-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_5897756-6152288

-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 CodingQuarry_transcript_19983-T1
Valid prediction for snap_scaffold_16-snap.1176-T1
Valid prediction for CodingQuarry_transcript_19986-T1
Valid prediction for CodingQuarry_transcript_19987-T1
Valid prediction for snap_scaffold_16-snap.1159-T1
Valid prediction for snap_scaffold_16-snap.1169-T1
Valid prediction for GlimmerHMM_glimmerT_38429-T1
Valid prediction for pasa_asmbl_16284.p1
Valid prediction for pasa_asmbl_16266.p1
Valid prediction for snap_scaffold_16-snap.1138-T1
Couldn't classify 215675, 216161
Couldn't classify 217706, 217909
Sorry, prediction pasa_asmbl_16265.p1 fails validation.
(CGA)	 AC	215675-216161	GT	AGG
(ATT)	 AG	216271-216338	GT	CCG
(GGT)	 AG	216434-216661	GT	AGG
(GAA)	 AG	216904-216972	GT	CCG
(GTT)	 AG	217373-217450	GT	AGG
(GAT)	 AG	217706-217909	GA	AGG
-recovered pasa_asmbl_16265.p1, internal, 216271, 216338
-recovered pasa_asmbl_16265.p1, internal, 216434, 216661
-recovered pasa_asmbl_16265.p1, internal, 216904, 216972
-recovered pasa_asmbl_16265.p1, internal, 217373, 217450
Couldn't classify 65911, 66020
Sorry, prediction pasa_asmbl_16250.p1 fails validation.
(ATG)	 CG	62922-62986	GT	GCG
(ATA)	 AG	64505-64614	GT	TGG
(AAA)	 AG	65415-65480	GT	AGG
(GAG)	 AG	65911-66020	GG	TCG
-recovered pasa_asmbl_16250.p1, initial, 62922, 62986
-recovered pasa_asmbl_16250.p1, internal, 64505, 64614
-recovered pasa_asmbl_16250.p1, internal, 65415, 65480
Valid prediction for snap_scaffold_16-snap.1174-T1
Couldn't classify 37099, 37175
Couldn't classify 43621, 43868
Sorry, prediction pasa_asmbl_16237.p1 fails validation.
(AGC)	 AC	37099-37175	GT	GGG
(TTC)	 AG	37403-37560	GT	AGG
(ATC)	 AG	37664-37687	GT	GGG
(GTC)	 AG	38046-38272	GT	AGG
(GTC)	 AG	40628-40732	GT	AGG
(GTG)	 AG	40915-41002	GT	CGG
(TTG)	 AG	42612-42709	GT	AGG
(ATC)	 AG	42827-42959	GT	CGG
(AAC)	 AG	43621-43868	GT	AGG
-recovered pasa_asmbl_16237.p1, internal, 37403, 37560
-recovered pasa_asmbl_16237.p1, internal, 37664, 37687
-recovered pasa_asmbl_16237.p1, internal, 38046, 38272
-recovered pasa_asmbl_16237.p1, internal, 40628, 40732
-recovered pasa_asmbl_16237.p1, internal, 40915, 41002
-recovered pasa_asmbl_16237.p1, internal, 42612, 42709
-recovered pasa_asmbl_16237.p1, internal, 42827, 42959
-recovered pasa_asmbl_16237.p1, internal, 43621, 43868
Valid prediction for GlimmerHMM_glimmerT_38434-T1
Couldn't classify 47419, 47631
Sorry, prediction pasa_asmbl_16239.p1 fails validation.
(GCG)	 AG	47419-47631	GT	AGG
(GTG)	 AG	49414-49602	GT	AGG
(GTG)	 AG	49892-49958	GT	AGG
(GTG)	 AG	50176-50306	GT	AGG
(GAG)	 AG	52136-52306	GG	GAG
-recovered pasa_asmbl_16239.p1, terminal, 52136, 52306
-recovered pasa_asmbl_16239.p1, internal, 47419, 47631
-recovered pasa_asmbl_16239.p1, internal, 49414, 49602
-recovered pasa_asmbl_16239.p1, internal, 49892, 49958
-recovered pasa_asmbl_16239.p1, internal, 50176, 50306
Valid prediction for pasa_asmbl_16235.p1
Valid prediction for snap_scaffold_16-snap.1180-T1
Valid prediction for snap_scaffold_16-snap.1163-T1
Valid prediction for Augustus_model.g25653.t1
Valid prediction for snap_scaffold_16-snap.1166-T1
Valid prediction for snap_scaffold_16-snap.1151-T1
Valid prediction for GlimmerHMM_glimmerT_38424-T1
Valid prediction for Augustus_model.g25657.t1
Valid prediction for Augustus_model.g25643.t1
Valid prediction for GlimmerHMM_glimmerT_38419-T1
Valid prediction for HiQ_model.g25659.t1
Valid prediction for GlimmerHMM_glimmerT_38422-T1
Valid prediction for Augustus_model.g25636.t1
Valid prediction for GlimmerHMM_glimmerT_38415-T1
Valid prediction for Augustus_model.g25642.t1
Valid prediction for GlimmerHMM_glimmerT_38416-T1
Couldn't classify 229284, 229361
Sorry, prediction pasa_asmbl_16273.p1 fails validation.
(CCA)	 CT	229284-229361	GT	AGG
(TGT)	 AG	229448-229642	GT	TGG
(TCA)	 AG	229753-229874	GT	CAG
(GAA)	 AG	229982-230150	GT	AGG
(GAG)	 AG	230613-230770	GT	AGG
(TTG)	 AG	230862-230923	GT	AGG
(ACG)	 AG	231014-231189	CA	AAC
-recovered pasa_asmbl_16273.p1, terminal, 231014, 231189
-recovered pasa_asmbl_16273.p1, internal, 229448, 229642
-recovered pasa_asmbl_16273.p1, internal, 229753, 229874
-recovered pasa_asmbl_16273.p1, internal, 229982, 230150
-recovered pasa_asmbl_16273.p1, internal, 230613, 230770
-recovered pasa_asmbl_16273.p1, internal, 230862, 230923
Valid prediction for snap_scaffold_16-snap.1165-T1
Valid prediction for snap_scaffold_16-snap.1146-T1
Valid prediction for HiQ_model.g25634.t1
Valid prediction for GlimmerHMM_glimmerT_38417-T1
Valid prediction for pasa_asmbl_16275.p1
Valid prediction for snap_scaffold_16-snap.1173-T1
Valid prediction for snap_scaffold_16-snap.1178-T1
Valid prediction for GlimmerHMM_glimmerT_38427-T1
Valid prediction for snap_scaffold_16-snap.1145-T1
Valid prediction for snap_scaffold_16-snap.1137-T1
Valid prediction for snap_scaffold_16-snap.1144-T1
Valid prediction for snap_scaffold_16-snap.1135-T1
Valid prediction for GlimmerHMM_glimmerT_38425-T1
Valid prediction for Augustus_model.g25649.t1
Valid prediction for HiQ_model.g25656.t1
Valid prediction for Augustus_model.g25637.t1
Valid prediction for GlimmerHMM_glimmerT_38428-T1
Couldn't classify 228023, 228082
Couldn't classify 229170, 229211
Sorry, prediction pasa_asmbl_16272.p1 fails validation.
(AGG)	 CC	228023-228082	GT	AGG
(ATT)	 AG	228261-228407	GT	AGG
(GAG)	 AG	228615-228764	GT	AGG
(AGT)	 AG	228858-228986	GT	TGG
(GAA)	 AG	229170-229211	CC	CCC
-recovered pasa_asmbl_16272.p1, internal, 228261, 228407
-recovered pasa_asmbl_16272.p1, internal, 228615, 228764
-recovered pasa_asmbl_16272.p1, internal, 228858, 228986
Valid prediction for snap_scaffold_16-snap.1149-T1
Valid prediction for snap_scaffold_16-snap.1139-T1
Valid prediction for GlimmerHMM_glimmerT_38420-T1
Valid prediction for snap_scaffold_16-snap.1141-T1
Valid prediction for pasa_asmbl_16251.p1
Valid prediction for snap_scaffold_16-snap.1134-T1
Couldn't classify 216045, 216053
Couldn't classify 216099, 216161
Sorry, prediction CodingQuarry_transcript_19980-T1 fails validation.
(ATG)	 AG	216045-216053	AG	CAA
(AGG)	 GC	216099-216161	GT	AGG
(ATT)	 AG	216271-216338	GT	CCG
(GGT)	 AG	216434-216653	AA	GAA
-recovered CodingQuarry_transcript_19980-T1, terminal, 216434, 216653
-recovered CodingQuarry_transcript_19980-T1, internal, 216271, 216338
Valid prediction for GlimmerHMM_glimmerT_38436-T1
Valid prediction for snap_scaffold_16-snap.1132-T1
Valid prediction for GlimmerHMM_glimmerT_38432-T1
Valid prediction for snap_scaffold_16-snap.1140-T1
Valid prediction for CodingQuarry_transcript_19989-T1
Valid prediction for GlimmerHMM_glimmerT_38430-T1
Valid prediction for CodingQuarry_transcript_19976-T1
Valid prediction for CodingQuarry_transcript_19982-T1
Valid prediction for GlimmerHMM_glimmerT_38431-T1
Valid prediction for snap_scaffold_16-snap.1161-T1
Valid prediction for HiQ_model.g25661.t1
Couldn't classify 33818, 33928
Sorry, prediction pasa_asmbl_16236.p1 fails validation.
(ATG)	 TC	30350-30415	GT	AGG
(GAG)	 AG	30638-30691	GT	AGG
(GAT)	 AG	30821-30895	GT	AAG
(TAT)	 AG	31014-31160	GT	TGG
(ATC)	 AG	31268-31383	GT	AGG
(ACT)	 AG	31484-31641	GT	AGG
(GAT)	 AG	31784-31937	GT	AGG
(GCA)	 AG	33031-33251	GT	GGG
(GCT)	 AG	33467-33618	GT	AGG
(GTG)	 AG	33818-33928	GA	GCG
-recovered pasa_asmbl_16236.p1, initial, 30350, 30415
-recovered pasa_asmbl_16236.p1, internal, 30638, 30691
-recovered pasa_asmbl_16236.p1, internal, 30821, 30895
-recovered pasa_asmbl_16236.p1, internal, 31014, 31160
-recovered pasa_asmbl_16236.p1, internal, 31268, 31383
-recovered pasa_asmbl_16236.p1, internal, 31484, 31641
-recovered pasa_asmbl_16236.p1, internal, 31784, 31937
-recovered pasa_asmbl_16236.p1, internal, 33031, 33251
-recovered pasa_asmbl_16236.p1, internal, 33467, 33618
Valid prediction for snap_scaffold_16-snap.1168-T1
Valid prediction for GlimmerHMM_glimmerT_38410-T1
Valid prediction for GlimmerHMM_glimmerT_38437-T1
Valid prediction for CodingQuarry_transcript_19977-T1
Valid prediction for Augustus_model.g25639.t1
Valid prediction for CodingQuarry_transcript_19981-T1
Valid prediction for Augustus_model.g25638.t1
Valid prediction for snap_scaffold_16-snap.1164-T1
Valid prediction for GlimmerHMM_glimmerT_38413-T1
Valid prediction for Augustus_model.g25640.t1
Valid prediction for snap_scaffold_16-snap.1156-T1
Valid prediction for CodingQuarry_transcript_19988-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_38433-T1
Valid prediction for snap_scaffold_16-snap.1170-T1
Valid prediction for Augustus_model.g25651.t1
Valid prediction for Augustus_model.g25635.t1
Valid prediction for HiQ_model.g25658.t1
Valid prediction for Augustus_model.g25633.t1
Valid prediction for snap_scaffold_16-snap.1136-T1
Valid prediction for snap_scaffold_16-snap.1142-T1
Valid prediction for pasa_asmbl_17143.p1
Valid prediction for snap_scaffold_16-snap.1158-T1
Valid prediction for snap_scaffold_16-snap.1155-T1
Valid prediction for GlimmerHMM_glimmerT_38411-T1
Valid prediction for Augustus_model.g25646.t1
Valid prediction for CodingQuarry_transcript_19978-T1
Valid prediction for snap_scaffold_16-snap.1175-T1
Valid prediction for snap_scaffold_16-snap.1157-T1
Valid prediction for GlimmerHMM_glimmerT_38426-T1
Valid prediction for GlimmerHMM_glimmerT_38414-T1
Valid prediction for pasa_asmbl_17141.p1
Valid prediction for HiQ_model.g25660.t1
Valid prediction for snap_scaffold_16-snap.1154-T1
Valid prediction for Augustus_model.g25645.t1
Valid prediction for pasa_asmbl_17142.p1
Valid prediction for snap_scaffold_16-snap.1162-T1
Valid prediction for Augustus_model.g25644.t1
Valid prediction for CodingQuarry_transcript_19979-T1
Valid prediction for Augustus_model.g25648.t1
Valid prediction for Augustus_model.g25650.t1
Valid prediction for snap_scaffold_16-snap.1147-T1
Valid prediction for snap_scaffold_16-snap.1152-T1
Valid prediction for CodingQuarry_transcript_19984-T1
Valid prediction for pasa_asmbl_17136.p1
Valid prediction for Augustus_model.g25652.t1
Valid prediction for GlimmerHMM_glimmerT_38435-T1
Valid prediction for snap_scaffold_16-snap.1177-T1
Valid prediction for Augustus_model.g25654.t1
Valid prediction for GlimmerHMM_glimmerT_38418-T1
Valid prediction for CodingQuarry_transcript_19985-T1
Valid prediction for Augustus_model.g25641.t1
Valid prediction for HiQ_model.g25655.t1
Valid prediction for snap_scaffold_16-snap.1171-T1
Valid prediction for snap_scaffold_16-snap.1172-T1
Valid prediction for GlimmerHMM_glimmerT_38421-T1
Valid prediction for Augustus_model.g25647.t1
Valid prediction for snap_scaffold_16-snap.1133-T1
Valid prediction for GlimmerHMM_glimmerT_38412-T1
Valid prediction for snap_scaffold_16-snap.1167-T1
Valid prediction for GlimmerHMM_glimmerT_38423-T1
Valid prediction for snap_scaffold_16-snap.1153-T1
Valid prediction for snap_scaffold_16-snap.1179-T1
Valid prediction for snap_scaffold_16-snap.1143-T1
Valid prediction for snap_scaffold_16-snap.1160-T1
Valid prediction for snap_scaffold_16-snap.1150-T1
Valid prediction for snap_scaffold_16-snap.1148-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 50546, rend_intergenic: 49171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72209, rend_intergenic: 70743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93942, rend_intergenic: 89084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134307, rend_intergenic: 131737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147897, rend_intergenic: 144983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148801, rend_intergenic: 148487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163675, rend_intergenic: 150196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176945, rend_intergenic: 171627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 249381, rend_intergenic: 245822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 252212, rend_intergenic: 249965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 254533
-exon list size: 489


building trellis

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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    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 50546, rend_intergenic: 49171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72209, rend_intergenic: 70743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93942, rend_intergenic: 89084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134307, rend_intergenic: 131737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147897, rend_intergenic: 144983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148801, rend_intergenic: 148487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163675, rend_intergenic: 150196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176945, rend_intergenic: 171627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 249381, rend_intergenic: 245822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 252212, rend_intergenic: 249965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support