHMM_glimmerT_35850-T1
Valid prediction for snap_scaffold_15-snap.701-T1
Valid prediction for snap_scaffold_15-snap.683-T1
Valid prediction for Augustus_model.g23913.t1
Valid prediction for snap_scaffold_15-snap.696-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 Augustus_model.g23906.t1
Valid prediction for snap_scaffold_15-snap.681-T1
Valid prediction for snap_scaffold_15-snap.713-T1
Valid prediction for snap_scaffold_15-snap.698-T1
Valid prediction for snap_scaffold_15-snap.686-T1
Valid prediction for GlimmerHMM_glimmerT_35845-T1
Couldn't classify 39180, 39296
Sorry, prediction pasa_asmbl_14086.p2 fails validation.
(GGT)	 CA	39180-39296	GT	ACG
(GTA)	 AG	41427-41542	GT	AGG
(GTG)	 AG	41696-41827	GT	CGG
(GGT)	 AG	42226-42373	GT	AGG
(ACT)	 AG	44365-44532	GT	AGG
(GAC)	 AG	47181-47309	AC	AGA
-recovered pasa_asmbl_14086.p2, terminal, 47181, 47309
-recovered pasa_asmbl_14086.p2, internal, 41427, 41542
-recovered pasa_asmbl_14086.p2, internal, 41696, 41827
-recovered pasa_asmbl_14086.p2, internal, 42226, 42373
-recovered pasa_asmbl_14086.p2, internal, 44365, 44532
Valid prediction for GlimmerHMM_glimmerT_35848-T1
Valid prediction for snap_scaffold_15-snap.682-T1
Valid prediction for snap_scaffold_15-snap.695-T1
Valid prediction for GlimmerHMM_glimmerT_35864-T1
Valid prediction for Augustus_model.g23909.t1
Valid prediction for GlimmerHMM_glimmerT_35854-T1
Valid prediction for snap_scaffold_15-snap.692-T1
Valid prediction for GlimmerHMM_glimmerT_35867-T1
Valid prediction for GlimmerHMM_glimmerT_35862-T1
Valid prediction for snap_scaffold_15-snap.703-T1
Valid prediction for GlimmerHMM_glimmerT_35849-T1
Valid prediction for snap_scaffold_15-snap.708-T1
Valid prediction for GlimmerHMM_glimmerT_35868-T1
Valid prediction for snap_scaffold_15-snap.706-T1
Valid prediction for snap_scaffold_15-snap.716-T1
Valid prediction for GlimmerHMM_glimmerT_35852-T1
Valid prediction for GlimmerHMM_glimmerT_35857-T1
Valid prediction for HiQ_model.g23915.t1
Valid prediction for snap_scaffold_15-snap.699-T1
Valid prediction for GlimmerHMM_glimmerT_35851-T1
Valid prediction for GlimmerHMM_glimmerT_35853-T1
Valid prediction for snap_scaffold_15-snap.709-T1
Valid prediction for snap_scaffold_15-snap.693-T1
Valid prediction for snap_scaffold_15-snap.707-T1
Valid prediction for Augustus_model.g23910.t1
Valid prediction for CodingQuarry_transcript_17955-T1
Couldn't classify 36013, 36126
Sorry, prediction pasa_asmbl_14087.p1 fails validation.
(ATG)	 GC	32878-33274	GT	AGG
(CTG)	 AG	33623-33990	GT	AAG
(AAC)	 AG	34124-34281	GT	AGG
(GCT)	 AG	35290-35461	GT	AGG
(GAC)	 AG	35659-35907	GT	AGG
(TTC)	 AG	36013-36126	AC	GTA
-recovered pasa_asmbl_14087.p1, initial, 32878, 33274
-recovered pasa_asmbl_14087.p1, internal, 33623, 33990
-recovered pasa_asmbl_14087.p1, internal, 34124, 34281
-recovered pasa_asmbl_14087.p1, internal, 35290, 35461
-recovered pasa_asmbl_14087.p1, internal, 35659, 35907
Valid prediction for GlimmerHMM_glimmerT_35863-T1
Valid prediction for GlimmerHMM_glimmerT_35869-T1
Valid prediction for snap_scaffold_15-snap.680-T1
Couldn't classify 14863, 14973
Sorry, prediction pasa_asmbl_14095.p2 fails validation.
(ATG)	 AG	12908-13049	GT	TGG
(ACC)	 AG	13573-13694	GT	AGG
(TTG)	 AG	14198-14281	GT	TGG
(GTG)	 AG	14378-14461	GT	CTG
(TGG)	 AG	14863-14973	TG	GGT
-recovered pasa_asmbl_14095.p2, initial, 12908, 13049
-recovered pasa_asmbl_14095.p2, internal, 12908, 13049
-recovered pasa_asmbl_14095.p2, internal, 13573, 13694
-recovered pasa_asmbl_14095.p2, internal, 14198, 14281
-recovered pasa_asmbl_14095.p2, internal, 14378, 14461
Valid prediction for snap_scaffold_15-snap.689-T1
Valid prediction for snap_scaffold_15-snap.711-T1
Valid prediction for Augustus_model.g23914.t1
Valid prediction for Augustus_model.g23908.t1
Valid prediction for snap_scaffold_15-snap.710-T1
Valid prediction for GlimmerHMM_glimmerT_35843-T1
Valid prediction for snap_scaffold_15-snap.704-T1
Valid prediction for snap_scaffold_15-snap.714-T1
Valid prediction for Augustus_model.g23917.t1
Valid prediction for GlimmerHMM_glimmerT_35860-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 42052, rend_intergenic: 42049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28697, rend_intergenic: 14633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32203, rend_intergenic: 28906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51373, rend_intergenic: 45926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135811, rend_intergenic: 132326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194243, rend_intergenic: 189195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 200368
-exon list size: 257


building trellis

0.4    
0.8    
1.2    
1.5    
1.9    
2.3    
2.7    
3.1    
3.5    
3.9    
4.2    
4.6    
5.0    
5.4    
5.8    
6.2    
6.6    
6.9    
7.3    
7.7    
8.1    
8.5    
8.9    
9.3    
9.7    
10.0    
10.4    
10.8    
11.2    
11.6    
12.0    
12.4    
12.7    
13.1    
13.5    
13.9    
14.3    
14.7    
15.1    
15.4    
15.8    
16.2    
16.6    
17.0    
17.4    
17.8    
18.1    
18.5    
18.9    
19.3    
19.7    
20.1    
20.5    
20.8    
21.2    
21.6    
22.0    
22.4    
22.8    
23.2    
23.6    
23.9    
24.3    
24.7    
25.1    
25.5    
25.9    
26.3    
26.6    
27.0    
27.4    
27.8    
28.2    
28.6    
29.0    
29.3    
29.7    
30.1    
30.5    
30.9    
31.3    
31.7    
32.0    
32.4    
32.8    
33.2    
33.6    
34.0    
34.4    
34.7    
35.1    
35.5    
35.9    
36.3    
36.7    
37.1    
37.5    
37.8    
38.2    
38.6    
39.0    
39.4    
39.8    
40.2    
40.5    
40.9    
41.3    
41.7    
42.1    
42.5    
42.9    
43.2    
43.6    
44.0    
44.4    
44.8    
45.2    
45.6    
45.9    
46.3    
46.7    
47.1    
47.5    
47.9    
48.3    
48.6    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.4    
51.7    
52.1    
52.5    
52.9    
53.3    
53.7    
54.1    
54.4    
54.8    
55.2    
55.6    
56.0    
56.4    
56.8    
57.1    
57.5    
57.9    
58.3    
58.7    
59.1    
59.5    
59.8    
60.2    
60.6    
61.0    
61.4    
61.8    
62.2    
62.5    
62.9    
63.3    
63.7    
64.1    
64.5    
64.9    
65.3    
65.6    
66.0    
66.4    
66.8    
67.2    
67.6    
68.0    
68.3    
68.7    
69.1    
69.5    
69.9    
70.3    
70.7    
71.0    
71.4    
71.8    
72.2    
72.6    
73.0    
73.4    
73.7    
74.1    
74.5    
74.9    
75.3    
75.7    
76.1    
76.4    
76.8    
77.2    
77.6    
78.0    
78.4    
78.8    
79.2    
79.5    
79.9    
80.3    
80.7    
81.1    
81.5    
81.9    
82.2    
82.6    
83.0    
83.4    
83.8    
84.2    
84.6    
84.9    
85.3    
85.7    
86.1    
86.5    
86.9    
87.3    
87.6    
88.0    
88.4    
88.8    
89.2    
89.6    
90.0    
90.3    
90.7    
91.1    
91.5    
91.9    
92.3    
92.7    
93.1    
93.4    
93.8    
94.2    
94.6    
95.0    
95.4    
95.8    
96.1    
96.5    
96.9    
97.3    
97.7    
98.1    
98.5    
98.8    
99.2    
99.6    
-found 29 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 42052, rend_intergenic: 42049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28697, rend_intergenic: 14633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32203, rend_intergenic: 28906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51373, rend_intergenic: 45926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135811, rend_intergenic: 132326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194243, rend_intergenic: 189195  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