-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_1-141708

-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.g7392.t1
Valid prediction for GlimmerHMM_glimmerT_11307-T1
Valid prediction for CodingQuarry_transcript_51956-T1
Valid prediction for snap_scaffold_5-snap.6-T1
Valid prediction for CodingQuarry_transcript_51955-T1
Couldn't classify 63119, 63189
Sorry, prediction pasa_asmbl_45063.p1 fails validation.
(ATG)	 GG	58414-58527	GT	AGG
(GTG)	 AG	60221-60313	GT	AGG
(GGC)	 AG	60973-61100	GT	ACG
(GCA)	 AG	61622-61712	GC	AGG
(GTG)	 AG	61932-62049	GT	AGG
(ATG)	 AG	63119-63189	AG	AAA
-recovered pasa_asmbl_45063.p1, initial, 58414, 58527
-recovered pasa_asmbl_45063.p1, internal, 60221, 60313
-recovered pasa_asmbl_45063.p1, internal, 60973, 61100
-recovered pasa_asmbl_45063.p1, internal, 61622, 61712
-recovered pasa_asmbl_45063.p1, internal, 61932, 62049
Valid prediction for GlimmerHMM_glimmerT_11310-T1
Valid prediction for pasa_asmbl_45076.p1
Valid prediction for snap_scaffold_5-snap.11-T1
Valid prediction for Augustus_model.g7391.t1
Valid prediction for GlimmerHMM_glimmerT_11303-T1
Valid prediction for GlimmerHMM_glimmerT_11299-T1
Valid prediction for GlimmerHMM_glimmerT_11297-T1
Valid prediction for GlimmerHMM_glimmerT_11296-T1
Valid prediction for pasa_asmbl_45069.p1
Valid prediction for snap_scaffold_5-snap.18-T1
Valid prediction for snap_scaffold_5-snap.9-T1
Valid prediction for Augustus_model.g7400.t1
Valid prediction for snap_scaffold_5-snap.14-T1
Valid prediction for snap_scaffold_5-snap.15-T1
Valid prediction for GlimmerHMM_glimmerT_11302-T1
Valid prediction for GlimmerHMM_glimmerT_11300-T1
Valid prediction for Augustus_model.g7390.t1
Valid prediction for snap_scaffold_5-snap.7-T1
Valid prediction for GlimmerHMM_glimmerT_11304-T1
Valid prediction for Augustus_model.g7396.t1
Valid prediction for snap_scaffold_5-snap.12-T1
Valid prediction for GlimmerHMM_glimmerT_11294-T1
add_exon() Sorry, GlimmerHMM_glimmerT_11294-T1 5031-5548-terminal-1 is invalid.
Valid prediction for HiQ_model.g7395.t1
Valid prediction for snap_scaffold_5-snap.27-T1
Valid prediction for GlimmerHMM_glimmerT_11311-T1
Valid prediction for snap_scaffold_5-snap.2-T1
Couldn't classify 136997, 137107
Sorry, prediction pasa_asmbl_45072.p1 fails validation.
(ATG)	 CC	131738-132163	GT	AGG
(GTG)	 AG	134540-134622	GT	AAG
(GTA)	 AG	136010-136166	GT	ACG
(GAA)	 AG	136526-136690	GT	AGG
(ATC)	 AG	136997-137107	TC	AGT
-recovered pasa_asmbl_45072.p1, initial, 131738, 132163
-recovered pasa_asmbl_45072.p1, internal, 134540, 134622
-recovered pasa_asmbl_45072.p1, internal, 136010, 136166
-recovered pasa_asmbl_45072.p1, internal, 136526, 136690
Valid prediction for snap_scaffold_5-snap.23-T1
Valid prediction for GlimmerHMM_glimmerT_11295-T1
Valid prediction for snap_scaffold_5-snap.4-T1
Valid prediction for snap_scaffold_5-snap.25-T1
Valid prediction for HiQ_model.g7394.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 GlimmerHMM_glimmerT_11309-T1
Couldn't classify 28417, 28887
Sorry, prediction pasa_asmbl_43755.p1 fails validation.
(ATC)	 AG	28417-28887	GT	AGG
(GTG)	 AG	30513-30721	GT	AAG
(GTA)	 AG	31405-31465	GT	AGG
(GAT)	 AG	31618-31713	GT	AGG
(GAG)	 AG	32121-32285	GT	AGG
(TAT)	 AG	32558-32683	GT	AGG
(CGG)	 AG	33065-33285	GT	AGG
(GCT)	 AG	33500-33543	GT	CAG
(CGG)	 AG	33899-34173	GG	GAG
-recovered pasa_asmbl_43755.p1, terminal, 33899, 34173
-recovered pasa_asmbl_43755.p1, internal, 28417, 28887
-recovered pasa_asmbl_43755.p1, internal, 30513, 30721
-recovered pasa_asmbl_43755.p1, internal, 31405, 31465
-recovered pasa_asmbl_43755.p1, internal, 31618, 31713
-recovered pasa_asmbl_43755.p1, internal, 32121, 32285
-recovered pasa_asmbl_43755.p1, internal, 32558, 32683
-recovered pasa_asmbl_43755.p1, internal, 33065, 33285
-recovered pasa_asmbl_43755.p1, internal, 33500, 33543
Valid prediction for snap_scaffold_5-snap.28-T1
Valid prediction for GlimmerHMM_glimmerT_11298-T1
Valid prediction for Augustus_model.g7399.t1
Valid prediction for snap_scaffold_5-snap.22-T1
Valid prediction for Augustus_model.g7397.t1
Valid prediction for GlimmerHMM_glimmerT_11308-T1
Valid prediction for Augustus_model.g7398.t1
Valid prediction for snap_scaffold_5-snap.17-T1
Valid prediction for HiQ_model.g7393.t1
Valid prediction for GlimmerHMM_glimmerT_11305-T1
Valid prediction for GlimmerHMM_glimmerT_11301-T1
Valid prediction for snap_scaffold_5-snap.1-T1
Valid prediction for snap_scaffold_5-snap.5-T1
Valid prediction for GlimmerHMM_glimmerT_11306-T1
Valid prediction for snap_scaffold_5-snap.20-T1
Valid prediction for snap_scaffold_5-snap.24-T1
Valid prediction for snap_scaffold_5-snap.19-T1
Valid prediction for pasa_asmbl_43749.p1
Valid prediction for snap_scaffold_5-snap.3-T1
Valid prediction for snap_scaffold_5-snap.16-T1
Valid prediction for snap_scaffold_5-snap.13-T1
Valid prediction for snap_scaffold_5-snap.26-T1
Valid prediction for snap_scaffold_5-snap.8-T1
Couldn't classify 40709, 41026
Sorry, prediction pasa_asmbl_45027.p1 fails validation.
(ATG)	 TC	40709-41026	GG	GTG
Valid prediction for CodingQuarry_transcript_51954-T1
Valid prediction for snap_scaffold_5-snap.21-T1
Valid prediction for snap_scaffold_5-snap.10-T1
Couldn't classify 41009, 41257
Sorry, prediction pasa_asmbl_43752.p1 fails validation.
(GGT)	 TC	41009-41257	GT	AGG
(GTG)	 AG	42932-43140	GT	AAG
(ATA)	 AG	43226-43286	GT	AGG
(GAT)	 AG	43405-43500	GT	CGG
(GAG)	 AG	43721-43885	GT	AGG
(TTT)	 AG	44116-44241	GT	AGG
(CGG)	 AG	44452-44672	GT	AGG
(GAT)	 AG	44884-44954	GT	TGG
(GCT)	 AG	45135-45385	AT	AAA
-recovered pasa_asmbl_43752.p1, terminal, 45135, 45385
-recovered pasa_asmbl_43752.p1, internal, 42932, 43140
-recovered pasa_asmbl_43752.p1, internal, 43226, 43286
-recovered pasa_asmbl_43752.p1, internal, 43405, 43500
-recovered pasa_asmbl_43752.p1, internal, 43721, 43885
-recovered pasa_asmbl_43752.p1, internal, 44116, 44241
-recovered pasa_asmbl_43752.p1, internal, 44452, 44672
-recovered pasa_asmbl_43752.p1, internal, 44884, 44954

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13723, rend_intergenic: 2590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31007, rend_intergenic: 14548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42840, rend_intergenic: 34928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51140, rend_intergenic: 47333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56169, rend_intergenic: 52710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64884, rend_intergenic: 58414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72834, rend_intergenic: 69710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78047, rend_intergenic: 74522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89916, rend_intergenic: 78180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104190, rend_intergenic: 103482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109155, rend_intergenic: 107536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120774, rend_intergenic: 111105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125252, rend_intergenic: 122268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139326, rend_intergenic: 127466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 141708
-exon list size: 291


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.0    
2.4    
2.7    
3.1    
3.4    
3.8    
4.1    
4.4    
4.8    
5.1    
5.5    
5.8    
6.1    
6.5    
6.8    
7.2    
7.5    
7.8    
8.2    
8.5    
8.9    
9.2    
9.6    
9.9    
10.2    
10.6    
10.9    
11.3    
11.6    
11.9    
12.3    
12.6    
13.0    
13.3    
13.7    
14.0    
14.3    
14.7    
15.0    
15.4    
15.7    
16.0    
16.4    
16.7    
17.1    
17.4    
17.7    
18.1    
18.4    
18.8    
19.1    
19.5    
19.8    
20.1    
20.5    
20.8    
21.2    
21.5    
21.8    
22.2    
22.5    
22.9    
23.2    
23.5    
23.9    
24.2    
24.6    
24.9    
25.3    
25.6    
25.9    
26.3    
26.6    
27.0    
27.3    
27.6    
28.0    
28.3    
28.7    
29.0    
29.4    
29.7    
30.0    
30.4    
30.7    
31.1    
31.4    
31.7    
32.1    
32.4    
32.8    
33.1    
33.4    
33.8    
34.1    
34.5    
34.8    
35.2    
35.5    
35.8    
36.2    
36.5    
36.9    
37.2    
37.5    
37.9    
38.2    
38.6    
38.9    
39.2    
39.6    
39.9    
40.3    
40.6    
41.0    
41.3    
41.6    
42.0    
42.3    
42.7    
43.0    
43.3    
43.7    
44.0    
44.4    
44.7    
45.1    
45.4    
45.7    
46.1    
46.4    
46.8    
47.1    
47.4    
47.8    
48.1    
48.5    
48.8    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.2    
51.5    
51.9    
52.2    
52.6    
52.9    
53.2    
53.6    
53.9    
54.3    
54.6    
54.9    
55.3    
55.6    
56.0    
56.3    
56.7    
57.0    
57.3    
57.7    
58.0    
58.4    
58.7    
59.0    
59.4    
59.7    
60.1    
60.4    
60.8    
61.1    
61.4    
61.8    
62.1    
62.5    
62.8    
63.1    
63.5    
63.8    
64.2    
64.5    
64.8    
65.2    
65.5    
65.9    
66.2    
66.6    
66.9    
67.2    
67.6    
67.9    
68.3    
68.6    
68.9    
69.3    
69.6    
70.0    
70.3    
70.6    
71.0    
71.3    
71.7    
72.0    
72.4    
72.7    
73.0    
73.4    
73.7    
74.1    
74.4    
74.7    
75.1    
75.4    
75.8    
76.1    
76.5    
76.8    
77.1    
77.5    
77.8    
78.2    
78.5    
78.8    
79.2    
79.5    
79.9    
80.2    
80.5    
80.9    
81.2    
81.6    
81.9    
82.3    
82.6    
82.9    
83.3    
83.6    
84.0    
84.3    
84.6    
85.0    
85.3    
85.7    
86.0    
86.3    
86.7    
87.0    
87.4    
87.7    
88.1    
88.4    
88.7    
89.1    
89.4    
89.8    
90.1    
90.4    
90.8    
91.1    
91.5    
91.8    
92.2    
92.5    
92.8    
93.2    
93.5    
93.9    
94.2    
94.5    
94.9    
95.2    
95.6    
95.9    
96.2    
96.6    
96.9    
97.3    
97.6    
98.0    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 16 predictions from path traversal
Error with prediction: snap lend_intergenic: 13723, rend_intergenic: 2590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31007, rend_intergenic: 14548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42840, rend_intergenic: 34928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51140, rend_intergenic: 47333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56169, rend_intergenic: 52710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64884, rend_intergenic: 58414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72834, rend_intergenic: 69710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78047, rend_intergenic: 74522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89916, rend_intergenic: 78180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104190, rend_intergenic: 103482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109155, rend_intergenic: 107536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120774, rend_intergenic: 111105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125252, rend_intergenic: 122268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139326, rend_intergenic: 127466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support