-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_7658301-7980781

-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_45442-T1
Valid prediction for GeneMark_model.79365_t
Valid prediction for snap_scaffold_19-snap.1522-T1
Valid prediction for GeneMark_model.79347_t
Valid prediction for snap_scaffold_19-snap.1528-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for HiQ_model.g30299.t1
Valid prediction for GeneMark_model.79379_t
Valid prediction for Augustus_model.g30306.t1
Valid prediction for GeneMark_model.79376_t
Valid prediction for snap_scaffold_19-snap.1520-T1
Valid prediction for GlimmerHMM_glimmerT_45438-T1
Valid prediction for snap_scaffold_19-snap.1538-T1
Valid prediction for snap_scaffold_19-snap.1549-T1
Valid prediction for GlimmerHMM_glimmerT_45452-T1
Valid prediction for HiQ_model.g30291.t1
Valid prediction for snap_scaffold_19-snap.1526-T1
Valid prediction for pasa_asmbl_22293.p1
Valid prediction for Augustus_model.g30288.t1
Valid prediction for GlimmerHMM_glimmerT_45456-T1
Valid prediction for Augustus_model.g30292.t1
Valid prediction for GlimmerHMM_glimmerT_45433-T1
Valid prediction for GeneMark_model.79378_t
Valid prediction for GlimmerHMM_glimmerT_45435-T1
Valid prediction for snap_scaffold_19-snap.1548-T1
Valid prediction for GeneMark_model.79360_t
Valid prediction for snap_scaffold_19-snap.1551-T1
Valid prediction for pasa_asmbl_22298.p1
Valid prediction for GeneMark_model.79380_t
Valid prediction for GlimmerHMM_glimmerT_45453-T1
Valid prediction for GeneMark_model.79351_t
Valid prediction for GeneMark_model.79372_t
Valid prediction for snap_scaffold_19-snap.1552-T1
Valid prediction for GlimmerHMM_glimmerT_45437-T1
Valid prediction for GlimmerHMM_glimmerT_45432-T1
Valid prediction for GeneMark_model.79353_t
Valid prediction for CodingQuarry_transcript_25659-T1
Valid prediction for GeneMark_model.79364_t
Valid prediction for GlimmerHMM_glimmerT_45449-T1
Valid prediction for snap_scaffold_19-snap.1529-T1
Valid prediction for GlimmerHMM_glimmerT_45455-T1
Valid prediction for CodingQuarry_transcript_25658-T1
Valid prediction for CodingQuarry_transcript_25661-T1
Valid prediction for Augustus_model.g30304.t1
Valid prediction for snap_scaffold_19-snap.1534-T1
Valid prediction for GeneMark_model.79357_t
Valid prediction for GeneMark_model.79344_t
Valid prediction for snap_scaffold_19-snap.1542-T1
Valid prediction for GeneMark_model.79374_t
Valid prediction for GlimmerHMM_glimmerT_45441-T1
Valid prediction for GlimmerHMM_glimmerT_45429-T1
Valid prediction for GlimmerHMM_glimmerT_45445-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.g30289.t1
Couldn't classify 292190, 292398
Couldn't classify 294457, 294582
Sorry, prediction pasa_asmbl_21463.p1 fails validation.
(GCG)	 CA	292190-292398	GT	AGG
(GTC)	 AG	293300-293507	GT	GGG
(ACA)	 AG	294457-294582	AA	AGA
-recovered pasa_asmbl_21463.p1, internal, 293300, 293507
Valid prediction for CodingQuarry_transcript_25662-T1
Valid prediction for pasa_asmbl_21477.p1
Valid prediction for GeneMark_model.79375_t
Valid prediction for GeneMark_model.79346_t
Valid prediction for snap_scaffold_19-snap.1537-T1
Valid prediction for snap_scaffold_19-snap.1546-T1
Valid prediction for snap_scaffold_19-snap.1541-T1
Valid prediction for snap_scaffold_19-snap.1527-T1
Couldn't classify 285106, 287085
Sorry, prediction pasa_asmbl_21465.p1 fails validation.
(CAT)	 CA	285106-287085	GC	GAG
Valid prediction for snap_scaffold_19-snap.1523-T1
Valid prediction for pasa_asmbl_21459.p1
Valid prediction for CodingQuarry_transcript_25663-T1
Couldn't classify 262405, 263247
Sorry, prediction pasa_asmbl_21466.p1 fails validation.
(AAA)	 CG	262405-263247	GC	GAG
Valid prediction for GlimmerHMM_glimmerT_45448-T1
Valid prediction for GeneMark_model.79358_t
Valid prediction for snap_scaffold_19-snap.1545-T1
Valid prediction for GeneMark_model.79366_t
Valid prediction for snap_scaffold_19-snap.1535-T1
Valid prediction for GeneMark_model.79370_t
Valid prediction for GeneMark_model.79361_t
Valid prediction for GeneMark_model.79369_t
Valid prediction for GeneMark_model.79342_t
Valid prediction for Augustus_model.g30297.t1
Valid prediction for snap_scaffold_19-snap.1532-T1
Valid prediction for snap_scaffold_19-snap.1550-T1
Valid prediction for GeneMark_model.79373_t
Valid prediction for GeneMark_model.79352_t
Valid prediction for GlimmerHMM_glimmerT_45431-T1
Valid prediction for HiQ_model.g30302.t1
Valid prediction for GlimmerHMM_glimmerT_45446-T1
Valid prediction for GlimmerHMM_glimmerT_45430-T1
Valid prediction for Augustus_model.g30298.t1
Valid prediction for snap_scaffold_19-snap.1547-T1
Valid prediction for GeneMark_model.79350_t
Valid prediction for Augustus_model.g30303.t1
Valid prediction for snap_scaffold_19-snap.1521-T1
Valid prediction for Augustus_model.g30301.t1
Valid prediction for GeneMark_model.79354_t
Couldn't classify 235012, 235181
Sorry, prediction pasa_asmbl_21469.p1 fails validation.
(GGC)	 CA	235012-235181	GT	CTG
(GTT)	 AG	235493-235756	GT	AGG
(GAC)	 AG	237605-237724	GT	GGG
(GTA)	 AG	240698-240793	GT	AAG
(GGA)	 AG	241968-242025	GT	AGG
(AAT)	 AG	243185-243262	GT	AGG
(CCT)	 AG	243366-243491	CT	AAC
-recovered pasa_asmbl_21469.p1, terminal, 243366, 243491
-recovered pasa_asmbl_21469.p1, internal, 235493, 235756
-recovered pasa_asmbl_21469.p1, internal, 237605, 237724
-recovered pasa_asmbl_21469.p1, internal, 240698, 240793
-recovered pasa_asmbl_21469.p1, internal, 241968, 242025
-recovered pasa_asmbl_21469.p1, internal, 243185, 243262
Valid prediction for GlimmerHMM_glimmerT_45440-T1
Valid prediction for GeneMark_model.79368_t
Valid prediction for snap_scaffold_19-snap.1531-T1
Valid prediction for Augustus_model.g30290.t1
Valid prediction for Augustus_model.g30294.t1
Valid prediction for GeneMark_model.79363_t
Valid prediction for snap_scaffold_19-snap.1539-T1
Valid prediction for GlimmerHMM_glimmerT_45443-T1
Valid prediction for GeneMark_model.79362_t
Valid prediction for GlimmerHMM_glimmerT_45428-T1
Valid prediction for GlimmerHMM_glimmerT_45436-T1
Couldn't classify 259849, 260134
Couldn't classify 260273, 260661
Sorry, prediction pasa_asmbl_21927.p1 fails validation.
(CCC)	 AT	259849-260134	GT	TGG
(GGG)	 AG	260273-260661	GG	GGG
Valid prediction for snap_scaffold_19-snap.1544-T1
Valid prediction for snap_scaffold_19-snap.1536-T1
Valid prediction for Augustus_model.g30300.t1
Valid prediction for Augustus_model.g30295.t1
Couldn't classify 261523, 261954
Sorry, prediction pasa_asmbl_21467.p1 fails validation.
(GAG)	 AG	261523-261954	CT	TCC
Valid prediction for GlimmerHMM_glimmerT_45434-T1
Valid prediction for GeneMark_model.79356_t
Valid prediction for Augustus_model.g30293.t1
Valid prediction for snap_scaffold_19-snap.1543-T1
Valid prediction for GlimmerHMM_glimmerT_45451-T1
Valid prediction for GeneMark_model.79345_t
Valid prediction for snap_scaffold_19-snap.1530-T1
Valid prediction for GlimmerHMM_glimmerT_45454-T1
Valid prediction for snap_scaffold_19-snap.1533-T1
Valid prediction for GlimmerHMM_glimmerT_45447-T1
Valid prediction for snap_scaffold_19-snap.1525-T1
Valid prediction for Augustus_model.g30305.t1
Valid prediction for Augustus_model.g30296.t1
Valid prediction for GeneMark_model.79367_t
Valid prediction for GeneMark_model.79348_t
Valid prediction for GeneMark_model.79343_t
Couldn't classify 96768, 96985
Sorry, prediction pasa_asmbl_21474.p1 fails validation.
(ATG)	 TG	96507-96639	GT	AGG
(GTG)	 AG	96768-96985	CC	CCC
-recovered pasa_asmbl_21474.p1, initial, 96507, 96639
Valid prediction for GeneMark_model.79371_t
Couldn't classify 260887, 261188
Couldn't classify 261339, 261447
Sorry, prediction pasa_asmbl_21468.p1 fails validation.
(AAC)	 TG	260887-261188	GT	AGG
(CTT)	 AG	261339-261447	GA	ACG
Valid prediction for GeneMark_model.79349_t
Valid prediction for GlimmerHMM_glimmerT_45450-T1
Valid prediction for pasa_asmbl_21476.p1
Valid prediction for CodingQuarry_transcript_25656-T1
Valid prediction for GeneMark_model.79359_t
Valid prediction for snap_scaffold_19-snap.1524-T1
Valid prediction for snap_scaffold_19-snap.1540-T1
Valid prediction for GeneMark_model.79377_t
Valid prediction for GlimmerHMM_glimmerT_45444-T1
Valid prediction for GeneMark_model.79355_t
Valid prediction for GlimmerHMM_glimmerT_45439-T1
Valid prediction for HiQ_model.g30287.t1

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

-building trellis in range 1 - 322481
-exon list size: 443


building trellis

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97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 26 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13085
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-found 1 predictions from path traversal

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