-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_2598575-2805423

-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_58250-T1
Valid prediction for pasa_asmbl_36073.p1
Valid prediction for HiQ_model.g38814.t1
Valid prediction for GeneMark_model.101396_t
Valid prediction for snap_scaffold_27-snap.665-T1
Valid prediction for GlimmerHMM_glimmerT_58256-T1
Valid prediction for HiQ_model.g38815.t1
Valid prediction for GeneMark_model.101364_t
Valid prediction for GeneMark_model.101372_t
Valid prediction for GeneMark_model.101361_t
Valid prediction for CodingQuarry_transcript_41717-T1
Valid prediction for CodingQuarry_transcript_41729-T1
Couldn't classify 185193, 185257
Sorry, prediction pasa_asmbl_36063.p1 fails validation.
(CGG)	 GT	185193-185257	GT	AAG
(GTC)	 AG	186040-186137	GT	AGG
(TGG)	 AG	186282-186410	GT	CTG
(CTG)	 AG	186657-186871	GT	GAG
(GTT)	 AG	186970-187107	GT	CTG
(GAT)	 AG	187275-187426	GT	CCG
(CTG)	 AG	187593-187755	GT	AGG
(CTT)	 AG	187966-188074	GT	AGG
(GGA)	 AG	188207-188329	GT	TGG
(ACA)	 AG	188422-188536	GT	GCG
(TGT)	 AG	188760-188823	GT	AGG
(GTG)	 AG	188934-189137	GT	AGG
(GCA)	 AG	189307-189401	GT	AGG
(GTT)	 AG	189631-189802	GT	AGG
(GAC)	 AG	189927-190019	GC	AAG
-recovered pasa_asmbl_36063.p1, terminal, 189927, 190019
-recovered pasa_asmbl_36063.p1, internal, 186040, 186137
-recovered pasa_asmbl_36063.p1, internal, 186282, 186410
-recovered pasa_asmbl_36063.p1, internal, 186657, 186871
-recovered pasa_asmbl_36063.p1, internal, 186970, 187107
-recovered pasa_asmbl_36063.p1, internal, 187275, 187426
-recovered pasa_asmbl_36063.p1, internal, 187593, 187755
-recovered pasa_asmbl_36063.p1, internal, 187966, 188074
-recovered pasa_asmbl_36063.p1, internal, 188207, 188329
-recovered pasa_asmbl_36063.p1, internal, 188422, 188536
-recovered pasa_asmbl_36063.p1, internal, 188760, 188823
-recovered pasa_asmbl_36063.p1, internal, 188934, 189137
-recovered pasa_asmbl_36063.p1, internal, 189307, 189401
-recovered pasa_asmbl_36063.p1, internal, 189631, 189802
-recovered pasa_asmbl_36063.p1, internal, 189927, 190019
Valid prediction for GeneMark_model.101389_t
Valid prediction for CodingQuarry_transcript_41726-T1
Valid prediction for snap_scaffold_27-snap.651-T1
Valid prediction for snap_scaffold_27-snap.652-T1
Valid prediction for snap_scaffold_27-snap.667-T1
Valid prediction for snap_scaffold_27-snap.653-T1
Couldn't classify 127314, 127388
Couldn't classify 127913, 127981
Sorry, prediction pasa_asmbl_36570.p1 fails validation.
(TTC)	 AC	127314-127388	GT	ATG
(ACA)	 AG	127482-127643	GT	AGG
(GCC)	 AG	127913-127981	AG	TGA
-recovered pasa_asmbl_36570.p1, internal, 127482, 127643
Valid prediction for GlimmerHMM_glimmerT_58249-T1
Valid prediction for GlimmerHMM_glimmerT_58264-T1
Couldn't classify 130445, 130552
Sorry, prediction pasa_asmbl_36544.p1 fails validation.
(TCC)	 GT	130445-130552	GT	AGG
(GAT)	 AG	130800-130922	GT	AGG
(GCA)	 AG	131155-131283	GT	AGG
(ATG)	 AG	131388-131516	GT	AGG
(TGC)	 AG	131884-132014	GT	TGG
(GAA)	 AG	132217-132343	GT	AGG
(GAC)	 AG	132755-132878	GT	GGG
(GGT)	 AG	133063-133184	GT	AGG
(AGA)	 AG	133523-133561	GA	GAG
-recovered pasa_asmbl_36544.p1, initial, 131388, 131516
-recovered pasa_asmbl_36544.p1, terminal, 133523, 133561
-recovered pasa_asmbl_36544.p1, internal, 130800, 130922
-recovered pasa_asmbl_36544.p1, internal, 131155, 131283
-recovered pasa_asmbl_36544.p1, internal, 131388, 131516
-recovered pasa_asmbl_36544.p1, internal, 131884, 132014
-recovered pasa_asmbl_36544.p1, internal, 132217, 132343
-recovered pasa_asmbl_36544.p1, internal, 132755, 132878
-recovered pasa_asmbl_36544.p1, internal, 133063, 133184
Valid prediction for CodingQuarry_transcript_41732-T1
Valid prediction for GlimmerHMM_glimmerT_58266-T1
Valid prediction for Augustus_model.g38805.t1
Valid prediction for HiQ_model.g38795.t1
Valid prediction for pasa_asmbl_36056.p1
Valid prediction for GeneMark_model.101398_t
Valid prediction for snap_scaffold_27-snap.635-T1
Valid prediction for GeneMark_model.101382_t
Valid prediction for snap_scaffold_27-snap.640-T1
Valid prediction for GeneMark_model.101368_t
Valid prediction for CodingQuarry_transcript_41718-T1
Valid prediction for GeneMark_model.101397_t
Valid prediction for snap_scaffold_27-snap.660-T1
Valid prediction for GlimmerHMM_glimmerT_58274-T1
Valid prediction for GeneMark_model.101365_t
Valid prediction for GlimmerHMM_glimmerT_58273-T1
Valid prediction for snap_scaffold_27-snap.633-T1
Valid prediction for Augustus_model.g38794.t1
Valid prediction for GeneMark_model.101383_t
Valid prediction for GlimmerHMM_glimmerT_58251-T1
Valid prediction for GeneMark_model.101369_t
Valid prediction for GeneMark_model.101393_t
Valid prediction for snap_scaffold_27-snap.641-T1
Valid prediction for GlimmerHMM_glimmerT_58257-T1
Valid prediction for Augustus_model.g38817.t1
Valid prediction for snap_scaffold_27-snap.642-T1
Valid prediction for GlimmerHMM_glimmerT_58248-T1
Valid prediction for snap_scaffold_27-snap.634-T1
Valid prediction for Augustus_model.g38799.t1
Valid prediction for Augustus_model.g38800.t1
Valid prediction for snap_scaffold_27-snap.664-T1
Valid prediction for GeneMark_model.101390_t
Valid prediction for HiQ_model.g38811.t1
Couldn't classify 128280, 128624
Couldn't classify 129810, 129818
Sorry, prediction pasa_asmbl_36061.p1 fails validation.
(GTG)	 TG	128280-128624	GT	ATG
(GAG)	 AG	129351-129444	GC	AGG
(ATT)	 AG	129550-129566	GT	AGG
(GAT)	 AG	129810-129818	GT	AGG
add_exon() Sorry, pasa_asmbl_36061.p1 129351-129444-terminal-3 is invalid.
-recovered pasa_asmbl_36061.p1, terminal, 129351, 129444
-recovered pasa_asmbl_36061.p1, internal, 129351, 129444
-recovered pasa_asmbl_36061.p1, internal, 129550, 129566
-recovered pasa_asmbl_36061.p1, internal, 129810, 129818
Valid prediction for GeneMark_model.101373_t
Valid prediction for GlimmerHMM_glimmerT_58275-T1
Valid prediction for Augustus_model.g38806.t1
Valid prediction for GlimmerHMM_glimmerT_58260-T1
Valid prediction for GlimmerHMM_glimmerT_58271-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_27-snap.650-T1
Valid prediction for GeneMark_model.101380_t
Couldn't classify 138367, 138963
Sorry, prediction pasa_asmbl_36795.p1 fails validation.
(ATG)	 GG	138367-138963	GG	GCG
Valid prediction for GlimmerHMM_glimmerT_58265-T1
Valid prediction for GeneMark_model.101394_t
Valid prediction for HiQ_model.g38792.t1
Valid prediction for Augustus_model.g38803.t1
Valid prediction for GlimmerHMM_glimmerT_58272-T1
Valid prediction for GeneMark_model.101378_t
Valid prediction for snap_scaffold_27-snap.649-T1
Valid prediction for Augustus_model.g38810.t1
Valid prediction for GlimmerHMM_glimmerT_58254-T1
Valid prediction for HiQ_model.g38796.t1
Valid prediction for GeneMark_model.101388_t
Valid prediction for GlimmerHMM_glimmerT_58261-T1
Valid prediction for snap_scaffold_27-snap.646-T1
Valid prediction for Augustus_model.g38790.t1
Valid prediction for pasa_asmbl_36793.p1
Valid prediction for CodingQuarry_transcript_41716-T1
Valid prediction for CodingQuarry_transcript_41724-T1
Valid prediction for GlimmerHMM_glimmerT_58259-T1
Valid prediction for CodingQuarry_transcript_41730-T1
Couldn't classify 183808, 183846
Sorry, prediction pasa_asmbl_36784.p1 fails validation.
(TCG)	 TC	183808-183846	GT	CAG
(GTG)	 AG	184065-184265	GT	GGG
(CTC)	 AG	184413-184505	GT	AGG
(ATG)	 AG	184612-184674	GT	CTG
(ATG)	 AG	184783-184881	GT	AGG
(GGC)	 AG	184967-185100	GT	ACG
(GTG)	 AG	185302-185413	GT	AGG
(GAG)	 AG	185894-186127	CT	AAC
-recovered pasa_asmbl_36784.p1, initial, 184612, 184674
-recovered pasa_asmbl_36784.p1, initial, 184783, 184881
-recovered pasa_asmbl_36784.p1, terminal, 185894, 186127
-recovered pasa_asmbl_36784.p1, internal, 184065, 184265
-recovered pasa_asmbl_36784.p1, internal, 184413, 184505
-recovered pasa_asmbl_36784.p1, internal, 184612, 184674
-recovered pasa_asmbl_36784.p1, internal, 184783, 184881
-recovered pasa_asmbl_36784.p1, internal, 184967, 185100
-recovered pasa_asmbl_36784.p1, internal, 185302, 185413
Valid prediction for snap_scaffold_27-snap.648-T1
Valid prediction for GlimmerHMM_glimmerT_58269-T1
Valid prediction for snap_scaffold_27-snap.632-T1
Couldn't classify 155512, 155655
Couldn't classify 156715, 157008
Sorry, prediction pasa_asmbl_36792.p1 fails validation.
(GTG)	 AT	155512-155655	GT	AGG
(GCT)	 AG	155770-155889	GT	AAG
(GCC)	 AG	156057-156151	GT	AAG
(GTA)	 AG	156237-156360	GT	AGG
(GAA)	 AG	156471-156548	GT	GGG
(GCT)	 AG	156715-157008	GA	AAG
-recovered pasa_asmbl_36792.p1, internal, 155770, 155889
-recovered pasa_asmbl_36792.p1, internal, 156057, 156151
-recovered pasa_asmbl_36792.p1, internal, 156237, 156360
-recovered pasa_asmbl_36792.p1, internal, 156471, 156548
Valid prediction for pasa_asmbl_36796.p1
Valid prediction for GlimmerHMM_glimmerT_58267-T1
Valid prediction for GeneMark_model.101370_t
Valid prediction for GlimmerHMM_glimmerT_58245-T1
Valid prediction for GeneMark_model.101392_t
Valid prediction for HiQ_model.g38798.t1
Valid prediction for CodingQuarry_transcript_41722-T1
Valid prediction for Augustus_model.g38816.t1
Valid prediction for pasa_asmbl_36799.p1
Couldn't classify 138661, 139761
Sorry, prediction pasa_asmbl_36794.p1 fails validation.
(CAG)	 TT	138661-139761	GC	AGG
Valid prediction for snap_scaffold_27-snap.656-T1
Valid prediction for GeneMark_model.101385_t
Valid prediction for GlimmerHMM_glimmerT_58247-T1
Valid prediction for GeneMark_model.101363_t
Valid prediction for snap_scaffold_27-snap.644-T1
Valid prediction for HiQ_model.g38793.t1
Valid prediction for pasa_asmbl_36800.p1
Valid prediction for GeneMark_model.101395_t
Valid prediction for snap_scaffold_27-snap.638-T1
Valid prediction for Augustus_model.g38807.t1
Valid prediction for snap_scaffold_27-snap.655-T1
Valid prediction for Augustus_model.g38808.t1
Valid prediction for HiQ_model.g38802.t1
Valid prediction for GeneMark_model.101384_t
Valid prediction for GlimmerHMM_glimmerT_58262-T1
Valid prediction for snap_scaffold_27-snap.654-T1
Valid prediction for GlimmerHMM_glimmerT_58268-T1
Valid prediction for Augustus_model.g38791.t1
Valid prediction for CodingQuarry_transcript_41723-T1
Valid prediction for snap_scaffold_27-snap.636-T1
Valid prediction for GeneMark_model.101367_t
Valid prediction for snap_scaffold_27-snap.658-T1
Valid prediction for snap_scaffold_27-snap.657-T1
Valid prediction for CodingQuarry_transcript_41720-T1
Valid prediction for GeneMark_model.101391_t
Valid prediction for CodingQuarry_transcript_41727-T1
Valid prediction for GeneMark_model.101379_t
Valid prediction for snap_scaffold_27-snap.666-T1
Valid prediction for GeneMark_model.101374_t
Valid prediction for snap_scaffold_27-snap.643-T1
Valid prediction for snap_scaffold_27-snap.663-T1
Couldn't classify 65308, 65430
Sorry, prediction pasa_asmbl_36802.p1 fails validation.
(ATG)	 GA	62827-62902	GT	CGG
(GTG)	 AG	63386-63569	GT	AGG
(GTT)	 AG	64441-64552	GT	AAG
(ATC)	 AG	64994-65131	GT	AGG
(GCA)	 AG	65308-65430	CC	GCC
-recovered pasa_asmbl_36802.p1, initial, 62827, 62902
-recovered pasa_asmbl_36802.p1, internal, 63386, 63569
-recovered pasa_asmbl_36802.p1, internal, 64441, 64552
-recovered pasa_asmbl_36802.p1, internal, 64994, 65131
Valid prediction for GeneMark_model.101362_t
Valid prediction for GeneMark_model.101371_t
Valid prediction for CodingQuarry_transcript_41719-T1
Valid prediction for GlimmerHMM_glimmerT_58255-T1
Valid prediction for GlimmerHMM_glimmerT_58253-T1
Valid prediction for Augustus_model.g38797.t1
Valid prediction for GeneMark_model.101377_t
Valid prediction for GlimmerHMM_glimmerT_58244-T1
Valid prediction for snap_scaffold_27-snap.662-T1
Valid prediction for GlimmerHMM_glimmerT_58263-T1
Valid prediction for CodingQuarry_transcript_41725-T1
Valid prediction for snap_scaffold_27-snap.647-T1
Couldn't classify 159889, 160120
Sorry, prediction pasa_asmbl_36790.p1 fails validation.
(GAA)	 CA	159889-160120	GT	AGG
(TGA)	 AG	160498-160610	GT	AAG
(TGT)	 AG	160750-160859	GT	ATG
(GGC)	 AG	160992-161056	GT	AGG
(GGG)	 AG	161168-161283	AT	GAA
-recovered pasa_asmbl_36790.p1, terminal, 161168, 161283
-recovered pasa_asmbl_36790.p1, internal, 160498, 160610
-recovered pasa_asmbl_36790.p1, internal, 160750, 160859
-recovered pasa_asmbl_36790.p1, internal, 160992, 161056
Valid prediction for CodingQuarry_transcript_41728-T1
Valid prediction for HiQ_model.g38804.t1
Valid prediction for snap_scaffold_27-snap.639-T1
Valid prediction for pasa_asmbl_36787.p1
Valid prediction for snap_scaffold_27-snap.645-T1
Valid prediction for Augustus_model.g38813.t1
Valid prediction for HiQ_model.g38801.t1
Couldn't classify 70071, 70197
Sorry, prediction pasa_asmbl_37148.p2 fails validation.
(ATC)	 CT	70071-70197	GT	AGG
(GGA)	 AG	70368-70470	GT	AGG
(GAA)	 AG	70658-70799	AA	GAA
-recovered pasa_asmbl_37148.p2, terminal, 70658, 70799
-recovered pasa_asmbl_37148.p2, internal, 70368, 70470
Valid prediction for GlimmerHMM_glimmerT_58246-T1
Valid prediction for GeneMark_model.101381_t
Valid prediction for GeneMark_model.101386_t
Valid prediction for pasa_asmbl_36803.p1
Valid prediction for pasa_asmbl_36789.p1
Valid prediction for snap_scaffold_27-snap.659-T1
Couldn't classify 157410, 157649
Sorry, prediction pasa_asmbl_36791.p1 fails validation.
(CTG)	 CT	157410-157649	GT	AGG
(GAA)	 AG	157774-157949	GT	AGG
(GTT)	 AG	158391-158490	GT	AGG
(GTG)	 AG	158616-158909	TT	GAT
-recovered pasa_asmbl_36791.p1, terminal, 158616, 158909
-recovered pasa_asmbl_36791.p1, internal, 157774, 157949
-recovered pasa_asmbl_36791.p1, internal, 158391, 158490
Valid prediction for GlimmerHMM_glimmerT_58258-T1
Valid prediction for GlimmerHMM_glimmerT_58270-T1
Valid prediction for snap_scaffold_27-snap.637-T1
Valid prediction for GlimmerHMM_glimmerT_58252-T1
Valid prediction for HiQ_model.g38809.t1
Valid prediction for GeneMark_model.101366_t
Valid prediction for HiQ_model.g38812.t1
Valid prediction for snap_scaffold_27-snap.661-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15874, rend_intergenic: 5286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 206849
-exon list size: 541


building trellis

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64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 15874, rend_intergenic: 5286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support