-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_12890940-13153270

-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_52306-T1
Valid prediction for HiQ_model.g8530.t1
Valid prediction for snap_scaffold_5-snap.2417-T1
Couldn't classify 206640, 206659
Sorry, prediction pasa_asmbl_45852.p1 fails validation.
(TTT)	 GA	206640-206659	GT	AGG
(GAT)	 AG	207559-207733	GT	TGG
(GTG)	 AG	207854-208005	GT	CTG
(GTA)	 AG	208256-208391	TA	GAT
-recovered pasa_asmbl_45852.p1, terminal, 208256, 208391
-recovered pasa_asmbl_45852.p1, internal, 207559, 207733
-recovered pasa_asmbl_45852.p1, internal, 207854, 208005
Valid prediction for snap_scaffold_5-snap.2391-T1
Valid prediction for CodingQuarry_transcript_52296-T1
Valid prediction for CodingQuarry_transcript_52303-T1
Valid prediction for GlimmerHMM_glimmerT_12879-T1
Valid prediction for GlimmerHMM_glimmerT_12877-T1
Couldn't classify 91860, 91884
Sorry, prediction pasa_asmbl_45837.p1 fails validation.
(AAC)	 AA	91860-91884	GT	AGG
(GCG)	 AG	92959-93107	GT	GGG
(ACA)	 AG	93298-93423	GT	TGG
(GTT)	 AG	93705-93851	GC	GAG
-recovered pasa_asmbl_45837.p1, terminal, 93705, 93851
-recovered pasa_asmbl_45837.p1, internal, 92959, 93107
-recovered pasa_asmbl_45837.p1, internal, 93298, 93423
-recovered pasa_asmbl_45837.p1, internal, 93705, 93851
Valid prediction for snap_scaffold_5-snap.2392-T1
Valid prediction for pasa_asmbl_45832.p1
Valid prediction for pasa_asmbl_45834.p1
Valid prediction for snap_scaffold_5-snap.2415-T1
Valid prediction for Augustus_model.g8531.t1
Valid prediction for GlimmerHMM_glimmerT_12881-T1
Valid prediction for snap_scaffold_5-snap.2413-T1
Valid prediction for HiQ_model.g8546.t1
Valid prediction for HiQ_model.g8536.t1
Valid prediction for GlimmerHMM_glimmerT_12891-T1
Valid prediction for GlimmerHMM_glimmerT_12871-T1
Valid prediction for pasa_asmbl_45835.p1
Valid prediction for GlimmerHMM_glimmerT_12869-T1
Valid prediction for HiQ_model.g8540.t1
Valid prediction for snap_scaffold_5-snap.2422-T1
Valid prediction for GlimmerHMM_glimmerT_12874-T1
Valid prediction for GlimmerHMM_glimmerT_12867-T1
Valid prediction for GlimmerHMM_glimmerT_12884-T1
Valid prediction for snap_scaffold_5-snap.2411-T1
Valid prediction for snap_scaffold_5-snap.2405-T1
Valid prediction for snap_scaffold_5-snap.2404-T1
Valid prediction for Augustus_model.g8539.t1
Couldn't classify 188522, 188648
Couldn't classify 188788, 188957
Sorry, prediction pasa_asmbl_45849.p1 fails validation.
(AAC)	 TC	188522-188648	GT	TGG
(GTG)	 AG	188788-188957	GC	CCG
-recovered pasa_asmbl_45849.p1, internal, 188788, 188957
Valid prediction for CodingQuarry_transcript_52313-T1
Valid prediction for CodingQuarry_transcript_52311-T1
Valid prediction for GlimmerHMM_glimmerT_12859-T1
Valid prediction for GlimmerHMM_glimmerT_12875-T1
Valid prediction for CodingQuarry_transcript_52305-T1
Valid prediction for CodingQuarry_transcript_52294-T1
Valid prediction for Augustus_model.g8544.t1
Valid prediction for HiQ_model.g8529.t1
Valid prediction for Augustus_model.g8538.t1
Valid prediction for HiQ_model.g8534.t1
Valid prediction for pasa_asmbl_45846.p1
Valid prediction for snap_scaffold_5-snap.2389-T1
Valid prediction for CodingQuarry_transcript_52308-T1
Valid prediction for snap_scaffold_5-snap.2414-T1
Valid prediction for snap_scaffold_5-snap.2410-T1
Valid prediction for snap_scaffold_5-snap.2402-T1
Valid prediction for pasa_asmbl_45841.p1
Valid prediction for snap_scaffold_5-snap.2419-T1
Valid prediction for snap_scaffold_5-snap.2407-T1
Valid prediction for GlimmerHMM_glimmerT_12880-T1
Valid prediction for CodingQuarry_transcript_52307-T1
Valid prediction for HiQ_model.g8518.t1
Valid prediction for HiQ_model.g8519.t1
Valid prediction for Augustus_model.g8533.t1
Valid prediction for snap_scaffold_5-snap.2409-T1
Valid prediction for GlimmerHMM_glimmerT_12889-T1
Valid prediction for HiQ_model.g8527.t1
Valid prediction for Augustus_model.g8532.t1
Valid prediction for HiQ_model.g8535.t1
Valid prediction for Augustus_model.g8542.t1
Valid prediction for pasa_asmbl_45836.p1
Valid prediction for GlimmerHMM_glimmerT_12870-T1
Valid prediction for CodingQuarry_transcript_52295-T1
Valid prediction for GlimmerHMM_glimmerT_12873-T1
Valid prediction for snap_scaffold_5-snap.2406-T1
Valid prediction for CodingQuarry_transcript_52301-T1
Valid prediction for pasa_asmbl_45850.p1
Valid prediction for pasa_asmbl_45854.p1
Valid prediction for GlimmerHMM_glimmerT_12872-T1
Valid prediction for pasa_asmbl_45844.p1
Valid prediction for snap_scaffold_5-snap.2393-T1
Valid prediction for GlimmerHMM_glimmerT_12886-T1
Valid prediction for CodingQuarry_transcript_52304-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 pasa_asmbl_44502.p1
Valid prediction for CodingQuarry_transcript_52298-T1
Valid prediction for GlimmerHMM_glimmerT_12888-T1
Couldn't classify 203311, 203481
Sorry, prediction pasa_asmbl_44503.p1 fails validation.
(ATG)	 CG	200884-201036	GT	CGG
(GAC)	 AG	202449-202526	GT	AGG
(GCA)	 AG	202921-203043	GT	AGG
(CTG)	 AG	203311-203481	GT	TGG
-recovered pasa_asmbl_44503.p1, initial, 200884, 201036
-recovered pasa_asmbl_44503.p1, internal, 202449, 202526
-recovered pasa_asmbl_44503.p1, internal, 202921, 203043
-recovered pasa_asmbl_44503.p1, internal, 203311, 203481
Valid prediction for snap_scaffold_5-snap.2426-T1
Valid prediction for CodingQuarry_transcript_52314-T1
Valid prediction for GlimmerHMM_glimmerT_12878-T1
Valid prediction for CodingQuarry_transcript_52310-T1
Valid prediction for Augustus_model.g8517.t1
Valid prediction for HiQ_model.g8549.t1
Valid prediction for snap_scaffold_5-snap.2399-T1
Valid prediction for snap_scaffold_5-snap.2424-T1
Valid prediction for GlimmerHMM_glimmerT_12866-T1
Valid prediction for snap_scaffold_5-snap.2401-T1
Valid prediction for Augustus_model.g8521.t1
Valid prediction for snap_scaffold_5-snap.2418-T1
Valid prediction for HiQ_model.g8524.t1
Valid prediction for snap_scaffold_5-snap.2425-T1
Couldn't classify 48145, 48171
Sorry, prediction pasa_asmbl_44516.p1 fails validation.
(TTC)	 TC	48145-48171	GT	AGG
(AAA)	 AG	48257-48371	GT	GGG
(GCT)	 AG	48502-48727	GT	CGG
(TAA)	 AG	48807-48983	GT	AGG
(ATT)	 AG	49171-49357	AT	AAA
-recovered pasa_asmbl_44516.p1, terminal, 49171, 49357
-recovered pasa_asmbl_44516.p1, internal, 48257, 48371
-recovered pasa_asmbl_44516.p1, internal, 48502, 48727
-recovered pasa_asmbl_44516.p1, internal, 48807, 48983
Valid prediction for GlimmerHMM_glimmerT_12863-T1
Valid prediction for HiQ_model.g8526.t1
Valid prediction for GlimmerHMM_glimmerT_12862-T1
Valid prediction for GlimmerHMM_glimmerT_12883-T1
Valid prediction for HiQ_model.g8547.t1
Valid prediction for snap_scaffold_5-snap.2397-T1
Valid prediction for snap_scaffold_5-snap.2396-T1
Valid prediction for Augustus_model.g8537.t1
Valid prediction for CodingQuarry_transcript_52300-T1
Valid prediction for pasa_asmbl_44524.p1
Valid prediction for GlimmerHMM_glimmerT_12865-T1
Valid prediction for snap_scaffold_5-snap.2388-T1
Valid prediction for pasa_asmbl_44501.p1
Valid prediction for HiQ_model.g8523.t1
Valid prediction for Augustus_model.g8543.t1
Valid prediction for GlimmerHMM_glimmerT_12890-T1
Valid prediction for snap_scaffold_5-snap.2416-T1
Valid prediction for HiQ_model.g8548.t1
Valid prediction for GlimmerHMM_glimmerT_12885-T1
Valid prediction for GlimmerHMM_glimmerT_12864-T1
Valid prediction for Augustus_model.g8525.t1
Valid prediction for CodingQuarry_transcript_52309-T1
Valid prediction for snap_scaffold_5-snap.2403-T1
Valid prediction for snap_scaffold_5-snap.2400-T1
Valid prediction for snap_scaffold_5-snap.2423-T1
Valid prediction for pasa_asmbl_44504.p1
Valid prediction for CodingQuarry_transcript_52299-T1
Valid prediction for CodingQuarry_transcript_52312-T1
Valid prediction for HiQ_model.g8550.t1
Valid prediction for pasa_asmbl_44508.p1
Valid prediction for GlimmerHMM_glimmerT_12876-T1
Couldn't classify 65489, 65536
Sorry, prediction pasa_asmbl_44510.p1 fails validation.
(TTT)	 GC	65489-65536	GC	TGG
(GTG)	 AG	65678-65771	GT	GGG
(ACC)	 AG	65939-66142	GT	AAG
(GTA)	 AG	66237-66271	GC	GAG
-recovered pasa_asmbl_44510.p1, terminal, 66237, 66271
-recovered pasa_asmbl_44510.p1, internal, 65678, 65771
-recovered pasa_asmbl_44510.p1, internal, 65939, 66142
-recovered pasa_asmbl_44510.p1, internal, 66237, 66271
Valid prediction for Augustus_model.g8522.t1
Valid prediction for Augustus_model.g8520.t1
Valid prediction for HiQ_model.g8541.t1
Valid prediction for pasa_asmbl_44494.p1
Valid prediction for Augustus_model.g8528.t1
Valid prediction for CodingQuarry_transcript_52297-T1
Valid prediction for GlimmerHMM_glimmerT_12887-T1
Valid prediction for GlimmerHMM_glimmerT_12868-T1
Valid prediction for snap_scaffold_5-snap.2394-T1
Valid prediction for GlimmerHMM_glimmerT_12882-T1
Valid prediction for Augustus_model.g8545.t1
Couldn't classify 62881, 63016
Couldn't classify 63528, 63557
Sorry, prediction pasa_asmbl_44513.p1 fails validation.
(TCA)	 CG	62881-63016	GT	CGG
(ATA)	 AG	63105-63211	GT	CAG
(GTG)	 AG	63306-63404	GT	AGG
(TAT)	 AG	63528-63557	GC	AGG
-recovered pasa_asmbl_44513.p1, internal, 63105, 63211
-recovered pasa_asmbl_44513.p1, internal, 63306, 63404
-recovered pasa_asmbl_44513.p1, internal, 63528, 63557
Valid prediction for pasa_asmbl_44496.p1
Valid prediction for GlimmerHMM_glimmerT_12861-T1
Valid prediction for snap_scaffold_5-snap.2395-T1
Valid prediction for GlimmerHMM_glimmerT_12860-T1
Valid prediction for pasa_asmbl_44523.p1
Valid prediction for snap_scaffold_5-snap.2408-T1
Valid prediction for GlimmerHMM_glimmerT_12893-T1
Valid prediction for pasa_asmbl_44519.p1
Valid prediction for GlimmerHMM_glimmerT_12892-T1
Valid prediction for snap_scaffold_5-snap.2398-T1
Valid prediction for snap_scaffold_5-snap.2421-T1
Valid prediction for CodingQuarry_transcript_52315-T1
Valid prediction for snap_scaffold_5-snap.2390-T1
Valid prediction for pasa_asmbl_44526.p1
Valid prediction for snap_scaffold_5-snap.2412-T1
Valid prediction for snap_scaffold_5-snap.2420-T1
Valid prediction for GlimmerHMM_glimmerT_12858-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)
-building DP trellis

-building trellis in range 1 - 262331
-exon list size: 445


building trellis

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-found 37 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 37 predictions persist after filtering for low support