-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_2923400-3161191

-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: +)Couldn't classify 21700, 21769
Couldn't classify 22896, 23138
Sorry, prediction pasa_asmbl_32121.p1 fails validation.
(AGC)	 AC	21700-21769	GT	ACG
(TGG)	 AG	21879-21958	GT	AGG
(GGT)	 AG	22347-22541	GT	AGG
(CTG)	 AG	22896-23138	AC	ACA
-recovered pasa_asmbl_32121.p1, internal, 21879, 21958
-recovered pasa_asmbl_32121.p1, internal, 22347, 22541
Couldn't classify 155093, 155148
Couldn't classify 161954, 161980
Sorry, prediction pasa_asmbl_32638.p1 fails validation.
(GCG)	 TG	155093-155148	GT	GGG
(ATC)	 AG	155716-155788	GT	TGG
(CCA)	 AG	156011-156081	GT	CAG
(GTA)	 AG	156219-156293	GT	AAG
(GTC)	 AG	156404-156482	GT	TGG
(ACT)	 AG	156863-156961	GT	AGG
(GAG)	 AG	157299-157830	GT	AGG
(AGG)	 AG	158020-158200	GT	TGG
(GGT)	 AG	158654-158784	GT	TGG
(ATC)	 AG	158928-159031	GT	TGG
(CGG)	 AG	159125-159202	GT	AGG
(CAC)	 AG	159453-159535	GT	GGG
(GTT)	 AG	159847-159898	GT	AGG
(GAG)	 AG	161954-161980	GA	CAG
-recovered pasa_asmbl_32638.p1, internal, 155716, 155788
-recovered pasa_asmbl_32638.p1, internal, 156011, 156081
-recovered pasa_asmbl_32638.p1, internal, 156219, 156293
-recovered pasa_asmbl_32638.p1, internal, 156404, 156482
-recovered pasa_asmbl_32638.p1, internal, 156863, 156961
-recovered pasa_asmbl_32638.p1, internal, 157299, 157830
-recovered pasa_asmbl_32638.p1, internal, 158020, 158200
-recovered pasa_asmbl_32638.p1, internal, 158654, 158784
-recovered pasa_asmbl_32638.p1, internal, 158928, 159031
-recovered pasa_asmbl_32638.p1, internal, 159125, 159202
-recovered pasa_asmbl_32638.p1, internal, 159453, 159535
-recovered pasa_asmbl_32638.p1, internal, 159847, 159898
Valid prediction for snap_scaffold_24-snap.666-T1
Valid prediction for GlimmerHMM_glimmerT_52225-T1
Valid prediction for HiQ_model.g34786.t1
Valid prediction for Augustus_model.g34800.t1
Valid prediction for Augustus_model.g34794.t1
Valid prediction for GlimmerHMM_glimmerT_52208-T1
Valid prediction for GlimmerHMM_glimmerT_52206-T1
Couldn't classify 164704, 165024
Sorry, prediction pasa_asmbl_32135.p1 fails validation.
(GAT)	 GT	164704-165024	TC	AAT
Valid prediction for snap_scaffold_24-snap.662-T1
Couldn't classify 66749, 66773
Sorry, prediction pasa_asmbl_32125.p1 fails validation.
(GGA)	 TG	66749-66773	GT	AGG
(ATG)	 AG	66946-67158	GT	CGG
(GCG)	 AG	67254-67385	GT	AGG
(GTG)	 AG	67822-68117	AA	GAA
add_exon() Sorry, pasa_asmbl_32125.p1 66946-67158-initial-1 is invalid.
-recovered pasa_asmbl_32125.p1, initial, 66946, 67158
-recovered pasa_asmbl_32125.p1, terminal, 67822, 68117
-recovered pasa_asmbl_32125.p1, internal, 66946, 67158
-recovered pasa_asmbl_32125.p1, internal, 67254, 67385
Couldn't classify 76383, 76511
Sorry, prediction pasa_asmbl_32127.p1 fails validation.
(CAG)	 TG	76383-76511	GT	AGG
(ATG)	 AG	76649-76716	GT	AGG
(GAC)	 AG	77012-77150	GT	GGG
(GCT)	 AG	77696-77765	GT	AGG
(GTG)	 AG	77891-77907	TG	GAT
-recovered pasa_asmbl_32127.p1, initial, 76649, 76716
-recovered pasa_asmbl_32127.p1, terminal, 77891, 77907
-recovered pasa_asmbl_32127.p1, internal, 76649, 76716
-recovered pasa_asmbl_32127.p1, internal, 77012, 77150
-recovered pasa_asmbl_32127.p1, internal, 77696, 77765
Couldn't classify 20416, 20572
Couldn't classify 21391, 21489
Sorry, prediction pasa_asmbl_32120.p2 fails validation.
(ACC)	 GA	20416-20572	GT	CAG
(GTG)	 AG	20957-21111	GT	AGG
(AAC)	 AG	21391-21489	TC	AGT
-recovered pasa_asmbl_32120.p2, internal, 20957, 21111
Couldn't classify 26285, 26421
Sorry, prediction pasa_asmbl_32122.p1 fails validation.
(ATG)	 AG	23399-23422	GT	ATG
(GTG)	 AG	24323-24415	GT	AGG
(ATG)	 AG	24621-24795	GT	AGG
(GAT)	 AG	25145-25342	GT	AGG
(GCT)	 AG	26285-26421	GT	AGG
-recovered pasa_asmbl_32122.p1, initial, 23399, 23422
-recovered pasa_asmbl_32122.p1, initial, 24621, 24795
-recovered pasa_asmbl_32122.p1, internal, 23399, 23422
-recovered pasa_asmbl_32122.p1, internal, 24323, 24415
-recovered pasa_asmbl_32122.p1, internal, 24621, 24795
-recovered pasa_asmbl_32122.p1, internal, 25145, 25342
-recovered pasa_asmbl_32122.p1, internal, 26285, 26421
Valid prediction for HiQ_model.g34785.t1
Valid prediction for Augustus_model.g34790.t1
Couldn't classify 167636, 167743
Sorry, prediction pasa_asmbl_32136.p1 fails validation.
(ATG)	 CC	165651-166048	GT	AGG
(GAA)	 AG	166387-166615	GT	GGG
(TAC)	 AG	166850-167023	GT	CGG
(AAC)	 AG	167636-167743	GT	CTG
-recovered pasa_asmbl_32136.p1, initial, 165651, 166048
-recovered pasa_asmbl_32136.p1, internal, 166387, 166615
-recovered pasa_asmbl_32136.p1, internal, 166850, 167023
-recovered pasa_asmbl_32136.p1, internal, 167636, 167743
Valid prediction for GlimmerHMM_glimmerT_52219-T1
Valid prediction for Augustus_model.g34784.t1
Couldn't classify 27034, 27248
Couldn't classify 27563, 27779
Sorry, prediction pasa_asmbl_32123.p1 fails validation.
(ACC)	 AG	27034-27248	GT	AGG
(GTC)	 AG	27563-27779	AC	ACA
-recovered pasa_asmbl_32123.p1, internal, 27034, 27248
Valid prediction for snap_scaffold_24-snap.680-T1
Valid prediction for GlimmerHMM_glimmerT_52218-T1
Valid prediction for Augustus_model.g34793.t1
Valid prediction for GlimmerHMM_glimmerT_52214-T1
Valid prediction for Augustus_model.g34799.t1
Valid prediction for Augustus_model.g34795.t1
Valid prediction for snap_scaffold_24-snap.668-T1
Valid prediction for snap_scaffold_24-snap.690-T1
Valid prediction for GlimmerHMM_glimmerT_52227-T1
Valid prediction for snap_scaffold_24-snap.677-T1
Couldn't classify 50098, 50198
Sorry, prediction pasa_asmbl_32674.p2 fails validation.
(ATG)	 CC	49862-50072	GT	CGG
(ACA)	 AG	50098-50198	TG	CTT
-recovered pasa_asmbl_32674.p2, initial, 49862, 50072
Couldn't classify 15198, 15755
Sorry, prediction pasa_asmbl_32118.p1 fails validation.
(TCG)	 GG	15198-15755	GG	GGG
Couldn't classify 143788, 144161
Couldn't classify 144273, 144294
Sorry, prediction pasa_asmbl_32623.p1 fails validation.
(CCC)	 GC	143788-144161	GT	AGG
(GTA)	 AG	144273-144294	AT	AGA
Valid prediction for snap_scaffold_24-snap.685-T1
Valid prediction for CodingQuarry_transcript_37268-T1
Couldn't classify 65834, 65894
Couldn't classify 66588, 66655
Sorry, prediction pasa_asmbl_32609.p1 fails validation.
(GTG)	 CG	65834-65894	GT	TGG
(TGC)	 AG	66009-66208	GT	AGG
(GTC)	 AG	66318-66504	GT	AGG
(CTT)	 AG	66588-66655	CC	CCC
-recovered pasa_asmbl_32609.p1, internal, 66009, 66208
-recovered pasa_asmbl_32609.p1, internal, 66318, 66504
Valid prediction for snap_scaffold_24-snap.675-T1
Valid prediction for snap_scaffold_24-snap.702-T1
Valid prediction for snap_scaffold_24-snap.698-T1
Valid prediction for GlimmerHMM_glimmerT_52221-T1
Valid prediction for GlimmerHMM_glimmerT_52216-T1
Valid prediction for GlimmerHMM_glimmerT_52226-T1
Valid prediction for GlimmerHMM_glimmerT_52222-T1
Valid prediction for GlimmerHMM_glimmerT_52209-T1
Valid prediction for GlimmerHMM_glimmerT_52230-T1
Valid prediction for Augustus_model.g34787.t1
Valid prediction for snap_scaffold_24-snap.678-T1
Valid prediction for snap_scaffold_24-snap.696-T1
Valid prediction for snap_scaffold_24-snap.664-T1
Valid prediction for GlimmerHMM_glimmerT_52229-T1
Valid prediction for GlimmerHMM_glimmerT_52228-T1
Valid prediction for Augustus_model.g34798.t1
Valid prediction for GlimmerHMM_glimmerT_52234-T1
Valid prediction for snap_scaffold_24-snap.691-T1
Couldn't classify 12090, 12104
Couldn't classify 12396, 12860
Sorry, prediction pasa_asmbl_32116.p1 fails validation.
(AGC)	 AC	12090-12104	GT	AGG
(GGT)	 AG	12396-12860	GT	GAG
-recovered pasa_asmbl_32116.p1, internal, 12396, 12860
Valid prediction for GlimmerHMM_glimmerT_52210-T1
Valid prediction for snap_scaffold_24-snap.700-T1
Valid prediction for CodingQuarry_transcript_37271-T1
Couldn't classify 72368, 72468
Sorry, prediction pasa_asmbl_32126.p2 fails validation.
(ATG)	 CG	69613-69773	GT	AGG
(GGA)	 AG	71275-71360	GT	AGG
(AGT)	 AG	72368-72468	AA	ATA
-recovered pasa_asmbl_32126.p2, initial, 69613, 69773
-recovered pasa_asmbl_32126.p2, internal, 71275, 71360
Valid prediction for GlimmerHMM_glimmerT_52207-T1
Valid prediction for GlimmerHMM_glimmerT_52220-T1
Valid prediction for snap_scaffold_24-snap.681-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 Augustus_model.g34789.t1
Valid prediction for GlimmerHMM_glimmerT_52224-T1
Valid prediction for snap_scaffold_24-snap.695-T1
Valid prediction for GlimmerHMM_glimmerT_52233-T1
Valid prediction for pasa_asmbl_33227.p1
Valid prediction for CodingQuarry_transcript_37270-T1
Valid prediction for snap_scaffold_24-snap.688-T1
Valid prediction for snap_scaffold_24-snap.694-T1
Valid prediction for pasa_asmbl_33261.p1
Valid prediction for snap_scaffold_24-snap.670-T1
Valid prediction for snap_scaffold_24-snap.671-T1
Valid prediction for CodingQuarry_transcript_37265-T1
Valid prediction for snap_scaffold_24-snap.697-T1
Valid prediction for snap_scaffold_24-snap.706-T1
Valid prediction for snap_scaffold_24-snap.679-T1
Valid prediction for snap_scaffold_24-snap.707-T1
Valid prediction for HiQ_model.g34791.t1
Valid prediction for snap_scaffold_24-snap.672-T1
Valid prediction for snap_scaffold_24-snap.673-T1
Valid prediction for GlimmerHMM_glimmerT_52213-T1
Valid prediction for Augustus_model.g34796.t1
Valid prediction for snap_scaffold_24-snap.669-T1
Valid prediction for GlimmerHMM_glimmerT_52212-T1
Valid prediction for snap_scaffold_24-snap.699-T1
Valid prediction for snap_scaffold_24-snap.692-T1
Valid prediction for GlimmerHMM_glimmerT_52217-T1
Valid prediction for GlimmerHMM_glimmerT_52223-T1
Valid prediction for snap_scaffold_24-snap.676-T1
Valid prediction for snap_scaffold_24-snap.663-T1
Valid prediction for snap_scaffold_24-snap.703-T1
Valid prediction for Augustus_model.g34788.t1
Valid prediction for GlimmerHMM_glimmerT_52232-T1
Valid prediction for snap_scaffold_24-snap.665-T1
Valid prediction for snap_scaffold_24-snap.705-T1
Valid prediction for snap_scaffold_24-snap.682-T1
Valid prediction for snap_scaffold_24-snap.674-T1
Valid prediction for snap_scaffold_24-snap.686-T1
Valid prediction for GlimmerHMM_glimmerT_52215-T1
Valid prediction for CodingQuarry_transcript_37266-T1
Valid prediction for CodingQuarry_transcript_37267-T1
Valid prediction for snap_scaffold_24-snap.687-T1
Valid prediction for pasa_asmbl_32806.p1
Valid prediction for Augustus_model.g34801.t1
Valid prediction for snap_scaffold_24-snap.684-T1
Valid prediction for snap_scaffold_24-snap.693-T1
Valid prediction for GlimmerHMM_glimmerT_52211-T1
Valid prediction for GlimmerHMM_glimmerT_52235-T1
Valid prediction for snap_scaffold_24-snap.689-T1
Valid prediction for HiQ_model.g34792.t1
Valid prediction for HiQ_model.g34797.t1
Couldn't classify 139918, 140304
Sorry, prediction pasa_asmbl_32129.p1 fails validation.
(CAC)	 GC	139918-140304	TG	GAT
Valid prediction for snap_scaffold_24-snap.683-T1
Valid prediction for snap_scaffold_24-snap.667-T1
Valid prediction for snap_scaffold_24-snap.701-T1
Valid prediction for pasa_asmbl_32812.p1
Valid prediction for GlimmerHMM_glimmerT_52231-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5129, rend_intergenic: 4060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7045, rend_intergenic: 5225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7700, rend_intergenic: 7582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20656, rend_intergenic: 7735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23461, rend_intergenic: 20784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38138, rend_intergenic: 24269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50370, rend_intergenic: 39528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51442, rend_intergenic: 50445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56735, rend_intergenic: 51475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87662, rend_intergenic: 69779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88114, rend_intergenic: 87780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100918, rend_intergenic: 88558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107437, rend_intergenic: 102761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154169, rend_intergenic: 110849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157991, rend_intergenic: 157250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165009, rend_intergenic: 157995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170294, rend_intergenic: 165998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184848, rend_intergenic: 170482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201560, rend_intergenic: 185257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206856, rend_intergenic: 201621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 237792
-exon list size: 560


building trellis

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66.5    
66.7    
66.9    
67.1    
67.3    
67.4    
67.6    
67.8    
68.0    
68.1    
68.3    
68.5    
68.7    
68.9    
69.0    
69.2    
69.4    
69.6    
69.8    
69.9    
70.1    
70.3    
70.5    
70.6    
70.8    
71.0    
71.2    
71.4    
71.5    
71.7    
71.9    
72.1    
72.2    
72.4    
72.6    
72.8    
73.0    
73.1    
73.3    
73.5    
73.7    
73.8    
74.0    
74.2    
74.4    
74.6    
74.7    
74.9    
75.1    
75.3    
75.4    
75.6    
75.8    
76.0    
76.2    
76.3    
76.5    
76.7    
76.9    
77.0    
77.2    
77.4    
77.6    
77.8    
77.9    
78.1    
78.3    
78.5    
78.6    
78.8    
79.0    
79.2    
79.4    
79.5    
79.7    
79.9    
80.1    
80.2    
80.4    
80.6    
80.8    
81.0    
81.1    
81.3    
81.5    
81.7    
81.9    
82.0    
82.2    
82.4    
82.6    
82.7    
82.9    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.2    
84.3    
84.5    
84.7    
84.9    
85.1    
85.2    
85.4    
85.6    
85.8    
85.9    
86.1    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
89.7    
89.9    
90.0    
90.2    
90.4    
90.6    
90.7    
90.9    
91.1    
91.3    
91.5    
91.6    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.9    
98.0    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 5129, rend_intergenic: 4060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7045, rend_intergenic: 5225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7700, rend_intergenic: 7582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20656, rend_intergenic: 7735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23461, rend_intergenic: 20784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38138, rend_intergenic: 24269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50370, rend_intergenic: 39528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51442, rend_intergenic: 50445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56735, rend_intergenic: 51475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87662, rend_intergenic: 69779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88114, rend_intergenic: 87780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100918, rend_intergenic: 88558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107437, rend_intergenic: 102761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154169, rend_intergenic: 110849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157991, rend_intergenic: 157250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165009, rend_intergenic: 157995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170294, rend_intergenic: 165998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184848, rend_intergenic: 170482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201560, rend_intergenic: 185257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206856, rend_intergenic: 201621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support