-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_3789316-3952947

-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 Augustus_model.g9542.t1
Valid prediction for GlimmerHMM_glimmerT_14412-T1
Valid prediction for snap_scaffold_6-snap.923-T1
Valid prediction for snap_scaffold_6-snap.911-T1
Valid prediction for GlimmerHMM_glimmerT_14397-T1
Valid prediction for snap_scaffold_6-snap.908-T1
Valid prediction for pasa_asmbl_46868.p1
Valid prediction for GlimmerHMM_glimmerT_14421-T1
Valid prediction for CodingQuarry_transcript_54997-T1
Valid prediction for GlimmerHMM_glimmerT_14411-T1
Valid prediction for snap_scaffold_6-snap.905-T1
Valid prediction for HiQ_model.g9535.t1
Valid prediction for GlimmerHMM_glimmerT_14391-T1
Valid prediction for Augustus_model.g9548.t1
Valid prediction for HiQ_model.g9536.t1
Valid prediction for GlimmerHMM_glimmerT_14417-T1
Valid prediction for GlimmerHMM_glimmerT_14403-T1
Valid prediction for Augustus_model.g9549.t1
Valid prediction for CodingQuarry_transcript_54995-T1
Valid prediction for Augustus_model.g9546.t1
Valid prediction for Augustus_model.g9544.t1
Valid prediction for GlimmerHMM_glimmerT_14401-T1
Valid prediction for Augustus_model.g9541.t1
Valid prediction for CodingQuarry_transcript_55000-T1
Valid prediction for snap_scaffold_6-snap.921-T1
Couldn't classify 29448, 29606
Sorry, prediction pasa_asmbl_46872.p1 fails validation.
(CCC)	 CC	29448-29606	GT	AGG
(CCC)	 AG	29690-29773	GT	AGG
(GTT)	 AG	29983-30117	GT	AGG
(GCT)	 AG	30673-30781	GT	AGG
(GGG)	 AG	31699-31784	GT	AGG
(GTG)	 AG	31890-32006	GT	CGG
(GAG)	 AG	32103-32280	GT	AGG
(ATG)	 AG	32429-32484	CA	GAC
-recovered pasa_asmbl_46872.p1, terminal, 32429, 32484
-recovered pasa_asmbl_46872.p1, internal, 29690, 29773
-recovered pasa_asmbl_46872.p1, internal, 29983, 30117
-recovered pasa_asmbl_46872.p1, internal, 30673, 30781
-recovered pasa_asmbl_46872.p1, internal, 31699, 31784
-recovered pasa_asmbl_46872.p1, internal, 31890, 32006
-recovered pasa_asmbl_46872.p1, internal, 32103, 32280
Valid prediction for HiQ_model.g9538.t1
Valid prediction for snap_scaffold_6-snap.906-T1
Valid prediction for pasa_asmbl_46861.p1
Valid prediction for GlimmerHMM_glimmerT_14418-T1
Valid prediction for pasa_asmbl_46859.p1
Valid prediction for CodingQuarry_transcript_54996-T1
Valid prediction for GlimmerHMM_glimmerT_14406-T1
Valid prediction for snap_scaffold_6-snap.920-T1
Valid prediction for snap_scaffold_6-snap.902-T1
Valid prediction for snap_scaffold_6-snap.912-T1
Valid prediction for GlimmerHMM_glimmerT_14402-T1
Valid prediction for Augustus_model.g9539.t1
Valid prediction for snap_scaffold_6-snap.922-T1
Valid prediction for snap_scaffold_6-snap.915-T1
Valid prediction for snap_scaffold_6-snap.894-T1
Valid prediction for GlimmerHMM_glimmerT_14404-T1
Valid prediction for snap_scaffold_6-snap.914-T1
Valid prediction for snap_scaffold_6-snap.895-T1
Valid prediction for GlimmerHMM_glimmerT_14413-T1
Valid prediction for snap_scaffold_6-snap.926-T1
Valid prediction for GlimmerHMM_glimmerT_14392-T1
Valid prediction for snap_scaffold_6-snap.898-T1
Valid prediction for GlimmerHMM_glimmerT_14419-T1
Valid prediction for snap_scaffold_6-snap.900-T1
Valid prediction for Augustus_model.g9547.t1
Couldn't classify 28656, 29384
Sorry, prediction pasa_asmbl_46870.p1 fails validation.
(ATG)	 CA	28335-28349	GT	TGG
(CAA)	 AG	28494-28547	GT	AGG
(GAT)	 AG	28656-29384	CG	GGC
-recovered pasa_asmbl_46870.p1, initial, 28335, 28349
-recovered pasa_asmbl_46870.p1, internal, 28494, 28547
Valid prediction for CodingQuarry_transcript_54994-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.924-T1
Valid prediction for GlimmerHMM_glimmerT_14410-T1
Valid prediction for GlimmerHMM_glimmerT_14408-T1
Valid prediction for CodingQuarry_transcript_54999-T1
Valid prediction for snap_scaffold_6-snap.925-T1
Valid prediction for GlimmerHMM_glimmerT_14394-T1
Valid prediction for Augustus_model.g9545.t1
Valid prediction for snap_scaffold_6-snap.909-T1
Valid prediction for snap_scaffold_6-snap.896-T1
Valid prediction for GlimmerHMM_glimmerT_14393-T1
Valid prediction for CodingQuarry_transcript_54998-T1
Valid prediction for GlimmerHMM_glimmerT_14415-T1
Valid prediction for snap_scaffold_6-snap.907-T1
Valid prediction for GlimmerHMM_glimmerT_14398-T1
Valid prediction for snap_scaffold_6-snap.910-T1
Valid prediction for snap_scaffold_6-snap.919-T1
Valid prediction for snap_scaffold_6-snap.903-T1
Valid prediction for snap_scaffold_6-snap.899-T1
Valid prediction for snap_scaffold_6-snap.897-T1
Couldn't classify 138660, 138754
Sorry, prediction pasa_asmbl_48281.p1 fails validation.
(TTA)	 GT	138660-138754	GT	AGG
(GTC)	 AG	139381-139998	GT	AGG
(CAA)	 AG	140138-140519	GA	GAG
-recovered pasa_asmbl_48281.p1, terminal, 140138, 140519
-recovered pasa_asmbl_48281.p1, internal, 139381, 139998
Valid prediction for GlimmerHMM_glimmerT_14407-T1
Valid prediction for GlimmerHMM_glimmerT_14399-T1
Valid prediction for GlimmerHMM_glimmerT_14396-T1
Valid prediction for Augustus_model.g9540.t1
Valid prediction for snap_scaffold_6-snap.916-T1
Valid prediction for snap_scaffold_6-snap.904-T1
Valid prediction for snap_scaffold_6-snap.913-T1
Valid prediction for snap_scaffold_6-snap.918-T1
Valid prediction for GlimmerHMM_glimmerT_14409-T1
Valid prediction for snap_scaffold_6-snap.927-T1
Valid prediction for GlimmerHMM_glimmerT_14414-T1
Valid prediction for GlimmerHMM_glimmerT_14416-T1
Valid prediction for pasa_asmbl_48283.p1
Valid prediction for Augustus_model.g9543.t1
Valid prediction for GlimmerHMM_glimmerT_14405-T1
Valid prediction for snap_scaffold_6-snap.901-T1
Valid prediction for Augustus_model.g9537.t1
Valid prediction for GlimmerHMM_glimmerT_14420-T1
Valid prediction for GlimmerHMM_glimmerT_14395-T1
Valid prediction for snap_scaffold_6-snap.917-T1
Valid prediction for GlimmerHMM_glimmerT_14400-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 32484, rend_intergenic: 29992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43857, rend_intergenic: 39494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51430, rend_intergenic: 47523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70458, rend_intergenic: 51459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76053, rend_intergenic: 73921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87194, rend_intergenic: 82320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91833, rend_intergenic: 88200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147517, rend_intergenic: 146481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 163632
-exon list size: 312


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.2    
2.5    
2.9    
3.2    
3.5    
3.8    
4.1    
4.5    
4.8    
5.1    
5.4    
5.7    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
8.0    
8.3    
8.6    
8.9    
9.2    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.5    
11.8    
12.1    
12.4    
12.7    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
15.0    
15.3    
15.6    
15.9    
16.2    
16.6    
16.9    
17.2    
17.5    
17.8    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
20.1    
20.4    
20.7    
21.0    
21.3    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.6    
23.9    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.1    
26.4    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.7    
29.0    
29.3    
29.6    
29.9    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.2    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.0    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.3    
37.6    
37.9    
38.2    
38.5    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.8    
41.1    
41.4    
41.7    
42.0    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.3    
44.6    
44.9    
45.2    
45.5    
45.9    
46.2    
46.5    
46.8    
47.1    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.4    
49.7    
50.0    
50.3    
50.6    
51.0    
51.3    
51.6    
51.9    
52.2    
52.5    
52.9    
53.2    
53.5    
53.8    
54.1    
54.5    
54.8    
55.1    
55.4    
55.7    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
58.0    
58.3    
58.6    
58.9    
59.2    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.5    
61.8    
62.1    
62.4    
62.7    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
65.0    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.8    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.1    
70.4    
70.7    
71.0    
71.3    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.6    
73.9    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.1    
76.4    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.7    
79.0    
79.3    
79.6    
79.9    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.2    
82.5    
82.8    
83.1    
83.4    
83.8    
84.1    
84.4    
84.7    
85.0    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.3    
87.6    
87.9    
88.2    
88.5    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.8    
91.1    
91.4    
91.7    
92.0    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.3    
94.6    
94.9    
95.2    
95.5    
95.9    
96.2    
96.5    
96.8    
97.1    
97.5    
97.8    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 32484, rend_intergenic: 29992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43857, rend_intergenic: 39494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51430, rend_intergenic: 47523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70458, rend_intergenic: 51459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76053, rend_intergenic: 73921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87194, rend_intergenic: 82320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91833, rend_intergenic: 88200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147517, rend_intergenic: 146481  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