-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_4460492-4800889

-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 snap_scaffold_7-snap.1052-T1
Valid prediction for Augustus_model.g11881.t1
Valid prediction for GlimmerHMM_glimmerT_17726-T1
Valid prediction for Augustus_model.g11899.t1
Valid prediction for GlimmerHMM_glimmerT_17735-T1
Valid prediction for GeneMark_model.29857_t
Couldn't classify 67258, 67433
Couldn't classify 67538, 67658
Sorry, prediction pasa_asmbl_51432.p1 fails validation.
(GGT)	 CA	67258-67433	GT	AAG
(GTT)	 AG	67538-67658	AG	TCA
Valid prediction for snap_scaffold_7-snap.1044-T1
Valid prediction for snap_scaffold_7-snap.1019-T1
Valid prediction for GlimmerHMM_glimmerT_17715-T1
Valid prediction for Augustus_model.g11909.t1
Valid prediction for Augustus_model.g11913.t1
Valid prediction for snap_scaffold_7-snap.1027-T1
Valid prediction for snap_scaffold_7-snap.1032-T1
Valid prediction for GlimmerHMM_glimmerT_17751-T1
Valid prediction for Augustus_model.g11907.t1
Valid prediction for GeneMark_model.29835_t
Valid prediction for GlimmerHMM_glimmerT_17749-T1
Valid prediction for Augustus_model.g11890.t1
Valid prediction for Augustus_model.g11882.t1
Valid prediction for GeneMark_model.29851_t
Valid prediction for GeneMark_model.29836_t
Valid prediction for GeneMark_model.29845_t
Valid prediction for snap_scaffold_7-snap.1053-T1
Valid prediction for GeneMark_model.29834_t
Valid prediction for GlimmerHMM_glimmerT_17752-T1
Valid prediction for snap_scaffold_7-snap.1064-T1
Valid prediction for Augustus_model.g11903.t1
Valid prediction for snap_scaffold_7-snap.1057-T1
Valid prediction for GlimmerHMM_glimmerT_17737-T1
Valid prediction for Augustus_model.g11886.t1
Valid prediction for snap_scaffold_7-snap.1026-T1
Valid prediction for GlimmerHMM_glimmerT_17710-T1
Valid prediction for snap_scaffold_7-snap.1029-T1
Valid prediction for GlimmerHMM_glimmerT_17742-T1
Valid prediction for GeneMark_model.29832_t
Valid prediction for Augustus_model.g11888.t1
Valid prediction for snap_scaffold_7-snap.1035-T1
Valid prediction for Augustus_model.g11883.t1
Valid prediction for snap_scaffold_7-snap.1031-T1
Valid prediction for GlimmerHMM_glimmerT_17711-T1
Valid prediction for snap_scaffold_7-snap.1023-T1
Couldn't classify 70819, 71004
Couldn't classify 73055, 73160
Sorry, prediction pasa_asmbl_50621.p1 fails validation.
(ACT)	 CA	70819-71004	GT	AGG
(GTG)	 AG	71152-71278	GT	AGG
(GCC)	 AG	71370-71548	GT	AGG
(GTC)	 AG	71649-71763	GT	AGG
(GTG)	 AG	72742-72904	GT	ATG
(CTC)	 AG	73055-73160	GG	AAG
-recovered pasa_asmbl_50621.p1, internal, 71152, 71278
-recovered pasa_asmbl_50621.p1, internal, 71370, 71548
-recovered pasa_asmbl_50621.p1, internal, 71649, 71763
-recovered pasa_asmbl_50621.p1, internal, 72742, 72904
Valid prediction for GlimmerHMM_glimmerT_17719-T1
Valid prediction for GlimmerHMM_glimmerT_17747-T1
Valid prediction for GeneMark_model.29831_t
Valid prediction for Augustus_model.g11894.t1
Couldn't classify 76422, 76467
Couldn't classify 79338, 79451
Sorry, prediction pasa_asmbl_50622.p1 fails validation.
(GCA)	 CA	76422-76467	GT	CAG
(TCA)	 AG	76842-76978	GT	ATG
(CCC)	 AG	77086-77230	GT	TGG
(CTT)	 AG	77347-77409	GT	GGG
(GCC)	 AG	77611-77678	GT	AGG
(GTG)	 AG	79338-79451	GT	AGG
-recovered pasa_asmbl_50622.p1, internal, 76842, 76978
-recovered pasa_asmbl_50622.p1, internal, 77086, 77230
-recovered pasa_asmbl_50622.p1, internal, 77347, 77409
-recovered pasa_asmbl_50622.p1, internal, 77611, 77678
-recovered pasa_asmbl_50622.p1, internal, 79338, 79451
Valid prediction for Augustus_model.g11884.t1
Valid prediction for GlimmerHMM_glimmerT_17724-T1
Valid prediction for GeneMark_model.29827_t
Valid prediction for GeneMark_model.29830_t
Valid prediction for GeneMark_model.29840_t
Valid prediction for Augustus_model.g11876.t1
Valid prediction for GlimmerHMM_glimmerT_17757-T1
Valid prediction for GlimmerHMM_glimmerT_17730-T1
Valid prediction for GlimmerHMM_glimmerT_17744-T1
Valid prediction for snap_scaffold_7-snap.1033-T1
Valid prediction for GeneMark_model.29842_t
Valid prediction for snap_scaffold_7-snap.1051-T1
Valid prediction for snap_scaffold_7-snap.1066-T1
Valid prediction for GlimmerHMM_glimmerT_17728-T1
Valid prediction for snap_scaffold_7-snap.1028-T1
Valid prediction for snap_scaffold_7-snap.1060-T1
Valid prediction for GeneMark_model.29847_t
Valid prediction for pasa_asmbl_50626.p1
Valid prediction for GlimmerHMM_glimmerT_17716-T1
Valid prediction for Augustus_model.g11904.t1
Valid prediction for snap_scaffold_7-snap.1034-T1
Valid prediction for GlimmerHMM_glimmerT_17731-T1
Valid prediction for GlimmerHMM_glimmerT_17738-T1
Valid prediction for snap_scaffold_7-snap.1063-T1
Valid prediction for Augustus_model.g11893.t1
Valid prediction for GlimmerHMM_glimmerT_17722-T1
Valid prediction for GeneMark_model.29826_t
Valid prediction for Augustus_model.g11887.t1
Valid prediction for GlimmerHMM_glimmerT_17755-T1
Valid prediction for GlimmerHMM_glimmerT_17718-T1
Valid prediction for Augustus_model.g11877.t1
Valid prediction for Augustus_model.g11897.t1
Couldn't classify 60662, 60847
Sorry, prediction pasa_asmbl_50616.p1 fails validation.
(ATG)	 CT	53583-53668	GT	AGG
(TTC)	 AG	54983-55040	GT	TGG
(GTG)	 AG	55181-55335	GT	TGG
(GTA)	 AG	55460-55546	GT	AAG
(GTG)	 AG	57092-57180	GT	GAG
(GGT)	 AG	57318-57368	GT	AAG
(TTC)	 AG	58292-58456	GT	TGG
(AGC)	 AG	58568-58729	GT	AGG
(ATG)	 AG	59030-59171	GT	AAG
(GTG)	 AG	59394-59593	GT	TGG
(CTA)	 AG	59781-59834	GT	AGG
(CTG)	 AG	60454-60581	GT	AGG
(AGC)	 AG	60662-60847	AA	GTA
-recovered pasa_asmbl_50616.p1, initial, 53583, 53668
add_exon() Sorry, pasa_asmbl_50616.p1 59030-59171-initial-1 is invalid.
-recovered pasa_asmbl_50616.p1, initial, 59030, 59171
add_exon() Sorry, pasa_asmbl_50616.p1 55460-55546-terminal-1 is invalid.
-recovered pasa_asmbl_50616.p1, terminal, 55460, 55546
-recovered pasa_asmbl_50616.p1, internal, 54983, 55040
-recovered pasa_asmbl_50616.p1, internal, 55181, 55335
-recovered pasa_asmbl_50616.p1, internal, 55460, 55546
-recovered pasa_asmbl_50616.p1, internal, 57092, 57180
-recovered pasa_asmbl_50616.p1, internal, 57318, 57368
-recovered pasa_asmbl_50616.p1, internal, 58292, 58456
-recovered pasa_asmbl_50616.p1, internal, 58568, 58729
-recovered pasa_asmbl_50616.p1, internal, 59030, 59171
-recovered pasa_asmbl_50616.p1, internal, 59394, 59593
-recovered pasa_asmbl_50616.p1, internal, 59781, 59834
-recovered pasa_asmbl_50616.p1, internal, 60454, 60581
Valid prediction for GlimmerHMM_glimmerT_17723-T1
Valid prediction for CodingQuarry_transcript_57337-T1
Valid prediction for GeneMark_model.29849_t
Valid prediction for GeneMark_model.29848_t
Valid prediction for GlimmerHMM_glimmerT_17745-T1
Valid prediction for GlimmerHMM_glimmerT_17721-T1
Valid prediction for snap_scaffold_7-snap.1030-T1
Valid prediction for snap_scaffold_7-snap.1020-T1
Valid prediction for GlimmerHMM_glimmerT_17714-T1
Valid prediction for GeneMark_model.29828_t
Valid prediction for GeneMark_model.29839_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 Augustus_model.g11901.t1
Valid prediction for GlimmerHMM_glimmerT_17750-T1
Valid prediction for GeneMark_model.29841_t
Valid prediction for Augustus_model.g11879.t1
Valid prediction for snap_scaffold_7-snap.1043-T1
Valid prediction for snap_scaffold_7-snap.1056-T1
Valid prediction for snap_scaffold_7-snap.1062-T1
Valid prediction for GeneMark_model.29846_t
Valid prediction for GeneMark_model.29825_t
Valid prediction for GlimmerHMM_glimmerT_17756-T1
Valid prediction for snap_scaffold_7-snap.1021-T1
Valid prediction for snap_scaffold_7-snap.1050-T1
Valid prediction for snap_scaffold_7-snap.1036-T1
Valid prediction for snap_scaffold_7-snap.1061-T1
Valid prediction for GeneMark_model.29829_t
Valid prediction for GlimmerHMM_glimmerT_17712-T1
Valid prediction for GeneMark_model.29856_t
Valid prediction for snap_scaffold_7-snap.1038-T1
Sorry, intron length (9) is less than minimum required (10)
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_17753-T1
Valid prediction for Augustus_model.g11895.t1
Valid prediction for snap_scaffold_7-snap.1022-T1
Valid prediction for GeneMark_model.29838_t
Valid prediction for GlimmerHMM_glimmerT_17754-T1
Valid prediction for Augustus_model.g11885.t1
Valid prediction for Augustus_model.g11906.t1
Valid prediction for Augustus_model.g11874.t1
Valid prediction for snap_scaffold_7-snap.1039-T1
Valid prediction for GlimmerHMM_glimmerT_17709-T1
Valid prediction for snap_scaffold_7-snap.1042-T1
Valid prediction for snap_scaffold_7-snap.1025-T1
Valid prediction for pasa_asmbl_49677.p1
Valid prediction for snap_scaffold_7-snap.1054-T1
Valid prediction for snap_scaffold_7-snap.1049-T1
Valid prediction for Augustus_model.g11912.t1
Valid prediction for Augustus_model.g11891.t1
Valid prediction for GlimmerHMM_glimmerT_17736-T1
Valid prediction for snap_scaffold_7-snap.1017-T1
Valid prediction for GeneMark_model.29823_t
Valid prediction for GeneMark_model.29854_t
Valid prediction for Augustus_model.g11902.t1
Valid prediction for GeneMark_model.29850_t
Valid prediction for GlimmerHMM_glimmerT_17733-T1
Valid prediction for Augustus_model.g11892.t1
Valid prediction for snap_scaffold_7-snap.1045-T1
Valid prediction for GlimmerHMM_glimmerT_17746-T1
Valid prediction for GeneMark_model.29855_t
Valid prediction for GlimmerHMM_glimmerT_17734-T1
Valid prediction for GlimmerHMM_glimmerT_17729-T1
Valid prediction for GeneMark_model.29843_t
Valid prediction for GlimmerHMM_glimmerT_17720-T1
Valid prediction for GlimmerHMM_glimmerT_17740-T1
Valid prediction for GlimmerHMM_glimmerT_17717-T1
Valid prediction for Augustus_model.g11905.t1
Valid prediction for snap_scaffold_7-snap.1018-T1
Valid prediction for GeneMark_model.29858_t
Valid prediction for snap_scaffold_7-snap.1058-T1
Valid prediction for Augustus_model.g11900.t1
Valid prediction for Augustus_model.g11914.t1
Valid prediction for Augustus_model.g11889.t1
Valid prediction for Augustus_model.g11896.t1
Valid prediction for Augustus_model.g11898.t1
Valid prediction for Augustus_model.g11875.t1
Valid prediction for GlimmerHMM_glimmerT_17743-T1
Valid prediction for GeneMark_model.29852_t
Valid prediction for GeneMark_model.29837_t
Valid prediction for GeneMark_model.29833_t
Valid prediction for snap_scaffold_7-snap.1065-T1
Valid prediction for Augustus_model.g11911.t1
Valid prediction for snap_scaffold_7-snap.1024-T1
Valid prediction for GlimmerHMM_glimmerT_17748-T1
Valid prediction for CodingQuarry_transcript_57336-T1
Valid prediction for snap_scaffold_7-snap.1040-T1
Valid prediction for Augustus_model.g11878.t1
Valid prediction for snap_scaffold_7-snap.1047-T1
Valid prediction for snap_scaffold_7-snap.1048-T1
Valid prediction for Augustus_model.g11908.t1
Valid prediction for GeneMark_model.29844_t
Valid prediction for Augustus_model.g11910.t1
Valid prediction for snap_scaffold_7-snap.1046-T1
Valid prediction for GlimmerHMM_glimmerT_17741-T1
Valid prediction for snap_scaffold_7-snap.1037-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.1059-T1
Valid prediction for HiQ_model.g11880.t1
Valid prediction for snap_scaffold_7-snap.1067-T1
Valid prediction for snap_scaffold_7-snap.1041-T1
Valid prediction for GlimmerHMM_glimmerT_17732-T1
Valid prediction for GlimmerHMM_glimmerT_17725-T1
Valid prediction for GlimmerHMM_glimmerT_17739-T1
Valid prediction for GeneMark_model.29824_t
Valid prediction for snap_scaffold_7-snap.1055-T1
Valid prediction for GlimmerHMM_glimmerT_17713-T1
Valid prediction for GlimmerHMM_glimmerT_17727-T1

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

-building trellis in range 1 - 340398
-exon list size: 617


building trellis

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88.9    
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89.8    
90.0    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.9    
94.0    
94.2    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 58 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 55 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 309053 - 340398
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 311317 - 340398
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 311927 - 340398