-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_5983496-6193488

-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 GlimmerHMM_glimmerT_12287-T1
Valid prediction for GlimmerHMM_glimmerT_12291-T1
Valid prediction for GeneMark_model.20806_t
Valid prediction for GeneMark_model.20813_t
Valid prediction for Augustus_model.g8117.t1
Valid prediction for HiQ_model.g8112.t1
Valid prediction for snap_scaffold_5-snap.1226-T1
Valid prediction for snap_scaffold_5-snap.1200-T1
Valid prediction for HiQ_model.g8107.t1
Valid prediction for GeneMark_model.20841_t
Valid prediction for snap_scaffold_5-snap.1191-T1
Valid prediction for Augustus_model.g8114.t1
Couldn't classify 10228, 10344
Sorry, prediction pasa_asmbl_44049.p1 fails validation.
(TGT)	 AG	10228-10344	GT	AGG
(TCG)	 AG	10669-10866	AA	GAA
-recovered pasa_asmbl_44049.p1, terminal, 10669, 10866
-recovered pasa_asmbl_44049.p1, internal, 10228, 10344
Valid prediction for GeneMark_model.20839_t
Valid prediction for pasa_asmbl_44050.p1
Valid prediction for GeneMark_model.20852_t
Valid prediction for GeneMark_model.20826_t
Valid prediction for GlimmerHMM_glimmerT_12281-T1
Valid prediction for GeneMark_model.20829_t
Valid prediction for pasa_asmbl_44055.p1
Valid prediction for GeneMark_model.20860_t
Valid prediction for GlimmerHMM_glimmerT_12302-T1
Valid prediction for GeneMark_model.20817_t
Valid prediction for Augustus_model.g8124.t1
Couldn't classify 7759, 7766
Couldn't classify 9661, 9756
Sorry, prediction pasa_asmbl_44048.p1 fails validation.
(CAG)	 TA	7759-7766	GT	GAG
(GTC)	 AG	7881-7908	GT	AGG
(GAA)	 AG	8024-8053	GT	AGG
(GAG)	 AG	8195-8290	GT	CAG
(ATC)	 AG	8821-8892	GT	AGG
(AAG)	 AG	9180-9320	GT	AGG
(GAG)	 AG	9431-9568	GT	AGG
(ATG)	 AG	9661-9756	GA	AGG
-recovered pasa_asmbl_44048.p1, internal, 7881, 7908
-recovered pasa_asmbl_44048.p1, internal, 8024, 8053
-recovered pasa_asmbl_44048.p1, internal, 8195, 8290
-recovered pasa_asmbl_44048.p1, internal, 8821, 8892
-recovered pasa_asmbl_44048.p1, internal, 9180, 9320
-recovered pasa_asmbl_44048.p1, internal, 9431, 9568
Couldn't classify 69121, 69138
Sorry, prediction pasa_asmbl_44057.p1 fails validation.
(AGA)	 TG	69121-69138	GT	AGG
(GTG)	 AG	69232-69447	GT	CTG
(ATC)	 AG	69626-69736	GT	CAG
(GTG)	 AG	69884-69985	GT	AGG
(GAC)	 AG	70298-70373	GT	CAG
(GTC)	 AG	70639-70766	GT	AGG
(AAA)	 AG	70995-71216	GA	GAG
-recovered pasa_asmbl_44057.p1, terminal, 70995, 71216
-recovered pasa_asmbl_44057.p1, internal, 69232, 69447
-recovered pasa_asmbl_44057.p1, internal, 69626, 69736
-recovered pasa_asmbl_44057.p1, internal, 69884, 69985
-recovered pasa_asmbl_44057.p1, internal, 70298, 70373
-recovered pasa_asmbl_44057.p1, internal, 70639, 70766
Valid prediction for CodingQuarry_transcript_51960-T1
Valid prediction for HiQ_model.g8105.t1
Valid prediction for CodingQuarry_transcript_51954-T1
Valid prediction for GlimmerHMM_glimmerT_12286-T1
Valid prediction for snap_scaffold_5-snap.1214-T1
Valid prediction for snap_scaffold_5-snap.1215-T1
Valid prediction for GeneMark_model.20856_t
Valid prediction for GlimmerHMM_glimmerT_12285-T1
Valid prediction for Augustus_model.g8104.t1
Valid prediction for snap_scaffold_5-snap.1221-T1
Valid prediction for GeneMark_model.20819_t
Valid prediction for GeneMark_model.20835_t
Valid prediction for snap_scaffold_5-snap.1224-T1
Valid prediction for GeneMark_model.20824_t
Valid prediction for CodingQuarry_transcript_51959-T1
Valid prediction for Augustus_model.g8123.t1
Valid prediction for Augustus_model.g8111.t1
Valid prediction for GeneMark_model.20815_t
Valid prediction for CodingQuarry_transcript_51958-T1
Valid prediction for snap_scaffold_5-snap.1211-T1
Valid prediction for GlimmerHMM_glimmerT_12277-T1
Valid prediction for snap_scaffold_5-snap.1208-T1
Valid prediction for Augustus_model.g8120.t1
Valid prediction for snap_scaffold_5-snap.1205-T1
Valid prediction for GeneMark_model.20858_t
Valid prediction for GlimmerHMM_glimmerT_12301-T1
Couldn't classify 182935, 182985
Couldn't classify 184877, 184975
Sorry, prediction pasa_asmbl_44063.p1 fails validation.
(AGG)	 TC	182935-182985	GT	AAG
(GCT)	 AG	183507-183631	GT	AGG
(AAG)	 AG	184072-184171	GT	CTG
(CTT)	 AG	184877-184975	GT	TGG
-recovered pasa_asmbl_44063.p1, internal, 183507, 183631
-recovered pasa_asmbl_44063.p1, internal, 184072, 184171
-recovered pasa_asmbl_44063.p1, internal, 184877, 184975
Valid prediction for snap_scaffold_5-snap.1206-T1
Valid prediction for GlimmerHMM_glimmerT_12296-T1
Valid prediction for GlimmerHMM_glimmerT_12283-T1
Couldn't classify 204200, 204567
Couldn't classify 205562, 205666
Sorry, prediction pasa_asmbl_44068.p1 fails validation.
(CAG)	 AC	204200-204567	GT	CGG
(GTT)	 AG	205238-205460	GT	CGG
(AAA)	 AG	205562-205666	GT	CCG
-recovered pasa_asmbl_44068.p1, internal, 205238, 205460
-recovered pasa_asmbl_44068.p1, internal, 205562, 205666
Couldn't classify 200475, 200637
Couldn't classify 203189, 203455
Sorry, prediction pasa_asmbl_44066.p1 fails validation.
(GGG)	 AG	200475-200637	GT	CTG
(TGG)	 AG	200857-200949	GT	CAG
(CCT)	 AG	201980-202179	GT	CGG
(ATG)	 AG	202666-202827	GT	AGG
(AAG)	 AG	202914-203027	GT	AGG
(GAG)	 AG	203189-203455	CC	CTC
-recovered pasa_asmbl_44066.p1, initial, 202666, 202827
-recovered pasa_asmbl_44066.p1, internal, 200475, 200637
-recovered pasa_asmbl_44066.p1, internal, 200857, 200949
-recovered pasa_asmbl_44066.p1, internal, 201980, 202179
-recovered pasa_asmbl_44066.p1, internal, 202666, 202827
-recovered pasa_asmbl_44066.p1, internal, 202914, 203027
Valid prediction for GlimmerHMM_glimmerT_12295-T1
Valid prediction for GeneMark_model.20844_t
Valid prediction for snap_scaffold_5-snap.1231-T1
Valid prediction for Augustus_model.g8122.t1
Valid prediction for pasa_asmbl_44059.p1
Valid prediction for snap_scaffold_5-snap.1203-T1
Valid prediction for snap_scaffold_5-snap.1212-T1
Valid prediction for snap_scaffold_5-snap.1192-T1
Valid prediction for GeneMark_model.20837_t
Valid prediction for snap_scaffold_5-snap.1230-T1
Valid prediction for snap_scaffold_5-snap.1232-T1
Valid prediction for GeneMark_model.20816_t
Valid prediction for snap_scaffold_5-snap.1228-T1
Valid prediction for snap_scaffold_5-snap.1229-T1
Valid prediction for GeneMark_model.20820_t
Valid prediction for GlimmerHMM_glimmerT_12274-T1
Valid prediction for GeneMark_model.20854_t
Couldn't classify 205763, 206282
Sorry, prediction pasa_asmbl_44070.p1 fails validation.
(TTC)	 CC	205763-206282	GT	AGG
(GTG)	 AG	206590-206760	GT	CGG
(GTA)	 AG	206878-207058	GT	AGG
(CCG)	 AG	207221-207254	GC	GAG
-recovered pasa_asmbl_44070.p1, terminal, 207221, 207254
-recovered pasa_asmbl_44070.p1, internal, 206590, 206760
-recovered pasa_asmbl_44070.p1, internal, 206878, 207058
-recovered pasa_asmbl_44070.p1, internal, 207221, 207254
Valid prediction for snap_scaffold_5-snap.1194-T1
Valid prediction for GlimmerHMM_glimmerT_12280-T1
Valid prediction for snap_scaffold_5-snap.1199-T1
Valid prediction for GlimmerHMM_glimmerT_12282-T1
Valid prediction for snap_scaffold_5-snap.1218-T1
Valid prediction for CodingQuarry_transcript_51961-T1
Valid prediction for snap_scaffold_5-snap.1220-T1
Valid prediction for GlimmerHMM_glimmerT_12288-T1
Valid prediction for snap_scaffold_5-snap.1202-T1
Valid prediction for GeneMark_model.20807_t
Valid prediction for HiQ_model.g8125.t1
Valid prediction for Augustus_model.g8118.t1
Valid prediction for GeneMark_model.20848_t
Valid prediction for Augustus_model.g8103.t1
Valid prediction for GlimmerHMM_glimmerT_12293-T1
Valid prediction for snap_scaffold_5-snap.1193-T1
Valid prediction for snap_scaffold_5-snap.1227-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 GlimmerHMM_glimmerT_12279-T1
Valid prediction for snap_scaffold_5-snap.1204-T1
Valid prediction for GeneMark_model.20809_t
Valid prediction for GeneMark_model.20853_t
Valid prediction for snap_scaffold_5-snap.1222-T1
Valid prediction for snap_scaffold_5-snap.1217-T1
Valid prediction for snap_scaffold_5-snap.1201-T1
Valid prediction for snap_scaffold_5-snap.1197-T1
Valid prediction for Augustus_model.g8113.t1
Valid prediction for GlimmerHMM_glimmerT_12292-T1
Valid prediction for GlimmerHMM_glimmerT_12289-T1
Valid prediction for GeneMark_model.20847_t
Valid prediction for GlimmerHMM_glimmerT_12284-T1
Valid prediction for GeneMark_model.20850_t
Valid prediction for GlimmerHMM_glimmerT_12294-T1
Valid prediction for snap_scaffold_5-snap.1195-T1
Valid prediction for GeneMark_model.20845_t
Valid prediction for CodingQuarry_transcript_51956-T1
Valid prediction for GeneMark_model.20857_t
Valid prediction for Augustus_model.g8116.t1
Valid prediction for pasa_asmbl_45471.p1
Valid prediction for GlimmerHMM_glimmerT_12278-T1
Valid prediction for GlimmerHMM_glimmerT_12300-T1
Valid prediction for Augustus_model.g8110.t1
Valid prediction for GeneMark_model.20846_t
Valid prediction for GeneMark_model.20851_t
Valid prediction for HiQ_model.g8106.t1
Valid prediction for GeneMark_model.20855_t
Valid prediction for snap_scaffold_5-snap.1196-T1
Valid prediction for GeneMark_model.20840_t
Valid prediction for snap_scaffold_5-snap.1210-T1
Valid prediction for GlimmerHMM_glimmerT_12299-T1
Valid prediction for GeneMark_model.20818_t
Valid prediction for GeneMark_model.20814_t
Valid prediction for pasa_asmbl_45460.p1
Valid prediction for snap_scaffold_5-snap.1216-T1
Valid prediction for GeneMark_model.20838_t
Valid prediction for snap_scaffold_5-snap.1213-T1
Valid prediction for pasa_asmbl_45465.p1
Valid prediction for snap_scaffold_5-snap.1207-T1
Valid prediction for GeneMark_model.20842_t
Valid prediction for GeneMark_model.20821_t
Valid prediction for snap_scaffold_5-snap.1219-T1
Valid prediction for GeneMark_model.20811_t
Valid prediction for GlimmerHMM_glimmerT_12298-T1
Valid prediction for GlimmerHMM_glimmerT_12276-T1
Valid prediction for snap_scaffold_5-snap.1190-T1
Valid prediction for snap_scaffold_5-snap.1198-T1
Valid prediction for Augustus_model.g8115.t1
Valid prediction for GlimmerHMM_glimmerT_12290-T1
Valid prediction for HiQ_model.g8109.t1
Valid prediction for GeneMark_model.20825_t
Valid prediction for GeneMark_model.20822_t
Valid prediction for GlimmerHMM_glimmerT_12303-T1
Valid prediction for snap_scaffold_5-snap.1209-T1
Valid prediction for GeneMark_model.20827_t
Valid prediction for GeneMark_model.20805_t
Valid prediction for GeneMark_model.20830_t
Valid prediction for CodingQuarry_transcript_51957-T1
Valid prediction for snap_scaffold_5-snap.1223-T1
Valid prediction for GeneMark_model.20849_t
Valid prediction for GlimmerHMM_glimmerT_12273-T1
Valid prediction for GeneMark_model.20832_t
Valid prediction for Augustus_model.g8119.t1
Valid prediction for GeneMark_model.20836_t
Valid prediction for pasa_asmbl_45463.p1
Valid prediction for HiQ_model.g8108.t1
Valid prediction for Augustus_model.g8121.t1
Valid prediction for snap_scaffold_5-snap.1225-T1
Valid prediction for CodingQuarry_transcript_51955-T1
Valid prediction for GeneMark_model.20831_t
Valid prediction for GeneMark_model.20812_t
Valid prediction for GeneMark_model.20810_t
Valid prediction for GeneMark_model.20859_t
Valid prediction for GeneMark_model.20823_t
Valid prediction for GeneMark_model.20828_t
Valid prediction for GeneMark_model.20808_t
Valid prediction for HiQ_model.g8102.t1
Valid prediction for GlimmerHMM_glimmerT_12297-T1
Valid prediction for GeneMark_model.20833_t
Valid prediction for GlimmerHMM_glimmerT_12304-T1
Valid prediction for GeneMark_model.20843_t
Valid prediction for CodingQuarry_transcript_51953-T1
Valid prediction for GlimmerHMM_glimmerT_12275-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 53361, rend_intergenic: 51089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95447, rend_intergenic: 94223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105168, rend_intergenic: 96301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137647, rend_intergenic: 133973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142132, rend_intergenic: 138211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147594, rend_intergenic: 147458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156571, rend_intergenic: 148449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167760, rend_intergenic: 157434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178087, rend_intergenic: 168200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 209993
-exon list size: 745


building trellis

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64.4    
64.5    
64.7    
64.8    
64.9    
65.1    
65.2    
65.3    
65.5    
65.6    
65.7    
65.9    
66.0    
66.1    
66.3    
66.4    
66.5    
66.7    
66.8    
66.9    
67.1    
67.2    
67.3    
67.5    
67.6    
67.7    
67.9    
68.0    
68.1    
68.3    
68.4    
68.5    
68.7    
68.8    
68.9    
69.1    
69.2    
69.3    
69.5    
69.6    
69.7    
69.9    
70.0    
70.1    
70.3    
70.4    
70.5    
70.7    
70.8    
71.0    
71.1    
71.2    
71.4    
71.5    
71.6    
71.8    
71.9    
72.0    
72.2    
72.3    
72.4    
72.6    
72.7    
72.8    
73.0    
73.1    
73.2    
73.4    
73.5    
73.6    
73.8    
73.9    
74.0    
74.2    
74.3    
74.4    
74.6    
74.7    
74.8    
75.0    
75.1    
75.2    
75.4    
75.5    
75.6    
75.8    
75.9    
76.0    
76.2    
76.3    
76.4    
76.6    
76.7    
76.8    
77.0    
77.1    
77.2    
77.4    
77.5    
77.6    
77.8    
77.9    
78.0    
78.2    
78.3    
78.4    
78.6    
78.7    
78.8    
79.0    
79.1    
79.3    
79.4    
79.5    
79.7    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.7    
80.9    
81.0    
81.1    
81.3    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.3    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.3    
83.4    
83.5    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.5    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.5    
86.6    
86.7    
86.9    
87.0    
87.1    
87.3    
87.4    
87.6    
87.7    
87.8    
88.0    
88.1    
88.2    
88.4    
88.5    
88.6    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 45 predictions from path traversal
Error with prediction: snap lend_intergenic: 53361, rend_intergenic: 51089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95447, rend_intergenic: 94223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105168, rend_intergenic: 96301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137647, rend_intergenic: 133973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142132, rend_intergenic: 138211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147594, rend_intergenic: 147458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156571, rend_intergenic: 148449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167760, rend_intergenic: 157434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178087, rend_intergenic: 168200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support