-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_7232799-7472985

-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_1-snap.1303-T1
Valid prediction for GlimmerHMM_glimmerT_1056-T1
Valid prediction for snap_scaffold_1-snap.1313-T1
Valid prediction for snap_scaffold_1-snap.1264-T1
Valid prediction for Augustus_model.g764.t1
Valid prediction for Augustus_model.g771.t1
Valid prediction for GeneMark_model.1290_t
Valid prediction for Augustus_model.g774.t1
Valid prediction for Augustus_model.g768.t1
Valid prediction for GeneMark_model.1314_t
Valid prediction for GeneMark_model.1270_t
Valid prediction for GeneMark_model.1289_t
Valid prediction for snap_scaffold_1-snap.1295-T1
Valid prediction for GlimmerHMM_glimmerT_1058-T1
Valid prediction for pasa_asmbl_1894.p1
Valid prediction for CodingQuarry_transcript_2685-T1
Valid prediction for GlimmerHMM_glimmerT_1034-T1
Valid prediction for snap_scaffold_1-snap.1312-T1
Valid prediction for GeneMark_model.1296_t
Valid prediction for snap_scaffold_1-snap.1308-T1
Valid prediction for GeneMark_model.1321_t
Valid prediction for GeneMark_model.1299_t
Valid prediction for GeneMark_model.1277_t
Valid prediction for GlimmerHMM_glimmerT_1049-T1
Valid prediction for GeneMark_model.1268_t
Valid prediction for GeneMark_model.1316_t
Valid prediction for snap_scaffold_1-snap.1286-T1
Valid prediction for GlimmerHMM_glimmerT_1061-T1
Valid prediction for snap_scaffold_1-snap.1280-T1
Valid prediction for GlimmerHMM_glimmerT_1048-T1
Valid prediction for GeneMark_model.1307_t
Valid prediction for GeneMark_model.1283_t
Valid prediction for GeneMark_model.1302_t
Valid prediction for GeneMark_model.1298_t
Valid prediction for snap_scaffold_1-snap.1307-T1
Valid prediction for GlimmerHMM_glimmerT_1054-T1
Valid prediction for GlimmerHMM_glimmerT_1033-T1
Valid prediction for snap_scaffold_1-snap.1279-T1
Valid prediction for snap_scaffold_1-snap.1305-T1
Valid prediction for GeneMark_model.1319_t
Valid prediction for Augustus_model.g769.t1
Valid prediction for GeneMark_model.1310_t
Valid prediction for GeneMark_model.1294_t
Valid prediction for snap_scaffold_1-snap.1271-T1
Valid prediction for snap_scaffold_1-snap.1288-T1
Valid prediction for snap_scaffold_1-snap.1292-T1
Valid prediction for GeneMark_model.1313_t
Valid prediction for snap_scaffold_1-snap.1301-T1
Valid prediction for snap_scaffold_1-snap.1283-T1
Valid prediction for GeneMark_model.1281_t
Valid prediction for GeneMark_model.1286_t
Valid prediction for GeneMark_model.1280_t
Valid prediction for snap_scaffold_1-snap.1269-T1
Valid prediction for snap_scaffold_1-snap.1267-T1
Valid prediction for Augustus_model.g758.t1
Valid prediction for GlimmerHMM_glimmerT_1044-T1
Valid prediction for GeneMark_model.1288_t
Valid prediction for snap_scaffold_1-snap.1298-T1
Valid prediction for GlimmerHMM_glimmerT_1042-T1
Valid prediction for GlimmerHMM_glimmerT_1045-T1
Valid prediction for snap_scaffold_1-snap.1284-T1
Valid prediction for GeneMark_model.1292_t
Valid prediction for Augustus_model.g766.t1
Valid prediction for GeneMark_model.1278_t
Valid prediction for snap_scaffold_1-snap.1273-T1
Valid prediction for GeneMark_model.1305_t

-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_2689-T1
Valid prediction for GlimmerHMM_glimmerT_1062-T1
Valid prediction for GeneMark_model.1309_t
Valid prediction for GeneMark_model.1318_t
Valid prediction for GeneMark_model.1312_t
Valid prediction for GlimmerHMM_glimmerT_1039-T1
Valid prediction for CodingQuarry_transcript_2681-T1
Valid prediction for snap_scaffold_1-snap.1277-T1
Valid prediction for snap_scaffold_1-snap.1270-T1
Valid prediction for pasa_asmbl_422.p1
Valid prediction for snap_scaffold_1-snap.1275-T1
Valid prediction for GlimmerHMM_glimmerT_1031-T1
Valid prediction for GeneMark_model.1320_t
Valid prediction for GlimmerHMM_glimmerT_1043-T1
Valid prediction for GeneMark_model.1295_t
Valid prediction for GlimmerHMM_glimmerT_1030-T1
Valid prediction for GeneMark_model.1276_t
Valid prediction for HiQ_model.g762.t1
Valid prediction for snap_scaffold_1-snap.1299-T1
Valid prediction for GeneMark_model.1303_t
Valid prediction for HiQ_model.g767.t1
Valid prediction for GeneMark_model.1304_t
Valid prediction for GlimmerHMM_glimmerT_1040-T1
Valid prediction for HiQ_model.g760.t1
Valid prediction for HiQ_model.g763.t1
Valid prediction for GeneMark_model.1297_t
Valid prediction for CodingQuarry_transcript_2686-T1
Valid prediction for GlimmerHMM_glimmerT_1055-T1
Valid prediction for GlimmerHMM_glimmerT_1059-T1
Valid prediction for Augustus_model.g757.t1
Valid prediction for GlimmerHMM_glimmerT_1036-T1
Valid prediction for Augustus_model.g773.t1
Valid prediction for CodingQuarry_transcript_2682-T1
Valid prediction for snap_scaffold_1-snap.1274-T1
Valid prediction for snap_scaffold_1-snap.1290-T1
Valid prediction for pasa_asmbl_432.p1
Valid prediction for GeneMark_model.1311_t
Valid prediction for snap_scaffold_1-snap.1300-T1
Valid prediction for GeneMark_model.1282_t
Valid prediction for pasa_asmbl_446.p1
Valid prediction for snap_scaffold_1-snap.1311-T1
Valid prediction for HiQ_model.g761.t1
Valid prediction for snap_scaffold_1-snap.1265-T1
Valid prediction for snap_scaffold_1-snap.1266-T1
Valid prediction for snap_scaffold_1-snap.1310-T1
Valid prediction for snap_scaffold_1-snap.1289-T1
Valid prediction for snap_scaffold_1-snap.1306-T1
Valid prediction for GlimmerHMM_glimmerT_1052-T1
Valid prediction for GlimmerHMM_glimmerT_1051-T1
Valid prediction for CodingQuarry_transcript_2687-T1
Valid prediction for snap_scaffold_1-snap.1287-T1
Valid prediction for GlimmerHMM_glimmerT_1041-T1
Valid prediction for pasa_asmbl_440.p1
Valid prediction for GeneMark_model.1306_t
Valid prediction for GeneMark_model.1272_t
Valid prediction for GlimmerHMM_glimmerT_1053-T1
Valid prediction for Augustus_model.g765.t1
Valid prediction for GlimmerHMM_glimmerT_1035-T1
Couldn't classify 52767, 52793
Sorry, prediction pasa_asmbl_445.p1 fails validation.
(TTG)	 AT	52767-52793	GT	AGG
(CAA)	 AG	53230-53340	GT	ACG
(GCT)	 AG	53532-53627	GT	AGG
(TCC)	 AG	53864-53944	CT	AGC
-recovered pasa_asmbl_445.p1, terminal, 53864, 53944
-recovered pasa_asmbl_445.p1, internal, 53230, 53340
-recovered pasa_asmbl_445.p1, internal, 53532, 53627
Valid prediction for CodingQuarry_transcript_2688-T1
Valid prediction for Augustus_model.g756.t1
Valid prediction for HiQ_model.g759.t1
Valid prediction for snap_scaffold_1-snap.1309-T1
Valid prediction for snap_scaffold_1-snap.1297-T1
Couldn't classify 236865, 237200
Sorry, prediction pasa_asmbl_1889.p1 fails validation.
(ATG)	 CA	236865-237200	GG	CAG
Valid prediction for CodingQuarry_transcript_2680-T1
Valid prediction for pasa_asmbl_428.p1
Valid prediction for GlimmerHMM_glimmerT_1050-T1
Valid prediction for pasa_asmbl_434.p1
Valid prediction for CodingQuarry_transcript_2683-T1
Valid prediction for snap_scaffold_1-snap.1285-T1
Valid prediction for snap_scaffold_1-snap.1302-T1
Valid prediction for GeneMark_model.1271_t
Valid prediction for GlimmerHMM_glimmerT_1038-T1
Valid prediction for GeneMark_model.1274_t
Valid prediction for pasa_asmbl_430.p1
Valid prediction for snap_scaffold_1-snap.1304-T1
Valid prediction for GeneMark_model.1291_t
Valid prediction for GeneMark_model.1279_t
Valid prediction for snap_scaffold_1-snap.1282-T1
Valid prediction for GlimmerHMM_glimmerT_1057-T1
Valid prediction for GlimmerHMM_glimmerT_1060-T1
Valid prediction for Augustus_model.g772.t1
Valid prediction for GeneMark_model.1273_t
Valid prediction for Augustus_model.g755.t1
Valid prediction for snap_scaffold_1-snap.1278-T1
Valid prediction for GeneMark_model.1285_t
Valid prediction for GlimmerHMM_glimmerT_1047-T1
Valid prediction for GeneMark_model.1315_t
Valid prediction for snap_scaffold_1-snap.1291-T1
Valid prediction for CodingQuarry_transcript_2684-T1
Valid prediction for GlimmerHMM_glimmerT_1032-T1
Valid prediction for GeneMark_model.1269_t
Valid prediction for GlimmerHMM_glimmerT_1037-T1
Valid prediction for snap_scaffold_1-snap.1293-T1
Valid prediction for snap_scaffold_1-snap.1272-T1
Valid prediction for GeneMark_model.1317_t
Valid prediction for snap_scaffold_1-snap.1296-T1
Valid prediction for GeneMark_model.1300_t
Valid prediction for GeneMark_model.1301_t
Valid prediction for GeneMark_model.1275_t
Valid prediction for HiQ_model.g770.t1
Valid prediction for snap_scaffold_1-snap.1268-T1
Valid prediction for GeneMark_model.1308_t
Valid prediction for GeneMark_model.1284_t
Valid prediction for snap_scaffold_1-snap.1276-T1
Valid prediction for GlimmerHMM_glimmerT_1046-T1
Valid prediction for GeneMark_model.1293_t
Valid prediction for snap_scaffold_1-snap.1281-T1
Valid prediction for snap_scaffold_1-snap.1294-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28793, rend_intergenic: 22802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37686, rend_intergenic: 35499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39878, rend_intergenic: 39376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43859, rend_intergenic: 42398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46021, rend_intergenic: 44993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65260, rend_intergenic: 60655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69777, rend_intergenic: 66939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83127, rend_intergenic: 71990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87548, rend_intergenic: 85666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90665, rend_intergenic: 89958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96780, rend_intergenic: 90674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114195, rend_intergenic: 98905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114768, rend_intergenic: 114457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116448, rend_intergenic: 115009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136054, rend_intergenic: 117130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153353, rend_intergenic: 149213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168405, rend_intergenic: 164249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172896, rend_intergenic: 168689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176837, rend_intergenic: 174642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184608, rend_intergenic: 179636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198249, rend_intergenic: 193735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 240187
-exon list size: 872


building trellis

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68.4    
68.5    
68.6    
68.8    
68.9    
69.0    
69.1    
69.2    
69.3    
69.5    
69.6    
69.7    
69.8    
69.9    
70.0    
70.1    
70.3    
70.4    
70.5    
70.6    
70.7    
70.8    
70.9    
71.1    
71.2    
71.3    
71.4    
71.5    
71.6    
71.7    
71.9    
72.0    
72.1    
72.2    
72.3    
72.4    
72.5    
72.7    
72.8    
72.9    
73.0    
73.1    
73.2    
73.3    
73.5    
73.6    
73.7    
73.8    
73.9    
74.0    
74.1    
74.3    
74.4    
74.5    
74.6    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.4    
75.5    
75.6    
75.7    
75.9    
76.0    
76.1    
76.2    
76.3    
76.4    
76.5    
76.7    
76.8    
76.9    
77.0    
77.1    
77.2    
77.3    
77.5    
77.6    
77.7    
77.8    
77.9    
78.0    
78.1    
78.3    
78.4    
78.5    
78.6    
78.7    
78.8    
78.9    
79.1    
79.2    
79.3    
79.4    
79.5    
79.6    
79.7    
79.9    
80.0    
80.1    
80.2    
80.3    
80.4    
80.5    
80.7    
80.8    
80.9    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.7    
81.8    
81.9    
82.0    
82.2    
82.3    
82.4    
82.5    
82.6    
82.7    
82.8    
83.0    
83.1    
83.2    
83.3    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.1    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
84.9    
85.0    
85.1    
85.2    
85.4    
85.5    
85.6    
85.7    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.5    
86.6    
86.7    
86.8    
87.0    
87.1    
87.2    
87.3    
87.4    
87.5    
87.6    
87.8    
87.9    
88.0    
88.1    
88.2    
88.3    
88.4    
88.6    
88.7    
88.8    
88.9    
89.0    
89.1    
89.2    
89.4    
89.5    
89.6    
89.7    
89.8    
89.9    
90.0    
90.2    
90.3    
90.4    
90.5    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.3    
91.4    
91.5    
91.6    
91.8    
91.9    
92.0    
92.1    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
92.9    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.7    
93.8    
93.9    
94.1    
94.2    
94.3    
94.4    
94.5    
94.6    
94.7    
94.9    
95.0    
95.1    
95.2    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.0    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.8    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.6    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.4    
98.5    
98.6    
98.7    
98.9    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.7    
99.8    
99.9    
-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 28793, rend_intergenic: 22802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37686, rend_intergenic: 35499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39878, rend_intergenic: 39376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43859, rend_intergenic: 42398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46021, rend_intergenic: 44993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65260, rend_intergenic: 60655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69777, rend_intergenic: 66939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83127, rend_intergenic: 71990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87548, rend_intergenic: 85666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90665, rend_intergenic: 89958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96780, rend_intergenic: 90674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114195, rend_intergenic: 98905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114768, rend_intergenic: 114457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116448, rend_intergenic: 115009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136054, rend_intergenic: 117130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153353, rend_intergenic: 149213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168405, rend_intergenic: 164249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172896, rend_intergenic: 168689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176837, rend_intergenic: 174642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184608, rend_intergenic: 179636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198249, rend_intergenic: 193735  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

-building DP trellis

-building trellis in range 222400 - 240187
-exon list size: 15


building trellis

5.9    
11.8    
17.6    
23.5    
29.4    
35.3    
41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 223099 - 240187
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 223099 - 237610
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 223099 - 236911
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 223099 - 234727
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 223767 - 234727
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support