-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_5241359-5456175

-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 snap_scaffold_1-snap.833-T1
Valid prediction for snap_scaffold_1-snap.826-T1
Couldn't classify 70055, 70154
Sorry, prediction pasa_asmbl_2791.p1 fails validation.
(GTC)	 CT	70055-70154	GT	CAG
(CTC)	 AG	70972-71222	AG	GAA
-recovered pasa_asmbl_2791.p1, terminal, 70972, 71222
Valid prediction for snap_scaffold_1-snap.832-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_673-T1
Valid prediction for Augustus_model.g493.t1
Valid prediction for Augustus_model.g517.t1
Valid prediction for GlimmerHMM_glimmerT_656-T1
Valid prediction for snap_scaffold_1-snap.845-T1
Valid prediction for snap_scaffold_1-snap.831-T1
Valid prediction for snap_scaffold_1-snap.829-T1
Valid prediction for GlimmerHMM_glimmerT_662-T1
Valid prediction for Augustus_model.g500.t1
Valid prediction for GlimmerHMM_glimmerT_645-T1
Valid prediction for snap_scaffold_1-snap.830-T1
Valid prediction for GeneMark_model.855_t
Valid prediction for GlimmerHMM_glimmerT_654-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.823-T1
Valid prediction for snap_scaffold_1-snap.853-T1
Valid prediction for GeneMark_model.812_t
Valid prediction for GeneMark_model.844_t
Valid prediction for GeneMark_model.816_t
Valid prediction for GlimmerHMM_glimmerT_651-T1
Valid prediction for snap_scaffold_1-snap.839-T1
Valid prediction for GeneMark_model.852_t
Valid prediction for snap_scaffold_1-snap.837-T1
Valid prediction for Augustus_model.g501.t1
Valid prediction for GeneMark_model.833_t
Valid prediction for GeneMark_model.814_t
Valid prediction for snap_scaffold_1-snap.820-T1
Valid prediction for GlimmerHMM_glimmerT_666-T1
Valid prediction for GeneMark_model.830_t
Valid prediction for Augustus_model.g495.t1
Valid prediction for pasa_asmbl_1716.p1
Valid prediction for GlimmerHMM_glimmerT_658-T1
Valid prediction for GeneMark_model.854_t
Valid prediction for GeneMark_model.832_t
Valid prediction for GeneMark_model.822_t
Valid prediction for snap_scaffold_1-snap.825-T1
Valid prediction for GlimmerHMM_glimmerT_647-T1
Valid prediction for snap_scaffold_1-snap.856-T1
Couldn't classify 16230, 16325
Couldn't classify 17204, 17242
Sorry, prediction pasa_asmbl_2822.p1 fails validation.
(ATC)	 TG	16230-16325	GT	AGG
(ATG)	 AG	16570-16684	GT	AGG
(GAA)	 AG	16821-16945	GT	GAG
(ATC)	 AG	17204-17242	GA	GGG
-recovered pasa_asmbl_2822.p1, initial, 16570, 16684
-recovered pasa_asmbl_2822.p1, internal, 16570, 16684
-recovered pasa_asmbl_2822.p1, internal, 16821, 16945
Valid prediction for GeneMark_model.823_t
Valid prediction for GeneMark_model.839_t
Valid prediction for GeneMark_model.841_t
Valid prediction for GlimmerHMM_glimmerT_652-T1
Valid prediction for GlimmerHMM_glimmerT_649-T1
Valid prediction for GlimmerHMM_glimmerT_653-T1
Valid prediction for GeneMark_model.848_t
Valid prediction for snap_scaffold_1-snap.835-T1
Valid prediction for snap_scaffold_1-snap.843-T1
Valid prediction for GeneMark_model.819_t
Valid prediction for GeneMark_model.850_t
Valid prediction for GeneMark_model.825_t
Valid prediction for HiQ_model.g498.t1
Valid prediction for GeneMark_model.836_t
Valid prediction for GeneMark_model.827_t
Valid prediction for GeneMark_model.817_t
Valid prediction for GeneMark_model.837_t
Valid prediction for GlimmerHMM_glimmerT_644-T1
Valid prediction for CodingQuarry_transcript_2604-T1
Valid prediction for Augustus_model.g496.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_669-T1
Valid prediction for GlimmerHMM_glimmerT_650-T1
Valid prediction for Augustus_model.g511.t1
Valid prediction for GlimmerHMM_glimmerT_670-T1
Valid prediction for snap_scaffold_1-snap.846-T1
Valid prediction for Augustus_model.g508.t1
Valid prediction for snap_scaffold_1-snap.860-T1
Valid prediction for snap_scaffold_1-snap.838-T1
Valid prediction for Augustus_model.g510.t1
Couldn't classify 17550, 17791
Sorry, prediction pasa_asmbl_266.p1 fails validation.
(CCT)	 AG	17550-17791	GT	AAG
(GTG)	 AG	17940-18174	GT	AGG
(GTG)	 AG	20805-20984	GT	AGG
(GTT)	 AG	21110-21197	GT	AGG
(GTA)	 AG	21590-21696	GT	TGG
(GGA)	 AG	22569-22760	GT	AGG
(GAC)	 AG	22975-23188	GT	GGG
(GCG)	 AG	23527-23738	GT	AGG
(ATT)	 AG	24060-24167	GT	AGG
(GTG)	 AG	24303-24485	GT	AGG
(ATC)	 AG	25262-25436	GT	CCG
(AGT)	 AG	25960-25967	GA	AAG
-recovered pasa_asmbl_266.p1, terminal, 25960, 25967
-recovered pasa_asmbl_266.p1, internal, 17550, 17791
-recovered pasa_asmbl_266.p1, internal, 17940, 18174
-recovered pasa_asmbl_266.p1, internal, 20805, 20984
-recovered pasa_asmbl_266.p1, internal, 21110, 21197
-recovered pasa_asmbl_266.p1, internal, 21590, 21696
-recovered pasa_asmbl_266.p1, internal, 22569, 22760
-recovered pasa_asmbl_266.p1, internal, 22975, 23188
-recovered pasa_asmbl_266.p1, internal, 23527, 23738
-recovered pasa_asmbl_266.p1, internal, 24060, 24167
-recovered pasa_asmbl_266.p1, internal, 24303, 24485
-recovered pasa_asmbl_266.p1, internal, 25262, 25436
Valid prediction for GlimmerHMM_glimmerT_660-T1
Valid prediction for GeneMark_model.838_t
Valid prediction for snap_scaffold_1-snap.836-T1
Valid prediction for GeneMark_model.829_t
Valid prediction for GlimmerHMM_glimmerT_659-T1
Valid prediction for GeneMark_model.851_t
Valid prediction for GlimmerHMM_glimmerT_672-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g503.t1
Valid prediction for snap_scaffold_1-snap.821-T1
Valid prediction for Augustus_model.g515.t1
Valid prediction for Augustus_model.g506.t1
Valid prediction for GlimmerHMM_glimmerT_668-T1
Valid prediction for Augustus_model.g513.t1
Valid prediction for GeneMark_model.835_t
Valid prediction for GeneMark_model.828_t
Valid prediction for snap_scaffold_1-snap.850-T1
Valid prediction for GlimmerHMM_glimmerT_664-T1
Valid prediction for GeneMark_model.818_t
Valid prediction for snap_scaffold_1-snap.824-T1
Valid prediction for snap_scaffold_1-snap.827-T1
Valid prediction for snap_scaffold_1-snap.840-T1
Couldn't classify 10648, 10878
Sorry, prediction pasa_asmbl_268.p1 fails validation.
(ATG)	 AT	7972-7993	GT	AGG
(TCA)	 AG	9072-9236	GT	AGG
(GTC)	 AG	10154-10368	GT	AGG
(AAA)	 AG	10648-10878	AC	CCA
-recovered pasa_asmbl_268.p1, initial, 7972, 7993
-recovered pasa_asmbl_268.p1, internal, 9072, 9236
-recovered pasa_asmbl_268.p1, internal, 10154, 10368
Valid prediction for Augustus_model.g512.t1
Valid prediction for snap_scaffold_1-snap.855-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.853_t
Valid prediction for GeneMark_model.811_t
Valid prediction for GlimmerHMM_glimmerT_643-T1
Valid prediction for Augustus_model.g516.t1
Valid prediction for snap_scaffold_1-snap.852-T1
Valid prediction for snap_scaffold_1-snap.818-T1
Valid prediction for snap_scaffold_1-snap.859-T1
Valid prediction for Augustus_model.g507.t1
Valid prediction for GeneMark_model.846_t
Valid prediction for GlimmerHMM_glimmerT_657-T1
Valid prediction for snap_scaffold_1-snap.847-T1
Valid prediction for GlimmerHMM_glimmerT_663-T1
Valid prediction for Augustus_model.g504.t1
Valid prediction for GeneMark_model.813_t
Valid prediction for Augustus_model.g494.t1
Couldn't classify 123347, 123427
Sorry, prediction pasa_asmbl_263.p1 fails validation.
(ATG)	 CG	110114-110279	GT	TGG
(GCG)	 AG	111069-111123	GT	GTG
(AGA)	 AG	111217-111334	GT	AGG
(ATA)	 AG	111721-111798	GT	CGG
(GAT)	 AG	111884-112000	GT	AGG
(ATC)	 AG	112695-112841	GT	AGG
(GTG)	 AG	112971-113059	GT	TGG
(GGG)	 AG	113380-113501	GT	AGG
(GAT)	 AG	113987-114077	GT	AGG
(ACT)	 AG	114201-114345	GT	TGG
(GGC)	 AG	114569-114727	GT	TGG
(AAC)	 AG	117089-117283	GT	AGG
(CTG)	 AG	117673-117909	GT	ATG
(TCC)	 AG	118537-118652	GT	GGG
(AGG)	 AG	120487-120562	GT	AGG
(ATC)	 AG	123347-123427	GT	CCG
-recovered pasa_asmbl_263.p1, initial, 110114, 110279
-recovered pasa_asmbl_263.p1, internal, 111069, 111123
-recovered pasa_asmbl_263.p1, internal, 111217, 111334
-recovered pasa_asmbl_263.p1, internal, 111721, 111798
-recovered pasa_asmbl_263.p1, internal, 111884, 112000
-recovered pasa_asmbl_263.p1, internal, 112695, 112841
-recovered pasa_asmbl_263.p1, internal, 112971, 113059
-recovered pasa_asmbl_263.p1, internal, 113380, 113501
-recovered pasa_asmbl_263.p1, internal, 113987, 114077
-recovered pasa_asmbl_263.p1, internal, 114201, 114345
-recovered pasa_asmbl_263.p1, internal, 114569, 114727
-recovered pasa_asmbl_263.p1, internal, 117089, 117283
-recovered pasa_asmbl_263.p1, internal, 117673, 117909
-recovered pasa_asmbl_263.p1, internal, 118537, 118652
-recovered pasa_asmbl_263.p1, internal, 120487, 120562
-recovered pasa_asmbl_263.p1, internal, 123347, 123427
Valid prediction for GeneMark_model.856_t
Valid prediction for snap_scaffold_1-snap.854-T1
Valid prediction for GeneMark_model.849_t
Valid prediction for Augustus_model.g518.t1
Valid prediction for GlimmerHMM_glimmerT_655-T1
Valid prediction for GlimmerHMM_glimmerT_674-T1
Valid prediction for GeneMark_model.843_t
Valid prediction for GlimmerHMM_glimmerT_667-T1
Valid prediction for snap_scaffold_1-snap.841-T1
Valid prediction for Augustus_model.g505.t1
Valid prediction for snap_scaffold_1-snap.819-T1
Valid prediction for GlimmerHMM_glimmerT_671-T1
Valid prediction for GeneMark_model.826_t
Valid prediction for snap_scaffold_1-snap.828-T1
Valid prediction for snap_scaffold_1-snap.857-T1
Valid prediction for Augustus_model.g509.t1
Valid prediction for GeneMark_model.842_t
Valid prediction for snap_scaffold_1-snap.851-T1
Valid prediction for Augustus_model.g492.t1
Valid prediction for snap_scaffold_1-snap.842-T1
Valid prediction for GlimmerHMM_glimmerT_665-T1
Valid prediction for Augustus_model.g499.t1
Valid prediction for GeneMark_model.831_t
Valid prediction for snap_scaffold_1-snap.848-T1
Valid prediction for GeneMark_model.840_t
Valid prediction for GlimmerHMM_glimmerT_648-T1
Valid prediction for GeneMark_model.820_t
Valid prediction for snap_scaffold_1-snap.834-T1
Valid prediction for GeneMark_model.815_t
Valid prediction for snap_scaffold_1-snap.844-T1
Valid prediction for snap_scaffold_1-snap.822-T1
Valid prediction for GlimmerHMM_glimmerT_646-T1
Valid prediction for snap_scaffold_1-snap.858-T1
Valid prediction for GlimmerHMM_glimmerT_661-T1
Valid prediction for snap_scaffold_1-snap.849-T1
Valid prediction for GeneMark_model.834_t
Valid prediction for GeneMark_model.824_t
Valid prediction for GeneMark_model.821_t
Valid prediction for Augustus_model.g514.t1
Valid prediction for Augustus_model.g502.t1
Valid prediction for Augustus_model.g497.t1
Valid prediction for GeneMark_model.810_t
Valid prediction for GeneMark_model.847_t
Valid prediction for GeneMark_model.845_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13219, rend_intergenic: 8866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47701, rend_intergenic: 45017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81165, rend_intergenic: 78464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88174, rend_intergenic: 81225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89694, rend_intergenic: 88576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90351, rend_intergenic: 90062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97805, rend_intergenic: 93234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197505, rend_intergenic: 194912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 214817
-exon list size: 694


building trellis

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76.7    
76.9    
77.0    
77.2    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.2    
78.3    
78.4    
78.6    
78.7    
78.9    
79.0    
79.2    
79.3    
79.5    
79.6    
79.7    
79.9    
80.0    
80.2    
80.3    
80.5    
80.6    
80.7    
80.9    
81.0    
81.2    
81.3    
81.5    
81.6    
81.8    
81.9    
82.0    
82.2    
82.3    
82.5    
82.6    
82.8    
82.9    
83.0    
83.2    
83.3    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.6    
87.8    
87.9    
88.1    
88.2    
88.4    
88.5    
88.6    
88.8    
88.9    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 13219, rend_intergenic: 8866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47701, rend_intergenic: 45017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81165, rend_intergenic: 78464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88174, rend_intergenic: 81225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89694, rend_intergenic: 88576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90351, rend_intergenic: 90062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97805, rend_intergenic: 93234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197505, rend_intergenic: 194912  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