-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_1251049-1431158

-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 GlimmerHMM_glimmerT_47106-T1
Valid prediction for GlimmerHMM_glimmerT_47107-T1
Valid prediction for GlimmerHMM_glimmerT_47092-T1
Valid prediction for GlimmerHMM_glimmerT_47109-T1
Valid prediction for GlimmerHMM_glimmerT_47105-T1
Valid prediction for Augustus_model.g31377.t1
Valid prediction for snap_scaffold_21-snap.230-T1
Valid prediction for snap_scaffold_21-snap.217-T1
Valid prediction for GlimmerHMM_glimmerT_47098-T1
Valid prediction for Augustus_model.g31381.t1
Valid prediction for snap_scaffold_21-snap.240-T1
Valid prediction for snap_scaffold_21-snap.245-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_21-snap.231-T1
Valid prediction for Augustus_model.g31383.t1
Valid prediction for snap_scaffold_21-snap.249-T1
Valid prediction for snap_scaffold_21-snap.236-T1
Valid prediction for GlimmerHMM_glimmerT_47099-T1
Valid prediction for snap_scaffold_21-snap.222-T1
Valid prediction for snap_scaffold_21-snap.224-T1
Valid prediction for snap_scaffold_21-snap.233-T1
Valid prediction for GlimmerHMM_glimmerT_47097-T1
Valid prediction for GlimmerHMM_glimmerT_47103-T1
Valid prediction for snap_scaffold_21-snap.232-T1
Valid prediction for GlimmerHMM_glimmerT_47089-T1
Valid prediction for Augustus_model.g31384.t1
Valid prediction for snap_scaffold_21-snap.226-T1
Valid prediction for snap_scaffold_21-snap.247-T1
Valid prediction for snap_scaffold_21-snap.216-T1
Valid prediction for snap_scaffold_21-snap.228-T1
Valid prediction for snap_scaffold_21-snap.242-T1
Valid prediction for snap_scaffold_21-snap.214-T1
Valid prediction for snap_scaffold_21-snap.234-T1
Valid prediction for snap_scaffold_21-snap.251-T1
Valid prediction for snap_scaffold_21-snap.223-T1
Valid prediction for snap_scaffold_21-snap.243-T1
Valid prediction for GlimmerHMM_glimmerT_47113-T1
Valid prediction for snap_scaffold_21-snap.219-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 CodingQuarry_transcript_32441-T1
Valid prediction for GlimmerHMM_glimmerT_47091-T1
Couldn't classify 133702, 133808
Couldn't classify 134017, 134030
Sorry, prediction CodingQuarry_transcript_32439-T1 fails validation.
(ATG)	 GG	127220-127535	GT	AGG
(AGG)	 AG	127776-127898	GT	AGG
(ATG)	 AG	128081-128275	GT	AGG
(GGG)	 AG	128395-128622	GT	AGG
(GCA)	 AG	128773-128879	GT	GGG
(GTG)	 AG	129022-129251	GT	AGG
(GCT)	 AG	129744-129933	GT	AGG
(GTG)	 AG	130736-130859	GT	AAG
(GCA)	 AG	131691-131793	GT	CGG
(GAC)	 AG	131938-132053	GT	AGG
(ATC)	 AG	132195-132394	GT	AGG
(GCG)	 AG	132664-132811	GT	AGG
(TGC)	 AG	133074-133195	GT	AGG
(GAG)	 AG	133509-133585	GT	AAG
(TGT)	 AG	133702-133808	AC	TCA
(CAG)	 TC	134017-134030	AG	GAA
-recovered CodingQuarry_transcript_32439-T1, initial, 127220, 127535
add_exon() Sorry, CodingQuarry_transcript_32439-T1 128081-128275-initial-1 is invalid.
-recovered CodingQuarry_transcript_32439-T1, initial, 128081, 128275
-recovered CodingQuarry_transcript_32439-T1, terminal, 128395, 128622
-recovered CodingQuarry_transcript_32439-T1, internal, 127776, 127898
-recovered CodingQuarry_transcript_32439-T1, internal, 128081, 128275
-recovered CodingQuarry_transcript_32439-T1, internal, 128395, 128622
-recovered CodingQuarry_transcript_32439-T1, internal, 128773, 128879
-recovered CodingQuarry_transcript_32439-T1, internal, 129022, 129251
-recovered CodingQuarry_transcript_32439-T1, internal, 129744, 129933
-recovered CodingQuarry_transcript_32439-T1, internal, 130736, 130859
-recovered CodingQuarry_transcript_32439-T1, internal, 131691, 131793
-recovered CodingQuarry_transcript_32439-T1, internal, 131938, 132053
-recovered CodingQuarry_transcript_32439-T1, internal, 132195, 132394
-recovered CodingQuarry_transcript_32439-T1, internal, 132664, 132811
-recovered CodingQuarry_transcript_32439-T1, internal, 133074, 133195
-recovered CodingQuarry_transcript_32439-T1, internal, 133509, 133585
Valid prediction for GlimmerHMM_glimmerT_47095-T1
Valid prediction for snap_scaffold_21-snap.225-T1
Valid prediction for snap_scaffold_21-snap.213-T1
Valid prediction for snap_scaffold_21-snap.253-T1
Valid prediction for GlimmerHMM_glimmerT_47094-T1
Valid prediction for pasa_asmbl_27406.p1
Valid prediction for snap_scaffold_21-snap.229-T1
Valid prediction for GlimmerHMM_glimmerT_47112-T1
Valid prediction for GlimmerHMM_glimmerT_47104-T1
Valid prediction for Augustus_model.g31380.t1
Valid prediction for Augustus_model.g31382.t1
Valid prediction for snap_scaffold_21-snap.252-T1
Valid prediction for Augustus_model.g31378.t1
Valid prediction for snap_scaffold_21-snap.215-T1
Valid prediction for Augustus_model.g31379.t1
Valid prediction for GlimmerHMM_glimmerT_47101-T1
Valid prediction for snap_scaffold_21-snap.237-T1
Valid prediction for snap_scaffold_21-snap.250-T1
Valid prediction for snap_scaffold_21-snap.218-T1
Valid prediction for snap_scaffold_21-snap.227-T1
Couldn't classify 113845, 113979
Sorry, prediction pasa_asmbl_27410.p1 fails validation.
(ATG)	 AC	110595-110672	GT	AGG
(GCC)	 AG	110968-111139	GT	GGG
(GTA)	 AG	113338-113522	GT	CGG
(GCC)	 AG	113845-113979	CC	ATC
-recovered pasa_asmbl_27410.p1, initial, 110595, 110672
-recovered pasa_asmbl_27410.p1, internal, 110968, 111139
-recovered pasa_asmbl_27410.p1, internal, 113338, 113522
Valid prediction for GlimmerHMM_glimmerT_47111-T1
Valid prediction for snap_scaffold_21-snap.244-T1
Valid prediction for snap_scaffold_21-snap.235-T1
Valid prediction for GlimmerHMM_glimmerT_47090-T1
Valid prediction for CodingQuarry_transcript_32440-T1
Valid prediction for Augustus_model.g31375.t1
Valid prediction for GlimmerHMM_glimmerT_47096-T1
Valid prediction for GlimmerHMM_glimmerT_47108-T1
Valid prediction for GlimmerHMM_glimmerT_47093-T1
Couldn't classify 148001, 148142
Sorry, prediction pasa_asmbl_27397.p1 fails validation.
(GTG)	 GG	148001-148142	GT	AGG
(GTC)	 AG	148405-148587	GT	AGG
(GTA)	 AG	148788-148946	GT	AGG
(GGC)	 AG	149279-149453	GT	AAG
(TGT)	 AG	149572-149705	GT	AGG
(GCG)	 AG	152267-152489	GT	AGG
(TCT)	 AG	154570-154706	GT	TGG
(CCG)	 AG	155355-155457	GT	AGG
(GTA)	 AG	155605-155810	GT	GGG
(GTA)	 AG	156045-156196	GT	AGG
(GTG)	 AG	156424-156532	GT	AGG
(GCT)	 AG	156812-157002	AG	AGA
add_exon() Sorry, pasa_asmbl_27397.p1 148405-148587-terminal-1 is invalid.
-recovered pasa_asmbl_27397.p1, terminal, 148405, 148587
add_exon() Sorry, pasa_asmbl_27397.p1 156424-156532-terminal-3 is invalid.
-recovered pasa_asmbl_27397.p1, terminal, 156424, 156532
-recovered pasa_asmbl_27397.p1, terminal, 156812, 157002
-recovered pasa_asmbl_27397.p1, internal, 148405, 148587
-recovered pasa_asmbl_27397.p1, internal, 148788, 148946
-recovered pasa_asmbl_27397.p1, internal, 149279, 149453
-recovered pasa_asmbl_27397.p1, internal, 149572, 149705
-recovered pasa_asmbl_27397.p1, internal, 152267, 152489
-recovered pasa_asmbl_27397.p1, internal, 154570, 154706
-recovered pasa_asmbl_27397.p1, internal, 155355, 155457
-recovered pasa_asmbl_27397.p1, internal, 155605, 155810
-recovered pasa_asmbl_27397.p1, internal, 156045, 156196
-recovered pasa_asmbl_27397.p1, internal, 156424, 156532
Valid prediction for snap_scaffold_21-snap.246-T1
Valid prediction for snap_scaffold_21-snap.220-T1
Valid prediction for GlimmerHMM_glimmerT_47102-T1
Valid prediction for GlimmerHMM_glimmerT_47100-T1
Valid prediction for GlimmerHMM_glimmerT_47110-T1
Valid prediction for HiQ_model.g31376.t1
Valid prediction for snap_scaffold_21-snap.221-T1
Valid prediction for snap_scaffold_21-snap.241-T1
Valid prediction for snap_scaffold_21-snap.248-T1
Valid prediction for snap_scaffold_21-snap.239-T1
Valid prediction for snap_scaffold_21-snap.238-T1
Valid prediction for CodingQuarry_transcript_32438-T1
Valid prediction for GlimmerHMM_glimmerT_47114-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19102, rend_intergenic: 10525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32155, rend_intergenic: 27742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52891, rend_intergenic: 46310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74996, rend_intergenic: 58808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80431, rend_intergenic: 77295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84273, rend_intergenic: 81400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90621, rend_intergenic: 86848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109124, rend_intergenic: 90812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110053, rend_intergenic: 109134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117163, rend_intergenic: 114290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136486, rend_intergenic: 133887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147795, rend_intergenic: 141262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156221, rend_intergenic: 149553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159490, rend_intergenic: 159286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166383, rend_intergenic: 163337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178328, rend_intergenic: 172777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 180110
-exon list size: 341


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.7    
2.0    
2.3    
2.6    
2.9    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
7.9    
8.2    
8.5    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.2    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.7    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.2    
52.5    
52.8    
53.1    
53.4    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.1    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 19102, rend_intergenic: 10525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32155, rend_intergenic: 27742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52891, rend_intergenic: 46310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74996, rend_intergenic: 58808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80431, rend_intergenic: 77295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84273, rend_intergenic: 81400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90621, rend_intergenic: 86848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109124, rend_intergenic: 90812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110053, rend_intergenic: 109134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117163, rend_intergenic: 114290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136486, rend_intergenic: 133887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147795, rend_intergenic: 141262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156221, rend_intergenic: 149553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159490, rend_intergenic: 159286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166383, rend_intergenic: 163337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178328, rend_intergenic: 172777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support