-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_11788897-12076610

-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.21956_t
Valid prediction for GeneMark_model.21995_t
Valid prediction for snap_scaffold_5-snap.2207-T1
Valid prediction for GeneMark_model.21977_t
Valid prediction for GlimmerHMM_glimmerT_13017-T1
Valid prediction for GlimmerHMM_glimmerT_13028-T1
Valid prediction for GeneMark_model.21975_t
Valid prediction for CodingQuarry_transcript_52140-T1
Valid prediction for GeneMark_model.21955_t
Couldn't classify 105037, 105102
Couldn't classify 108894, 108914
Sorry, prediction pasa_asmbl_45100.p1 fails validation.
(TTT)	 TC	105037-105102	GT	GGG
(AAG)	 AG	105997-106098	GT	CGG
(GCC)	 AG	106261-106395	GT	AGG
(AGG)	 AG	107866-108006	GT	AGG
(GAC)	 AG	108894-108914	GT	CAG
-recovered pasa_asmbl_45100.p1, internal, 105997, 106098
-recovered pasa_asmbl_45100.p1, internal, 106261, 106395
-recovered pasa_asmbl_45100.p1, internal, 107866, 108006
-recovered pasa_asmbl_45100.p1, internal, 108894, 108914
Valid prediction for GeneMark_model.21990_t
Valid prediction for GlimmerHMM_glimmerT_13027-T1
Valid prediction for GlimmerHMM_glimmerT_12998-T1
Valid prediction for Augustus_model.g8664.t1
Valid prediction for Augustus_model.g8668.t1
Valid prediction for snap_scaffold_5-snap.2209-T1
Valid prediction for GeneMark_model.21959_t
Valid prediction for Augustus_model.g8666.t1
Valid prediction for GeneMark_model.21988_t
Valid prediction for GlimmerHMM_glimmerT_13031-T1
Valid prediction for GeneMark_model.21991_t
Couldn't classify 52577, 52600
Couldn't classify 55384, 55869
Sorry, prediction pasa_asmbl_44436.p1 fails validation.
(AAG)	 AG	52577-52600	GT	AGG
(ATG)	 AG	54634-54891	GT	AGG
(GTG)	 AG	55011-55214	GT	AGG
(GTG)	 AG	55384-55869	AC	GCA
-recovered pasa_asmbl_44436.p1, initial, 54634, 54891
-recovered pasa_asmbl_44436.p1, internal, 52577, 52600
-recovered pasa_asmbl_44436.p1, internal, 54634, 54891
-recovered pasa_asmbl_44436.p1, internal, 55011, 55214
Valid prediction for Augustus_model.g8681.t1
Valid prediction for GeneMark_model.21978_t
Valid prediction for snap_scaffold_5-snap.2228-T1
Valid prediction for Augustus_model.g8660.t1
Valid prediction for Augustus_model.g8655.t1
Valid prediction for snap_scaffold_5-snap.2213-T1
Valid prediction for CodingQuarry_transcript_52145-T1
Valid prediction for GlimmerHMM_glimmerT_13002-T1
Valid prediction for GlimmerHMM_glimmerT_13004-T1
Valid prediction for GlimmerHMM_glimmerT_13011-T1
Valid prediction for GlimmerHMM_glimmerT_13014-T1
Valid prediction for GlimmerHMM_glimmerT_13001-T1
Valid prediction for snap_scaffold_5-snap.2222-T1
Valid prediction for snap_scaffold_5-snap.2211-T1
Valid prediction for GeneMark_model.21985_t
Valid prediction for GeneMark_model.21969_t
Valid prediction for HiQ_model.g8685.t1
Valid prediction for GlimmerHMM_glimmerT_13010-T1
Valid prediction for CodingQuarry_transcript_52142-T1
Valid prediction for snap_scaffold_5-snap.2235-T1
Valid prediction for GeneMark_model.21957_t
Valid prediction for Augustus_model.g8663.t1
Valid prediction for snap_scaffold_5-snap.2219-T1
Couldn't classify 121708, 121859
Couldn't classify 121950, 122136
Sorry, prediction pasa_asmbl_45039.p1 fails validation.
(AGA)	 CC	121708-121859	GT	AGG
(ATG)	 AG	121950-122136	GG	CCG
Valid prediction for snap_scaffold_5-snap.2199-T1
Valid prediction for GlimmerHMM_glimmerT_13016-T1
Valid prediction for Augustus_model.g8683.t1
Valid prediction for GeneMark_model.21965_t
Valid prediction for GeneMark_model.21994_t
Valid prediction for snap_scaffold_5-snap.2218-T1
Valid prediction for Augustus_model.g8665.t1
Valid prediction for GlimmerHMM_glimmerT_13013-T1
Valid prediction for pasa_asmbl_44453.p1
Valid prediction for snap_scaffold_5-snap.2203-T1
Valid prediction for Augustus_model.g8677.t1
Valid prediction for snap_scaffold_5-snap.2200-T1
Valid prediction for GeneMark_model.21961_t
Valid prediction for snap_scaffold_5-snap.2237-T1
Valid prediction for pasa_asmbl_44433.p1
Valid prediction for GeneMark_model.21984_t
Valid prediction for pasa_asmbl_44452.p1
Valid prediction for snap_scaffold_5-snap.2221-T1
Valid prediction for Augustus_model.g8673.t1
Valid prediction for GlimmerHMM_glimmerT_13018-T1
Valid prediction for GeneMark_model.21962_t
Valid prediction for GlimmerHMM_glimmerT_13020-T1
Valid prediction for snap_scaffold_5-snap.2196-T1
Valid prediction for GlimmerHMM_glimmerT_13008-T1
Valid prediction for GeneMark_model.21971_t
Valid prediction for snap_scaffold_5-snap.2201-T1
Valid prediction for Augustus_model.g8669.t1
Valid prediction for Augustus_model.g8658.t1
Valid prediction for snap_scaffold_5-snap.2216-T1
Valid prediction for snap_scaffold_5-snap.2206-T1
Valid prediction for HiQ_model.g8676.t1
Valid prediction for GlimmerHMM_glimmerT_13006-T1
Valid prediction for GeneMark_model.21980_t
Valid prediction for snap_scaffold_5-snap.2215-T1
Valid prediction for snap_scaffold_5-snap.2205-T1
Valid prediction for snap_scaffold_5-snap.2220-T1
Valid prediction for GlimmerHMM_glimmerT_13015-T1
Valid prediction for HiQ_model.g8674.t1
Valid prediction for GlimmerHMM_glimmerT_13019-T1
Valid prediction for snap_scaffold_5-snap.2229-T1
Valid prediction for GeneMark_model.21973_t
Valid prediction for GlimmerHMM_glimmerT_12996-T1
Valid prediction for GeneMark_model.21997_t
Valid prediction for GeneMark_model.21981_t
Valid prediction for snap_scaffold_5-snap.2212-T1
Valid prediction for Augustus_model.g8672.t1
Valid prediction for snap_scaffold_5-snap.2232-T1
Valid prediction for GlimmerHMM_glimmerT_13022-T1
Couldn't classify 123360, 123429
Sorry, prediction pasa_asmbl_44443.p1 fails validation.
(GTT)	 AA	123360-123429	GT	AGG
(ACG)	 AG	124151-124290	GT	GAG
(TTC)	 AG	124423-124579	GT	AGG
(GAC)	 AG	125546-125611	GT	GGG
(AGG)	 AG	125723-125838	GC	GAG
-recovered pasa_asmbl_44443.p1, terminal, 125723, 125838
-recovered pasa_asmbl_44443.p1, internal, 124151, 124290
-recovered pasa_asmbl_44443.p1, internal, 124423, 124579
-recovered pasa_asmbl_44443.p1, internal, 125546, 125611
-recovered pasa_asmbl_44443.p1, internal, 125723, 125838
Valid prediction for GlimmerHMM_glimmerT_13021-T1
Valid prediction for CodingQuarry_transcript_52139-T1
Valid prediction for Augustus_model.g8671.t1
Couldn't classify 51093, 51173
Couldn't classify 52354, 52423
Sorry, prediction pasa_asmbl_44435.p1 fails validation.
(CGT)	 CT	51093-51173	GT	AGG
(GTG)	 AG	52038-52252	GT	AGG
(CCC)	 AG	52354-52423	GC	AGG
-recovered pasa_asmbl_44435.p1, internal, 52038, 52252
-recovered pasa_asmbl_44435.p1, internal, 52354, 52423
Valid prediction for GeneMark_model.21952_t
Valid prediction for snap_scaffold_5-snap.2233-T1
Valid prediction for CodingQuarry_transcript_52137-T1
Valid prediction for Augustus_model.g8661.t1
Valid prediction for GeneMark_model.21983_t
Valid prediction for GeneMark_model.21968_t
Valid prediction for Augustus_model.g8662.t1
Valid prediction for GlimmerHMM_glimmerT_13034-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_5-snap.2236-T1
Valid prediction for GeneMark_model.21974_t
Valid prediction for snap_scaffold_5-snap.2197-T1
Valid prediction for GlimmerHMM_glimmerT_13003-T1
Valid prediction for Augustus_model.g8682.t1
Valid prediction for GeneMark_model.21963_t
Valid prediction for GeneMark_model.21989_t
Valid prediction for snap_scaffold_5-snap.2225-T1
Valid prediction for GeneMark_model.21960_t
Valid prediction for GlimmerHMM_glimmerT_12995-T1
Valid prediction for CodingQuarry_transcript_52141-T1
Valid prediction for GeneMark_model.21996_t
Valid prediction for GeneMark_model.21970_t
Valid prediction for GeneMark_model.21976_t
Valid prediction for GlimmerHMM_glimmerT_12999-T1
Valid prediction for GlimmerHMM_glimmerT_13026-T1
Valid prediction for pasa_asmbl_45817.p1
Valid prediction for GlimmerHMM_glimmerT_13033-T1
Valid prediction for pasa_asmbl_45812.p1
Valid prediction for GlimmerHMM_glimmerT_13030-T1
Valid prediction for GlimmerHMM_glimmerT_13023-T1
Valid prediction for Augustus_model.g8667.t1
Valid prediction for Augustus_model.g8670.t1
Valid prediction for GlimmerHMM_glimmerT_13000-T1
Valid prediction for GlimmerHMM_glimmerT_13024-T1
Valid prediction for HiQ_model.g8678.t1
Valid prediction for snap_scaffold_5-snap.2195-T1
Valid prediction for GeneMark_model.21979_t
Valid prediction for snap_scaffold_5-snap.2202-T1
Valid prediction for CodingQuarry_transcript_52138-T1
Valid prediction for CodingQuarry_transcript_52143-T1
Valid prediction for GlimmerHMM_glimmerT_13025-T1
Valid prediction for snap_scaffold_5-snap.2231-T1
Valid prediction for snap_scaffold_5-snap.2234-T1
Valid prediction for GeneMark_model.21954_t
Valid prediction for GeneMark_model.21993_t
Valid prediction for Augustus_model.g8656.t1
Valid prediction for HiQ_model.g8684.t1
Valid prediction for snap_scaffold_5-snap.2217-T1
Valid prediction for Augustus_model.g8679.t1
Valid prediction for GeneMark_model.21992_t
Valid prediction for snap_scaffold_5-snap.2227-T1
Valid prediction for HiQ_model.g8657.t1
Valid prediction for pasa_asmbl_45810.p1
Valid prediction for GeneMark_model.21966_t
Valid prediction for GlimmerHMM_glimmerT_13009-T1
Valid prediction for GeneMark_model.21987_t
Valid prediction for snap_scaffold_5-snap.2230-T1
Valid prediction for snap_scaffold_5-snap.2223-T1
Valid prediction for GeneMark_model.21972_t
Couldn't classify 264530, 264631
Sorry, prediction pasa_asmbl_45809.p1 fails validation.
(TTT)	 AG	264530-264631	GT	TGG
(CAC)	 AG	265074-265189	GT	TGG
(GGT)	 AG	265299-265480	GT	TGG
(GTT)	 AG	265701-265726	GG	GAG
-recovered pasa_asmbl_45809.p1, terminal, 265701, 265726
-recovered pasa_asmbl_45809.p1, internal, 264530, 264631
-recovered pasa_asmbl_45809.p1, internal, 265074, 265189
-recovered pasa_asmbl_45809.p1, internal, 265299, 265480
Valid prediction for GlimmerHMM_glimmerT_13012-T1
Valid prediction for GeneMark_model.21986_t
Valid prediction for snap_scaffold_5-snap.2208-T1
Valid prediction for GeneMark_model.21982_t
Valid prediction for GlimmerHMM_glimmerT_13029-T1
Valid prediction for GeneMark_model.21958_t
Valid prediction for GlimmerHMM_glimmerT_13032-T1
Valid prediction for GeneMark_model.21953_t
Valid prediction for GeneMark_model.21951_t
Valid prediction for snap_scaffold_5-snap.2224-T1
Valid prediction for Augustus_model.g8654.t1
Valid prediction for snap_scaffold_5-snap.2226-T1
Valid prediction for snap_scaffold_5-snap.2198-T1
Valid prediction for Augustus_model.g8680.t1
Valid prediction for GlimmerHMM_glimmerT_13007-T1
Valid prediction for GeneMark_model.21964_t
Valid prediction for Augustus_model.g8659.t1
Valid prediction for snap_scaffold_5-snap.2214-T1
Valid prediction for HiQ_model.g8675.t1
Valid prediction for GeneMark_model.21967_t
Valid prediction for snap_scaffold_5-snap.2204-T1
Valid prediction for GlimmerHMM_glimmerT_13005-T1
Valid prediction for snap_scaffold_5-snap.2210-T1
Valid prediction for GlimmerHMM_glimmerT_12997-T1
Valid prediction for CodingQuarry_transcript_52144-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 34836, rend_intergenic: 34029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41654, rend_intergenic: 37412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50109, rend_intergenic: 42364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82948, rend_intergenic: 71875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91776, rend_intergenic: 83632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116090, rend_intergenic: 92406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143148, rend_intergenic: 142944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147309, rend_intergenic: 143586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227215, rend_intergenic: 224261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233360, rend_intergenic: 228440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 242467, rend_intergenic: 241130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 287714
-exon list size: 736


building trellis

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69.8    
69.9    
70.1    
70.2    
70.3    
70.5    
70.6    
70.7    
70.9    
71.0    
71.1    
71.3    
71.4    
71.5    
71.7    
71.8    
72.0    
72.1    
72.2    
72.4    
72.5    
72.6    
72.8    
72.9    
73.0    
73.2    
73.3    
73.4    
73.6    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.5    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.5    
75.6    
75.7    
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    
78.5    
78.6    
78.7    
78.9    
79.0    
79.1    
79.3    
79.4    
79.5    
79.7    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
80.6    
80.8    
80.9    
81.0    
81.2    
81.3    
81.4    
81.6    
81.7    
81.8    
82.0    
82.1    
82.2    
82.4    
82.5    
82.7    
82.8    
82.9    
83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.9    
84.0    
84.1    
84.3    
84.4    
84.6    
84.7    
84.8    
85.0    
85.1    
85.2    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.6    
86.7    
86.9    
87.0    
87.1    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
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    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 34836, rend_intergenic: 34029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41654, rend_intergenic: 37412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50109, rend_intergenic: 42364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82948, rend_intergenic: 71875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91776, rend_intergenic: 83632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116090, rend_intergenic: 92406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143148, rend_intergenic: 142944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147309, rend_intergenic: 143586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227215, rend_intergenic: 224261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233360, rend_intergenic: 228440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 242467, rend_intergenic: 241130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support