-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_13578126-13765932

-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_35802-T1
Valid prediction for Augustus_model.g24101.t1
Couldn't classify 166032, 166184
Couldn't classify 170695, 170825
Sorry, prediction pasa_asmbl_12487.p1 fails validation.
(GCC)	 CT	166032-166184	GT	CTG
(GGC)	 AG	166424-166616	GT	AGG
(GTT)	 AG	169160-169273	GT	GGG
(TGA)	 AG	170695-170825	GT	CGG
-recovered pasa_asmbl_12487.p1, internal, 166424, 166616
-recovered pasa_asmbl_12487.p1, internal, 169160, 169273
-recovered pasa_asmbl_12487.p1, internal, 170695, 170825
Valid prediction for pasa_asmbl_12467.p1
Valid prediction for snap_scaffold_14-snap.2855-T1
Valid prediction for GlimmerHMM_glimmerT_35786-T1
Valid prediction for snap_scaffold_14-snap.2825-T1
Valid prediction for GeneMark_model.61352_t
Valid prediction for GeneMark_model.61364_t
Couldn't classify 37720, 37906
Couldn't classify 39647, 39797
Sorry, prediction pasa_asmbl_12478.p1 fails validation.
(GCC)	 TG	37720-37906	GT	AGG
(ACG)	 AG	38057-38309	GT	GGG
(GAT)	 AG	39647-39797	GC	CCG
-recovered pasa_asmbl_12478.p1, internal, 38057, 38309
-recovered pasa_asmbl_12478.p1, internal, 39647, 39797
Valid prediction for GlimmerHMM_glimmerT_35797-T1
Valid prediction for HiQ_model.g24093.t1
Valid prediction for GeneMark_model.61355_t
Valid prediction for CodingQuarry_transcript_15865-T1
Valid prediction for CodingQuarry_transcript_15863-T1
Couldn't classify 95455, 95548
Sorry, prediction pasa_asmbl_12483.p1 fails validation.
(ATG)	 AC	93878-94011	GT	CGG
(GAC)	 AG	94520-94645	GT	AGG
(AGA)	 AG	95004-95136	GT	GAG
(GAA)	 AG	95231-95358	GT	AGG
(AGT)	 AG	95455-95548	AT	TGA
-recovered pasa_asmbl_12483.p1, initial, 93878, 94011
-recovered pasa_asmbl_12483.p1, internal, 94520, 94645
-recovered pasa_asmbl_12483.p1, internal, 95004, 95136
-recovered pasa_asmbl_12483.p1, internal, 95231, 95358
Valid prediction for GeneMark_model.61347_t
Valid prediction for GlimmerHMM_glimmerT_35798-T1
Valid prediction for snap_scaffold_14-snap.2847-T1
Valid prediction for GeneMark_model.61361_t
Valid prediction for Augustus_model.g24090.t1
Valid prediction for GlimmerHMM_glimmerT_35776-T1
Valid prediction for snap_scaffold_14-snap.2852-T1
Valid prediction for GlimmerHMM_glimmerT_35801-T1
Valid prediction for GeneMark_model.61336_t
Valid prediction for GeneMark_model.61363_t
Couldn't classify 90363, 90622
Couldn't classify 91344, 91572
Sorry, prediction pasa_asmbl_12482.p1 fails validation.
(CAG)	 CA	90363-90622	GT	AGG
(GTT)	 AG	91344-91572	GG	CGG
Valid prediction for snap_scaffold_14-snap.2849-T1
Valid prediction for GeneMark_model.61350_t
Valid prediction for pasa_asmbl_12748.p1
Valid prediction for GeneMark_model.61343_t
Valid prediction for snap_scaffold_14-snap.2853-T1
Valid prediction for snap_scaffold_14-snap.2841-T1
Valid prediction for GeneMark_model.61339_t
Valid prediction for Augustus_model.g24104.t1
Valid prediction for GlimmerHMM_glimmerT_35784-T1
Valid prediction for snap_scaffold_14-snap.2821-T1
Valid prediction for snap_scaffold_14-snap.2835-T1
Valid prediction for Augustus_model.g24105.t1
Valid prediction for snap_scaffold_14-snap.2827-T1
Valid prediction for snap_scaffold_14-snap.2837-T1
Valid prediction for snap_scaffold_14-snap.2844-T1
Valid prediction for snap_scaffold_14-snap.2830-T1
Valid prediction for snap_scaffold_14-snap.2826-T1
Valid prediction for HiQ_model.g24096.t1
Valid prediction for GeneMark_model.61359_t
Valid prediction for CodingQuarry_transcript_15866-T1
Valid prediction for snap_scaffold_14-snap.2829-T1
Valid prediction for CodingQuarry_transcript_15868-T1
Valid prediction for GlimmerHMM_glimmerT_35793-T1
Valid prediction for GlimmerHMM_glimmerT_35800-T1
Valid prediction for GeneMark_model.61345_t
Valid prediction for GeneMark_model.61349_t
Valid prediction for HiQ_model.g24086.t1
Valid prediction for snap_scaffold_14-snap.2838-T1
Valid prediction for GeneMark_model.61335_t
Valid prediction for Augustus_model.g24100.t1
Valid prediction for HiQ_model.g24088.t1
Valid prediction for pasa_asmbl_12481.p1
Valid prediction for GlimmerHMM_glimmerT_35794-T1
Couldn't classify 100410, 100471
Sorry, prediction pasa_asmbl_12484.p1 fails validation.
(ATC)	 CC	100410-100471	GT	AGG
(GCC)	 AG	101906-102068	GT	AGG
(TTT)	 AG	102240-102373	GT	AGG
(CTC)	 AG	102476-102640	GT	AGG
(GCT)	 AG	102998-103178	GT	AGG
(TAC)	 AG	103315-103463	GT	AGG
(AGC)	 AG	103560-103730	GT	ATG
(GGT)	 AG	104027-104220	GT	CGG
(ACG)	 AG	104676-104819	GT	TGG
(AGG)	 AG	104990-105117	GT	GGG
(GAC)	 AG	105325-105434	GT	AAG
(AGA)	 AG	106322-106431	GT	AGG
(GTA)	 AG	106603-106706	AG	AGA
-recovered pasa_asmbl_12484.p1, terminal, 106603, 106706
-recovered pasa_asmbl_12484.p1, internal, 101906, 102068
-recovered pasa_asmbl_12484.p1, internal, 102240, 102373
-recovered pasa_asmbl_12484.p1, internal, 102476, 102640
-recovered pasa_asmbl_12484.p1, internal, 102998, 103178
-recovered pasa_asmbl_12484.p1, internal, 103315, 103463
-recovered pasa_asmbl_12484.p1, internal, 103560, 103730
-recovered pasa_asmbl_12484.p1, internal, 104027, 104220
-recovered pasa_asmbl_12484.p1, internal, 104676, 104819
-recovered pasa_asmbl_12484.p1, internal, 104990, 105117
-recovered pasa_asmbl_12484.p1, internal, 105325, 105434
-recovered pasa_asmbl_12484.p1, internal, 106322, 106431
Couldn't classify 48977, 49200
Sorry, prediction pasa_asmbl_12480.p1 fails validation.
(GGA)	 CA	48977-49200	GT	AAG
(GGA)	 AG	49386-49486	GT	GGG
(AGT)	 AG	49749-49868	GT	TGG
(ACT)	 AG	51276-51442	GT	CGG
(GGA)	 AG	52150-52221	TA	GAT
-recovered pasa_asmbl_12480.p1, terminal, 52150, 52221
-recovered pasa_asmbl_12480.p1, internal, 49386, 49486
-recovered pasa_asmbl_12480.p1, internal, 49749, 49868
-recovered pasa_asmbl_12480.p1, internal, 51276, 51442
Valid prediction for snap_scaffold_14-snap.2840-T1
Valid prediction for GlimmerHMM_glimmerT_35787-T1
Valid prediction for GlimmerHMM_glimmerT_35790-T1
Valid prediction for GlimmerHMM_glimmerT_35780-T1
Valid prediction for Augustus_model.g24095.t1
Valid prediction for snap_scaffold_14-snap.2839-T1
Valid prediction for snap_scaffold_14-snap.2848-T1
Valid prediction for Augustus_model.g24106.t1
Valid prediction for snap_scaffold_14-snap.2842-T1
Couldn't classify 33897, 34114
Sorry, prediction pasa_asmbl_12476.p1 fails validation.
(TTT)	 AG	33897-34114	GT	TGG
(CTG)	 AG	34515-34596	GT	AGG
(GTC)	 AG	35002-35178	CC	GAC
-recovered pasa_asmbl_12476.p1, terminal, 35002, 35178
-recovered pasa_asmbl_12476.p1, internal, 33897, 34114
-recovered pasa_asmbl_12476.p1, internal, 34515, 34596
Valid prediction for GlimmerHMM_glimmerT_35795-T1
Valid prediction for GlimmerHMM_glimmerT_35791-T1
Valid prediction for GeneMark_model.61356_t
Valid prediction for snap_scaffold_14-snap.2831-T1
Valid prediction for GlimmerHMM_glimmerT_35792-T1
Valid prediction for GeneMark_model.61342_t
Couldn't classify 26484, 26600
Sorry, prediction pasa_asmbl_12475.p1 fails validation.
(ATG)	 AA	25329-25433	GT	CAG
(AAA)	 AG	25798-25953	GT	AGG
(AAA)	 AG	26484-26600	GT	AAG
-recovered pasa_asmbl_12475.p1, initial, 25329, 25433
-recovered pasa_asmbl_12475.p1, internal, 25798, 25953
-recovered pasa_asmbl_12475.p1, internal, 26484, 26600
Valid prediction for GeneMark_model.61340_t
Valid prediction for GlimmerHMM_glimmerT_35781-T1
Valid prediction for GeneMark_model.61330_t
Valid prediction for GlimmerHMM_glimmerT_35783-T1
Valid prediction for snap_scaffold_14-snap.2818-T1
Valid prediction for GlimmerHMM_glimmerT_35789-T1
Valid prediction for snap_scaffold_14-snap.2851-T1
Couldn't classify 40272, 40352
Couldn't classify 42470, 42568
Sorry, prediction pasa_asmbl_12479.p1 fails validation.
(CGC)	 GA	40272-40352	GT	TGG
(GAT)	 AG	41467-41562	GT	AAG
(AAC)	 AG	42082-42171	GT	CTG
(AAG)	 AG	42470-42568	CT	GCC
-recovered pasa_asmbl_12479.p1, internal, 41467, 41562
-recovered pasa_asmbl_12479.p1, internal, 42082, 42171
Valid prediction for HiQ_model.g24098.t1
Valid prediction for Augustus_model.g24099.t1
Valid prediction for snap_scaffold_14-snap.2823-T1
Valid prediction for Augustus_model.g24103.t1
Valid prediction for Augustus_model.g24102.t1
Valid prediction for Augustus_model.g24094.t1
Valid prediction for pasa_asmbl_12473.p2

-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_14-snap.2822-T1
Valid prediction for snap_scaffold_14-snap.2833-T1
Valid prediction for snap_scaffold_14-snap.2846-T1
Valid prediction for snap_scaffold_14-snap.2856-T1
Valid prediction for GeneMark_model.61357_t
Couldn't classify 119753, 119953
Sorry, prediction pasa_asmbl_13638.p1 fails validation.
(ATG)	 AG	118223-118459	GT	AGG
(GCT)	 AG	119753-119953	GT	AGG
-recovered pasa_asmbl_13638.p1, initial, 118223, 118459
-recovered pasa_asmbl_13638.p1, internal, 118223, 118459
-recovered pasa_asmbl_13638.p1, internal, 119753, 119953
Valid prediction for GeneMark_model.61351_t
Valid prediction for snap_scaffold_14-snap.2850-T1
Valid prediction for snap_scaffold_14-snap.2843-T1
Valid prediction for GlimmerHMM_glimmerT_35782-T1
Valid prediction for snap_scaffold_14-snap.2854-T1
Valid prediction for HiQ_model.g24085.t1
Valid prediction for GeneMark_model.61344_t
Valid prediction for snap_scaffold_14-snap.2819-T1
Valid prediction for Augustus_model.g24092.t1
Valid prediction for GeneMark_model.61358_t
Valid prediction for snap_scaffold_14-snap.2834-T1
Valid prediction for snap_scaffold_14-snap.2824-T1
Valid prediction for GlimmerHMM_glimmerT_35785-T1
Valid prediction for pasa_asmbl_13628.p1
Valid prediction for CodingQuarry_transcript_15864-T1
Valid prediction for CodingQuarry_transcript_15861-T1
Valid prediction for GeneMark_model.61346_t
Valid prediction for GeneMark_model.61353_t
Valid prediction for GeneMark_model.61333_t
Valid prediction for snap_scaffold_14-snap.2820-T1
Couldn't classify 171830, 171858
Sorry, prediction pasa_asmbl_13631.p2 fails validation.
(GAG)	 CG	171830-171858	GT	ACG
(ACT)	 AG	171960-172101	GT	AGG
(AGG)	 AG	172468-172732	GT	AGG
(GTG)	 AG	172827-172898	GT	GGG
(GAA)	 AG	173018-173100	AC	AGA
-recovered pasa_asmbl_13631.p2, terminal, 173018, 173100
-recovered pasa_asmbl_13631.p2, internal, 171960, 172101
-recovered pasa_asmbl_13631.p2, internal, 172468, 172732
-recovered pasa_asmbl_13631.p2, internal, 172827, 172898
Valid prediction for GeneMark_model.61337_t
Valid prediction for GeneMark_model.61362_t
Valid prediction for GlimmerHMM_glimmerT_35796-T1
Valid prediction for snap_scaffold_14-snap.2828-T1
Valid prediction for snap_scaffold_14-snap.2832-T1
Valid prediction for Augustus_model.g24087.t1
Valid prediction for snap_scaffold_14-snap.2817-T1
Valid prediction for GeneMark_model.61338_t
Valid prediction for pasa_asmbl_13633.p1
Valid prediction for GeneMark_model.61348_t
Valid prediction for HiQ_model.g24089.t1
Valid prediction for pasa_asmbl_13634.p1
Couldn't classify 128604, 128831
Sorry, prediction pasa_asmbl_13636.p1 fails validation.
(TGT)	 AG	128604-128831	GT	AGG
(AGA)	 AG	129466-129579	CC	AGC
-recovered pasa_asmbl_13636.p1, terminal, 129466, 129579
-recovered pasa_asmbl_13636.p1, internal, 128604, 128831
Valid prediction for GlimmerHMM_glimmerT_35777-T1
Valid prediction for GlimmerHMM_glimmerT_35803-T1
Valid prediction for Augustus_model.g24091.t1
Valid prediction for GeneMark_model.61331_t
Valid prediction for HiQ_model.g24097.t1
Valid prediction for GeneMark_model.61332_t
Valid prediction for CodingQuarry_transcript_15862-T1
Valid prediction for GeneMark_model.61360_t
Valid prediction for GlimmerHMM_glimmerT_35799-T1
Valid prediction for CodingQuarry_transcript_15867-T1
Valid prediction for GlimmerHMM_glimmerT_35775-T1
Valid prediction for GeneMark_model.61354_t
Valid prediction for GlimmerHMM_glimmerT_35778-T1
Valid prediction for snap_scaffold_14-snap.2836-T1
Valid prediction for GeneMark_model.61329_t
Valid prediction for snap_scaffold_14-snap.2845-T1
Valid prediction for GeneMark_model.61341_t
Valid prediction for GlimmerHMM_glimmerT_35779-T1
Valid prediction for GlimmerHMM_glimmerT_35788-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 43111, rend_intergenic: 39677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67035, rend_intergenic: 66272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106868, rend_intergenic: 100175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173257, rend_intergenic: 170711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 187807
-exon list size: 529


building trellis

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87.6    
87.8    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 43111, rend_intergenic: 39677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67035, rend_intergenic: 66272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106868, rend_intergenic: 100175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173257, rend_intergenic: 170711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support