-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_7631317-7934466

-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_28611-T1
Valid prediction for GlimmerHMM_glimmerT_4122-T1
Valid prediction for GlimmerHMM_glimmerT_4111-T1
Valid prediction for pasa_asmbl_24589.p1
Valid prediction for pasa_asmbl_24573.p2
Valid prediction for Augustus_model.g2766.t1
Valid prediction for Augustus_model.g2772.t1
Valid prediction for snap_scaffold_2-snap.1636-T1
Valid prediction for GlimmerHMM_glimmerT_4108-T1
Valid prediction for CodingQuarry_transcript_28603-T1
Valid prediction for snap_scaffold_2-snap.1629-T1
Valid prediction for GlimmerHMM_glimmerT_4107-T1
Valid prediction for snap_scaffold_2-snap.1602-T1
Valid prediction for GlimmerHMM_glimmerT_4123-T1
Valid prediction for Augustus_model.g2780.t1
Valid prediction for snap_scaffold_2-snap.1595-T1
Valid prediction for snap_scaffold_2-snap.1617-T1
Valid prediction for Augustus_model.g2771.t1
Valid prediction for GlimmerHMM_glimmerT_4112-T1
Valid prediction for CodingQuarry_transcript_28612-T1
Valid prediction for snap_scaffold_2-snap.1601-T1
Valid prediction for snap_scaffold_2-snap.1632-T1
Valid prediction for CodingQuarry_transcript_28605-T1
Valid prediction for CodingQuarry_transcript_28607-T1
Valid prediction for snap_scaffold_2-snap.1603-T1
Valid prediction for snap_scaffold_2-snap.1613-T1
Valid prediction for snap_scaffold_2-snap.1633-T1
Valid prediction for snap_scaffold_2-snap.1614-T1
Valid prediction for snap_scaffold_2-snap.1612-T1
Valid prediction for CodingQuarry_transcript_28604-T1
Valid prediction for pasa_asmbl_24582.p1
Valid prediction for Augustus_model.g2762.t1
Valid prediction for Augustus_model.g2769.t1
Valid prediction for snap_scaffold_2-snap.1606-T1
Valid prediction for GlimmerHMM_glimmerT_4127-T1
Valid prediction for snap_scaffold_2-snap.1616-T1
Valid prediction for GlimmerHMM_glimmerT_4121-T1
Valid prediction for snap_scaffold_2-snap.1609-T1
Valid prediction for GlimmerHMM_glimmerT_4125-T1
Valid prediction for GlimmerHMM_glimmerT_4129-T1
Valid prediction for snap_scaffold_2-snap.1630-T1
Valid prediction for snap_scaffold_2-snap.1607-T1
Valid prediction for snap_scaffold_2-snap.1605-T1
Couldn't classify 262819, 263043
Sorry, prediction pasa_asmbl_24593.p1 fails validation.
(AAG)	 GT	262819-263043	GT	AGG
(AAT)	 AG	263176-263293	GT	AGG
(GGC)	 AG	263393-263550	AT	AAA
add_exon() Sorry, pasa_asmbl_24593.p1 263176-263293-terminal-3 is invalid.
-recovered pasa_asmbl_24593.p1, terminal, 263176, 263293
-recovered pasa_asmbl_24593.p1, terminal, 263393, 263550
-recovered pasa_asmbl_24593.p1, internal, 263176, 263293
Valid prediction for GlimmerHMM_glimmerT_4120-T1
Valid prediction for pasa_asmbl_24580.p1
Valid prediction for snap_scaffold_2-snap.1615-T1
Valid prediction for GlimmerHMM_glimmerT_4115-T1
Valid prediction for GlimmerHMM_glimmerT_4131-T1
Valid prediction for CodingQuarry_transcript_28606-T1
Valid prediction for HiQ_model.g2781.t1
Valid prediction for HiQ_model.g2770.t1
Valid prediction for snap_scaffold_2-snap.1611-T1
Valid prediction for pasa_asmbl_24583.p1
Valid prediction for CodingQuarry_transcript_28614-T1
Valid prediction for Augustus_model.g2786.t1
Valid prediction for HiQ_model.g2775.t1
Valid prediction for Augustus_model.g2768.t1
Valid prediction for snap_scaffold_2-snap.1625-T1
Valid prediction for snap_scaffold_2-snap.1608-T1
Valid prediction for snap_scaffold_2-snap.1610-T1
Valid prediction for Augustus_model.g2773.t1
Valid prediction for HiQ_model.g2783.t1
Valid prediction for Augustus_model.g2765.t1
Valid prediction for CodingQuarry_transcript_28615-T1
Valid prediction for snap_scaffold_2-snap.1631-T1
Valid prediction for snap_scaffold_2-snap.1620-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 snap_scaffold_2-snap.1597-T1
Valid prediction for GlimmerHMM_glimmerT_4130-T1
Valid prediction for Augustus_model.g2779.t1
Valid prediction for snap_scaffold_2-snap.1618-T1
Valid prediction for GlimmerHMM_glimmerT_4113-T1
Valid prediction for GlimmerHMM_glimmerT_4132-T1
Valid prediction for Augustus_model.g2763.t1
Valid prediction for pasa_asmbl_23291.p1
Valid prediction for GlimmerHMM_glimmerT_4117-T1
Valid prediction for snap_scaffold_2-snap.1621-T1
Valid prediction for HiQ_model.g2774.t1
Valid prediction for Augustus_model.g2784.t1
Valid prediction for GlimmerHMM_glimmerT_4116-T1
Valid prediction for Augustus_model.g2777.t1
Valid prediction for GlimmerHMM_glimmerT_4110-T1
Valid prediction for GlimmerHMM_glimmerT_4128-T1
Valid prediction for GlimmerHMM_glimmerT_4109-T1
Valid prediction for HiQ_model.g2776.t1
Valid prediction for HiQ_model.g2787.t1
Valid prediction for snap_scaffold_2-snap.1634-T1
Valid prediction for snap_scaffold_2-snap.1604-T1
Valid prediction for snap_scaffold_2-snap.1600-T1
Valid prediction for snap_scaffold_2-snap.1594-T1
Valid prediction for Augustus_model.g2761.t1
Valid prediction for CodingQuarry_transcript_28613-T1
Valid prediction for snap_scaffold_2-snap.1635-T1
Valid prediction for snap_scaffold_2-snap.1638-T1
Valid prediction for snap_scaffold_2-snap.1599-T1
Couldn't classify 94284, 94403
Couldn't classify 100707, 100856
Sorry, prediction pasa_asmbl_23286.p1 fails validation.
(CTC)	 CC	94284-94403	GT	TGG
(CTC)	 AG	95770-95999	GT	AGG
(CTA)	 AG	97590-97745	GT	CGG
(CTC)	 AG	99103-99340	GT	AGG
(TCT)	 AG	100707-100856	GT	AGG
-recovered pasa_asmbl_23286.p1, internal, 95770, 95999
-recovered pasa_asmbl_23286.p1, internal, 97590, 97745
-recovered pasa_asmbl_23286.p1, internal, 99103, 99340
-recovered pasa_asmbl_23286.p1, internal, 100707, 100856
Valid prediction for CodingQuarry_transcript_28617-T1
Valid prediction for CodingQuarry_transcript_28610-T1
Couldn't classify 263325, 263684
Sorry, prediction pasa_asmbl_23273.p1 fails validation.
(ATC)	 TG	263325-263684	CA	TCC
Valid prediction for snap_scaffold_2-snap.1598-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for pasa_asmbl_23277.p1
Valid prediction for CodingQuarry_transcript_28609-T1
Valid prediction for Augustus_model.g2764.t1
Valid prediction for HiQ_model.g2782.t1
Valid prediction for GlimmerHMM_glimmerT_4126-T1
Couldn't classify 74815, 74922
Sorry, prediction pasa_asmbl_23288.p1 fails validation.
(ATG)	 AA	69044-69217	GT	AGG
(CCC)	 AG	71175-71342	GT	CTG
(ACA)	 AG	71540-71606	GT	TGG
(CTC)	 AG	71779-71896	GT	AGG
(GAC)	 AG	71990-72101	GT	GGG
(GAG)	 AG	72567-72707	GT	AGG
(GTC)	 AG	72819-72974	GT	AGG
(GAG)	 AG	73070-73212	GT	AGG
(AGA)	 AG	73318-73399	GT	AGG
(CAT)	 AG	73499-73651	GT	TGG
(ATC)	 AG	74815-74922	GT	TGG
-recovered pasa_asmbl_23288.p1, initial, 69044, 69217
-recovered pasa_asmbl_23288.p1, internal, 71175, 71342
-recovered pasa_asmbl_23288.p1, internal, 71540, 71606
-recovered pasa_asmbl_23288.p1, internal, 71779, 71896
-recovered pasa_asmbl_23288.p1, internal, 71990, 72101
-recovered pasa_asmbl_23288.p1, internal, 72567, 72707
-recovered pasa_asmbl_23288.p1, internal, 72819, 72974
-recovered pasa_asmbl_23288.p1, internal, 73070, 73212
-recovered pasa_asmbl_23288.p1, internal, 73318, 73399
-recovered pasa_asmbl_23288.p1, internal, 73499, 73651
-recovered pasa_asmbl_23288.p1, internal, 74815, 74922
Valid prediction for snap_scaffold_2-snap.1622-T1
Valid prediction for snap_scaffold_2-snap.1624-T1
Valid prediction for pasa_asmbl_23295.p1
Couldn't classify 26219, 26391
Sorry, prediction pasa_asmbl_23959.p1 fails validation.
(TGT)	 GG	26219-26391	GT	CAG
(GTC)	 AG	26481-26640	GT	AGG
(AGT)	 AG	26785-27042	GT	GGG
(TCA)	 AG	27293-27405	GT	TGG
(GTA)	 AG	27944-28085	GT	AGG
(GAG)	 AG	28307-28834	GA	AAG
-recovered pasa_asmbl_23959.p1, terminal, 28307, 28834
-recovered pasa_asmbl_23959.p1, internal, 26481, 26640
-recovered pasa_asmbl_23959.p1, internal, 26785, 27042
-recovered pasa_asmbl_23959.p1, internal, 27293, 27405
-recovered pasa_asmbl_23959.p1, internal, 27944, 28085
Valid prediction for snap_scaffold_2-snap.1637-T1
Valid prediction for snap_scaffold_2-snap.1627-T1
Valid prediction for snap_scaffold_2-snap.1619-T1
Valid prediction for Augustus_model.g2785.t1
Couldn't classify 67138, 67173
Sorry, prediction pasa_asmbl_23289.p1 fails validation.
(ATG)	 GT	61716-61769	GT	CTG
(GCA)	 AG	63289-63406	GT	AGG
(CAA)	 AG	64092-64168	GT	AGG
(AAT)	 AG	64524-64721	GT	AGG
(GAG)	 AG	67138-67173	TT	ACT
-recovered pasa_asmbl_23289.p1, initial, 61716, 61769
-recovered pasa_asmbl_23289.p1, internal, 63289, 63406
-recovered pasa_asmbl_23289.p1, internal, 64092, 64168
-recovered pasa_asmbl_23289.p1, internal, 64524, 64721
Valid prediction for GlimmerHMM_glimmerT_4118-T1
Valid prediction for snap_scaffold_2-snap.1626-T1
Valid prediction for Augustus_model.g2767.t1
Valid prediction for GlimmerHMM_glimmerT_4133-T1
Valid prediction for GlimmerHMM_glimmerT_4119-T1
Valid prediction for CodingQuarry_transcript_28616-T1
Valid prediction for GlimmerHMM_glimmerT_4134-T1
Valid prediction for GlimmerHMM_glimmerT_4114-T1
Valid prediction for snap_scaffold_2-snap.1639-T1
Couldn't classify 22918, 23397
Sorry, prediction pasa_asmbl_23293.p1 fails validation.
(ATG)	 GC	22918-23397	GA	CCG
Valid prediction for GlimmerHMM_glimmerT_4124-T1
Valid prediction for snap_scaffold_2-snap.1628-T1
Valid prediction for snap_scaffold_2-snap.1623-T1
Couldn't classify 105930, 105977
Sorry, prediction pasa_asmbl_23281.p1 fails validation.
(CCT)	 CA	105930-105977	GT	TGG
(GTG)	 AG	106273-106464	GT	AGG
(GAC)	 AG	107099-107147	GT	AGG
(AGA)	 AG	107351-107454	TC	AAT
-recovered pasa_asmbl_23281.p1, terminal, 107351, 107454
-recovered pasa_asmbl_23281.p1, internal, 106273, 106464
-recovered pasa_asmbl_23281.p1, internal, 107099, 107147
Valid prediction for Augustus_model.g2778.t1
Valid prediction for snap_scaffold_2-snap.1596-T1
Valid prediction for CodingQuarry_transcript_28608-T1

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

-building trellis in range 1 - 303150
-exon list size: 485


building trellis

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99.8    
-found 34 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11440
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support