-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_6479825-6626026

-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 snap_scaffold_1-snap.1094-T1
Valid prediction for Augustus_model.g651.t1
Valid prediction for GlimmerHMM_glimmerT_863-T1
Valid prediction for Augustus_model.g667.t1
Valid prediction for snap_scaffold_1-snap.1096-T1
Valid prediction for snap_scaffold_1-snap.1066-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.1084-T1
Valid prediction for GlimmerHMM_glimmerT_885-T1
Valid prediction for snap_scaffold_1-snap.1078-T1
Valid prediction for snap_scaffold_1-snap.1090-T1
Valid prediction for CodingQuarry_transcript_2660-T1
Valid prediction for snap_scaffold_1-snap.1071-T1
Valid prediction for GlimmerHMM_glimmerT_878-T1
Valid prediction for snap_scaffold_1-snap.1085-T1
Valid prediction for GlimmerHMM_glimmerT_874-T1
Valid prediction for snap_scaffold_1-snap.1080-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.1067-T1
Valid prediction for pasa_asmbl_1840.p1
Valid prediction for Augustus_model.g654.t1
Valid prediction for snap_scaffold_1-snap.1097-T1
Valid prediction for GlimmerHMM_glimmerT_861-T1
Valid prediction for Augustus_model.g662.t1
Valid prediction for snap_scaffold_1-snap.1083-T1
Valid prediction for GlimmerHMM_glimmerT_860-T1
Valid prediction for GlimmerHMM_glimmerT_871-T1
Valid prediction for Augustus_model.g663.t1
Valid prediction for GlimmerHMM_glimmerT_872-T1
Valid prediction for snap_scaffold_1-snap.1088-T1
Valid prediction for snap_scaffold_1-snap.1089-T1
Valid prediction for GlimmerHMM_glimmerT_877-T1
Valid prediction for GlimmerHMM_glimmerT_879-T1
Valid prediction for GlimmerHMM_glimmerT_884-T1
Valid prediction for HiQ_model.g664.t1
Valid prediction for Augustus_model.g658.t1
Valid prediction for GlimmerHMM_glimmerT_882-T1
Valid prediction for Augustus_model.g660.t1
Valid prediction for snap_scaffold_1-snap.1087-T1
Valid prediction for GlimmerHMM_glimmerT_865-T1
Valid prediction for Augustus_model.g669.t1
Valid prediction for snap_scaffold_1-snap.1092-T1
Valid prediction for snap_scaffold_1-snap.1073-T1
Valid prediction for snap_scaffold_1-snap.1074-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.g655.t1
Valid prediction for GlimmerHMM_glimmerT_886-T1
Valid prediction for GlimmerHMM_glimmerT_868-T1
Valid prediction for snap_scaffold_1-snap.1091-T1
Valid prediction for snap_scaffold_1-snap.1095-T1
Valid prediction for GlimmerHMM_glimmerT_869-T1
Couldn't classify 65826, 65933
Couldn't classify 66994, 67209
Sorry, prediction pasa_asmbl_1240.p1 fails validation.
(GAG)	 TG	65826-65933	GT	AGG
(GTA)	 AG	66509-66604	GT	AGG
(GGG)	 AG	66994-67209	GA	ATG
-recovered pasa_asmbl_1240.p1, internal, 66509, 66604
Valid prediction for Augustus_model.g656.t1
Valid prediction for pasa_asmbl_367.p1
Valid prediction for GlimmerHMM_glimmerT_867-T1
Valid prediction for GlimmerHMM_glimmerT_866-T1
Valid prediction for snap_scaffold_1-snap.1072-T1
Valid prediction for snap_scaffold_1-snap.1082-T1
Valid prediction for Augustus_model.g668.t1
Valid prediction for Augustus_model.g653.t1
Valid prediction for pasa_asmbl_376.p1
Valid prediction for GlimmerHMM_glimmerT_870-T1
Valid prediction for snap_scaffold_1-snap.1076-T1
Couldn't classify 49574, 49613
Couldn't classify 52081, 52222
Sorry, prediction pasa_asmbl_372.p1 fails validation.
(GAT)	 CC	49574-49613	GT	TGG
(AGC)	 AG	49741-49812	GT	CGG
(ATG)	 AG	49945-50060	GT	CGG
(GGT)	 AG	50567-50628	GT	AGG
(GTG)	 AG	50765-51077	GT	CGG
(TTG)	 AG	51736-51836	GT	AGG
(CAA)	 AG	52081-52222	GT	GGG
add_exon() Sorry, pasa_asmbl_372.p1 49945-50060-initial-1 is invalid.
-recovered pasa_asmbl_372.p1, initial, 49945, 50060
-recovered pasa_asmbl_372.p1, internal, 49741, 49812
-recovered pasa_asmbl_372.p1, internal, 49945, 50060
-recovered pasa_asmbl_372.p1, internal, 50567, 50628
-recovered pasa_asmbl_372.p1, internal, 50765, 51077
-recovered pasa_asmbl_372.p1, internal, 51736, 51836
-recovered pasa_asmbl_372.p1, internal, 52081, 52222
Valid prediction for snap_scaffold_1-snap.1079-T1
Valid prediction for Augustus_model.g657.t1
Valid prediction for Augustus_model.g666.t1
Valid prediction for GlimmerHMM_glimmerT_864-T1
Valid prediction for GlimmerHMM_glimmerT_883-T1
Valid prediction for snap_scaffold_1-snap.1077-T1
Valid prediction for snap_scaffold_1-snap.1093-T1
Valid prediction for pasa_asmbl_364.p1
Valid prediction for GlimmerHMM_glimmerT_862-T1
Valid prediction for GlimmerHMM_glimmerT_873-T1
Valid prediction for GlimmerHMM_glimmerT_875-T1
Valid prediction for HiQ_model.g652.t1
Valid prediction for GlimmerHMM_glimmerT_876-T1
Valid prediction for Augustus_model.g659.t1
Valid prediction for Augustus_model.g661.t1
Valid prediction for snap_scaffold_1-snap.1070-T1
Valid prediction for snap_scaffold_1-snap.1068-T1
Valid prediction for snap_scaffold_1-snap.1081-T1
Valid prediction for Augustus_model.g665.t1
Valid prediction for CodingQuarry_transcript_2658-T1
Valid prediction for snap_scaffold_1-snap.1069-T1
Valid prediction for snap_scaffold_1-snap.1086-T1
Valid prediction for GlimmerHMM_glimmerT_881-T1
Valid prediction for GlimmerHMM_glimmerT_880-T1
Valid prediction for snap_scaffold_1-snap.1075-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 27001, rend_intergenic: 23347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29053, rend_intergenic: 27672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32804, rend_intergenic: 29293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72787, rend_intergenic: 66330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125106, rend_intergenic: 122076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132093, rend_intergenic: 128490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139376, rend_intergenic: 134776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 87365, rend_intergenic: 87362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 146202
-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 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 27001, rend_intergenic: 23347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29053, rend_intergenic: 27672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32804, rend_intergenic: 29293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72787, rend_intergenic: 66330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125106, rend_intergenic: 122076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132093, rend_intergenic: 128490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139376, rend_intergenic: 134776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 87365, rend_intergenic: 87362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support