-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_6177872-6419917

-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 Augustus_model.g21749.t1
Valid prediction for snap_scaffold_13-snap.1184-T1
Valid prediction for GeneMark_model.55522_t
Valid prediction for snap_scaffold_13-snap.1171-T1
Valid prediction for GeneMark_model.55538_t
Valid prediction for GeneMark_model.55518_t
Valid prediction for snap_scaffold_13-snap.1157-T1
Valid prediction for pasa_asmbl_10906.p1
Valid prediction for snap_scaffold_13-snap.1176-T1
Valid prediction for GeneMark_model.55535_t
Valid prediction for pasa_asmbl_10920.p1
Valid prediction for GeneMark_model.55511_t
Valid prediction for snap_scaffold_13-snap.1162-T1
Valid prediction for HiQ_model.g21748.t1
Valid prediction for HiQ_model.g21757.t1
Valid prediction for snap_scaffold_13-snap.1166-T1
Valid prediction for GlimmerHMM_glimmerT_32462-T1
Valid prediction for pasa_asmbl_11564.p1
Valid prediction for GlimmerHMM_glimmerT_32464-T1
Valid prediction for snap_scaffold_13-snap.1168-T1
Valid prediction for GlimmerHMM_glimmerT_32488-T1
Valid prediction for snap_scaffold_13-snap.1187-T1
Valid prediction for snap_scaffold_13-snap.1160-T1
Valid prediction for GeneMark_model.55533_t
Valid prediction for snap_scaffold_13-snap.1173-T1
Valid prediction for GlimmerHMM_glimmerT_32474-T1
Valid prediction for snap_scaffold_13-snap.1180-T1
Valid prediction for snap_scaffold_13-snap.1181-T1
Valid prediction for GeneMark_model.55510_t
Valid prediction for pasa_asmbl_10903.p1
Valid prediction for GlimmerHMM_glimmerT_32473-T1
Valid prediction for CodingQuarry_transcript_13033-T1
Valid prediction for Augustus_model.g21755.t1
Valid prediction for snap_scaffold_13-snap.1156-T1
Valid prediction for GlimmerHMM_glimmerT_32477-T1
Valid prediction for GeneMark_model.55514_t
Valid prediction for GlimmerHMM_glimmerT_32467-T1
Valid prediction for CodingQuarry_transcript_13027-T1
Valid prediction for GeneMark_model.55523_t
Valid prediction for snap_scaffold_13-snap.1167-T1
Couldn't classify 228639, 228779
Sorry, prediction pasa_asmbl_10918.p2 fails validation.
(ATG)	 CT	228041-228241	GT	AGG
(ACT)	 AG	228360-228503	GT	ACG
(ACC)	 AG	228639-228779	CA	ATC
-recovered pasa_asmbl_10918.p2, initial, 228041, 228241
-recovered pasa_asmbl_10918.p2, internal, 228360, 228503
Valid prediction for GeneMark_model.55513_t
Valid prediction for GlimmerHMM_glimmerT_32486-T1
Valid prediction for HiQ_model.g21751.t1
Valid prediction for GlimmerHMM_glimmerT_32483-T1
Valid prediction for GeneMark_model.55539_t
Valid prediction for pasa_asmbl_10900.p1
Valid prediction for pasa_asmbl_10909.p1
Valid prediction for Augustus_model.g21746.t1
Valid prediction for GeneMark_model.55527_t
Valid prediction for snap_scaffold_13-snap.1175-T1
Valid prediction for GlimmerHMM_glimmerT_32471-T1
Valid prediction for GlimmerHMM_glimmerT_32468-T1
Valid prediction for GlimmerHMM_glimmerT_32465-T1
Valid prediction for snap_scaffold_13-snap.1183-T1
Valid prediction for snap_scaffold_13-snap.1179-T1
Valid prediction for GeneMark_model.55516_t
Valid prediction for GeneMark_model.55517_t
Valid prediction for CodingQuarry_transcript_13034-T1
Valid prediction for GeneMark_model.55525_t
Valid prediction for CodingQuarry_transcript_13028-T1
Valid prediction for GeneMark_model.55531_t
Valid prediction for GeneMark_model.55528_t

-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_13-snap.1159-T1
Valid prediction for GeneMark_model.55532_t
Valid prediction for snap_scaffold_13-snap.1164-T1
Valid prediction for GlimmerHMM_glimmerT_32482-T1
Valid prediction for GlimmerHMM_glimmerT_32481-T1
Valid prediction for GlimmerHMM_glimmerT_32479-T1
Valid prediction for HiQ_model.g21752.t1
Valid prediction for GeneMark_model.55521_t
Couldn't classify 36796, 36838
Couldn't classify 37335, 37405
Sorry, prediction CodingQuarry_transcript_13032-T1 fails validation.
(ATG)	 AG	25520-25594	GT	AGG
(ATT)	 AG	26463-26695	GT	AGG
(ATC)	 AG	26807-26904	GT	AGG
(GAA)	 AG	27130-27239	GT	AGG
(ACC)	 AG	27407-27517	GT	TGG
(ATG)	 AG	27657-27742	GT	AGG
(GAT)	 AG	27841-27928	GT	GGG
(AAT)	 AG	28034-28202	GT	GGG
(GCT)	 AG	28319-28386	GT	AGG
(TTT)	 AG	28654-28797	GT	GGG
(GAG)	 AG	28904-29073	GT	GAG
(TGA)	 AG	29255-29344	GT	TGG
(GTA)	 AG	29425-29581	GT	GGG
(CAC)	 AG	29760-29879	GT	AGG
(AGG)	 AG	29956-30125	GT	AGG
(GCA)	 AG	30311-30428	GT	AGG
(TTC)	 AG	30564-30659	GT	CGG
(GTG)	 AG	30817-30920	GT	AAG
(GTT)	 AG	31008-31139	GT	CAG
(CTT)	 AG	31264-31426	GT	AGG
(GAT)	 AG	31541-31654	GT	AGG
(GTG)	 AG	31770-31868	GT	ATG
(AAA)	 AG	31977-32092	GT	AAG
(CCC)	 AG	32191-32337	GT	AGG
(GTT)	 AG	32490-32579	GT	GGG
(GGC)	 AG	32669-32804	GT	AGG
(GTA)	 AG	32913-32969	GT	GGG
(CCT)	 AG	33421-33553	GT	AGG
(CGG)	 AG	33732-33801	GT	AGG
(GTG)	 AG	33904-34093	GT	AGG
(CAA)	 AG	34506-34595	GT	AGG
(GGT)	 AG	34704-34790	GT	AAG
(GAA)	 AG	34916-34975	GT	CTG
(GGT)	 AG	35513-35584	GT	AGG
(CCC)	 AG	35785-35919	GT	TGG
(AAG)	 AG	36447-36579	GT	GGG
(CTG)	 AG	36796-36838	AG	CCA
(CTT)	 CC	37335-37405	GT	AGG
(GTG)	 AG	37508-37668	GT	AGG
(GTG)	 AG	37772-38098	CC	GAC
-recovered CodingQuarry_transcript_13032-T1, initial, 25520, 25594
-recovered CodingQuarry_transcript_13032-T1, initial, 27657, 27742
add_exon() Sorry, CodingQuarry_transcript_13032-T1 26463-26695-terminal-2 is invalid.
-recovered CodingQuarry_transcript_13032-T1, terminal, 26463, 26695
-recovered CodingQuarry_transcript_13032-T1, terminal, 37772, 38098
-recovered CodingQuarry_transcript_13032-T1, internal, 25520, 25594
-recovered CodingQuarry_transcript_13032-T1, internal, 26463, 26695
-recovered CodingQuarry_transcript_13032-T1, internal, 26807, 26904
-recovered CodingQuarry_transcript_13032-T1, internal, 27130, 27239
-recovered CodingQuarry_transcript_13032-T1, internal, 27407, 27517
-recovered CodingQuarry_transcript_13032-T1, internal, 27657, 27742
-recovered CodingQuarry_transcript_13032-T1, internal, 27841, 27928
-recovered CodingQuarry_transcript_13032-T1, internal, 28034, 28202
-recovered CodingQuarry_transcript_13032-T1, internal, 28319, 28386
-recovered CodingQuarry_transcript_13032-T1, internal, 28654, 28797
-recovered CodingQuarry_transcript_13032-T1, internal, 28904, 29073
-recovered CodingQuarry_transcript_13032-T1, internal, 29255, 29344
-recovered CodingQuarry_transcript_13032-T1, internal, 29425, 29581
-recovered CodingQuarry_transcript_13032-T1, internal, 29760, 29879
-recovered CodingQuarry_transcript_13032-T1, internal, 29956, 30125
-recovered CodingQuarry_transcript_13032-T1, internal, 30311, 30428
-recovered CodingQuarry_transcript_13032-T1, internal, 30564, 30659
-recovered CodingQuarry_transcript_13032-T1, internal, 30817, 30920
-recovered CodingQuarry_transcript_13032-T1, internal, 31008, 31139
-recovered CodingQuarry_transcript_13032-T1, internal, 31264, 31426
-recovered CodingQuarry_transcript_13032-T1, internal, 31541, 31654
-recovered CodingQuarry_transcript_13032-T1, internal, 31770, 31868
-recovered CodingQuarry_transcript_13032-T1, internal, 31977, 32092
-recovered CodingQuarry_transcript_13032-T1, internal, 32191, 32337
-recovered CodingQuarry_transcript_13032-T1, internal, 32490, 32579
-recovered CodingQuarry_transcript_13032-T1, internal, 32669, 32804
-recovered CodingQuarry_transcript_13032-T1, internal, 32913, 32969
-recovered CodingQuarry_transcript_13032-T1, internal, 33421, 33553
-recovered CodingQuarry_transcript_13032-T1, internal, 33732, 33801
-recovered CodingQuarry_transcript_13032-T1, internal, 33904, 34093
-recovered CodingQuarry_transcript_13032-T1, internal, 34506, 34595
-recovered CodingQuarry_transcript_13032-T1, internal, 34704, 34790
-recovered CodingQuarry_transcript_13032-T1, internal, 34916, 34975
-recovered CodingQuarry_transcript_13032-T1, internal, 35513, 35584
-recovered CodingQuarry_transcript_13032-T1, internal, 35785, 35919
-recovered CodingQuarry_transcript_13032-T1, internal, 36447, 36579
-recovered CodingQuarry_transcript_13032-T1, internal, 37508, 37668
Valid prediction for GeneMark_model.55537_t
Valid prediction for GeneMark_model.55515_t
Valid prediction for CodingQuarry_transcript_13030-T1
Valid prediction for GeneMark_model.55512_t
Valid prediction for snap_scaffold_13-snap.1178-T1
Valid prediction for GeneMark_model.55536_t
Valid prediction for GlimmerHMM_glimmerT_32466-T1
Valid prediction for CodingQuarry_transcript_13035-T1
Valid prediction for snap_scaffold_13-snap.1155-T1
Couldn't classify 120030, 120106
Sorry, prediction pasa_asmbl_9738.p1 fails validation.
(ACG)	 CC	120030-120106	GT	AGG
(TCT)	 AG	120218-120343	GT	AGG
(GGA)	 AG	120493-120638	GT	AGG
(GTA)	 AG	120975-121077	GT	AGG
(GTA)	 AG	121237-121330	CG	AAC
-recovered pasa_asmbl_9738.p1, terminal, 121237, 121330
-recovered pasa_asmbl_9738.p1, internal, 120218, 120343
-recovered pasa_asmbl_9738.p1, internal, 120493, 120638
-recovered pasa_asmbl_9738.p1, internal, 120975, 121077
Valid prediction for GeneMark_model.55529_t
Valid prediction for Augustus_model.g21747.t1
Valid prediction for snap_scaffold_13-snap.1169-T1
Valid prediction for snap_scaffold_13-snap.1161-T1
Valid prediction for GlimmerHMM_glimmerT_32487-T1
Valid prediction for GlimmerHMM_glimmerT_32475-T1
Valid prediction for GeneMark_model.55526_t
Valid prediction for snap_scaffold_13-snap.1165-T1
Valid prediction for Augustus_model.g21750.t1
Valid prediction for snap_scaffold_13-snap.1163-T1
Valid prediction for GlimmerHMM_glimmerT_32463-T1
Valid prediction for GeneMark_model.55524_t
Valid prediction for snap_scaffold_13-snap.1185-T1
Valid prediction for GlimmerHMM_glimmerT_32485-T1
Valid prediction for GeneMark_model.55520_t
Valid prediction for HiQ_model.g21754.t1
Valid prediction for snap_scaffold_13-snap.1186-T1
Valid prediction for GeneMark_model.55530_t
Valid prediction for GlimmerHMM_glimmerT_32469-T1
Valid prediction for pasa_asmbl_9741.p1
Valid prediction for pasa_asmbl_9739.p1
Valid prediction for GlimmerHMM_glimmerT_32478-T1
Valid prediction for GlimmerHMM_glimmerT_32470-T1
Valid prediction for GlimmerHMM_glimmerT_32480-T1
Valid prediction for GeneMark_model.55519_t
Valid prediction for GlimmerHMM_glimmerT_32484-T1
Valid prediction for snap_scaffold_13-snap.1188-T1
Valid prediction for snap_scaffold_13-snap.1170-T1
Valid prediction for HiQ_model.g21753.t1
Valid prediction for HiQ_model.g21756.t1
Valid prediction for snap_scaffold_13-snap.1177-T1
Valid prediction for pasa_asmbl_9744.p1
Valid prediction for GeneMark_model.55534_t
Valid prediction for snap_scaffold_13-snap.1158-T1
Valid prediction for snap_scaffold_13-snap.1182-T1
Valid prediction for snap_scaffold_13-snap.1174-T1
Valid prediction for GlimmerHMM_glimmerT_32461-T1
Valid prediction for GlimmerHMM_glimmerT_32472-T1
Valid prediction for CodingQuarry_transcript_13029-T1
Valid prediction for snap_scaffold_13-snap.1172-T1
Valid prediction for pasa_asmbl_9737.p1
Valid prediction for GlimmerHMM_glimmerT_32476-T1
Valid prediction for CodingQuarry_transcript_13031-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15532, rend_intergenic: 15207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30240, rend_intergenic: 23510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40581, rend_intergenic: 39088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128655, rend_intergenic: 121471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215554, rend_intergenic: 204346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238121, rend_intergenic: 232762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 242046
-exon list size: 572


building trellis

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92.0    
92.2    
92.3    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.6    
93.7    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 15532, rend_intergenic: 15207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30240, rend_intergenic: 23510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40581, rend_intergenic: 39088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128655, rend_intergenic: 121471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215554, rend_intergenic: 204346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238121, rend_intergenic: 232762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support