-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_3711734-3852040

-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.g5864.t1
Valid prediction for snap_scaffold_4-snap.856-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.869-T1
Valid prediction for snap_scaffold_4-snap.883-T1
Valid prediction for GlimmerHMM_glimmerT_9136-T1
Valid prediction for snap_scaffold_4-snap.874-T1
Valid prediction for snap_scaffold_4-snap.863-T1
Valid prediction for GlimmerHMM_glimmerT_9135-T1
Valid prediction for GlimmerHMM_glimmerT_9154-T1
Valid prediction for GlimmerHMM_glimmerT_9148-T1
Valid prediction for snap_scaffold_4-snap.887-T1
Valid prediction for GlimmerHMM_glimmerT_9145-T1
Couldn't classify 126541, 126691
Sorry, prediction pasa_asmbl_41203.p1 fails validation.
(CAT)	 GG	126541-126691	GT	AGG
(CCT)	 AG	127343-127429	GT	AAG
(GTT)	 AG	127808-127901	GT	AGG
(AAG)	 AG	128100-128140	GT	AGG
(GCT)	 AG	128245-128352	GT	CGG
(ACT)	 AG	130056-130492	CC	GAC
-recovered pasa_asmbl_41203.p1, terminal, 130056, 130492
-recovered pasa_asmbl_41203.p1, internal, 127343, 127429
-recovered pasa_asmbl_41203.p1, internal, 127808, 127901
-recovered pasa_asmbl_41203.p1, internal, 128100, 128140
-recovered pasa_asmbl_41203.p1, internal, 128245, 128352
Valid prediction for snap_scaffold_4-snap.859-T1
Valid prediction for snap_scaffold_4-snap.870-T1
Valid prediction for snap_scaffold_4-snap.875-T1
Valid prediction for GlimmerHMM_glimmerT_9139-T1
Valid prediction for snap_scaffold_4-snap.857-T1
Valid prediction for snap_scaffold_4-snap.880-T1
Valid prediction for snap_scaffold_4-snap.884-T1
Valid prediction for snap_scaffold_4-snap.864-T1
Valid prediction for snap_scaffold_4-snap.878-T1
Valid prediction for GlimmerHMM_glimmerT_9150-T1
Couldn't classify 122966, 123011
Couldn't classify 126269, 126282
Sorry, prediction pasa_asmbl_41202.p1 fails validation.
(TCA)	 GT	122966-123011	GT	AGG
(ATC)	 AG	124673-124724	GT	AGG
(CGT)	 AG	124814-124886	GT	ACG
(ACC)	 AG	125320-125453	GT	ATG
(GGG)	 AG	125775-125812	GT	AGG
(AGT)	 AG	125958-126152	GT	AGG
(GGA)	 AG	126269-126282	GG	GCG
-recovered pasa_asmbl_41202.p1, internal, 124673, 124724
-recovered pasa_asmbl_41202.p1, internal, 124814, 124886
-recovered pasa_asmbl_41202.p1, internal, 125320, 125453
-recovered pasa_asmbl_41202.p1, internal, 125775, 125812
-recovered pasa_asmbl_41202.p1, internal, 125958, 126152
Valid prediction for GlimmerHMM_glimmerT_9143-T1
Valid prediction for GlimmerHMM_glimmerT_9156-T1
Valid prediction for Augustus_model.g5870.t1
Valid prediction for snap_scaffold_4-snap.876-T1
Valid prediction for GlimmerHMM_glimmerT_9152-T1
Valid prediction for Augustus_model.g5867.t1
Valid prediction for Augustus_model.g5873.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_4-snap.882-T1
Valid prediction for GlimmerHMM_glimmerT_9138-T1
Valid prediction for snap_scaffold_4-snap.862-T1
Valid prediction for snap_scaffold_4-snap.877-T1
Valid prediction for snap_scaffold_4-snap.889-T1
Valid prediction for snap_scaffold_4-snap.865-T1
Valid prediction for snap_scaffold_4-snap.871-T1
Valid prediction for snap_scaffold_4-snap.867-T1
Valid prediction for Augustus_model.g5859.t1
Valid prediction for GlimmerHMM_glimmerT_9144-T1
Valid prediction for GlimmerHMM_glimmerT_9141-T1
Valid prediction for snap_scaffold_4-snap.881-T1
Valid prediction for GlimmerHMM_glimmerT_9134-T1
Valid prediction for snap_scaffold_4-snap.873-T1
Valid prediction for Augustus_model.g5865.t1
Valid prediction for GlimmerHMM_glimmerT_9149-T1
Valid prediction for snap_scaffold_4-snap.866-T1
Valid prediction for snap_scaffold_4-snap.879-T1
Valid prediction for Augustus_model.g5872.t1
Valid prediction for snap_scaffold_4-snap.888-T1
Valid prediction for snap_scaffold_4-snap.872-T1
Valid prediction for GlimmerHMM_glimmerT_9155-T1
Valid prediction for GlimmerHMM_glimmerT_9147-T1
Valid prediction for snap_scaffold_4-snap.861-T1
Valid prediction for GlimmerHMM_glimmerT_9142-T1
Valid prediction for snap_scaffold_4-snap.885-T1
Valid prediction for GlimmerHMM_glimmerT_9151-T1
Valid prediction for Augustus_model.g5874.t1
Valid prediction for Augustus_model.g5869.t1
Valid prediction for GlimmerHMM_glimmerT_9140-T1
Valid prediction for snap_scaffold_4-snap.868-T1
Valid prediction for Augustus_model.g5861.t1
Valid prediction for GlimmerHMM_glimmerT_9153-T1
Valid prediction for snap_scaffold_4-snap.886-T1
Valid prediction for GlimmerHMM_glimmerT_9146-T1
Valid prediction for Augustus_model.g5860.t1
Valid prediction for Augustus_model.g5862.t1
Valid prediction for snap_scaffold_4-snap.855-T1
Valid prediction for snap_scaffold_4-snap.858-T1
Valid prediction for Augustus_model.g5871.t1
Valid prediction for GlimmerHMM_glimmerT_9157-T1
Valid prediction for snap_scaffold_4-snap.860-T1
Valid prediction for Augustus_model.g5863.t1
Valid prediction for Augustus_model.g5868.t1
Valid prediction for Augustus_model.g5866.t1
Valid prediction for GlimmerHMM_glimmerT_9137-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18515, rend_intergenic: 13725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21112, rend_intergenic: 18935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33291, rend_intergenic: 30715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56931, rend_intergenic: 55485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65630, rend_intergenic: 61856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88342, rend_intergenic: 84682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89613, rend_intergenic: 88579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94001, rend_intergenic: 90022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106445, rend_intergenic: 100218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124124, rend_intergenic: 120710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 84855, rend_intergenic: 84852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 140307
-exon list size: 304


building trellis

0.3    
0.7    
1.0    
1.3    
1.6    
2.0    
2.3    
2.6    
2.9    
3.3    
3.6    
3.9    
4.2    
4.6    
4.9    
5.2    
5.6    
5.9    
6.2    
6.5    
6.9    
7.2    
7.5    
7.8    
8.2    
8.5    
8.8    
9.2    
9.5    
9.8    
10.1    
10.5    
10.8    
11.1    
11.4    
11.8    
12.1    
12.4    
12.7    
13.1    
13.4    
13.7    
14.1    
14.4    
14.7    
15.0    
15.4    
15.7    
16.0    
16.3    
16.7    
17.0    
17.3    
17.6    
18.0    
18.3    
18.6    
19.0    
19.3    
19.6    
19.9    
20.3    
20.6    
20.9    
21.2    
21.6    
21.9    
22.2    
22.5    
22.9    
23.2    
23.5    
23.9    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.1    
26.5    
26.8    
27.1    
27.5    
27.8    
28.1    
28.4    
28.8    
29.1    
29.4    
29.7    
30.1    
30.4    
30.7    
31.0    
31.4    
31.7    
32.0    
32.4    
32.7    
33.0    
33.3    
33.7    
34.0    
34.3    
34.6    
35.0    
35.3    
35.6    
35.9    
36.3    
36.6    
36.9    
37.3    
37.6    
37.9    
38.2    
38.6    
38.9    
39.2    
39.5    
39.9    
40.2    
40.5    
40.8    
41.2    
41.5    
41.8    
42.2    
42.5    
42.8    
43.1    
43.5    
43.8    
44.1    
44.4    
44.8    
45.1    
45.4    
45.8    
46.1    
46.4    
46.7    
47.1    
47.4    
47.7    
48.0    
48.4    
48.7    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.3    
51.6    
52.0    
52.3    
52.6    
52.9    
53.3    
53.6    
53.9    
54.2    
54.6    
54.9    
55.2    
55.6    
55.9    
56.2    
56.5    
56.9    
57.2    
57.5    
57.8    
58.2    
58.5    
58.8    
59.2    
59.5    
59.8    
60.1    
60.5    
60.8    
61.1    
61.4    
61.8    
62.1    
62.4    
62.7    
63.1    
63.4    
63.7    
64.1    
64.4    
64.7    
65.0    
65.4    
65.7    
66.0    
66.3    
66.7    
67.0    
67.3    
67.6    
68.0    
68.3    
68.6    
69.0    
69.3    
69.6    
69.9    
70.3    
70.6    
70.9    
71.2    
71.6    
71.9    
72.2    
72.5    
72.9    
73.2    
73.5    
73.9    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.1    
76.5    
76.8    
77.1    
77.5    
77.8    
78.1    
78.4    
78.8    
79.1    
79.4    
79.7    
80.1    
80.4    
80.7    
81.0    
81.4    
81.7    
82.0    
82.4    
82.7    
83.0    
83.3    
83.7    
84.0    
84.3    
84.6    
85.0    
85.3    
85.6    
85.9    
86.3    
86.6    
86.9    
87.3    
87.6    
87.9    
88.2    
88.6    
88.9    
89.2    
89.5    
89.9    
90.2    
90.5    
90.8    
91.2    
91.5    
91.8    
92.2    
92.5    
92.8    
93.1    
93.5    
93.8    
94.1    
94.4    
94.8    
95.1    
95.4    
95.8    
96.1    
96.4    
96.7    
97.1    
97.4    
97.7    
98.0    
98.4    
98.7    
99.0    
99.3    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 18515, rend_intergenic: 13725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21112, rend_intergenic: 18935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33291, rend_intergenic: 30715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56931, rend_intergenic: 55485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65630, rend_intergenic: 61856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88342, rend_intergenic: 84682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89613, rend_intergenic: 88579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94001, rend_intergenic: 90022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106445, rend_intergenic: 100218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124124, rend_intergenic: 120710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 84855, rend_intergenic: 84852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support