-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_17331549-17627546

-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_23736-T1
Valid prediction for snap_scaffold_9-snap.3517-T1
Couldn't classify 25281, 25495
Couldn't classify 26597, 26793
Sorry, prediction pasa_asmbl_54628.p1 fails validation.
(GAG)	 AG	25281-25495	GT	AGG
(TCG)	 AG	26051-26205	GT	AGG
(ACC)	 AG	26597-26793	AG	TCA
add_exon() Sorry, pasa_asmbl_54628.p1 25281-25495-terminal-2 is invalid.
-recovered pasa_asmbl_54628.p1, terminal, 25281, 25495
-recovered pasa_asmbl_54628.p1, internal, 25281, 25495
-recovered pasa_asmbl_54628.p1, internal, 26051, 26205
Valid prediction for GlimmerHMM_glimmerT_23733-T1
Valid prediction for Augustus_model.g15790.t1
Valid prediction for snap_scaffold_9-snap.3486-T1
Valid prediction for pasa_asmbl_54630.p1
Valid prediction for GlimmerHMM_glimmerT_23735-T1
Valid prediction for GlimmerHMM_glimmerT_23730-T1
Valid prediction for GlimmerHMM_glimmerT_23739-T1
Valid prediction for GlimmerHMM_glimmerT_23732-T1
Valid prediction for snap_scaffold_9-snap.3501-T1
Valid prediction for Augustus_model.g15787.t1
Valid prediction for GlimmerHMM_glimmerT_23743-T1
Valid prediction for snap_scaffold_9-snap.3513-T1
Valid prediction for CodingQuarry_transcript_62457-T1
Valid prediction for Augustus_model.g15789.t1
Valid prediction for snap_scaffold_9-snap.3514-T1
Valid prediction for HiQ_model.g15793.t1
Valid prediction for pasa_asmbl_54634.p1
Valid prediction for Augustus_model.g15800.t1
Valid prediction for GlimmerHMM_glimmerT_23745-T1
Valid prediction for snap_scaffold_9-snap.3488-T1
Valid prediction for snap_scaffold_9-snap.3494-T1
Valid prediction for snap_scaffold_9-snap.3508-T1
Valid prediction for CodingQuarry_transcript_62455-T1
Valid prediction for snap_scaffold_9-snap.3490-T1
Valid prediction for Augustus_model.g15796.t1
Valid prediction for snap_scaffold_9-snap.3516-T1
Valid prediction for GlimmerHMM_glimmerT_23727-T1
Valid prediction for snap_scaffold_9-snap.3510-T1
Valid prediction for GlimmerHMM_glimmerT_23723-T1
Valid prediction for snap_scaffold_9-snap.3484-T1
Valid prediction for GlimmerHMM_glimmerT_23744-T1
Valid prediction for GlimmerHMM_glimmerT_23725-T1
Couldn't classify 37239, 37302
Sorry, prediction pasa_asmbl_54629.p1 fails validation.
(TCA)	 CC	37239-37302	GT	AGG
(GCT)	 AG	37714-37773	GT	AGG
(ATC)	 AG	37904-37951	GT	AGG
(GCT)	 AG	38247-38776	GT	AAG
-recovered pasa_asmbl_54629.p1, terminal, 38247, 38776
-recovered pasa_asmbl_54629.p1, internal, 37714, 37773
-recovered pasa_asmbl_54629.p1, internal, 37904, 37951
-recovered pasa_asmbl_54629.p1, internal, 38247, 38776
Valid prediction for snap_scaffold_9-snap.3512-T1
Valid prediction for snap_scaffold_9-snap.3483-T1
Valid prediction for Augustus_model.g15783.t1
Valid prediction for snap_scaffold_9-snap.3492-T1
Valid prediction for GlimmerHMM_glimmerT_23729-T1
Valid prediction for snap_scaffold_9-snap.3500-T1
Valid prediction for HiQ_model.g15784.t1
Valid prediction for GlimmerHMM_glimmerT_23749-T1
Valid prediction for snap_scaffold_9-snap.3515-T1
Valid prediction for GlimmerHMM_glimmerT_23748-T1
Valid prediction for Augustus_model.g15802.t1
Valid prediction for GlimmerHMM_glimmerT_23746-T1
Valid prediction for CodingQuarry_transcript_62454-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_23721-T1
Valid prediction for Augustus_model.g15786.t1
Valid prediction for snap_scaffold_9-snap.3519-T1
Valid prediction for HiQ_model.g15797.t1
Valid prediction for snap_scaffold_9-snap.3502-T1
Valid prediction for Augustus_model.g15799.t1
Valid prediction for GlimmerHMM_glimmerT_23731-T1
Couldn't classify 131611, 132107
Sorry, prediction pasa_asmbl_55654.p1 fails validation.
(ATG)	 AG	130203-130314	GT	GGG
(ATG)	 AG	131611-132107	CT	AGC
-recovered pasa_asmbl_55654.p1, initial, 130203, 130314
-recovered pasa_asmbl_55654.p1, internal, 130203, 130314
Valid prediction for Augustus_model.g15791.t1
Valid prediction for GlimmerHMM_glimmerT_23742-T1
Valid prediction for GlimmerHMM_glimmerT_23724-T1
Valid prediction for pasa_asmbl_55648.p1
Valid prediction for GlimmerHMM_glimmerT_23750-T1
Valid prediction for GlimmerHMM_glimmerT_23734-T1
Valid prediction for pasa_asmbl_55660.p1
Valid prediction for snap_scaffold_9-snap.3491-T1
Valid prediction for HiQ_model.g15801.t1
Valid prediction for snap_scaffold_9-snap.3495-T1
Valid prediction for GlimmerHMM_glimmerT_23737-T1
Valid prediction for CodingQuarry_transcript_62459-T1
Valid prediction for pasa_asmbl_55650.p1
Valid prediction for snap_scaffold_9-snap.3493-T1
Valid prediction for snap_scaffold_9-snap.3503-T1
Valid prediction for pasa_asmbl_55644.p1
Valid prediction for snap_scaffold_9-snap.3509-T1
Valid prediction for CodingQuarry_transcript_62456-T1
Valid prediction for snap_scaffold_9-snap.3520-T1
Valid prediction for GlimmerHMM_glimmerT_23726-T1
Valid prediction for snap_scaffold_9-snap.3518-T1
Valid prediction for snap_scaffold_9-snap.3521-T1
Valid prediction for snap_scaffold_9-snap.3506-T1
Valid prediction for snap_scaffold_9-snap.3505-T1
Valid prediction for GlimmerHMM_glimmerT_23751-T1
Valid prediction for Augustus_model.g15785.t1
Valid prediction for Augustus_model.g15804.t1
Valid prediction for GlimmerHMM_glimmerT_23722-T1
Couldn't classify 170028, 170054
Sorry, prediction pasa_asmbl_55643.p1 fails validation.
(AAT)	 AG	170028-170054	GT	TGG
(AGG)	 AG	170271-170568	GT	GGG
(GAT)	 AG	170989-171054	GT	AGG
(AAT)	 AG	171375-171388	CA	GAC
-recovered pasa_asmbl_55643.p1, terminal, 171375, 171388
-recovered pasa_asmbl_55643.p1, internal, 170028, 170054
-recovered pasa_asmbl_55643.p1, internal, 170271, 170568
-recovered pasa_asmbl_55643.p1, internal, 170989, 171054
Valid prediction for GlimmerHMM_glimmerT_23747-T1
Valid prediction for snap_scaffold_9-snap.3507-T1
Couldn't classify 196863, 196924
Couldn't classify 200661, 200751
Sorry, prediction pasa_asmbl_55640.p1 fails validation.
(GCT)	 CT	196863-196924	GT	AAG
(CAT)	 AG	198163-198260	GT	TGG
(AGC)	 AG	199030-199093	GT	AAG
(TCT)	 AG	199478-199573	GT	CGG
(CCT)	 AG	200661-200751	CC	ACC
-recovered pasa_asmbl_55640.p1, internal, 198163, 198260
-recovered pasa_asmbl_55640.p1, internal, 199030, 199093
-recovered pasa_asmbl_55640.p1, internal, 199478, 199573
Valid prediction for GlimmerHMM_glimmerT_23738-T1
Valid prediction for GlimmerHMM_glimmerT_23741-T1
Valid prediction for snap_scaffold_9-snap.3499-T1
Valid prediction for Augustus_model.g15795.t1
Valid prediction for Augustus_model.g15794.t1
Valid prediction for snap_scaffold_9-snap.3482-T1
Valid prediction for snap_scaffold_9-snap.3522-T1
Valid prediction for CodingQuarry_transcript_62458-T1
Valid prediction for snap_scaffold_9-snap.3496-T1
Valid prediction for snap_scaffold_9-snap.3497-T1
Valid prediction for snap_scaffold_9-snap.3511-T1
Valid prediction for Augustus_model.g15792.t1
Valid prediction for snap_scaffold_9-snap.3485-T1
Valid prediction for snap_scaffold_9-snap.3487-T1
Valid prediction for snap_scaffold_9-snap.3504-T1
Valid prediction for HiQ_model.g15798.t1
Valid prediction for Augustus_model.g15788.t1
Valid prediction for GlimmerHMM_glimmerT_23740-T1
Valid prediction for CodingQuarry_transcript_62460-T1
Valid prediction for snap_scaffold_9-snap.3498-T1
Valid prediction for GlimmerHMM_glimmerT_23728-T1
Valid prediction for snap_scaffold_9-snap.3523-T1
Valid prediction for HiQ_model.g15803.t1
Valid prediction for snap_scaffold_9-snap.3489-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 31346, rend_intergenic: 29570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 295998
-exon list size: 360


building trellis

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97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 31346, rend_intergenic: 29570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11070
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 2 predictions from path traversal
GOT 5prime partial gene.

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