-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_9017312-9248686

-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_28-snap.2059-T1
Valid prediction for snap_scaffold_28-snap.2068-T1
Valid prediction for snap_scaffold_28-snap.2047-T1
Valid prediction for GlimmerHMM_glimmerT_59334-T1
Valid prediction for snap_scaffold_28-snap.2044-T1
Valid prediction for snap_scaffold_28-snap.2054-T1
Valid prediction for snap_scaffold_28-snap.2042-T1
Valid prediction for GlimmerHMM_glimmerT_59333-T1
Valid prediction for snap_scaffold_28-snap.2037-T1
Valid prediction for GlimmerHMM_glimmerT_59342-T1
Valid prediction for snap_scaffold_28-snap.2067-T1
Valid prediction for GlimmerHMM_glimmerT_59340-T1
Valid prediction for snap_scaffold_28-snap.2053-T1
Valid prediction for snap_scaffold_28-snap.2051-T1
Valid prediction for snap_scaffold_28-snap.2073-T1
Valid prediction for snap_scaffold_28-snap.2063-T1
Valid prediction for snap_scaffold_28-snap.2035-T1
Valid prediction for CodingQuarry_transcript_43755-T1
Valid prediction for snap_scaffold_28-snap.2057-T1
Valid prediction for snap_scaffold_28-snap.2070-T1
Valid prediction for snap_scaffold_28-snap.2056-T1
Valid prediction for GlimmerHMM_glimmerT_59329-T1
Valid prediction for snap_scaffold_28-snap.2038-T1
Valid prediction for HiQ_model.g39314.t1
Valid prediction for CodingQuarry_transcript_43757-T1
Valid prediction for GlimmerHMM_glimmerT_59336-T1
Valid prediction for GlimmerHMM_glimmerT_59341-T1
Valid prediction for snap_scaffold_28-snap.2066-T1
Couldn't classify 95051, 95659
Sorry, prediction pasa_asmbl_37771.p1 fails validation.
(GTG)	 CG	95051-95659	GT	AGG
(GAG)	 AG	95893-96110	GT	TGG
(CTA)	 AG	96671-96740	CC	GAC
-recovered pasa_asmbl_37771.p1, terminal, 96671, 96740
-recovered pasa_asmbl_37771.p1, internal, 95893, 96110
Valid prediction for snap_scaffold_28-snap.2045-T1
Valid prediction for GlimmerHMM_glimmerT_59339-T1
Valid prediction for snap_scaffold_28-snap.2061-T1
Valid prediction for GlimmerHMM_glimmerT_59347-T1
Valid prediction for GlimmerHMM_glimmerT_59344-T1
Valid prediction for snap_scaffold_28-snap.2040-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_59350-T1
Valid prediction for Augustus_model.g39317.t1
Valid prediction for snap_scaffold_28-snap.2041-T1
Valid prediction for GlimmerHMM_glimmerT_59332-T1
Valid prediction for GlimmerHMM_glimmerT_59335-T1
Valid prediction for Augustus_model.g39318.t1
Valid prediction for GlimmerHMM_glimmerT_59346-T1
Valid prediction for GlimmerHMM_glimmerT_59330-T1
Valid prediction for snap_scaffold_28-snap.2050-T1
Valid prediction for Augustus_model.g39316.t1
Valid prediction for Augustus_model.g39319.t1
Couldn't classify 19576, 19707
Sorry, prediction pasa_asmbl_38497.p1 fails validation.
(GGC)	 AG	19576-19707	GT	AGG
(GTG)	 AG	20550-20664	GT	TGG
(GCG)	 AG	21545-21969	GG	GAG
-recovered pasa_asmbl_38497.p1, terminal, 21545, 21969
-recovered pasa_asmbl_38497.p1, internal, 19576, 19707
-recovered pasa_asmbl_38497.p1, internal, 20550, 20664
Couldn't classify 84289, 84932
Couldn't classify 86157, 86270
Sorry, prediction pasa_asmbl_38495.p1 fails validation.
(CCG)	 AG	84289-84932	GT	AGG
(TTT)	 AG	85174-85291	GT	AGG
(GTG)	 AG	85638-85739	GT	CGG
(GTC)	 AG	86157-86270	CT	CTC
-recovered pasa_asmbl_38495.p1, internal, 84289, 84932
-recovered pasa_asmbl_38495.p1, internal, 85174, 85291
-recovered pasa_asmbl_38495.p1, internal, 85638, 85739
Valid prediction for snap_scaffold_28-snap.2052-T1
Valid prediction for snap_scaffold_28-snap.2062-T1
Valid prediction for Augustus_model.g39322.t1
Couldn't classify 80083, 80199
Couldn't classify 81983, 82155
Sorry, prediction pasa_asmbl_38548.p1 fails validation.
(GAC)	 CC	80083-80199	GT	GGG
(GAG)	 AG	80330-80474	GT	AGG
(CTG)	 AG	81983-82155	AC	TCA
-recovered pasa_asmbl_38548.p1, internal, 80330, 80474
Valid prediction for GlimmerHMM_glimmerT_59343-T1
Valid prediction for GlimmerHMM_glimmerT_59338-T1
Valid prediction for snap_scaffold_28-snap.2071-T1
Valid prediction for Augustus_model.g39320.t1
Valid prediction for snap_scaffold_28-snap.2046-T1
Valid prediction for Augustus_model.g39315.t1
Valid prediction for GlimmerHMM_glimmerT_59349-T1
Valid prediction for snap_scaffold_28-snap.2058-T1
Valid prediction for snap_scaffold_28-snap.2055-T1
Valid prediction for Augustus_model.g39321.t1
Valid prediction for HiQ_model.g39313.t1
Valid prediction for GlimmerHMM_glimmerT_59348-T1
Valid prediction for snap_scaffold_28-snap.2064-T1
Valid prediction for snap_scaffold_28-snap.2049-T1
Valid prediction for GlimmerHMM_glimmerT_59331-T1
Valid prediction for snap_scaffold_28-snap.2039-T1
Valid prediction for snap_scaffold_28-snap.2072-T1
Valid prediction for snap_scaffold_28-snap.2043-T1
Valid prediction for snap_scaffold_28-snap.2048-T1
Couldn't classify 126492, 126527
Sorry, prediction pasa_asmbl_38491.p1 fails validation.
(AAT)	 TG	126492-126527	GT	AGG
(GTG)	 AG	127325-127450	GT	GGG
(AAA)	 AG	127977-128042	GT	AGG
(GCG)	 AG	129092-129159	GT	TGG
(GGT)	 AG	129709-129757	GT	GAG
(CAA)	 AG	130137-130249	GT	CAG
(CGG)	 AG	130395-130467	GT	AGG
(CTA)	 AG	130644-130713	GT	AGG
(GGA)	 AG	130987-131063	GT	AGG
(TCA)	 AG	131154-131223	GT	AGG
(TCA)	 AG	131407-131491	GT	GTG
(CTA)	 AG	131900-132002	AG	AAA
-recovered pasa_asmbl_38491.p1, terminal, 131900, 132002
-recovered pasa_asmbl_38491.p1, internal, 127325, 127450
-recovered pasa_asmbl_38491.p1, internal, 127977, 128042
-recovered pasa_asmbl_38491.p1, internal, 129092, 129159
-recovered pasa_asmbl_38491.p1, internal, 129709, 129757
-recovered pasa_asmbl_38491.p1, internal, 130137, 130249
-recovered pasa_asmbl_38491.p1, internal, 130395, 130467
-recovered pasa_asmbl_38491.p1, internal, 130644, 130713
-recovered pasa_asmbl_38491.p1, internal, 130987, 131063
-recovered pasa_asmbl_38491.p1, internal, 131154, 131223
-recovered pasa_asmbl_38491.p1, internal, 131407, 131491
Valid prediction for snap_scaffold_28-snap.2065-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.2069-T1
Valid prediction for snap_scaffold_28-snap.2060-T1
Valid prediction for GlimmerHMM_glimmerT_59345-T1
Valid prediction for CodingQuarry_transcript_43756-T1
Valid prediction for GlimmerHMM_glimmerT_59337-T1
Couldn't classify 83299, 84015
Sorry, prediction pasa_asmbl_38496.p1 fails validation.
(CTG)	 AA	83299-84015	AC	ACA
Valid prediction for snap_scaffold_28-snap.2036-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 49929, rend_intergenic: 46286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64782, rend_intergenic: 63623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70612, rend_intergenic: 67807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105497, rend_intergenic: 102584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114035, rend_intergenic: 106763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153587, rend_intergenic: 152344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160677, rend_intergenic: 154782  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174974, rend_intergenic: 162550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189892, rend_intergenic: 184760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201600, rend_intergenic: 190062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211798, rend_intergenic: 209407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230727, rend_intergenic: 219953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 231375
-exon list size: 306


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.3    
2.6    
2.9    
3.2    
3.6    
3.9    
4.2    
4.5    
4.9    
5.2    
5.5    
5.8    
6.2    
6.5    
6.8    
7.1    
7.5    
7.8    
8.1    
8.4    
8.8    
9.1    
9.4    
9.7    
10.1    
10.4    
10.7    
11.0    
11.4    
11.7    
12.0    
12.3    
12.7    
13.0    
13.3    
13.6    
14.0    
14.3    
14.6    
14.9    
15.3    
15.6    
15.9    
16.2    
16.6    
16.9    
17.2    
17.5    
17.9    
18.2    
18.5    
18.8    
19.2    
19.5    
19.8    
20.1    
20.5    
20.8    
21.1    
21.4    
21.8    
22.1    
22.4    
22.7    
23.1    
23.4    
23.7    
24.0    
24.4    
24.7    
25.0    
25.3    
25.6    
26.0    
26.3    
26.6    
26.9    
27.3    
27.6    
27.9    
28.2    
28.6    
28.9    
29.2    
29.5    
29.9    
30.2    
30.5    
30.8    
31.2    
31.5    
31.8    
32.1    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.1    
35.4    
35.7    
36.0    
36.4    
36.7    
37.0    
37.3    
37.7    
38.0    
38.3    
38.6    
39.0    
39.3    
39.6    
39.9    
40.3    
40.6    
40.9    
41.2    
41.6    
41.9    
42.2    
42.5    
42.9    
43.2    
43.5    
43.8    
44.2    
44.5    
44.8    
45.1    
45.5    
45.8    
46.1    
46.4    
46.8    
47.1    
47.4    
47.7    
48.1    
48.4    
48.7    
49.0    
49.4    
49.7    
50.0    
50.3    
50.6    
51.0    
51.3    
51.6    
51.9    
52.3    
52.6    
52.9    
53.2    
53.6    
53.9    
54.2    
54.5    
54.9    
55.2    
55.5    
55.8    
56.2    
56.5    
56.8    
57.1    
57.5    
57.8    
58.1    
58.4    
58.8    
59.1    
59.4    
59.7    
60.1    
60.4    
60.7    
61.0    
61.4    
61.7    
62.0    
62.3    
62.7    
63.0    
63.3    
63.6    
64.0    
64.3    
64.6    
64.9    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.9    
68.2    
68.5    
68.8    
69.2    
69.5    
69.8    
70.1    
70.5    
70.8    
71.1    
71.4    
71.8    
72.1    
72.4    
72.7    
73.1    
73.4    
73.7    
74.0    
74.4    
74.7    
75.0    
75.3    
75.6    
76.0    
76.3    
76.6    
76.9    
77.3    
77.6    
77.9    
78.2    
78.6    
78.9    
79.2    
79.5    
79.9    
80.2    
80.5    
80.8    
81.2    
81.5    
81.8    
82.1    
82.5    
82.8    
83.1    
83.4    
83.8    
84.1    
84.4    
84.7    
85.1    
85.4    
85.7    
86.0    
86.4    
86.7    
87.0    
87.3    
87.7    
88.0    
88.3    
88.6    
89.0    
89.3    
89.6    
89.9    
90.3    
90.6    
90.9    
91.2    
91.6    
91.9    
92.2    
92.5    
92.9    
93.2    
93.5    
93.8    
94.2    
94.5    
94.8    
95.1    
95.5    
95.8    
96.1    
96.4    
96.8    
97.1    
97.4    
97.7    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 49929, rend_intergenic: 46286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64782, rend_intergenic: 63623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70612, rend_intergenic: 67807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105497, rend_intergenic: 102584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114035, rend_intergenic: 106763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153587, rend_intergenic: 152344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160677, rend_intergenic: 154782  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174974, rend_intergenic: 162550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189892, rend_intergenic: 184760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201600, rend_intergenic: 190062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211798, rend_intergenic: 209407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230727, rend_intergenic: 219953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support