-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_4809491-4989163

-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_19-snap.1014-T1
Valid prediction for GlimmerHMM_glimmerT_44047-T1
Valid prediction for snap_scaffold_19-snap.1010-T1
Valid prediction for GlimmerHMM_glimmerT_44055-T1
Valid prediction for GlimmerHMM_glimmerT_44063-T1
Valid prediction for snap_scaffold_19-snap.1035-T1
Valid prediction for GlimmerHMM_glimmerT_44049-T1
Valid prediction for CodingQuarry_transcript_25642-T1
Valid prediction for Augustus_model.g29191.t1
Valid prediction for GlimmerHMM_glimmerT_44042-T1
Valid prediction for snap_scaffold_19-snap.1017-T1
Valid prediction for pasa_asmbl_21344.p1
Valid prediction for snap_scaffold_19-snap.1038-T1
Valid prediction for GlimmerHMM_glimmerT_44065-T1
Valid prediction for GlimmerHMM_glimmerT_44045-T1
Valid prediction for snap_scaffold_19-snap.1021-T1
Valid prediction for GlimmerHMM_glimmerT_44056-T1
Valid prediction for GlimmerHMM_glimmerT_44060-T1
Valid prediction for Augustus_model.g29186.t1
Valid prediction for GlimmerHMM_glimmerT_44041-T1
Valid prediction for GlimmerHMM_glimmerT_44061-T1
Valid prediction for snap_scaffold_19-snap.1030-T1
Valid prediction for Augustus_model.g29189.t1
Valid prediction for snap_scaffold_19-snap.1023-T1
Valid prediction for snap_scaffold_19-snap.1013-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.1032-T1
Valid prediction for Augustus_model.g29188.t1
Valid prediction for snap_scaffold_19-snap.1034-T1
Valid prediction for GlimmerHMM_glimmerT_44046-T1
Valid prediction for snap_scaffold_19-snap.1011-T1
Valid prediction for CodingQuarry_transcript_25644-T1
Valid prediction for snap_scaffold_19-snap.1019-T1
Valid prediction for snap_scaffold_19-snap.1028-T1
Valid prediction for GlimmerHMM_glimmerT_44054-T1
Valid prediction for HiQ_model.g29196.t1
Valid prediction for snap_scaffold_19-snap.1036-T1
Couldn't classify 53889, 53932
Sorry, prediction pasa_asmbl_21345.p1 fails validation.
(GTT)	 CT	53889-53932	GT	GTG
(CGA)	 AG	56463-56657	GT	GAG
(ATA)	 AG	56928-56982	GT	AGG
(GGC)	 AG	57211-57307	GT	TGG
(CTT)	 AG	57444-57502	GT	AAG
(TCT)	 AG	58637-58709	GT	CGG
(CAA)	 AG	58815-58888	GT	AGG
(ATC)	 AG	59112-59246	CA	GAC
-recovered pasa_asmbl_21345.p1, terminal, 59112, 59246
-recovered pasa_asmbl_21345.p1, internal, 56463, 56657
-recovered pasa_asmbl_21345.p1, internal, 56928, 56982
-recovered pasa_asmbl_21345.p1, internal, 57211, 57307
-recovered pasa_asmbl_21345.p1, internal, 57444, 57502
-recovered pasa_asmbl_21345.p1, internal, 58637, 58709
-recovered pasa_asmbl_21345.p1, internal, 58815, 58888
Valid prediction for snap_scaffold_19-snap.1041-T1
Valid prediction for Augustus_model.g29187.t1
Valid prediction for pasa_asmbl_21347.p1
Valid prediction for GlimmerHMM_glimmerT_44058-T1
Valid prediction for GlimmerHMM_glimmerT_44052-T1
Valid prediction for Augustus_model.g29185.t1
Valid prediction for GlimmerHMM_glimmerT_44053-T1
Valid prediction for snap_scaffold_19-snap.1015-T1
Valid prediction for CodingQuarry_transcript_25641-T1
Valid prediction for GlimmerHMM_glimmerT_44048-T1
Valid prediction for GlimmerHMM_glimmerT_44066-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 snap_scaffold_19-snap.1026-T1
Valid prediction for GlimmerHMM_glimmerT_44062-T1
Valid prediction for snap_scaffold_19-snap.1020-T1
Valid prediction for GlimmerHMM_glimmerT_44043-T1
Valid prediction for GlimmerHMM_glimmerT_44051-T1
Valid prediction for Augustus_model.g29190.t1
Valid prediction for pasa_asmbl_22140.p1
Valid prediction for snap_scaffold_19-snap.1009-T1
Valid prediction for Augustus_model.g29192.t1
Valid prediction for GlimmerHMM_glimmerT_44044-T1
Valid prediction for GlimmerHMM_glimmerT_44040-T1
Valid prediction for snap_scaffold_19-snap.1025-T1
Valid prediction for Augustus_model.g29193.t1
Valid prediction for snap_scaffold_19-snap.1027-T1
Valid prediction for HiQ_model.g29194.t1
Valid prediction for snap_scaffold_19-snap.1042-T1
Couldn't classify 163979, 164119
Sorry, prediction pasa_asmbl_22138.p1 fails validation.
(ATG)	 CT	159487-159586	GT	AGG
(GGA)	 AG	159711-159755	GT	GTG
(CCT)	 AG	159928-160046	GT	AGG
(GGC)	 AG	160256-160372	GT	CGG
(ATG)	 AG	160570-160649	GT	AGG
(GTC)	 AG	160816-160927	GT	GGG
(ACG)	 AG	161029-161119	GT	AGG
(TGT)	 AG	161256-161403	GT	AGG
(AGT)	 AG	161538-161668	GT	GGG
(GTC)	 AG	161771-161875	GT	TGG
(ACC)	 AG	161983-162091	GT	CAG
(CAG)	 AG	163322-163508	GT	AGG
(ACT)	 AG	163634-163849	GT	GGG
(GAG)	 AG	163979-164119	GG	AAG
-recovered pasa_asmbl_22138.p1, initial, 159487, 159586
-recovered pasa_asmbl_22138.p1, initial, 160570, 160649
-recovered pasa_asmbl_22138.p1, internal, 159711, 159755
-recovered pasa_asmbl_22138.p1, internal, 159928, 160046
-recovered pasa_asmbl_22138.p1, internal, 160256, 160372
-recovered pasa_asmbl_22138.p1, internal, 160570, 160649
-recovered pasa_asmbl_22138.p1, internal, 160816, 160927
-recovered pasa_asmbl_22138.p1, internal, 161029, 161119
-recovered pasa_asmbl_22138.p1, internal, 161256, 161403
-recovered pasa_asmbl_22138.p1, internal, 161538, 161668
-recovered pasa_asmbl_22138.p1, internal, 161771, 161875
-recovered pasa_asmbl_22138.p1, internal, 161983, 162091
-recovered pasa_asmbl_22138.p1, internal, 163322, 163508
-recovered pasa_asmbl_22138.p1, internal, 163634, 163849
Valid prediction for Augustus_model.g29195.t1
Valid prediction for snap_scaffold_19-snap.1033-T1
Valid prediction for snap_scaffold_19-snap.1022-T1
Valid prediction for snap_scaffold_19-snap.1029-T1
Valid prediction for snap_scaffold_19-snap.1024-T1
Valid prediction for GlimmerHMM_glimmerT_44050-T1
Valid prediction for snap_scaffold_19-snap.1031-T1
Valid prediction for CodingQuarry_transcript_25643-T1
Valid prediction for snap_scaffold_19-snap.1040-T1
Valid prediction for GlimmerHMM_glimmerT_44059-T1
Valid prediction for GlimmerHMM_glimmerT_44064-T1
Valid prediction for snap_scaffold_19-snap.1016-T1
Couldn't classify 171200, 171352
Sorry, prediction pasa_asmbl_22137.p1 fails validation.
(ATG)	 TG	169672-169785	GT	CGG
(CTG)	 AG	169945-170068	GT	CGG
(GTG)	 AG	170217-170484	GT	AAG
(GTT)	 AG	170637-170734	GT	CTG
(GTC)	 AG	170861-170973	GT	AGG
(ATC)	 AG	171200-171352	AG	GCA
-recovered pasa_asmbl_22137.p1, initial, 169672, 169785
-recovered pasa_asmbl_22137.p1, internal, 169945, 170068
-recovered pasa_asmbl_22137.p1, internal, 170217, 170484
-recovered pasa_asmbl_22137.p1, internal, 170637, 170734
-recovered pasa_asmbl_22137.p1, internal, 170861, 170973
Valid prediction for snap_scaffold_19-snap.1018-T1
Valid prediction for snap_scaffold_19-snap.1039-T1
Valid prediction for snap_scaffold_19-snap.1037-T1
Valid prediction for GlimmerHMM_glimmerT_44057-T1
Valid prediction for Augustus_model.g29184.t1
Valid prediction for snap_scaffold_19-snap.1012-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23501, rend_intergenic: 6627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28328, rend_intergenic: 24615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59246, rend_intergenic: 48916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67739, rend_intergenic: 65944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93682, rend_intergenic: 92232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98392, rend_intergenic: 95752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115567, rend_intergenic: 109159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129789, rend_intergenic: 121156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136954, rend_intergenic: 134187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177578, rend_intergenic: 174190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179673
-exon list size: 307


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    
6.1    
6.5    
6.8    
7.1    
7.4    
7.8    
8.1    
8.4    
8.7    
9.1    
9.4    
9.7    
10.0    
10.4    
10.7    
11.0    
11.3    
11.7    
12.0    
12.3    
12.6    
12.9    
13.3    
13.6    
13.9    
14.2    
14.6    
14.9    
15.2    
15.5    
15.9    
16.2    
16.5    
16.8    
17.2    
17.5    
17.8    
18.1    
18.4    
18.8    
19.1    
19.4    
19.7    
20.1    
20.4    
20.7    
21.0    
21.4    
21.7    
22.0    
22.3    
22.7    
23.0    
23.3    
23.6    
23.9    
24.3    
24.6    
24.9    
25.2    
25.6    
25.9    
26.2    
26.5    
26.9    
27.2    
27.5    
27.8    
28.2    
28.5    
28.8    
29.1    
29.4    
29.8    
30.1    
30.4    
30.7    
31.1    
31.4    
31.7    
32.0    
32.4    
32.7    
33.0    
33.3    
33.7    
34.0    
34.3    
34.6    
35.0    
35.3    
35.6    
35.9    
36.2    
36.6    
36.9    
37.2    
37.5    
37.9    
38.2    
38.5    
38.8    
39.2    
39.5    
39.8    
40.1    
40.5    
40.8    
41.1    
41.4    
41.7    
42.1    
42.4    
42.7    
43.0    
43.4    
43.7    
44.0    
44.3    
44.7    
45.0    
45.3    
45.6    
46.0    
46.3    
46.6    
46.9    
47.2    
47.6    
47.9    
48.2    
48.5    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.5    
51.8    
52.1    
52.4    
52.8    
53.1    
53.4    
53.7    
54.0    
54.4    
54.7    
55.0    
55.3    
55.7    
56.0    
56.3    
56.6    
57.0    
57.3    
57.6    
57.9    
58.3    
58.6    
58.9    
59.2    
59.5    
59.9    
60.2    
60.5    
60.8    
61.2    
61.5    
61.8    
62.1    
62.5    
62.8    
63.1    
63.4    
63.8    
64.1    
64.4    
64.7    
65.0    
65.4    
65.7    
66.0    
66.3    
66.7    
67.0    
67.3    
67.6    
68.0    
68.3    
68.6    
68.9    
69.3    
69.6    
69.9    
70.2    
70.6    
70.9    
71.2    
71.5    
71.8    
72.2    
72.5    
72.8    
73.1    
73.5    
73.8    
74.1    
74.4    
74.8    
75.1    
75.4    
75.7    
76.1    
76.4    
76.7    
77.0    
77.3    
77.7    
78.0    
78.3    
78.6    
79.0    
79.3    
79.6    
79.9    
80.3    
80.6    
80.9    
81.2    
81.6    
81.9    
82.2    
82.5    
82.8    
83.2    
83.5    
83.8    
84.1    
84.5    
84.8    
85.1    
85.4    
85.8    
86.1    
86.4    
86.7    
87.1    
87.4    
87.7    
88.0    
88.3    
88.7    
89.0    
89.3    
89.6    
90.0    
90.3    
90.6    
90.9    
91.3    
91.6    
91.9    
92.2    
92.6    
92.9    
93.2    
93.5    
93.9    
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: 23501, rend_intergenic: 6627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28328, rend_intergenic: 24615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59246, rend_intergenic: 48916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67739, rend_intergenic: 65944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93682, rend_intergenic: 92232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98392, rend_intergenic: 95752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115567, rend_intergenic: 109159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129789, rend_intergenic: 121156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136954, rend_intergenic: 134187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177578, rend_intergenic: 174190  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