-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_5084738-5291403

-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 GeneMark_model.96784_t
Valid prediction for GlimmerHMM_glimmerT_55442-T1
Valid prediction for GlimmerHMM_glimmerT_55431-T1
Valid prediction for GlimmerHMM_glimmerT_55433-T1
Valid prediction for GeneMark_model.96798_t
Valid prediction for GeneMark_model.96759_t
Valid prediction for Augustus_model.g36983.t1
Valid prediction for Augustus_model.g36984.t1
Valid prediction for GeneMark_model.96748_t
Valid prediction for GlimmerHMM_glimmerT_55438-T1
Valid prediction for GeneMark_model.96793_t
Valid prediction for Augustus_model.g36978.t1
Valid prediction for snap_scaffold_25-snap.1112-T1
Valid prediction for GeneMark_model.96813_t
Valid prediction for GeneMark_model.96761_t
Valid prediction for snap_scaffold_25-snap.1134-T1
Valid prediction for GeneMark_model.96763_t
Valid prediction for snap_scaffold_25-snap.1096-T1
Valid prediction for GlimmerHMM_glimmerT_55428-T1
Valid prediction for snap_scaffold_25-snap.1121-T1
Valid prediction for GlimmerHMM_glimmerT_55426-T1
Valid prediction for GlimmerHMM_glimmerT_55440-T1
Valid prediction for snap_scaffold_25-snap.1105-T1
Valid prediction for Augustus_model.g36976.t1
Valid prediction for snap_scaffold_25-snap.1120-T1
Valid prediction for snap_scaffold_25-snap.1116-T1
Valid prediction for snap_scaffold_25-snap.1133-T1
Valid prediction for GeneMark_model.96767_t
Valid prediction for snap_scaffold_25-snap.1092-T1
Valid prediction for GeneMark_model.96787_t
Valid prediction for GeneMark_model.96753_t
Valid prediction for snap_scaffold_25-snap.1094-T1
Valid prediction for GeneMark_model.96806_t
Valid prediction for GeneMark_model.96804_t
Valid prediction for snap_scaffold_25-snap.1095-T1
Valid prediction for GeneMark_model.96802_t
Valid prediction for GeneMark_model.96807_t
Valid prediction for GeneMark_model.96775_t
Valid prediction for snap_scaffold_25-snap.1130-T1
Valid prediction for GlimmerHMM_glimmerT_55456-T1
Valid prediction for GeneMark_model.96769_t
Valid prediction for GeneMark_model.96791_t
Valid prediction for GeneMark_model.96779_t
Valid prediction for GeneMark_model.96771_t
Valid prediction for Augustus_model.g36989.t1
Valid prediction for snap_scaffold_25-snap.1114-T1
Valid prediction for snap_scaffold_25-snap.1135-T1
Valid prediction for GeneMark_model.96780_t
Valid prediction for snap_scaffold_25-snap.1131-T1
Valid prediction for GlimmerHMM_glimmerT_55457-T1
Valid prediction for GeneMark_model.96789_t
Valid prediction for Augustus_model.g36994.t1
Valid prediction for GlimmerHMM_glimmerT_55427-T1
Valid prediction for GeneMark_model.96809_t
Valid prediction for Augustus_model.g36973.t1
Valid prediction for snap_scaffold_25-snap.1122-T1
Valid prediction for GeneMark_model.96796_t
Valid prediction for GeneMark_model.96815_t
Valid prediction for GeneMark_model.96800_t
Valid prediction for GlimmerHMM_glimmerT_55432-T1
Valid prediction for Augustus_model.g36974.t1
Valid prediction for GeneMark_model.96782_t
Valid prediction for snap_scaffold_25-snap.1126-T1
Valid prediction for GeneMark_model.96765_t
Valid prediction for GlimmerHMM_glimmerT_55444-T1
Valid prediction for GlimmerHMM_glimmerT_55455-T1
Valid prediction for snap_scaffold_25-snap.1113-T1
Valid prediction for snap_scaffold_25-snap.1106-T1
Valid prediction for snap_scaffold_25-snap.1108-T1
Valid prediction for GlimmerHMM_glimmerT_55429-T1
Valid prediction for GlimmerHMM_glimmerT_55430-T1
Valid prediction for GeneMark_model.96772_t
Valid prediction for snap_scaffold_25-snap.1109-T1
Valid prediction for GeneMark_model.96811_t
Valid prediction for GeneMark_model.96751_t
Valid prediction for snap_scaffold_25-snap.1118-T1
Valid prediction for GlimmerHMM_glimmerT_55439-T1
Valid prediction for snap_scaffold_25-snap.1115-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g36975.t1
Valid prediction for snap_scaffold_25-snap.1093-T1
Sorry, intron length (4) is less than minimum required (10)

-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.96816_t
Valid prediction for GeneMark_model.96774_t
Valid prediction for Augustus_model.g36993.t1
Valid prediction for Augustus_model.g36996.t1
Valid prediction for GeneMark_model.96773_t
Valid prediction for GeneMark_model.96810_t
Valid prediction for GeneMark_model.96805_t
Valid prediction for HiQ_model.g36972.t1
Valid prediction for GeneMark_model.96752_t
Valid prediction for GeneMark_model.96757_t
Valid prediction for Augustus_model.g36990.t1
Valid prediction for Augustus_model.g36995.t1
Valid prediction for GeneMark_model.96814_t
Valid prediction for pasa_asmbl_34220.p1
Valid prediction for GeneMark_model.96747_t
Valid prediction for GeneMark_model.96790_t
Valid prediction for GlimmerHMM_glimmerT_55435-T1
Sorry, intron length (9) is less than minimum required (10)
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for HiQ_model.g36980.t1
Valid prediction for Augustus_model.g36981.t1
Valid prediction for snap_scaffold_25-snap.1110-T1
Valid prediction for GeneMark_model.96795_t
Couldn't classify 137408, 137546
Sorry, prediction pasa_asmbl_34222.p1 fails validation.
(GAG)	 GC	137408-137546	GT	GGG
(GTT)	 AG	137681-138036	CG	GAC
-recovered pasa_asmbl_34222.p1, terminal, 137681, 138036
Valid prediction for snap_scaffold_25-snap.1091-T1
Valid prediction for GeneMark_model.96758_t
Valid prediction for GeneMark_model.96812_t
Valid prediction for GlimmerHMM_glimmerT_55445-T1
Valid prediction for GlimmerHMM_glimmerT_55453-T1
Valid prediction for Augustus_model.g36986.t1
Valid prediction for snap_scaffold_25-snap.1102-T1
Valid prediction for GeneMark_model.96756_t
Valid prediction for GeneMark_model.96799_t
Valid prediction for GeneMark_model.96778_t
Valid prediction for GlimmerHMM_glimmerT_55446-T1
Valid prediction for GlimmerHMM_glimmerT_55434-T1
Valid prediction for GeneMark_model.96764_t
Valid prediction for snap_scaffold_25-snap.1097-T1
Valid prediction for snap_scaffold_25-snap.1127-T1
Valid prediction for snap_scaffold_25-snap.1128-T1
Valid prediction for snap_scaffold_25-snap.1125-T1
Valid prediction for GlimmerHMM_glimmerT_55423-T1
Valid prediction for GeneMark_model.96755_t
Valid prediction for GlimmerHMM_glimmerT_55437-T1
Valid prediction for snap_scaffold_25-snap.1107-T1
Valid prediction for GlimmerHMM_glimmerT_55443-T1
Valid prediction for GeneMark_model.96750_t
Valid prediction for GeneMark_model.96792_t
Valid prediction for snap_scaffold_25-snap.1098-T1
Valid prediction for Augustus_model.g36977.t1
Valid prediction for GlimmerHMM_glimmerT_55441-T1
Valid prediction for Augustus_model.g36991.t1
Valid prediction for Augustus_model.g36988.t1
Valid prediction for snap_scaffold_25-snap.1104-T1
Valid prediction for snap_scaffold_25-snap.1100-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_55447-T1
Valid prediction for GlimmerHMM_glimmerT_55454-T1
Valid prediction for GeneMark_model.96770_t
Valid prediction for Augustus_model.g36987.t1
Valid prediction for snap_scaffold_25-snap.1136-T1
Valid prediction for GeneMark_model.96781_t
Valid prediction for snap_scaffold_25-snap.1117-T1
Valid prediction for snap_scaffold_25-snap.1111-T1
Valid prediction for CodingQuarry_transcript_38639-T1
Valid prediction for GeneMark_model.96768_t
Valid prediction for snap_scaffold_25-snap.1103-T1
Valid prediction for GeneMark_model.96797_t
Valid prediction for GlimmerHMM_glimmerT_55449-T1
Valid prediction for GlimmerHMM_glimmerT_55448-T1
Valid prediction for Augustus_model.g36992.t1
Valid prediction for snap_scaffold_25-snap.1119-T1
Valid prediction for GeneMark_model.96777_t
Valid prediction for GlimmerHMM_glimmerT_55452-T1
Valid prediction for GlimmerHMM_glimmerT_55436-T1
Valid prediction for Augustus_model.g36979.t1
Valid prediction for GeneMark_model.96808_t
Valid prediction for GeneMark_model.96817_t
Valid prediction for Augustus_model.g36982.t1
Valid prediction for GlimmerHMM_glimmerT_55425-T1
Valid prediction for GeneMark_model.96803_t
Valid prediction for GeneMark_model.96776_t
Couldn't classify 132362, 132456
Sorry, prediction pasa_asmbl_34225.p1 fails validation.
(CGG)	 CA	132362-132456	GT	GGG
(CTC)	 AG	132804-132859	GT	ACG
(GTG)	 AG	132940-132995	GT	AGG
(AGA)	 AG	133171-133300	GT	CCG
(ACA)	 AG	133450-133562	GT	AGG
(ATG)	 AG	133869-134027	GT	AGG
(ATT)	 AG	134321-134462	GT	GGG
(TCA)	 AG	134567-134601	GT	AGG
(GTG)	 AG	135255-135361	GT	GGG
(GGC)	 AG	135963-136086	AA	GAA
-recovered pasa_asmbl_34225.p1, initial, 133869, 134027
-recovered pasa_asmbl_34225.p1, terminal, 135963, 136086
-recovered pasa_asmbl_34225.p1, internal, 132804, 132859
-recovered pasa_asmbl_34225.p1, internal, 132940, 132995
-recovered pasa_asmbl_34225.p1, internal, 133171, 133300
-recovered pasa_asmbl_34225.p1, internal, 133450, 133562
-recovered pasa_asmbl_34225.p1, internal, 133869, 134027
-recovered pasa_asmbl_34225.p1, internal, 134321, 134462
-recovered pasa_asmbl_34225.p1, internal, 134567, 134601
-recovered pasa_asmbl_34225.p1, internal, 135255, 135361
Valid prediction for GeneMark_model.96794_t
Valid prediction for GlimmerHMM_glimmerT_55450-T1
Valid prediction for GeneMark_model.96785_t
Valid prediction for CodingQuarry_transcript_38638-T1
Valid prediction for snap_scaffold_25-snap.1099-T1
Valid prediction for GeneMark_model.96766_t
Valid prediction for GlimmerHMM_glimmerT_55458-T1
Valid prediction for Augustus_model.g36985.t1
Valid prediction for GlimmerHMM_glimmerT_55424-T1
Valid prediction for snap_scaffold_25-snap.1101-T1
Valid prediction for GeneMark_model.96783_t
Valid prediction for GeneMark_model.96801_t
Valid prediction for GlimmerHMM_glimmerT_55451-T1
Valid prediction for snap_scaffold_25-snap.1129-T1
Valid prediction for snap_scaffold_25-snap.1132-T1
Valid prediction for snap_scaffold_25-snap.1124-T1
Valid prediction for GeneMark_model.96788_t
Valid prediction for snap_scaffold_25-snap.1123-T1
Valid prediction for GeneMark_model.96786_t
Valid prediction for GeneMark_model.96754_t
Valid prediction for GeneMark_model.96762_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 100087, rend_intergenic: 97208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105389, rend_intergenic: 102779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123565, rend_intergenic: 107670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127293, rend_intergenic: 123852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139937, rend_intergenic: 138535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153526, rend_intergenic: 148443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162695, rend_intergenic: 159495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174865, rend_intergenic: 162735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179365, rend_intergenic: 175040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185336, rend_intergenic: 180021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199787, rend_intergenic: 187590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203495, rend_intergenic: 200753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 206666
-exon list size: 940


building trellis

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63.2    
63.3    
63.4    
63.5    
63.6    
63.7    
63.8    
63.9    
64.0    
64.1    
64.2    
64.3    
64.4    
64.5    
64.6    
64.8    
64.9    
65.0    
65.1    
65.2    
65.3    
65.4    
65.5    
65.6    
65.7    
65.8    
65.9    
66.0    
66.1    
66.2    
66.3    
66.5    
66.6    
66.7    
66.8    
66.9    
67.0    
67.1    
67.2    
67.3    
67.4    
67.5    
67.6    
67.7    
67.8    
67.9    
68.0    
68.2    
68.3    
68.4    
68.5    
68.6    
68.7    
68.8    
68.9    
69.0    
69.1    
69.2    
69.3    
69.4    
69.5    
69.6    
69.7    
69.9    
70.0    
70.1    
70.2    
70.3    
70.4    
70.5    
70.6    
70.7    
70.8    
70.9    
71.0    
71.1    
71.2    
71.3    
71.4    
71.5    
71.7    
71.8    
71.9    
72.0    
72.1    
72.2    
72.3    
72.4    
72.5    
72.6    
72.7    
72.8    
72.9    
73.0    
73.1    
73.2    
73.4    
73.5    
73.6    
73.7    
73.8    
73.9    
74.0    
74.1    
74.2    
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    
75.8    
75.9    
76.0    
76.1    
76.2    
76.3    
76.4    
76.5    
76.6    
76.8    
76.9    
77.0    
77.1    
77.2    
77.3    
77.4    
77.5    
77.6    
77.7    
77.8    
77.9    
78.0    
78.1    
78.2    
78.3    
78.5    
78.6    
78.7    
78.8    
78.9    
79.0    
79.1    
79.2    
79.3    
79.4    
79.5    
79.6    
79.7    
79.8    
79.9    
80.0    
80.1    
80.3    
80.4    
80.5    
80.6    
80.7    
80.8    
80.9    
81.0    
81.1    
81.2    
81.3    
81.4    
81.5    
81.6    
81.7    
81.8    
82.0    
82.1    
82.2    
82.3    
82.4    
82.5    
82.6    
82.7    
82.8    
82.9    
83.0    
83.1    
83.2    
83.3    
83.4    
83.5    
83.7    
83.8    
83.9    
84.0    
84.1    
84.2    
84.3    
84.4    
84.5    
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    
86.1    
86.2    
86.3    
86.4    
86.5    
86.6    
86.7    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.5    
87.6    
87.7    
87.8    
87.9    
88.0    
88.1    
88.2    
88.3    
88.4    
88.5    
88.6    
88.7    
88.9    
89.0    
89.1    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.8    
89.9    
90.0    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.2    
91.3    
91.4    
91.5    
91.6    
91.7    
91.8    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.6    
92.7    
92.8    
92.9    
93.0    
93.1    
93.2    
93.3    
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    
94.8    
94.9    
95.0    
95.1    
95.2    
95.3    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.1    
96.2    
96.3    
96.4    
96.5    
96.6    
96.7    
96.8    
96.9    
97.0    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.8    
97.9    
98.0    
98.1    
98.2    
98.3    
98.4    
98.5    
98.6    
98.7    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.5    
99.6    
99.7    
99.8    
99.9    
-found 54 predictions from path traversal
Error with prediction: snap lend_intergenic: 100087, rend_intergenic: 97208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105389, rend_intergenic: 102779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123565, rend_intergenic: 107670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127293, rend_intergenic: 123852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139937, rend_intergenic: 138535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153526, rend_intergenic: 148443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162695, rend_intergenic: 159495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174865, rend_intergenic: 162735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179365, rend_intergenic: 175040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185336, rend_intergenic: 180021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199787, rend_intergenic: 187590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203495, rend_intergenic: 200753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support