-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_5935288-6143760

-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 CodingQuarry_transcript_57374-T1
Valid prediction for pasa_asmbl_50719.p1
Valid prediction for GeneMark_model.30057_t
Valid prediction for snap_scaffold_7-snap.1286-T1
Valid prediction for GeneMark_model.30051_t
Valid prediction for snap_scaffold_7-snap.1287-T1
Valid prediction for HiQ_model.g12027.t1
Valid prediction for snap_scaffold_7-snap.1280-T1
Valid prediction for GlimmerHMM_glimmerT_17910-T1
Valid prediction for snap_scaffold_7-snap.1268-T1
Valid prediction for snap_scaffold_7-snap.1236-T1
Valid prediction for snap_scaffold_7-snap.1259-T1
Valid prediction for GeneMark_model.30053_t
Valid prediction for GeneMark_model.30040_t
Valid prediction for snap_scaffold_7-snap.1251-T1
Valid prediction for GlimmerHMM_glimmerT_17909-T1
Valid prediction for GlimmerHMM_glimmerT_17917-T1
Valid prediction for Augustus_model.g12025.t1
Valid prediction for GlimmerHMM_glimmerT_17904-T1
Valid prediction for GlimmerHMM_glimmerT_17922-T1
Valid prediction for Augustus_model.g12030.t1
Valid prediction for GlimmerHMM_glimmerT_17892-T1
Valid prediction for snap_scaffold_7-snap.1279-T1
Valid prediction for GeneMark_model.30047_t
Valid prediction for snap_scaffold_7-snap.1262-T1
Valid prediction for GeneMark_model.30032_t
Couldn't classify 171508, 171534
Couldn't classify 172358, 172493
Sorry, prediction pasa_asmbl_50725.p1 fails validation.
(CTG)	 GG	171508-171534	GT	AGG
(TAT)	 AG	172112-172245	GT	AGG
(CTC)	 AG	172358-172493	AC	CCA
-recovered pasa_asmbl_50725.p1, internal, 172112, 172245
Valid prediction for snap_scaffold_7-snap.1288-T1
Couldn't classify 162025, 162125
Couldn't classify 163532, 163664
Sorry, prediction pasa_asmbl_50724.p1 fails validation.
(GAG)	 GG	162025-162125	GT	AGG
(GGA)	 AG	163023-163155	GT	GGG
(GAC)	 AG	163318-163445	GT	AGG
(AGT)	 AG	163532-163664	AG	GGA
-recovered pasa_asmbl_50724.p1, internal, 163023, 163155
-recovered pasa_asmbl_50724.p1, internal, 163318, 163445
Valid prediction for snap_scaffold_7-snap.1274-T1
Valid prediction for snap_scaffold_7-snap.1283-T1
Valid prediction for CodingQuarry_transcript_57371-T1
Valid prediction for GlimmerHMM_glimmerT_17916-T1
Valid prediction for Augustus_model.g12020.t1
Valid prediction for GeneMark_model.30030_t
Valid prediction for Augustus_model.g12022.t1
Valid prediction for Augustus_model.g12017.t1
Valid prediction for GeneMark_model.30074_t
Valid prediction for GeneMark_model.30044_t
Valid prediction for snap_scaffold_7-snap.1257-T1
Valid prediction for snap_scaffold_7-snap.1266-T1
Valid prediction for Augustus_model.g12019.t1
Valid prediction for GeneMark_model.30067_t
Valid prediction for snap_scaffold_7-snap.1277-T1
Valid prediction for snap_scaffold_7-snap.1239-T1
Valid prediction for snap_scaffold_7-snap.1243-T1
Valid prediction for snap_scaffold_7-snap.1247-T1
Valid prediction for snap_scaffold_7-snap.1235-T1
Valid prediction for GeneMark_model.30078_t
Valid prediction for snap_scaffold_7-snap.1245-T1
Valid prediction for GlimmerHMM_glimmerT_17901-T1
Valid prediction for GeneMark_model.30058_t
Valid prediction for snap_scaffold_7-snap.1273-T1
Valid prediction for GlimmerHMM_glimmerT_17898-T1
Valid prediction for GeneMark_model.30063_t
Valid prediction for CodingQuarry_transcript_57370-T1
Valid prediction for GlimmerHMM_glimmerT_17907-T1
Valid prediction for GeneMark_model.30035_t
Valid prediction for snap_scaffold_7-snap.1253-T1
Valid prediction for GlimmerHMM_glimmerT_17918-T1
Valid prediction for snap_scaffold_7-snap.1278-T1
Valid prediction for GlimmerHMM_glimmerT_17905-T1
Valid prediction for snap_scaffold_7-snap.1282-T1
Valid prediction for snap_scaffold_7-snap.1264-T1
Valid prediction for GlimmerHMM_glimmerT_17893-T1
Couldn't classify 172944, 173003
Sorry, prediction pasa_asmbl_50726.p1 fails validation.
(GAG)	 TG	172944-173003	GT	AGG
(TAC)	 AG	173789-173937	GT	AGG
(AGC)	 AG	174997-175167	GT	ATG
(GAT)	 AG	175385-175581	GT	GGG
(ACT)	 AG	175688-175831	GT	GGG
(AGG)	 AG	176377-176504	GT	AGG
(GAC)	 AG	177388-177497	GT	AAG
(GGA)	 AG	178175-178284	GT	AGG
(GTA)	 AG	178395-178498	AG	AGA
-recovered pasa_asmbl_50726.p1, terminal, 177388, 177497
-recovered pasa_asmbl_50726.p1, terminal, 178395, 178498
-recovered pasa_asmbl_50726.p1, internal, 173789, 173937
-recovered pasa_asmbl_50726.p1, internal, 174997, 175167
-recovered pasa_asmbl_50726.p1, internal, 175385, 175581
-recovered pasa_asmbl_50726.p1, internal, 175688, 175831
-recovered pasa_asmbl_50726.p1, internal, 176377, 176504
-recovered pasa_asmbl_50726.p1, internal, 177388, 177497
-recovered pasa_asmbl_50726.p1, internal, 178175, 178284
Valid prediction for GeneMark_model.30052_t
Valid prediction for GeneMark_model.30076_t
Valid prediction for GeneMark_model.30066_t
Valid prediction for snap_scaffold_7-snap.1255-T1
Valid prediction for snap_scaffold_7-snap.1271-T1
Valid prediction for GlimmerHMM_glimmerT_17914-T1
Valid prediction for snap_scaffold_7-snap.1237-T1
Valid prediction for GeneMark_model.30038_t
Valid prediction for CodingQuarry_transcript_57375-T1
Valid prediction for HiQ_model.g12023.t1
Valid prediction for GeneMark_model.30055_t
Valid prediction for Augustus_model.g12021.t1
Valid prediction for snap_scaffold_7-snap.1252-T1
Valid prediction for GeneMark_model.30049_t
Valid prediction for Augustus_model.g12028.t1
Valid prediction for GlimmerHMM_glimmerT_17903-T1
Valid prediction for GeneMark_model.30068_t
Valid prediction for GlimmerHMM_glimmerT_17919-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 GeneMark_model.30046_t
Valid prediction for snap_scaffold_7-snap.1244-T1
Valid prediction for GeneMark_model.30069_t
Valid prediction for GeneMark_model.30042_t
Valid prediction for GlimmerHMM_glimmerT_17895-T1
Valid prediction for snap_scaffold_7-snap.1248-T1
Valid prediction for snap_scaffold_7-snap.1254-T1
Valid prediction for snap_scaffold_7-snap.1256-T1
Valid prediction for GlimmerHMM_glimmerT_17899-T1
Valid prediction for snap_scaffold_7-snap.1240-T1
Valid prediction for GlimmerHMM_glimmerT_17921-T1
Valid prediction for snap_scaffold_7-snap.1272-T1
Valid prediction for GeneMark_model.30065_t
Valid prediction for GeneMark_model.30034_t
Valid prediction for snap_scaffold_7-snap.1281-T1
Valid prediction for GeneMark_model.30077_t
Valid prediction for GeneMark_model.30037_t
Valid prediction for GlimmerHMM_glimmerT_17912-T1
Valid prediction for GlimmerHMM_glimmerT_17911-T1
Valid prediction for GlimmerHMM_glimmerT_17920-T1
Valid prediction for snap_scaffold_7-snap.1267-T1
Valid prediction for Augustus_model.g12016.t1
Valid prediction for GeneMark_model.30075_t
Valid prediction for pasa_asmbl_49723.p1
Valid prediction for GeneMark_model.30039_t
Valid prediction for GlimmerHMM_glimmerT_17906-T1
Valid prediction for GlimmerHMM_glimmerT_17891-T1
Valid prediction for GlimmerHMM_glimmerT_17894-T1
Valid prediction for GeneMark_model.30061_t
Valid prediction for snap_scaffold_7-snap.1241-T1
Valid prediction for GlimmerHMM_glimmerT_17900-T1
Couldn't classify 78981, 79184
Sorry, prediction pasa_asmbl_49727.p1 fails validation.
(ATG)	 AG	76092-76328	GT	AGG
(GCC)	 AG	78981-79184	AG	TGA
-recovered pasa_asmbl_49727.p1, initial, 76092, 76328
-recovered pasa_asmbl_49727.p1, internal, 76092, 76328
Valid prediction for GeneMark_model.30080_t
Valid prediction for snap_scaffold_7-snap.1265-T1
Valid prediction for GeneMark_model.30060_t
Valid prediction for Augustus_model.g12014.t1
Valid prediction for snap_scaffold_7-snap.1270-T1
Valid prediction for snap_scaffold_7-snap.1275-T1
Valid prediction for Augustus_model.g12018.t1
Valid prediction for GeneMark_model.30048_t
Valid prediction for snap_scaffold_7-snap.1269-T1
Valid prediction for GeneMark_model.30045_t
Valid prediction for snap_scaffold_7-snap.1246-T1
Valid prediction for snap_scaffold_7-snap.1242-T1
Valid prediction for GeneMark_model.30054_t
Valid prediction for GeneMark_model.30056_t
Valid prediction for snap_scaffold_7-snap.1285-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.30043_t
Valid prediction for snap_scaffold_7-snap.1249-T1
Valid prediction for snap_scaffold_7-snap.1238-T1
Valid prediction for GeneMark_model.30033_t
Valid prediction for Augustus_model.g12015.t1
Valid prediction for GeneMark_model.30029_t
Valid prediction for GeneMark_model.30041_t
Valid prediction for snap_scaffold_7-snap.1261-T1
Valid prediction for snap_scaffold_7-snap.1260-T1
Valid prediction for GeneMark_model.30050_t
Valid prediction for snap_scaffold_7-snap.1258-T1
Valid prediction for snap_scaffold_7-snap.1284-T1
Valid prediction for GlimmerHMM_glimmerT_17915-T1
Valid prediction for GeneMark_model.30064_t
Valid prediction for GeneMark_model.30036_t
Valid prediction for Augustus_model.g12026.t1
Valid prediction for GeneMark_model.30073_t
Valid prediction for CodingQuarry_transcript_57372-T1
Valid prediction for snap_scaffold_7-snap.1263-T1
Valid prediction for GlimmerHMM_glimmerT_17902-T1
Valid prediction for HiQ_model.g12024.t1
Valid prediction for GlimmerHMM_glimmerT_17908-T1
Valid prediction for GlimmerHMM_glimmerT_17897-T1
Valid prediction for GeneMark_model.30059_t
Valid prediction for GeneMark_model.30062_t
Valid prediction for snap_scaffold_7-snap.1276-T1
Valid prediction for GeneMark_model.30070_t
Valid prediction for GeneMark_model.30071_t
Valid prediction for GlimmerHMM_glimmerT_17896-T1
Valid prediction for GlimmerHMM_glimmerT_17913-T1
Valid prediction for GeneMark_model.30079_t
Valid prediction for GlimmerHMM_glimmerT_17890-T1
Valid prediction for Augustus_model.g12029.t1
Valid prediction for GeneMark_model.30031_t
Couldn't classify 101087, 101088
Sorry, prediction CodingQuarry_transcript_57373-T1 fails validation.
(ATG)	 AC	98211-98261	GT	AGG
(CGC)	 AG	100355-100421	GT	GTG
(AGT)	 AG	101087-101088	TT	AGT
-recovered CodingQuarry_transcript_57373-T1, initial, 98211, 98261
-recovered CodingQuarry_transcript_57373-T1, internal, 100355, 100421
Valid prediction for snap_scaffold_7-snap.1250-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11013, rend_intergenic: 7444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16154, rend_intergenic: 13898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28614, rend_intergenic: 27595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36303, rend_intergenic: 32393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44553, rend_intergenic: 37466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53735, rend_intergenic: 49849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62014, rend_intergenic: 55331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70913, rend_intergenic: 64394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77051, rend_intergenic: 73354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91919, rend_intergenic: 86596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97419, rend_intergenic: 92613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175851, rend_intergenic: 160645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208473
-exon list size: 713


building trellis

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79.7    
79.9    
80.0    
80.1    
80.3    
80.4    
80.6    
80.7    
80.8    
81.0    
81.1    
81.3    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.2    
82.4    
82.5    
82.7    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.0    
85.2    
85.3    
85.5    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
86.4    
86.6    
86.7    
86.9    
87.0    
87.1    
87.3    
87.4    
87.6    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.4    
92.6    
92.7    
92.9    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 11013, rend_intergenic: 7444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16154, rend_intergenic: 13898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28614, rend_intergenic: 27595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36303, rend_intergenic: 32393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44553, rend_intergenic: 37466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53735, rend_intergenic: 49849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62014, rend_intergenic: 55331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70913, rend_intergenic: 64394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77051, rend_intergenic: 73354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91919, rend_intergenic: 86596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97419, rend_intergenic: 92613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175851, rend_intergenic: 160645  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

-building DP trellis

-building trellis in range 1 - 12567
-exon list size: 35


building trellis

2.7    
5.4    
8.1    
10.8    
13.5    
16.2    
18.9    
21.6    
24.3    
27.0    
29.7    
32.4    
35.1    
37.8    
40.5    
43.2    
45.9    
48.6    
51.4    
54.1    
56.8    
59.5    
62.2    
64.9    
67.6    
70.3    
73.0    
75.7    
78.4    
81.1    
83.8    
86.5    
89.2    
91.9    
94.6    
97.3    
-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 1 - 11839
-exon list size: 33


building trellis

2.9    
5.7    
8.6    
11.4    
14.3    
17.1    
20.0    
22.9    
25.7    
28.6    
31.4    
34.3    
37.1    
40.0    
42.9    
45.7    
48.6    
51.4    
54.3    
57.1    
60.0    
62.9    
65.7    
68.6    
71.4    
74.3    
77.1    
80.0    
82.9    
85.7    
88.6    
91.4    
94.3    
97.1    
-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