-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_8638207-8800183

-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: +)Couldn't classify 104840, 105377
Couldn't classify 107735, 107935
Couldn't classify 108172, 108191
Sorry, prediction pasa_asmbl_21543.p1 fails validation.
(TCA)	 AG	104840-105377	GT	AGG
(GCA)	 AG	105491-105786	GT	TGG
(GAA)	 AG	106126-106245	GT	AGG
(GAG)	 AG	106983-107196	GT	GGG
(GTC)	 AG	107497-107641	GT	AGG
(TGA)	 AG	107735-107935	AT	GAA
(GTT)	 AC	108172-108191	GT	TGG
(AAT)	 AG	108954-109075	AG	GAA
-recovered pasa_asmbl_21543.p1, terminal, 108954, 109075
-recovered pasa_asmbl_21543.p1, internal, 104840, 105377
-recovered pasa_asmbl_21543.p1, internal, 105491, 105786
-recovered pasa_asmbl_21543.p1, internal, 106126, 106245
-recovered pasa_asmbl_21543.p1, internal, 106983, 107196
-recovered pasa_asmbl_21543.p1, internal, 107497, 107641
Valid prediction for GlimmerHMM_glimmerT_44513-T1
Valid prediction for snap_scaffold_19-snap.1677-T1
Valid prediction for Augustus_model.g29515.t1
Valid prediction for GlimmerHMM_glimmerT_44504-T1
Valid prediction for snap_scaffold_19-snap.1672-T1
Valid prediction for HiQ_model.g29531.t1
Valid prediction for snap_scaffold_19-snap.1646-T1
Valid prediction for snap_scaffold_19-snap.1648-T1
Valid prediction for snap_scaffold_19-snap.1678-T1
Valid prediction for CodingQuarry_transcript_25744-T1
Valid prediction for snap_scaffold_19-snap.1675-T1
Valid prediction for snap_scaffold_19-snap.1673-T1
Couldn't classify 94305, 94670
Sorry, prediction pasa_asmbl_21539.p1 fails validation.
(CGT)	 GA	94305-94670	GA	GGG
Valid prediction for GlimmerHMM_glimmerT_44511-T1
Valid prediction for Augustus_model.g29529.t1
Valid prediction for snap_scaffold_19-snap.1674-T1
Valid prediction for Augustus_model.g29525.t1
Couldn't classify 116095, 116915
Couldn't classify 116994, 117135
Sorry, prediction CodingQuarry_transcript_25746-T1 fails validation.
(ATG)	 AT	114745-114877	GT	AGG
(ACA)	 AG	115009-115154	GT	GGG
(GCA)	 AG	115547-115664	GT	TGG
(GTG)	 AG	116095-116915	GA	ATG
(GAG)	 AT	116994-117135	GT	TGG
(AGG)	 AG	117264-117421	GT	CTG
(GCG)	 AG	117538-117655	GT	GGG
(GTG)	 AG	117917-118302	GG	AGG
-recovered CodingQuarry_transcript_25746-T1, initial, 114745, 114877
-recovered CodingQuarry_transcript_25746-T1, terminal, 117917, 118302
-recovered CodingQuarry_transcript_25746-T1, internal, 115009, 115154
-recovered CodingQuarry_transcript_25746-T1, internal, 115547, 115664
-recovered CodingQuarry_transcript_25746-T1, internal, 117264, 117421
-recovered CodingQuarry_transcript_25746-T1, internal, 117538, 117655
Valid prediction for Augustus_model.g29533.t1
Valid prediction for CodingQuarry_transcript_25745-T1
Valid prediction for GlimmerHMM_glimmerT_44496-T1
Valid prediction for GlimmerHMM_glimmerT_44509-T1
Couldn't classify 103158, 103222
Couldn't classify 104051, 104191
Sorry, prediction pasa_asmbl_21541.p1 fails validation.
(AAC)	 CC	103158-103222	GT	AGG
(TAC)	 AG	103379-103480	GT	AGG
(TTC)	 AG	103622-103682	GT	AGG
(GAG)	 AG	103820-103963	GT	AGG
(TGT)	 AG	104051-104191	CA	AGC
-recovered pasa_asmbl_21541.p1, internal, 103379, 103480
-recovered pasa_asmbl_21541.p1, internal, 103622, 103682
-recovered pasa_asmbl_21541.p1, internal, 103820, 103963
Valid prediction for snap_scaffold_19-snap.1651-T1
Valid prediction for Augustus_model.g29534.t1
Valid prediction for snap_scaffold_19-snap.1661-T1
Valid prediction for Augustus_model.g29518.t1
Valid prediction for GlimmerHMM_glimmerT_44507-T1
Valid prediction for snap_scaffold_19-snap.1649-T1
Valid prediction for HiQ_model.g29530.t1
Valid prediction for Augustus_model.g29522.t1
Valid prediction for GlimmerHMM_glimmerT_44512-T1
Valid prediction for pasa_asmbl_21546.p1
Valid prediction for snap_scaffold_19-snap.1664-T1
Valid prediction for snap_scaffold_19-snap.1666-T1
Valid prediction for GlimmerHMM_glimmerT_44499-T1
Valid prediction for snap_scaffold_19-snap.1653-T1
Valid prediction for snap_scaffold_19-snap.1668-T1
Valid prediction for snap_scaffold_19-snap.1670-T1
Couldn't classify 158801, 158918
Couldn't classify 159611, 159817
Sorry, prediction pasa_asmbl_21552.p1 fails validation.
(TTC)	 GA	158801-158918	GT	AGG
(GTG)	 AG	159411-159493	GT	ATG
(ATG)	 AG	159611-159817	GG	CCG
-recovered pasa_asmbl_21552.p1, internal, 159411, 159493
Valid prediction for snap_scaffold_19-snap.1680-T1
Valid prediction for Augustus_model.g29516.t1
Valid prediction for pasa_asmbl_21547.p1
Valid prediction for snap_scaffold_19-snap.1660-T1
Valid prediction for snap_scaffold_19-snap.1654-T1
Valid prediction for GlimmerHMM_glimmerT_44517-T1
Valid prediction for GlimmerHMM_glimmerT_44516-T1
Valid prediction for Augustus_model.g29527.t1
Valid prediction for snap_scaffold_19-snap.1644-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 HiQ_model.g29528.t1
Valid prediction for GlimmerHMM_glimmerT_44495-T1
Valid prediction for snap_scaffold_19-snap.1662-T1
Valid prediction for GlimmerHMM_glimmerT_44515-T1
Valid prediction for snap_scaffold_19-snap.1658-T1
Valid prediction for Augustus_model.g29519.t1
Valid prediction for CodingQuarry_transcript_25740-T1
Valid prediction for GlimmerHMM_glimmerT_44503-T1
Valid prediction for snap_scaffold_19-snap.1665-T1
Valid prediction for GlimmerHMM_glimmerT_44510-T1
Valid prediction for snap_scaffold_19-snap.1667-T1
Valid prediction for GlimmerHMM_glimmerT_44514-T1
Valid prediction for snap_scaffold_19-snap.1681-T1
Valid prediction for snap_scaffold_19-snap.1656-T1
Valid prediction for Augustus_model.g29521.t1
Valid prediction for snap_scaffold_19-snap.1671-T1
Valid prediction for HiQ_model.g29532.t1
Valid prediction for Augustus_model.g29523.t1
Valid prediction for GlimmerHMM_glimmerT_44500-T1
Valid prediction for pasa_asmbl_22311.p1
Valid prediction for GlimmerHMM_glimmerT_44505-T1
Valid prediction for snap_scaffold_19-snap.1663-T1
Valid prediction for snap_scaffold_19-snap.1679-T1
Valid prediction for CodingQuarry_transcript_25742-T1
Couldn't classify 71348, 71385
Couldn't classify 72650, 72805
Sorry, prediction pasa_asmbl_22304.p1 fails validation.
(GAA)	 AA	71348-71385	GT	AGG
(GTT)	 AG	71658-71787	GT	AGG
(GAG)	 AG	71889-72005	GT	AGG
(GTG)	 AG	72141-72215	GT	AGG
(AAG)	 AG	72650-72805	AC	CGA
-recovered pasa_asmbl_22304.p1, internal, 71658, 71787
-recovered pasa_asmbl_22304.p1, internal, 71889, 72005
-recovered pasa_asmbl_22304.p1, internal, 72141, 72215
Valid prediction for snap_scaffold_19-snap.1669-T1
Valid prediction for Augustus_model.g29520.t1
Valid prediction for Augustus_model.g29514.t1
Valid prediction for pasa_asmbl_22305.p1
Valid prediction for snap_scaffold_19-snap.1647-T1
Valid prediction for pasa_asmbl_22309.p1
Valid prediction for snap_scaffold_19-snap.1652-T1
Valid prediction for Augustus_model.g29517.t1
Valid prediction for HiQ_model.g29524.t1
Valid prediction for GlimmerHMM_glimmerT_44508-T1
Valid prediction for GlimmerHMM_glimmerT_44501-T1
Valid prediction for GlimmerHMM_glimmerT_44506-T1
Valid prediction for CodingQuarry_transcript_25743-T1
Valid prediction for snap_scaffold_19-snap.1676-T1
Valid prediction for HiQ_model.g29526.t1
Valid prediction for snap_scaffold_19-snap.1655-T1
Valid prediction for snap_scaffold_19-snap.1657-T1
Valid prediction for snap_scaffold_19-snap.1659-T1
Valid prediction for snap_scaffold_19-snap.1645-T1
Valid prediction for GlimmerHMM_glimmerT_44497-T1
Valid prediction for GlimmerHMM_glimmerT_44502-T1
Valid prediction for Augustus_model.g29513.t1
Valid prediction for pasa_asmbl_22307.p1
Valid prediction for CodingQuarry_transcript_25741-T1
Valid prediction for GlimmerHMM_glimmerT_44498-T1
Valid prediction for snap_scaffold_19-snap.1650-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 27779, rend_intergenic: 25728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38145, rend_intergenic: 34990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43109, rend_intergenic: 38933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51787, rend_intergenic: 46540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105813, rend_intergenic: 104305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106817, rend_intergenic: 106093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108764, rend_intergenic: 106977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110957, rend_intergenic: 109974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125455, rend_intergenic: 120238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130857, rend_intergenic: 125673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152781, rend_intergenic: 144619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160986, rend_intergenic: 155178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 161977
-exon list size: 322


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.4    
16.7    
17.0    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.1    
23.5    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
26.5    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.9    
52.2    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.5    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.5    
76.9    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.0    
83.3    
83.6    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 27779, rend_intergenic: 25728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38145, rend_intergenic: 34990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43109, rend_intergenic: 38933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51787, rend_intergenic: 46540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105813, rend_intergenic: 104305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106817, rend_intergenic: 106093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108764, rend_intergenic: 106977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110957, rend_intergenic: 109974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125455, rend_intergenic: 120238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130857, rend_intergenic: 125673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152781, rend_intergenic: 144619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160986, rend_intergenic: 155178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support