-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_1287178-1421268

-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_36357-T1
Couldn't classify 112950, 113066
Couldn't classify 113822, 113865
Sorry, prediction pasa_asmbl_14829.p1 fails validation.
(GAG)	 TG	112950-113066	GT	AGG
(AGC)	 AG	113451-113601	GT	TGG
(GGG)	 AG	113822-113865	GA	TGG
-recovered pasa_asmbl_14829.p1, internal, 113451, 113601
Valid prediction for snap_scaffold_15-snap.284-T1
Valid prediction for Augustus_model.g24432.t1
Valid prediction for snap_scaffold_15-snap.269-T1
Valid prediction for GlimmerHMM_glimmerT_36342-T1
Valid prediction for GeneMark_model.62503_t
Valid prediction for GeneMark_model.62533_t
Couldn't classify 62062, 62217
Sorry, prediction pasa_asmbl_13946.p1 fails validation.
(TTC)	 AC	62062-62217	GT	TTG
(GTC)	 AG	63202-63675	TA	AGT
-recovered pasa_asmbl_13946.p1, terminal, 63202, 63675
Valid prediction for GeneMark_model.62501_t
Valid prediction for GeneMark_model.62523_t
Valid prediction for GeneMark_model.62499_t
Valid prediction for GlimmerHMM_glimmerT_36358-T1
Valid prediction for snap_scaffold_15-snap.273-T1
Valid prediction for snap_scaffold_15-snap.278-T1
Valid prediction for GlimmerHMM_glimmerT_36348-T1
Valid prediction for GeneMark_model.62525_t
Valid prediction for GlimmerHMM_glimmerT_36355-T1
Valid prediction for snap_scaffold_15-snap.275-T1
Valid prediction for GeneMark_model.62535_t
Valid prediction for GeneMark_model.62513_t
Valid prediction for GeneMark_model.62509_t
Valid prediction for GeneMark_model.62527_t
Valid prediction for snap_scaffold_15-snap.289-T1
Valid prediction for GeneMark_model.62514_t
Valid prediction for Augustus_model.g24429.t1
Valid prediction for Augustus_model.g24433.t1
Couldn't classify 120274, 120426
Sorry, prediction pasa_asmbl_13948.p2 fails validation.
(CTG)	 AC	120274-120426	GT	AGG
(GAG)	 AG	120898-121059	GT	AGG
(GGC)	 AG	121652-121789	GT	AGG
(GTG)	 AG	121891-122029	GT	AGG
(GTG)	 AG	122262-122437	GT	AGG
(GGC)	 AG	122558-122689	GT	AGG
(CGC)	 AG	123036-123174	GT	CGG
(AAG)	 AG	123270-123370	GG	GAG
-recovered pasa_asmbl_13948.p2, terminal, 123270, 123370
-recovered pasa_asmbl_13948.p2, internal, 120898, 121059
-recovered pasa_asmbl_13948.p2, internal, 121652, 121789
-recovered pasa_asmbl_13948.p2, internal, 121891, 122029
-recovered pasa_asmbl_13948.p2, internal, 122262, 122437
-recovered pasa_asmbl_13948.p2, internal, 122558, 122689
-recovered pasa_asmbl_13948.p2, internal, 123036, 123174
Valid prediction for GeneMark_model.62516_t
Valid prediction for GeneMark_model.62529_t
Valid prediction for GeneMark_model.62518_t
Couldn't classify 52497, 52889
Sorry, prediction pasa_asmbl_13945.p1 fails validation.
(CAC)	 AG	52497-52889	GA	GAG
Valid prediction for GeneMark_model.62505_t
Valid prediction for Augustus_model.g24428.t1
Valid prediction for GeneMark_model.62521_t
Valid prediction for GlimmerHMM_glimmerT_36350-T1
Valid prediction for GeneMark_model.62531_t
Valid prediction for CodingQuarry_transcript_17861-T1
Valid prediction for CodingQuarry_transcript_17860-T1
Valid prediction for snap_scaffold_15-snap.272-T1
Valid prediction for GlimmerHMM_glimmerT_36345-T1
Valid prediction for GlimmerHMM_glimmerT_36354-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_36353-T1
Valid prediction for GeneMark_model.62507_t
Valid prediction for GeneMark_model.62504_t
Valid prediction for GeneMark_model.62530_t
Valid prediction for GeneMark_model.62534_t
Valid prediction for Augustus_model.g24424.t1
Valid prediction for snap_scaffold_15-snap.280-T1
Valid prediction for GeneMark_model.62524_t
Valid prediction for snap_scaffold_15-snap.276-T1
Couldn't classify 59862, 60742
Sorry, prediction pasa_asmbl_14960.p1 fails validation.
(TCC)	 TT	59862-60742	GT	AAG
(GGA)	 AG	60944-61043	GT	AAG
(ATT)	 AG	61173-61235	TC	GAT
-recovered pasa_asmbl_14960.p1, terminal, 61173, 61235
-recovered pasa_asmbl_14960.p1, internal, 60944, 61043
Valid prediction for Augustus_model.g24425.t1
Valid prediction for GlimmerHMM_glimmerT_36351-T1
Valid prediction for GlimmerHMM_glimmerT_36344-T1
Valid prediction for snap_scaffold_15-snap.288-T1
Valid prediction for snap_scaffold_15-snap.283-T1
Valid prediction for snap_scaffold_15-snap.267-T1
Valid prediction for snap_scaffold_15-snap.287-T1
Valid prediction for snap_scaffold_15-snap.281-T1
Valid prediction for GeneMark_model.62528_t
Valid prediction for Augustus_model.g24427.t1
Valid prediction for GlimmerHMM_glimmerT_36347-T1
Valid prediction for snap_scaffold_15-snap.286-T1
Couldn't classify 58038, 58104
Couldn't classify 58210, 59537
Sorry, prediction pasa_asmbl_14961.p1 fails validation.
(GTG)	 GC	58038-58104	GT	AGG
(ATT)	 AG	58210-59537	AC	TTA
Valid prediction for GeneMark_model.62526_t
Valid prediction for Augustus_model.g24430.t1
Valid prediction for snap_scaffold_15-snap.285-T1
Valid prediction for snap_scaffold_15-snap.274-T1
Valid prediction for GlimmerHMM_glimmerT_36356-T1
Valid prediction for GeneMark_model.62520_t
Valid prediction for snap_scaffold_15-snap.282-T1
Valid prediction for GeneMark_model.62522_t
Valid prediction for GeneMark_model.62515_t
Valid prediction for GeneMark_model.62506_t
Valid prediction for snap_scaffold_15-snap.268-T1
Valid prediction for Augustus_model.g24426.t1
Valid prediction for GeneMark_model.62511_t
Valid prediction for GeneMark_model.62502_t
Valid prediction for GeneMark_model.62517_t
Valid prediction for GlimmerHMM_glimmerT_36346-T1
Valid prediction for GeneMark_model.62508_t
Valid prediction for snap_scaffold_15-snap.271-T1
Valid prediction for GlimmerHMM_glimmerT_36352-T1
Valid prediction for GeneMark_model.62500_t
Valid prediction for GeneMark_model.62532_t
Valid prediction for GlimmerHMM_glimmerT_36349-T1
Valid prediction for GeneMark_model.62519_t
Valid prediction for GlimmerHMM_glimmerT_36343-T1
Valid prediction for snap_scaffold_15-snap.279-T1
Valid prediction for Augustus_model.g24431.t1
Valid prediction for snap_scaffold_15-snap.270-T1
Valid prediction for GeneMark_model.62512_t
Valid prediction for snap_scaffold_15-snap.277-T1
Valid prediction for GeneMark_model.62536_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 46493, rend_intergenic: 44844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53645, rend_intergenic: 48872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61225, rend_intergenic: 55388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65339, rend_intergenic: 62646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130932, rend_intergenic: 98756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 134091
-exon list size: 558


building trellis

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89.3    
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91.8    
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92.1    
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93.0    
93.2    
93.4    
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96.6    
96.8    
97.0    
97.1    
97.3    
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98.0    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 17 predictions from path traversal
Error with prediction: snap lend_intergenic: 46493, rend_intergenic: 44844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53645, rend_intergenic: 48872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61225, rend_intergenic: 55388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65339, rend_intergenic: 62646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130932, rend_intergenic: 98756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support