-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_11821340-12119387

-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_57490-T1
Valid prediction for GlimmerHMM_glimmerT_18628-T1
Valid prediction for pasa_asmbl_51094.p1
Valid prediction for snap_scaffold_7-snap.2254-T1
Valid prediction for CodingQuarry_transcript_57492-T1
Valid prediction for GeneMark_model.31222_t
Valid prediction for GlimmerHMM_glimmerT_18616-T1
Couldn't classify 28466, 28597
Sorry, prediction pasa_asmbl_51073.p2 fails validation.
(GGT)	 CA	28466-28597	GT	AGG
(GTG)	 AG	28742-28925	GT	AGG
(GCA)	 AG	29526-29692	GT	TTG
(GGA)	 AG	30458-30574	GG	GAG
-recovered pasa_asmbl_51073.p2, terminal, 30458, 30574
-recovered pasa_asmbl_51073.p2, internal, 28742, 28925
-recovered pasa_asmbl_51073.p2, internal, 29526, 29692
Valid prediction for Augustus_model.g12566.t1
Valid prediction for HiQ_model.g12576.t1
Valid prediction for CodingQuarry_transcript_57495-T1
Valid prediction for GlimmerHMM_glimmerT_18619-T1
Valid prediction for Augustus_model.g12572.t1
Valid prediction for snap_scaffold_7-snap.2291-T1
Valid prediction for snap_scaffold_7-snap.2255-T1
Valid prediction for snap_scaffold_7-snap.2270-T1
Valid prediction for GlimmerHMM_glimmerT_18613-T1
Valid prediction for HiQ_model.g12582.t1
Valid prediction for snap_scaffold_7-snap.2287-T1
Valid prediction for GeneMark_model.31202_t
Valid prediction for Augustus_model.g12557.t1
Valid prediction for GeneMark_model.31208_t
Valid prediction for Augustus_model.g12560.t1
Valid prediction for snap_scaffold_7-snap.2290-T1
Valid prediction for Augustus_model.g12558.t1
Couldn't classify 171824, 172342
Sorry, prediction pasa_asmbl_51083.p1 fails validation.
(GAC)	 TC	171824-172342	TC	AAT
Valid prediction for GeneMark_model.31209_t
Valid prediction for GeneMark_model.31199_t
Valid prediction for pasa_asmbl_51084.p1
Valid prediction for GlimmerHMM_glimmerT_18609-T1
Valid prediction for GeneMark_model.31224_t
Valid prediction for snap_scaffold_7-snap.2257-T1
Valid prediction for snap_scaffold_7-snap.2256-T1
Valid prediction for snap_scaffold_7-snap.2277-T1
Valid prediction for CodingQuarry_transcript_57496-T1
Valid prediction for CodingQuarry_transcript_57497-T1
Valid prediction for snap_scaffold_7-snap.2264-T1
Valid prediction for Augustus_model.g12565.t1
Valid prediction for HiQ_model.g12577.t1
Valid prediction for GlimmerHMM_glimmerT_18624-T1
Valid prediction for GeneMark_model.31218_t
Valid prediction for Augustus_model.g12564.t1
Valid prediction for pasa_asmbl_51092.p1
Couldn't classify 131985, 132170
Sorry, prediction pasa_asmbl_51080.p1 fails validation.
(GTC)	 TT	131985-132170	GT	AGG
(GTG)	 AG	132922-132975	GT	AGG
(TGT)	 AG	133080-133160	GT	AGG
(GAT)	 AG	133257-133307	GA	AAG
-recovered pasa_asmbl_51080.p1, terminal, 133257, 133307
-recovered pasa_asmbl_51080.p1, internal, 132922, 132975
-recovered pasa_asmbl_51080.p1, internal, 133080, 133160
Valid prediction for GeneMark_model.31211_t
Valid prediction for snap_scaffold_7-snap.2272-T1
Valid prediction for GeneMark_model.31206_t
Valid prediction for GeneMark_model.31196_t
Valid prediction for GlimmerHMM_glimmerT_18617-T1
Valid prediction for pasa_asmbl_51091.p1
Valid prediction for GlimmerHMM_glimmerT_18600-T1
Valid prediction for snap_scaffold_7-snap.2269-T1
Valid prediction for CodingQuarry_transcript_57500-T1
Valid prediction for snap_scaffold_7-snap.2286-T1
Valid prediction for HiQ_model.g12578.t1
Valid prediction for pasa_asmbl_51085.p1
Valid prediction for GlimmerHMM_glimmerT_18612-T1
Couldn't classify 123340, 123495
Couldn't classify 125048, 125112
Sorry, prediction pasa_asmbl_51450.p1 fails validation.
(GAG)	 CG	123340-123495	GT	AGG
(TTT)	 AG	123624-123726	GT	TGG
(GGA)	 AG	125048-125112	GT	ATG
-recovered pasa_asmbl_51450.p1, internal, 123624, 123726
-recovered pasa_asmbl_51450.p1, internal, 125048, 125112
Valid prediction for snap_scaffold_7-snap.2274-T1
Valid prediction for GlimmerHMM_glimmerT_18610-T1
Couldn't classify 55549, 55600
Couldn't classify 57375, 57392
Sorry, prediction pasa_asmbl_51479.p1 fails validation.
(CAG)	 CT	55549-55600	GT	AGG
(AGG)	 AG	56363-56450	GT	GGG
(GCC)	 AG	57059-57224	GT	ACG
(TTT)	 AG	57375-57392	TA	ACT
-recovered pasa_asmbl_51479.p1, internal, 56363, 56450
-recovered pasa_asmbl_51479.p1, internal, 57059, 57224
Couldn't classify 260002, 260172
Sorry, prediction pasa_asmbl_51098.p2 fails validation.
(GCT)	 AG	260002-260172	GT	AGG
(GAA)	 AG	260276-260379	GT	CGG
(GGA)	 AG	260614-261035	GT	CGG
(GTG)	 AG	261238-261364	GT	AGG
(AGA)	 AG	261488-261756	GT	GGG
(GAG)	 AG	262084-262268	GC	GAG
-recovered pasa_asmbl_51098.p2, terminal, 262084, 262268
-recovered pasa_asmbl_51098.p2, internal, 260002, 260172
-recovered pasa_asmbl_51098.p2, internal, 260276, 260379
-recovered pasa_asmbl_51098.p2, internal, 260614, 261035
-recovered pasa_asmbl_51098.p2, internal, 261238, 261364
-recovered pasa_asmbl_51098.p2, internal, 261488, 261756
-recovered pasa_asmbl_51098.p2, internal, 262084, 262268
Valid prediction for GlimmerHMM_glimmerT_18621-T1
Valid prediction for snap_scaffold_7-snap.2260-T1
Valid prediction for GlimmerHMM_glimmerT_18625-T1
Valid prediction for GeneMark_model.31197_t
Valid prediction for snap_scaffold_7-snap.2282-T1
Valid prediction for pasa_asmbl_51074.p1
Valid prediction for snap_scaffold_7-snap.2263-T1
Valid prediction for GlimmerHMM_glimmerT_18607-T1
Valid prediction for GlimmerHMM_glimmerT_18603-T1
Valid prediction for GlimmerHMM_glimmerT_18604-T1
Valid prediction for CodingQuarry_transcript_57501-T1
Valid prediction for CodingQuarry_transcript_57499-T1
Valid prediction for Augustus_model.g12568.t1
Valid prediction for HiQ_model.g12580.t1
Valid prediction for Augustus_model.g12571.t1
Valid prediction for GlimmerHMM_glimmerT_18608-T1
Couldn't classify 116176, 116541
Sorry, prediction pasa_asmbl_51078.p1 fails validation.
(ACC)	 AG	116176-116541	GG	AAG

-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.31191_t
Valid prediction for GeneMark_model.31203_t
Valid prediction for snap_scaffold_7-snap.2288-T1
Valid prediction for snap_scaffold_7-snap.2261-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.31198_t
Couldn't classify 50492, 50530
Sorry, prediction pasa_asmbl_49995.p1 fails validation.
(AAA)	 AG	50492-50530	GT	CTG
(GCA)	 AG	50896-51010	GT	CAG
(ATG)	 AG	51156-51297	GT	TTG
(CAC)	 AG	51393-51528	GT	AGG
(ACA)	 AG	51725-51828	GT	AGG
(GGG)	 AG	51915-52080	GT	CGG
(ATC)	 AG	52172-52222	GC	AGG
add_exon() Sorry, pasa_asmbl_49995.p1 51156-51297-initial-1 is invalid.
-recovered pasa_asmbl_49995.p1, initial, 51156, 51297
-recovered pasa_asmbl_49995.p1, terminal, 52172, 52222
-recovered pasa_asmbl_49995.p1, internal, 50492, 50530
-recovered pasa_asmbl_49995.p1, internal, 50896, 51010
-recovered pasa_asmbl_49995.p1, internal, 51156, 51297
-recovered pasa_asmbl_49995.p1, internal, 51393, 51528
-recovered pasa_asmbl_49995.p1, internal, 51725, 51828
-recovered pasa_asmbl_49995.p1, internal, 51915, 52080
-recovered pasa_asmbl_49995.p1, internal, 52172, 52222
Valid prediction for Augustus_model.g12574.t1
Valid prediction for GeneMark_model.31207_t
Valid prediction for GeneMark_model.31192_t
Valid prediction for Augustus_model.g12567.t1
Valid prediction for GeneMark_model.31204_t
Couldn't classify 121140, 121541
Sorry, prediction pasa_asmbl_49994.p1 fails validation.
(GCT)	 CA	121140-121541	TG	AGT
Valid prediction for Augustus_model.g12581.t1
Valid prediction for GeneMark_model.31215_t
Valid prediction for GlimmerHMM_glimmerT_18630-T1
Valid prediction for pasa_asmbl_49991.p1
Valid prediction for GlimmerHMM_glimmerT_18626-T1
Valid prediction for snap_scaffold_7-snap.2275-T1
Valid prediction for snap_scaffold_7-snap.2273-T1
Couldn't classify 255272, 255442
Sorry, prediction pasa_asmbl_49984.p1 fails validation.
(CCC)	 CC	255272-255442	GT	TCG
(CTC)	 AG	257414-257524	GT	CTG
(TAC)	 AG	257626-257746	GT	CGG
(ATG)	 AG	258625-258716	GT	AGG
(TCT)	 AG	259339-259450	GT	TGG
(GGG)	 AG	260909-261076	GT	TGG
(GCT)	 AG	261209-261481	GT	AGG
(ACA)	 AG	262115-262176	GT	GGG
(GAC)	 AG	262908-262980	GT	CTG
(GCC)	 AG	263100-263167	GT	AGG
(CCT)	 AG	263277-263372	GA	GAG
add_exon() Sorry, pasa_asmbl_49984.p1 258625-258716-initial-1 is invalid.
-recovered pasa_asmbl_49984.p1, initial, 258625, 258716
-recovered pasa_asmbl_49984.p1, terminal, 263277, 263372
-recovered pasa_asmbl_49984.p1, internal, 257414, 257524
-recovered pasa_asmbl_49984.p1, internal, 257626, 257746
-recovered pasa_asmbl_49984.p1, internal, 258625, 258716
-recovered pasa_asmbl_49984.p1, internal, 259339, 259450
-recovered pasa_asmbl_49984.p1, internal, 260909, 261076
-recovered pasa_asmbl_49984.p1, internal, 261209, 261481
-recovered pasa_asmbl_49984.p1, internal, 262115, 262176
-recovered pasa_asmbl_49984.p1, internal, 262908, 262980
-recovered pasa_asmbl_49984.p1, internal, 263100, 263167
Valid prediction for GlimmerHMM_glimmerT_18627-T1
Valid prediction for snap_scaffold_7-snap.2258-T1
Valid prediction for GeneMark_model.31225_t
Valid prediction for snap_scaffold_7-snap.2262-T1
Valid prediction for GlimmerHMM_glimmerT_18601-T1
Valid prediction for snap_scaffold_7-snap.2283-T1
Valid prediction for GlimmerHMM_glimmerT_18622-T1
Valid prediction for Augustus_model.g12563.t1
Couldn't classify 137036, 137170
Sorry, prediction pasa_asmbl_49990.p1 fails validation.
(GGT)	 CA	137036-137170	GT	AGG
(GTC)	 AG	137312-137482	GT	AGG
(CTG)	 AG	137619-137775	GT	GGG
(GTA)	 AG	137866-138062	GT	TGG
(ATC)	 AG	138149-138399	GT	AAG
(GAG)	 AG	138507-139389	TT	GAT
-recovered pasa_asmbl_49990.p1, terminal, 138507, 139389
-recovered pasa_asmbl_49990.p1, internal, 137312, 137482
-recovered pasa_asmbl_49990.p1, internal, 137619, 137775
-recovered pasa_asmbl_49990.p1, internal, 137866, 138062
-recovered pasa_asmbl_49990.p1, internal, 138149, 138399
Valid prediction for CodingQuarry_transcript_57493-T1
Valid prediction for CodingQuarry_transcript_57498-T1
Valid prediction for snap_scaffold_7-snap.2267-T1
Valid prediction for snap_scaffold_7-snap.2284-T1
Valid prediction for GlimmerHMM_glimmerT_18618-T1
Valid prediction for GeneMark_model.31226_t
Valid prediction for GeneMark_model.31195_t
Valid prediction for GeneMark_model.31212_t
Valid prediction for snap_scaffold_7-snap.2271-T1
Valid prediction for GeneMark_model.31201_t
Valid prediction for GeneMark_model.31190_t
Valid prediction for snap_scaffold_7-snap.2253-T1
Valid prediction for GlimmerHMM_glimmerT_18606-T1
Valid prediction for Augustus_model.g12575.t1
Valid prediction for snap_scaffold_7-snap.2285-T1
Valid prediction for Augustus_model.g12556.t1
Valid prediction for GeneMark_model.31217_t
Valid prediction for Augustus_model.g12573.t1
Valid prediction for GeneMark_model.31223_t
Valid prediction for GeneMark_model.31205_t
Valid prediction for snap_scaffold_7-snap.2281-T1
Valid prediction for GlimmerHMM_glimmerT_18623-T1
Valid prediction for snap_scaffold_7-snap.2259-T1
Valid prediction for HiQ_model.g12569.t1
Valid prediction for HiQ_model.g12559.t1
Valid prediction for GeneMark_model.31194_t
Valid prediction for GeneMark_model.31200_t
Valid prediction for GeneMark_model.31216_t
Valid prediction for GlimmerHMM_glimmerT_18615-T1
Valid prediction for snap_scaffold_7-snap.2276-T1
Valid prediction for HiQ_model.g12570.t1
Valid prediction for snap_scaffold_7-snap.2266-T1
Valid prediction for GlimmerHMM_glimmerT_18611-T1
Valid prediction for snap_scaffold_7-snap.2279-T1
Valid prediction for pasa_asmbl_49996.p1
Valid prediction for GeneMark_model.31221_t
Valid prediction for snap_scaffold_7-snap.2265-T1
Valid prediction for GeneMark_model.31193_t
Valid prediction for snap_scaffold_7-snap.2278-T1
Couldn't classify 129929, 130110
Couldn't classify 130321, 130334
Sorry, prediction CodingQuarry_transcript_57494-T1 fails validation.
(ATG)	 CA	129222-129378	GT	TGG
(GCC)	 AG	129717-129795	GT	AAG
(ATT)	 AG	129929-130110	AA	GGA
(TGC)	 GG	130321-130334	TA	GAT
-recovered CodingQuarry_transcript_57494-T1, initial, 129222, 129378
-recovered CodingQuarry_transcript_57494-T1, internal, 129717, 129795
Couldn't classify 284796, 284886
Sorry, prediction pasa_asmbl_49979.p1 fails validation.
(CGG)	 CT	284796-284886	GT	AGG
(CTC)	 AG	286330-287285	TA	GAT
-recovered pasa_asmbl_49979.p1, terminal, 286330, 287285
Valid prediction for GlimmerHMM_glimmerT_18629-T1
Valid prediction for GeneMark_model.31213_t
Valid prediction for GlimmerHMM_glimmerT_18602-T1
Valid prediction for GeneMark_model.31227_t
Valid prediction for snap_scaffold_7-snap.2252-T1
Valid prediction for snap_scaffold_7-snap.2289-T1
Valid prediction for GeneMark_model.31219_t
Valid prediction for Augustus_model.g12561.t1
Valid prediction for snap_scaffold_7-snap.2280-T1
Valid prediction for GlimmerHMM_glimmerT_18614-T1
Valid prediction for Augustus_model.g12562.t1
Valid prediction for HiQ_model.g12579.t1
Valid prediction for GlimmerHMM_glimmerT_18605-T1
Valid prediction for snap_scaffold_7-snap.2268-T1
Valid prediction for GlimmerHMM_glimmerT_18620-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 40086, rend_intergenic: 34677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43452, rend_intergenic: 42860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102760, rend_intergenic: 100362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187458, rend_intergenic: 186878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 298048
-exon list size: 600


building trellis

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65.3    
65.4    
65.6    
65.8    
65.9    
66.1    
66.3    
66.4    
66.6    
66.8    
66.9    
67.1    
67.3    
67.4    
67.6    
67.8    
67.9    
68.1    
68.3    
68.4    
68.6    
68.8    
68.9    
69.1    
69.3    
69.4    
69.6    
69.8    
69.9    
70.1    
70.3    
70.4    
70.6    
70.8    
70.9    
71.1    
71.3    
71.4    
71.6    
71.8    
71.9    
72.1    
72.3    
72.4    
72.6    
72.8    
72.9    
73.1    
73.3    
73.4    
73.6    
73.8    
73.9    
74.1    
74.3    
74.4    
74.6    
74.8    
74.9    
75.1    
75.2    
75.4    
75.6    
75.7    
75.9    
76.1    
76.2    
76.4    
76.6    
76.7    
76.9    
77.1    
77.2    
77.4    
77.6    
77.7    
77.9    
78.1    
78.2    
78.4    
78.6    
78.7    
78.9    
79.1    
79.2    
79.4    
79.6    
79.7    
79.9    
80.1    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.7    
81.9    
82.1    
82.2    
82.4    
82.6    
82.7    
82.9    
83.1    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.2    
84.4    
84.6    
84.7    
84.9    
85.0    
85.2    
85.4    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.5    
88.7    
88.9    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 40086, rend_intergenic: 34677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43452, rend_intergenic: 42860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102760, rend_intergenic: 100362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187458, rend_intergenic: 186878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support