-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_1-214049

-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.g37421.t1
Valid prediction for Augustus_model.g37414.t1
Valid prediction for snap_scaffold_27-snap.45-T1
Valid prediction for Augustus_model.g37409.t1
Valid prediction for GlimmerHMM_glimmerT_56482-T1
Valid prediction for snap_scaffold_27-snap.21-T1
Valid prediction for snap_scaffold_27-snap.16-T1
Valid prediction for GlimmerHMM_glimmerT_56483-T1
Valid prediction for GlimmerHMM_glimmerT_56478-T1
Valid prediction for snap_scaffold_27-snap.42-T1
Valid prediction for snap_scaffold_27-snap.23-T1
Valid prediction for pasa_asmbl_35941.p1
Valid prediction for snap_scaffold_27-snap.15-T1
Valid prediction for snap_scaffold_27-snap.24-T1
Valid prediction for CodingQuarry_transcript_41734-T1
Valid prediction for snap_scaffold_27-snap.26-T1
Valid prediction for GlimmerHMM_glimmerT_56472-T1
Valid prediction for Augustus_model.g37406.t1
Valid prediction for GlimmerHMM_glimmerT_56466-T1
add_exon() Sorry, GlimmerHMM_glimmerT_56466-T1 1410-1581-terminal-1 is invalid.
Valid prediction for snap_scaffold_27-snap.38-T1
Valid prediction for Augustus_model.g37433.t1
Valid prediction for Augustus_model.g37420.t1
Valid prediction for snap_scaffold_27-snap.11-T1
Valid prediction for Augustus_model.g37419.t1
Valid prediction for snap_scaffold_27-snap.41-T1
Valid prediction for snap_scaffold_27-snap.2-T1
Valid prediction for snap_scaffold_27-snap.40-T1
Valid prediction for GlimmerHMM_glimmerT_56471-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_56480-T1
Valid prediction for GlimmerHMM_glimmerT_56493-T1
Valid prediction for Augustus_model.g37431.t1
Valid prediction for GlimmerHMM_glimmerT_56490-T1
Valid prediction for GlimmerHMM_glimmerT_56489-T1
Valid prediction for snap_scaffold_27-snap.44-T1
Valid prediction for HiQ_model.g37430.t1
Valid prediction for GlimmerHMM_glimmerT_56476-T1
Valid prediction for GlimmerHMM_glimmerT_56468-T1
Valid prediction for snap_scaffold_27-snap.19-T1
Valid prediction for snap_scaffold_27-snap.4-T1
Valid prediction for Augustus_model.g37407.t1
Valid prediction for GlimmerHMM_glimmerT_56492-T1
Valid prediction for snap_scaffold_27-snap.43-T1
Valid prediction for Augustus_model.g37408.t1
Valid prediction for snap_scaffold_27-snap.39-T1
Valid prediction for GlimmerHMM_glimmerT_56467-T1
Valid prediction for snap_scaffold_27-snap.36-T1
Valid prediction for snap_scaffold_27-snap.3-T1
Valid prediction for snap_scaffold_27-snap.22-T1
Valid prediction for Augustus_model.g37426.t1
Valid prediction for GlimmerHMM_glimmerT_56469-T1
Valid prediction for GlimmerHMM_glimmerT_56491-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.g37413.t1
Valid prediction for snap_scaffold_27-snap.18-T1
Valid prediction for GlimmerHMM_glimmerT_56485-T1
Valid prediction for snap_scaffold_27-snap.7-T1
Valid prediction for GlimmerHMM_glimmerT_56486-T1
Couldn't classify 171192, 171729
Sorry, prediction pasa_asmbl_36628.p1 fails validation.
(AGT)	 CC	171192-171729	GT	AGG
(TGT)	 AG	171956-172276	GT	GGG
(ATG)	 AG	175108-175130	CT	AAC
-recovered pasa_asmbl_36628.p1, terminal, 175108, 175130
-recovered pasa_asmbl_36628.p1, internal, 171956, 172276
Valid prediction for snap_scaffold_27-snap.14-T1
Valid prediction for HiQ_model.g37422.t1
Valid prediction for Augustus_model.g37412.t1
Couldn't classify 153079, 153255
Couldn't classify 154163, 154359
Sorry, prediction pasa_asmbl_36632.p1 fails validation.
(AAC)	 TA	153079-153255	GT	AGG
(ATC)	 AG	153717-153825	GT	CGG
(TCT)	 AG	154163-154359	AT	AGA
-recovered pasa_asmbl_36632.p1, internal, 153717, 153825
Valid prediction for snap_scaffold_27-snap.33-T1
Valid prediction for snap_scaffold_27-snap.6-T1
Valid prediction for Augustus_model.g37429.t1
Valid prediction for snap_scaffold_27-snap.32-T1
Valid prediction for Augustus_model.g37427.t1
Valid prediction for snap_scaffold_27-snap.31-T1
Couldn't classify 66186, 66323
Couldn't classify 68125, 68393
Sorry, prediction pasa_asmbl_36643.p1 fails validation.
(CAG)	 AT	66186-66323	GT	AGG
(GGC)	 AG	66784-66884	GT	AGG
(GTC)	 AG	67017-67091	GT	ACG
(GTT)	 AG	67248-67330	GT	AGG
(GTT)	 AG	68125-68393	CC	CCC
add_exon() Sorry, pasa_asmbl_36643.p1 67248-67330-terminal-2 is invalid.
-recovered pasa_asmbl_36643.p1, terminal, 67248, 67330
-recovered pasa_asmbl_36643.p1, internal, 66784, 66884
-recovered pasa_asmbl_36643.p1, internal, 67017, 67091
-recovered pasa_asmbl_36643.p1, internal, 67248, 67330
Valid prediction for snap_scaffold_27-snap.35-T1
Valid prediction for snap_scaffold_27-snap.1-T1
Valid prediction for snap_scaffold_27-snap.30-T1
Valid prediction for snap_scaffold_27-snap.8-T1
Valid prediction for snap_scaffold_27-snap.13-T1
Valid prediction for snap_scaffold_27-snap.20-T1
Valid prediction for Augustus_model.g37428.t1
Valid prediction for snap_scaffold_27-snap.29-T1
Valid prediction for snap_scaffold_27-snap.9-T1
Valid prediction for CodingQuarry_transcript_41733-T1
Valid prediction for GlimmerHMM_glimmerT_56479-T1
Valid prediction for snap_scaffold_27-snap.27-T1
Valid prediction for pasa_asmbl_36631.p1
Valid prediction for Augustus_model.g37415.t1
Valid prediction for pasa_asmbl_36637.p1
Valid prediction for Augustus_model.g37432.t1
Valid prediction for pasa_asmbl_36648.p1
Valid prediction for Augustus_model.g37423.t1
Valid prediction for GlimmerHMM_glimmerT_56477-T1
Valid prediction for snap_scaffold_27-snap.28-T1
Valid prediction for snap_scaffold_27-snap.10-T1
Valid prediction for GlimmerHMM_glimmerT_56481-T1
Valid prediction for HiQ_model.g37411.t1
Valid prediction for CodingQuarry_transcript_41732-T1
Valid prediction for Augustus_model.g37425.t1
Valid prediction for Augustus_model.g37424.t1
Valid prediction for snap_scaffold_27-snap.12-T1
Valid prediction for snap_scaffold_27-snap.5-T1
Valid prediction for GlimmerHMM_glimmerT_56487-T1
Valid prediction for GlimmerHMM_glimmerT_56484-T1
Couldn't classify 147959, 148117
Couldn't classify 148985, 149122
Sorry, prediction pasa_asmbl_36633.p1 fails validation.
(CTG)	 AG	147959-148117	GT	AGG
(TTT)	 AG	148985-149122	CA	GAC
-recovered pasa_asmbl_36633.p1, internal, 147959, 148117
Valid prediction for pasa_asmbl_36650.p1
Valid prediction for snap_scaffold_27-snap.37-T1
Valid prediction for Augustus_model.g37416.t1
Valid prediction for snap_scaffold_27-snap.34-T1
Valid prediction for Augustus_model.g37418.t1
Valid prediction for GlimmerHMM_glimmerT_56474-T1
Valid prediction for GlimmerHMM_glimmerT_56488-T1
Valid prediction for Augustus_model.g37410.t1
Valid prediction for GlimmerHMM_glimmerT_56473-T1
Valid prediction for GlimmerHMM_glimmerT_56475-T1
Valid prediction for GlimmerHMM_glimmerT_56470-T1
Valid prediction for snap_scaffold_27-snap.17-T1
Valid prediction for snap_scaffold_27-snap.25-T1
Valid prediction for Augustus_model.g37417.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 113781, rend_intergenic: 110498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134881, rend_intergenic: 131955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179710, rend_intergenic: 178083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 214049
-exon list size: 369


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.2    
2.4    
2.7    
3.0    
3.2    
3.5    
3.8    
4.0    
4.3    
4.6    
4.9    
5.1    
5.4    
5.7    
5.9    
6.2    
6.5    
6.7    
7.0    
7.3    
7.5    
7.8    
8.1    
8.4    
8.6    
8.9    
9.2    
9.4    
9.7    
10.0    
10.2    
10.5    
10.8    
11.1    
11.3    
11.6    
11.9    
12.1    
12.4    
12.7    
12.9    
13.2    
13.5    
13.7    
14.0    
14.3    
14.6    
14.8    
15.1    
15.4    
15.6    
15.9    
16.2    
16.4    
16.7    
17.0    
17.3    
17.5    
17.8    
18.1    
18.3    
18.6    
18.9    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.0    
21.3    
21.6    
21.8    
22.1    
22.4    
22.6    
22.9    
23.2    
23.5    
23.7    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.1    
26.4    
26.7    
27.0    
27.2    
27.5    
27.8    
28.0    
28.3    
28.6    
28.8    
29.1    
29.4    
29.6    
29.9    
30.2    
30.5    
30.7    
31.0    
31.3    
31.5    
31.8    
32.1    
32.3    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.0    
35.3    
35.6    
35.8    
36.1    
36.4    
36.7    
36.9    
37.2    
37.5    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.2    
41.5    
41.8    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
43.9    
44.2    
44.5    
44.7    
45.0    
45.3    
45.6    
45.8    
46.1    
46.4    
46.6    
46.9    
47.2    
47.4    
47.7    
48.0    
48.2    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.8    
52.0    
52.3    
52.6    
52.8    
53.1    
53.4    
53.6    
53.9    
54.2    
54.4    
54.7    
55.0    
55.3    
55.5    
55.8    
56.1    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.2    
58.5    
58.8    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.2    
61.5    
61.7    
62.0    
62.3    
62.5    
62.8    
63.1    
63.3    
63.6    
63.9    
64.2    
64.4    
64.7    
65.0    
65.2    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.7    
67.9    
68.2    
68.5    
68.7    
69.0    
69.3    
69.5    
69.8    
70.1    
70.4    
70.6    
70.9    
71.2    
71.4    
71.7    
72.0    
72.2    
72.5    
72.8    
73.0    
73.3    
73.6    
73.9    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.3    
76.5    
76.8    
77.1    
77.4    
77.6    
77.9    
78.2    
78.4    
78.7    
79.0    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.1    
81.4    
81.7    
81.9    
82.2    
82.5    
82.7    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.6    
84.9    
85.2    
85.4    
85.7    
86.0    
86.3    
86.5    
86.8    
87.1    
87.3    
87.6    
87.9    
88.1    
88.4    
88.7    
88.9    
89.2    
89.5    
89.8    
90.0    
90.3    
90.6    
90.8    
91.1    
91.4    
91.6    
91.9    
92.2    
92.5    
92.7    
93.0    
93.3    
93.5    
93.8    
94.1    
94.3    
94.6    
94.9    
95.1    
95.4    
95.7    
96.0    
96.2    
96.5    
96.8    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 113781, rend_intergenic: 110498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134881, rend_intergenic: 131955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179710, rend_intergenic: 178083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support