-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_17440378-17591676

-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.g5413.t1
Valid prediction for Augustus_model.g5404.t1
Valid prediction for GlimmerHMM_glimmerT_8198-T1
Valid prediction for Augustus_model.g5408.t1
Valid prediction for GlimmerHMM_glimmerT_8202-T1
Valid prediction for GlimmerHMM_glimmerT_8216-T1
Valid prediction for snap_scaffold_3-snap.3389-T1
Valid prediction for GlimmerHMM_glimmerT_8215-T1
Valid prediction for GlimmerHMM_glimmerT_8203-T1
Valid prediction for snap_scaffold_3-snap.3405-T1
Valid prediction for GlimmerHMM_glimmerT_8195-T1
Valid prediction for GlimmerHMM_glimmerT_8218-T1
Valid prediction for GlimmerHMM_glimmerT_8212-T1
Valid prediction for GlimmerHMM_glimmerT_8204-T1
Valid prediction for snap_scaffold_3-snap.3414-T1
Valid prediction for GlimmerHMM_glimmerT_8206-T1
Valid prediction for snap_scaffold_3-snap.3388-T1
Valid prediction for snap_scaffold_3-snap.3420-T1
Valid prediction for snap_scaffold_3-snap.3399-T1
Valid prediction for snap_scaffold_3-snap.3413-T1
Valid prediction for snap_scaffold_3-snap.3412-T1
Valid prediction for GlimmerHMM_glimmerT_8210-T1
Valid prediction for HiQ_model.g5411.t1
Valid prediction for CodingQuarry_transcript_46449-T1
Valid prediction for GlimmerHMM_glimmerT_8199-T1
Valid prediction for GlimmerHMM_glimmerT_8200-T1
Valid prediction for snap_scaffold_3-snap.3403-T1
Valid prediction for snap_scaffold_3-snap.3406-T1
Valid prediction for snap_scaffold_3-snap.3422-T1
Valid prediction for snap_scaffold_3-snap.3396-T1
Valid prediction for GlimmerHMM_glimmerT_8217-T1
Valid prediction for GlimmerHMM_glimmerT_8207-T1
Valid prediction for GlimmerHMM_glimmerT_8197-T1
Valid prediction for Augustus_model.g5414.t1
Valid prediction for snap_scaffold_3-snap.3392-T1
Valid prediction for CodingQuarry_transcript_46448-T1
Valid prediction for snap_scaffold_3-snap.3415-T1
Valid prediction for HiQ_model.g5403.t1
Valid prediction for snap_scaffold_3-snap.3394-T1
Valid prediction for snap_scaffold_3-snap.3402-T1
Valid prediction for pasa_asmbl_40685.p1
Valid prediction for snap_scaffold_3-snap.3409-T1
Valid prediction for Augustus_model.g5409.t1
Valid prediction for snap_scaffold_3-snap.3424-T1
Valid prediction for snap_scaffold_3-snap.3387-T1
Valid prediction for pasa_asmbl_40679.p2
Valid prediction for Augustus_model.g5406.t1
Valid prediction for CodingQuarry_transcript_46444-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_3-snap.3397-T1
Valid prediction for snap_scaffold_3-snap.3417-T1
Valid prediction for snap_scaffold_3-snap.3393-T1
Valid prediction for snap_scaffold_3-snap.3404-T1
Valid prediction for snap_scaffold_3-snap.3416-T1
Valid prediction for GlimmerHMM_glimmerT_8208-T1
Valid prediction for snap_scaffold_3-snap.3401-T1
Valid prediction for snap_scaffold_3-snap.3418-T1
Valid prediction for snap_scaffold_3-snap.3407-T1
Valid prediction for GlimmerHMM_glimmerT_8196-T1
Valid prediction for CodingQuarry_transcript_46450-T1
Valid prediction for GlimmerHMM_glimmerT_8209-T1
Valid prediction for snap_scaffold_3-snap.3395-T1
Valid prediction for Augustus_model.g5416.t1
Valid prediction for GlimmerHMM_glimmerT_8213-T1
Valid prediction for CodingQuarry_transcript_46451-T1
Valid prediction for snap_scaffold_3-snap.3410-T1
Valid prediction for snap_scaffold_3-snap.3400-T1
Couldn't classify 89198, 89215
Sorry, prediction pasa_asmbl_39565.p2 fails validation.
(ATG)	 AC	86222-86251	GT	GGG
(GAT)	 AG	86594-86655	GT	AGG
(GGT)	 AG	87795-87884	GT	AGG
(GGT)	 AG	88984-89083	GT	AGG
(CAT)	 AG	89198-89215	AT	AGA
-recovered pasa_asmbl_39565.p2, initial, 86222, 86251
-recovered pasa_asmbl_39565.p2, internal, 86594, 86655
-recovered pasa_asmbl_39565.p2, internal, 87795, 87884
-recovered pasa_asmbl_39565.p2, internal, 88984, 89083
Valid prediction for snap_scaffold_3-snap.3421-T1
Valid prediction for snap_scaffold_3-snap.3411-T1
Valid prediction for Augustus_model.g5405.t1
Valid prediction for GlimmerHMM_glimmerT_8214-T1
Valid prediction for snap_scaffold_3-snap.3391-T1
Valid prediction for snap_scaffold_3-snap.3408-T1
Valid prediction for snap_scaffold_3-snap.3398-T1
Valid prediction for GlimmerHMM_glimmerT_8219-T1
Valid prediction for snap_scaffold_3-snap.3386-T1
Couldn't classify 73790, 73898
Couldn't classify 76569, 76646
Sorry, prediction pasa_asmbl_39566.p1 fails validation.
(GCC)	 AT	73790-73898	GT	CGG
(GTC)	 AG	74015-74089	GT	AAG
(GCA)	 AG	75336-75407	GT	TGG
(GTG)	 AG	75633-75712	GT	TGG
(AAC)	 AG	76569-76646	CT	GAC
-recovered pasa_asmbl_39566.p1, internal, 74015, 74089
-recovered pasa_asmbl_39566.p1, internal, 75336, 75407
-recovered pasa_asmbl_39566.p1, internal, 75633, 75712
Valid prediction for pasa_asmbl_39571.p1
Valid prediction for HiQ_model.g5412.t1
Valid prediction for GlimmerHMM_glimmerT_8220-T1
Valid prediction for GlimmerHMM_glimmerT_8211-T1
Valid prediction for snap_scaffold_3-snap.3390-T1
Valid prediction for snap_scaffold_3-snap.3423-T1
Valid prediction for GlimmerHMM_glimmerT_8205-T1
Valid prediction for Augustus_model.g5410.t1
Valid prediction for snap_scaffold_3-snap.3419-T1
Valid prediction for Augustus_model.g5407.t1
Valid prediction for Augustus_model.g5402.t1
Valid prediction for GlimmerHMM_glimmerT_8201-T1
Valid prediction for Augustus_model.g5415.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7052, rend_intergenic: 2278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29028, rend_intergenic: 28588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30615, rend_intergenic: 29185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32702, rend_intergenic: 31493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43824, rend_intergenic: 39241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44679, rend_intergenic: 44301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47972, rend_intergenic: 45676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67202, rend_intergenic: 59163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74225, rend_intergenic: 70920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80074, rend_intergenic: 75474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139143, rend_intergenic: 137780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142112, rend_intergenic: 140934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 151299
-exon list size: 300


building trellis

0.3    
0.7    
1.0    
1.3    
1.7    
2.0    
2.3    
2.6    
3.0    
3.3    
3.6    
4.0    
4.3    
4.6    
5.0    
5.3    
5.6    
6.0    
6.3    
6.6    
7.0    
7.3    
7.6    
7.9    
8.3    
8.6    
8.9    
9.3    
9.6    
9.9    
10.3    
10.6    
10.9    
11.3    
11.6    
11.9    
12.3    
12.6    
12.9    
13.2    
13.6    
13.9    
14.2    
14.6    
14.9    
15.2    
15.6    
15.9    
16.2    
16.6    
16.9    
17.2    
17.5    
17.9    
18.2    
18.5    
18.9    
19.2    
19.5    
19.9    
20.2    
20.5    
20.9    
21.2    
21.5    
21.9    
22.2    
22.5    
22.8    
23.2    
23.5    
23.8    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.2    
26.5    
26.8    
27.2    
27.5    
27.8    
28.1    
28.5    
28.8    
29.1    
29.5    
29.8    
30.1    
30.5    
30.8    
31.1    
31.5    
31.8    
32.1    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.8    
35.1    
35.4    
35.8    
36.1    
36.4    
36.8    
37.1    
37.4    
37.7    
38.1    
38.4    
38.7    
39.1    
39.4    
39.7    
40.1    
40.4    
40.7    
41.1    
41.4    
41.7    
42.1    
42.4    
42.7    
43.0    
43.4    
43.7    
44.0    
44.4    
44.7    
45.0    
45.4    
45.7    
46.0    
46.4    
46.7    
47.0    
47.4    
47.7    
48.0    
48.3    
48.7    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.3    
51.7    
52.0    
52.3    
52.6    
53.0    
53.3    
53.6    
54.0    
54.3    
54.6    
55.0    
55.3    
55.6    
56.0    
56.3    
56.6    
57.0    
57.3    
57.6    
57.9    
58.3    
58.6    
58.9    
59.3    
59.6    
59.9    
60.3    
60.6    
60.9    
61.3    
61.6    
61.9    
62.3    
62.6    
62.9    
63.2    
63.6    
63.9    
64.2    
64.6    
64.9    
65.2    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.9    
68.2    
68.5    
68.9    
69.2    
69.5    
69.9    
70.2    
70.5    
70.9    
71.2    
71.5    
71.9    
72.2    
72.5    
72.8    
73.2    
73.5    
73.8    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.2    
76.5    
76.8    
77.2    
77.5    
77.8    
78.1    
78.5    
78.8    
79.1    
79.5    
79.8    
80.1    
80.5    
80.8    
81.1    
81.5    
81.8    
82.1    
82.5    
82.8    
83.1    
83.4    
83.8    
84.1    
84.4    
84.8    
85.1    
85.4    
85.8    
86.1    
86.4    
86.8    
87.1    
87.4    
87.7    
88.1    
88.4    
88.7    
89.1    
89.4    
89.7    
90.1    
90.4    
90.7    
91.1    
91.4    
91.7    
92.1    
92.4    
92.7    
93.0    
93.4    
93.7    
94.0    
94.4    
94.7    
95.0    
95.4    
95.7    
96.0    
96.4    
96.7    
97.0    
97.4    
97.7    
98.0    
98.3    
98.7    
99.0    
99.3    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 7052, rend_intergenic: 2278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29028, rend_intergenic: 28588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30615, rend_intergenic: 29185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32702, rend_intergenic: 31493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43824, rend_intergenic: 39241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44679, rend_intergenic: 44301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47972, rend_intergenic: 45676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67202, rend_intergenic: 59163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74225, rend_intergenic: 70920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80074, rend_intergenic: 75474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139143, rend_intergenic: 137780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142112, rend_intergenic: 140934  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