-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_910220-1158494

-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_43570-T1
Valid prediction for snap_scaffold_19-snap.244-T1
Valid prediction for snap_scaffold_19-snap.218-T1
Couldn't classify 84307, 84555
Couldn't classify 84701, 84763
Sorry, prediction pasa_asmbl_21919.p1 fails validation.
(CCA)	 TT	84307-84555	GT	AGG
(ACT)	 AG	84701-84763	GT	AGG
-recovered pasa_asmbl_21919.p1, internal, 84701, 84763
Couldn't classify 125400, 126058
Couldn't classify 126770, 126873
Sorry, prediction pasa_asmbl_21227.p1 fails validation.
(CCT)	 NC	125400-126058	GT	AGG
(TCT)	 AG	126212-126381	GT	CGG
(GAA)	 AG	126770-126873	GT	GGG
-recovered pasa_asmbl_21227.p1, internal, 126212, 126381
-recovered pasa_asmbl_21227.p1, internal, 126770, 126873
Valid prediction for snap_scaffold_19-snap.214-T1
Valid prediction for snap_scaffold_19-snap.208-T1
Valid prediction for GlimmerHMM_glimmerT_43555-T1
Couldn't classify 73867, 74011
Couldn't classify 78385, 78417
Sorry, prediction pasa_asmbl_21222.p1 fails validation.
(CCC)	 CC	73867-74011	GT	AGG
(AGA)	 AG	75209-75301	GT	AGG
(CCA)	 AG	75462-75523	GT	AGG
(GAG)	 AG	75629-75694	GT	AGG
(GCC)	 AG	77243-77308	GC	AGG
(GAG)	 AG	77646-77690	GT	AGG
(GAG)	 AG	78385-78417	GT	GGG
-recovered pasa_asmbl_21222.p1, internal, 75209, 75301
-recovered pasa_asmbl_21222.p1, internal, 75462, 75523
-recovered pasa_asmbl_21222.p1, internal, 75629, 75694
-recovered pasa_asmbl_21222.p1, internal, 77243, 77308
-recovered pasa_asmbl_21222.p1, internal, 77646, 77690
-recovered pasa_asmbl_21222.p1, internal, 78385, 78417
Valid prediction for snap_scaffold_19-snap.226-T1
Valid prediction for snap_scaffold_19-snap.206-T1
Valid prediction for snap_scaffold_19-snap.239-T1
Valid prediction for GlimmerHMM_glimmerT_43575-T1
Valid prediction for snap_scaffold_19-snap.231-T1
Couldn't classify 68219, 68533
Sorry, prediction pasa_asmbl_21221.p1 fails validation.
(GGG)	 CA	68219-68533	GA	ATG
Couldn't classify 85310, 85344
Couldn't classify 87963, 88399
Sorry, prediction pasa_asmbl_21223.p1 fails validation.
(AAG)	 GG	85310-85344	GT	AAG
(GCT)	 AG	85713-85947	GT	AGG
(GAT)	 AG	86111-86173	GT	AGG
(CAA)	 AG	86503-86647	GT	AGG
(CTC)	 AG	87963-88399	TC	CAT
-recovered pasa_asmbl_21223.p1, internal, 85713, 85947
-recovered pasa_asmbl_21223.p1, internal, 86111, 86173
-recovered pasa_asmbl_21223.p1, internal, 86503, 86647
Valid prediction for snap_scaffold_19-snap.235-T1
Valid prediction for snap_scaffold_19-snap.236-T1
Valid prediction for Augustus_model.g28954.t1
Valid prediction for snap_scaffold_19-snap.227-T1
Valid prediction for GlimmerHMM_glimmerT_43557-T1
Valid prediction for Augustus_model.g28939.t1
Valid prediction for pasa_asmbl_21224.p1
Valid prediction for snap_scaffold_19-snap.210-T1
Valid prediction for GlimmerHMM_glimmerT_43560-T1
Valid prediction for snap_scaffold_19-snap.232-T1
Valid prediction for Augustus_model.g28943.t1
Valid prediction for Augustus_model.g28940.t1
Valid prediction for GlimmerHMM_glimmerT_43566-T1
Valid prediction for snap_scaffold_19-snap.225-T1
Valid prediction for Augustus_model.g28952.t1
Valid prediction for GlimmerHMM_glimmerT_43556-T1
Valid prediction for snap_scaffold_19-snap.223-T1
Valid prediction for Augustus_model.g28942.t1
Valid prediction for snap_scaffold_19-snap.205-T1
Valid prediction for Augustus_model.g28953.t1
Valid prediction for GlimmerHMM_glimmerT_43572-T1
Valid prediction for GlimmerHMM_glimmerT_43552-T1
Couldn't classify 221426, 221533
Sorry, prediction pasa_asmbl_21232.p1 fails validation.
(GTT)	 AG	221426-221533	GT	AGG
(GCC)	 AG	221949-222023	GT	AGG
(ATG)	 AG	222224-222349	GT	AGG
(GCT)	 AG	222456-222518	GT	AGG
(GAT)	 AG	222914-223012	AG	GAA
-recovered pasa_asmbl_21232.p1, initial, 222224, 222349
-recovered pasa_asmbl_21232.p1, terminal, 222914, 223012
-recovered pasa_asmbl_21232.p1, internal, 221426, 221533
-recovered pasa_asmbl_21232.p1, internal, 221949, 222023
-recovered pasa_asmbl_21232.p1, internal, 222224, 222349
-recovered pasa_asmbl_21232.p1, internal, 222456, 222518
Valid prediction for snap_scaffold_19-snap.247-T1
Valid prediction for Augustus_model.g28941.t1
Valid prediction for HiQ_model.g28951.t1
Valid prediction for snap_scaffold_19-snap.241-T1
Valid prediction for GlimmerHMM_glimmerT_43573-T1
Couldn't classify 218227, 218401
Sorry, prediction pasa_asmbl_21900.p1 fails validation.
(ATG)	 AG	216802-216849	GT	AGG
(GGT)	 AG	217115-217186	GT	AGG
(ATG)	 AG	217749-217868	GT	CTG
(GGT)	 AG	217980-218050	GT	AGG
(GCC)	 AG	218227-218401	CA	ACC
-recovered pasa_asmbl_21900.p1, initial, 216802, 216849
-recovered pasa_asmbl_21900.p1, initial, 217749, 217868
-recovered pasa_asmbl_21900.p1, internal, 216802, 216849
-recovered pasa_asmbl_21900.p1, internal, 217115, 217186
-recovered pasa_asmbl_21900.p1, internal, 217749, 217868
-recovered pasa_asmbl_21900.p1, internal, 217980, 218050
Valid prediction for snap_scaffold_19-snap.238-T1
Valid prediction for snap_scaffold_19-snap.237-T1
Valid prediction for snap_scaffold_19-snap.246-T1
Valid prediction for GlimmerHMM_glimmerT_43571-T1
Valid prediction for snap_scaffold_19-snap.250-T1
Valid prediction for GlimmerHMM_glimmerT_43558-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.g28937.t1
Valid prediction for snap_scaffold_19-snap.229-T1
Valid prediction for pasa_asmbl_22027.p1
Valid prediction for GlimmerHMM_glimmerT_43547-T1
Valid prediction for snap_scaffold_19-snap.228-T1
Valid prediction for snap_scaffold_19-snap.252-T1
Valid prediction for GlimmerHMM_glimmerT_43561-T1
Valid prediction for snap_scaffold_19-snap.220-T1
Valid prediction for snap_scaffold_19-snap.243-T1
Valid prediction for GlimmerHMM_glimmerT_43569-T1
Valid prediction for GlimmerHMM_glimmerT_43568-T1
Couldn't classify 105364, 105402
Sorry, prediction CodingQuarry_transcript_25590-T1 fails validation.
(ATG)	 CG	104841-104961	GT	GGG
(GAA)	 AG	105364-105402	AA	TGA
(GCC)	 AG	105872-106037	GT	AAG
(GTG)	 AG	106697-106754	CG	GAC
-recovered CodingQuarry_transcript_25590-T1, initial, 104841, 104961
-recovered CodingQuarry_transcript_25590-T1, terminal, 106697, 106754
-recovered CodingQuarry_transcript_25590-T1, internal, 105872, 106037
Valid prediction for snap_scaffold_19-snap.207-T1
Valid prediction for GlimmerHMM_glimmerT_43549-T1
Valid prediction for CodingQuarry_transcript_25591-T1
Valid prediction for GlimmerHMM_glimmerT_43554-T1
Valid prediction for GlimmerHMM_glimmerT_43565-T1
Couldn't classify 92320, 92441
Sorry, prediction pasa_asmbl_22018.p1 fails validation.
(ATG)	 CC	91031-91199	GT	TGG
(GTA)	 AG	91541-91576	GT	TGG
(GGT)	 AG	92320-92441	CT	CGC
-recovered pasa_asmbl_22018.p1, initial, 91031, 91199
-recovered pasa_asmbl_22018.p1, internal, 91541, 91576
Valid prediction for snap_scaffold_19-snap.222-T1
Valid prediction for snap_scaffold_19-snap.217-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_43553-T1
Valid prediction for Augustus_model.g28947.t1
Valid prediction for HiQ_model.g28936.t1
Couldn't classify 65923, 65929
Sorry, prediction pasa_asmbl_22021.p1 fails validation.
(TGT)	 TC	65923-65929	GT	AGG
(GCC)	 AG	66029-66251	GT	AGG
(GAC)	 AG	67057-67151	GT	GGG
(GGT)	 AG	68126-68242	GT	CGG
(ACT)	 AG	68862-69028	GT	CAG
(GGA)	 AG	70009-70107	TG	GAT
-recovered pasa_asmbl_22021.p1, terminal, 70009, 70107
-recovered pasa_asmbl_22021.p1, internal, 66029, 66251
-recovered pasa_asmbl_22021.p1, internal, 67057, 67151
-recovered pasa_asmbl_22021.p1, internal, 68126, 68242
-recovered pasa_asmbl_22021.p1, internal, 68862, 69028
Valid prediction for GlimmerHMM_glimmerT_43551-T1
Valid prediction for snap_scaffold_19-snap.211-T1
Valid prediction for GlimmerHMM_glimmerT_43548-T1
Valid prediction for Augustus_model.g28946.t1
Valid prediction for Augustus_model.g28944.t1
Valid prediction for snap_scaffold_19-snap.248-T1
Valid prediction for Augustus_model.g28945.t1
Valid prediction for snap_scaffold_19-snap.249-T1
Valid prediction for snap_scaffold_19-snap.216-T1
Valid prediction for CodingQuarry_transcript_25592-T1
Valid prediction for Augustus_model.g28948.t1
Valid prediction for HiQ_model.g28950.t1
Valid prediction for GlimmerHMM_glimmerT_43563-T1
Valid prediction for snap_scaffold_19-snap.224-T1
Valid prediction for snap_scaffold_19-snap.219-T1
Valid prediction for snap_scaffold_19-snap.242-T1
Valid prediction for snap_scaffold_19-snap.213-T1
Valid prediction for GlimmerHMM_glimmerT_43550-T1
Valid prediction for snap_scaffold_19-snap.230-T1
Couldn't classify 88173, 88358
Couldn't classify 89816, 89844
Sorry, prediction pasa_asmbl_22019.p1 fails validation.
(CCT)	 GT	88173-88358	GT	ACG
(GAT)	 AG	88714-88891	GT	TAG
(AGA)	 AG	89172-89309	GT	AGG
(CGA)	 AG	89816-89844	AC	AGA
-recovered pasa_asmbl_22019.p1, internal, 88714, 88891
-recovered pasa_asmbl_22019.p1, internal, 89172, 89309
Valid prediction for Augustus_model.g28949.t1
Valid prediction for snap_scaffold_19-snap.221-T1
Couldn't classify 114363, 114438
Sorry, prediction pasa_asmbl_22013.p1 fails validation.
(TTC)	 CA	114363-114438	GT	TGG
(ACC)	 AG	115088-115273	GT	AGG
(ACT)	 AG	115573-115796	GT	ACG
(GCG)	 AG	116032-116209	GT	GAG
(GAG)	 AG	116928-117089	GT	GGG
(GTG)	 AG	117197-117313	GT	GGG
(GAC)	 AG	117527-117730	GT	ACG
(GAT)	 AG	118163-118338	AG	GAA
-recovered pasa_asmbl_22013.p1, terminal, 118163, 118338
-recovered pasa_asmbl_22013.p1, internal, 115088, 115273
-recovered pasa_asmbl_22013.p1, internal, 115573, 115796
-recovered pasa_asmbl_22013.p1, internal, 116032, 116209
-recovered pasa_asmbl_22013.p1, internal, 116928, 117089
-recovered pasa_asmbl_22013.p1, internal, 117197, 117313
-recovered pasa_asmbl_22013.p1, internal, 117527, 117730
Valid prediction for snap_scaffold_19-snap.245-T1
Valid prediction for GlimmerHMM_glimmerT_43574-T1
Valid prediction for GlimmerHMM_glimmerT_43564-T1
Valid prediction for snap_scaffold_19-snap.233-T1
Valid prediction for Augustus_model.g28938.t1
Valid prediction for snap_scaffold_19-snap.212-T1
Valid prediction for snap_scaffold_19-snap.209-T1
Valid prediction for GlimmerHMM_glimmerT_43559-T1
Valid prediction for snap_scaffold_19-snap.234-T1
Valid prediction for CodingQuarry_transcript_25593-T1
Valid prediction for GlimmerHMM_glimmerT_43567-T1
Couldn't classify 95474, 95753
Couldn't classify 97212, 97315
Sorry, prediction pasa_asmbl_22015.p1 fails validation.
(CTG)	 AC	95474-95753	GT	CGG
(TCA)	 AG	97212-97315	CA	ACC
Valid prediction for snap_scaffold_19-snap.240-T1
Couldn't classify 65512, 65844
Sorry, prediction pasa_asmbl_22023.p1 fails validation.
(ATG)	 CG	65159-65338	GT	CGG
(GTG)	 AG	65512-65844	GC	AGG
-recovered pasa_asmbl_22023.p1, initial, 65159, 65338
-recovered pasa_asmbl_22023.p1, internal, 65512, 65844
Valid prediction for GlimmerHMM_glimmerT_43562-T1
Valid prediction for snap_scaffold_19-snap.215-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4997, rend_intergenic: 3169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11128, rend_intergenic: 9056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39567, rend_intergenic: 15146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68584, rend_intergenic: 50634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71940, rend_intergenic: 68862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93945, rend_intergenic: 73785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101145, rend_intergenic: 100968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106034, rend_intergenic: 104106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135250, rend_intergenic: 129938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152844, rend_intergenic: 138903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176645, rend_intergenic: 158276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189171, rend_intergenic: 179360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206257, rend_intergenic: 197667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223012, rend_intergenic: 219728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238553, rend_intergenic: 230893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 248275
-exon list size: 511


building trellis

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82.5    
82.7    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 4997, rend_intergenic: 3169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11128, rend_intergenic: 9056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39567, rend_intergenic: 15146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68584, rend_intergenic: 50634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71940, rend_intergenic: 68862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93945, rend_intergenic: 73785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101145, rend_intergenic: 100968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106034, rend_intergenic: 104106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135250, rend_intergenic: 129938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152844, rend_intergenic: 138903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176645, rend_intergenic: 158276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189171, rend_intergenic: 179360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206257, rend_intergenic: 197667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223012, rend_intergenic: 219728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238553, rend_intergenic: 230893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support