-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_13609180-13762102

-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_45257-T1
Couldn't classify 151306, 151535
Sorry, prediction GlimmerHMM_glimmerT_45279-T1 fails validation.
(ATG)	 GG	148022-149970	GT	AGG
(CTA)	 AG	151306-151535	GT	GGG
-recovered GlimmerHMM_glimmerT_45279-T1, initial, 148022, 149970
-recovered GlimmerHMM_glimmerT_45279-T1, internal, 151306, 151535
Valid prediction for GlimmerHMM_glimmerT_45266-T1
Valid prediction for CodingQuarry_transcript_25897-T1
Valid prediction for GlimmerHMM_glimmerT_45271-T1
Valid prediction for CodingQuarry_transcript_25896-T1
Couldn't classify 3113, 3451
Sorry, prediction pasa_asmbl_22665.p1 fails validation.
(TTC)	 TG	3113-3451	CA	CAC
Valid prediction for snap_scaffold_19-snap.2694-T1
Valid prediction for snap_scaffold_19-snap.2686-T1
Valid prediction for GlimmerHMM_glimmerT_45277-T1
Valid prediction for GlimmerHMM_glimmerT_45259-T1
Valid prediction for snap_scaffold_19-snap.2703-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.2682-T1
Valid prediction for GlimmerHMM_glimmerT_45274-T1
Valid prediction for GlimmerHMM_glimmerT_45269-T1
Valid prediction for snap_scaffold_19-snap.2698-T1
Valid prediction for GlimmerHMM_glimmerT_45268-T1
Valid prediction for snap_scaffold_19-snap.2689-T1
Valid prediction for snap_scaffold_19-snap.2687-T1
Couldn't classify 137960, 138037
Sorry, prediction pasa_asmbl_21885.p1 fails validation.
(TAT)	 GG	137960-138037	GT	TGG
(GCC)	 AG	138555-138649	GT	AGG
(TAT)	 AG	139105-139150	GT	AGG
(ACC)	 AG	139251-139397	GT	GGG
(GTT)	 AG	139623-139705	GT	AGG
(GGA)	 AG	139816-139855	GT	TGG
(ACT)	 AG	139946-140036	GT	GGG
(GCA)	 AG	140118-140222	GT	GGG
(TGA)	 AG	143081-143172	CC	GAC
add_exon() Sorry, pasa_asmbl_21885.p1 139623-139705-terminal-2 is invalid.
-recovered pasa_asmbl_21885.p1, terminal, 139623, 139705
-recovered pasa_asmbl_21885.p1, terminal, 143081, 143172
-recovered pasa_asmbl_21885.p1, internal, 138555, 138649
-recovered pasa_asmbl_21885.p1, internal, 139105, 139150
-recovered pasa_asmbl_21885.p1, internal, 139251, 139397
-recovered pasa_asmbl_21885.p1, internal, 139623, 139705
-recovered pasa_asmbl_21885.p1, internal, 139816, 139855
-recovered pasa_asmbl_21885.p1, internal, 139946, 140036
-recovered pasa_asmbl_21885.p1, internal, 140118, 140222
Valid prediction for GlimmerHMM_glimmerT_45260-T1
Couldn't classify 133096, 133287
Couldn't classify 134532, 134570
Sorry, prediction pasa_asmbl_21884.p1 fails validation.
(GCG)	 GA	133096-133287	GT	AGG
(AGA)	 AG	133535-133628	GT	CGG
(ATA)	 AG	133777-133883	GT	AGG
(GTC)	 AG	134532-134570	TA	AGT
-recovered pasa_asmbl_21884.p1, internal, 133535, 133628
-recovered pasa_asmbl_21884.p1, internal, 133777, 133883
Valid prediction for CodingQuarry_transcript_25895-T1
Valid prediction for snap_scaffold_19-snap.2695-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.2702-T1
Valid prediction for GlimmerHMM_glimmerT_45255-T1
Valid prediction for snap_scaffold_19-snap.2684-T1
Valid prediction for GlimmerHMM_glimmerT_45263-T1
Valid prediction for GlimmerHMM_glimmerT_45278-T1
Valid prediction for GlimmerHMM_glimmerT_45262-T1
Valid prediction for snap_scaffold_19-snap.2700-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_19-snap.2699-T1
Valid prediction for snap_scaffold_19-snap.2692-T1
Valid prediction for snap_scaffold_19-snap.2704-T1
Valid prediction for snap_scaffold_19-snap.2679-T1
Valid prediction for GlimmerHMM_glimmerT_45270-T1
Valid prediction for GlimmerHMM_glimmerT_45265-T1
Valid prediction for snap_scaffold_19-snap.2696-T1
Valid prediction for GlimmerHMM_glimmerT_45258-T1
Valid prediction for GlimmerHMM_glimmerT_45272-T1
Valid prediction for GlimmerHMM_glimmerT_45261-T1
Valid prediction for snap_scaffold_19-snap.2691-T1
Valid prediction for GlimmerHMM_glimmerT_45275-T1
Valid prediction for GlimmerHMM_glimmerT_45276-T1
Valid prediction for snap_scaffold_19-snap.2680-T1
Valid prediction for snap_scaffold_19-snap.2701-T1
Valid prediction for GlimmerHMM_glimmerT_45267-T1
Valid prediction for GlimmerHMM_glimmerT_45256-T1
Valid prediction for snap_scaffold_19-snap.2697-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.2681-T1
Valid prediction for snap_scaffold_19-snap.2690-T1
Valid prediction for snap_scaffold_19-snap.2693-T1
Couldn't classify 132800, 132892
Couldn't classify 135750, 135855
Sorry, prediction pasa_asmbl_22710.p1 fails validation.
(GAT)	 TA	132800-132892	GT	CAG
(GAT)	 AG	132967-133100	GT	AGG
(ACC)	 AG	135750-135855	GT	AGG
-recovered pasa_asmbl_22710.p1, internal, 132967, 133100
-recovered pasa_asmbl_22710.p1, internal, 135750, 135855
Valid prediction for snap_scaffold_19-snap.2688-T1
Valid prediction for snap_scaffold_19-snap.2685-T1
Valid prediction for GlimmerHMM_glimmerT_45264-T1
Valid prediction for GlimmerHMM_glimmerT_45273-T1
Valid prediction for snap_scaffold_19-snap.2683-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 130447, rend_intergenic: 127462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 152923
-exon list size: 167


building trellis

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79.3    
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84.6    
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91.7    
92.3    
92.9    
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94.1    
94.7    
95.3    
95.9    
96.4    
97.0    
97.6    
98.2    
98.8    
99.4    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 130447, rend_intergenic: 127462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 17068
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support