-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_2033932-2157424

-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 Augustus_model.g2264.t1
Valid prediction for GeneMark_model.5469_t
Valid prediction for Augustus_model.g2261.t1
Valid prediction for GeneMark_model.5474_t
Valid prediction for GlimmerHMM_glimmerT_3382-T1
Valid prediction for GlimmerHMM_glimmerT_3376-T1
Couldn't classify 29911, 30220
Sorry, prediction pasa_asmbl_24254.p1 fails validation.
(GTC)	 CG	29911-30220	GT	AGG
(ACC)	 AG	30499-30743	GC	GAG
-recovered pasa_asmbl_24254.p1, terminal, 30499, 30743
-recovered pasa_asmbl_24254.p1, internal, 30499, 30743
Valid prediction for snap_scaffold_2-snap.497-T1
Valid prediction for Augustus_model.g2270.t1
Valid prediction for snap_scaffold_2-snap.488-T1
Valid prediction for snap_scaffold_2-snap.490-T1
Valid prediction for GeneMark_model.5466_t
Valid prediction for snap_scaffold_2-snap.484-T1
Couldn't classify 36360, 36439
Couldn't classify 37593, 37695
Sorry, prediction pasa_asmbl_24256.p2 fails validation.
(AAG)	 AT	36360-36439	GT	AAG
(AGT)	 AG	36698-36865	GT	CGG
(GTA)	 AG	37593-37695	GC	CCG
-recovered pasa_asmbl_24256.p2, internal, 36698, 36865
-recovered pasa_asmbl_24256.p2, internal, 37593, 37695
Valid prediction for GeneMark_model.5438_t
Valid prediction for Augustus_model.g2262.t1
Valid prediction for GlimmerHMM_glimmerT_3381-T1
Valid prediction for snap_scaffold_2-snap.480-T1
Valid prediction for snap_scaffold_2-snap.505-T1
Valid prediction for snap_scaffold_2-snap.495-T1
Valid prediction for GeneMark_model.5468_t
Valid prediction for GlimmerHMM_glimmerT_3386-T1
Valid prediction for snap_scaffold_2-snap.498-T1
Valid prediction for snap_scaffold_2-snap.482-T1
Valid prediction for GeneMark_model.5447_t
Valid prediction for GlimmerHMM_glimmerT_3374-T1
Valid prediction for GlimmerHMM_glimmerT_3384-T1
Valid prediction for GeneMark_model.5459_t
Valid prediction for snap_scaffold_2-snap.504-T1
Valid prediction for GeneMark_model.5471_t
Valid prediction for GeneMark_model.5461_t
Valid prediction for snap_scaffold_2-snap.489-T1
Valid prediction for GeneMark_model.5445_t
Valid prediction for HiQ_model.g2263.t1
Valid prediction for GlimmerHMM_glimmerT_3388-T1
Valid prediction for Augustus_model.g2265.t1
Valid prediction for snap_scaffold_2-snap.486-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.5454_t
Valid prediction for GeneMark_model.5470_t
Valid prediction for GeneMark_model.5441_t
Valid prediction for snap_scaffold_2-snap.503-T1
Valid prediction for GlimmerHMM_glimmerT_3377-T1
Valid prediction for GeneMark_model.5472_t
Valid prediction for snap_scaffold_2-snap.496-T1
Valid prediction for GeneMark_model.5451_t
Valid prediction for GeneMark_model.5452_t
Valid prediction for GeneMark_model.5464_t
Valid prediction for GeneMark_model.5456_t
Valid prediction for snap_scaffold_2-snap.502-T1
Valid prediction for GeneMark_model.5465_t
Valid prediction for snap_scaffold_2-snap.493-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_3378-T1
Valid prediction for Augustus_model.g2268.t1
Valid prediction for snap_scaffold_2-snap.500-T1
Valid prediction for snap_scaffold_2-snap.485-T1
Valid prediction for GeneMark_model.5458_t
Valid prediction for snap_scaffold_2-snap.507-T1
Valid prediction for GeneMark_model.5440_t
Valid prediction for snap_scaffold_2-snap.494-T1
Valid prediction for Augustus_model.g2271.t1
Valid prediction for snap_scaffold_2-snap.487-T1
Valid prediction for snap_scaffold_2-snap.506-T1
Valid prediction for GlimmerHMM_glimmerT_3385-T1
Valid prediction for snap_scaffold_2-snap.501-T1
Valid prediction for GeneMark_model.5462_t
Valid prediction for GeneMark_model.5455_t
Valid prediction for snap_scaffold_2-snap.499-T1
Valid prediction for Augustus_model.g2267.t1
Valid prediction for GeneMark_model.5467_t
Valid prediction for GeneMark_model.5448_t
Valid prediction for snap_scaffold_2-snap.492-T1
Valid prediction for GlimmerHMM_glimmerT_3380-T1
Valid prediction for Augustus_model.g2266.t1
Valid prediction for Augustus_model.g2269.t1
Valid prediction for GeneMark_model.5450_t
Valid prediction for GeneMark_model.5446_t
Valid prediction for GeneMark_model.5439_t
Valid prediction for GeneMark_model.5449_t
Valid prediction for GeneMark_model.5463_t
Valid prediction for GeneMark_model.5442_t
Valid prediction for snap_scaffold_2-snap.491-T1
Valid prediction for GeneMark_model.5437_t
Valid prediction for GeneMark_model.5444_t
Valid prediction for GeneMark_model.5453_t
Valid prediction for GlimmerHMM_glimmerT_3387-T1
Valid prediction for snap_scaffold_2-snap.481-T1
Valid prediction for GeneMark_model.5473_t
Valid prediction for GeneMark_model.5457_t
Valid prediction for snap_scaffold_2-snap.483-T1
Valid prediction for GlimmerHMM_glimmerT_3389-T1
Valid prediction for GeneMark_model.5460_t
Valid prediction for GlimmerHMM_glimmerT_3379-T1
Valid prediction for GlimmerHMM_glimmerT_3390-T1
Valid prediction for GlimmerHMM_glimmerT_3383-T1
Valid prediction for GlimmerHMM_glimmerT_3375-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17996, rend_intergenic: 17009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28655, rend_intergenic: 18046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38904, rend_intergenic: 36681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55650, rend_intergenic: 48418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59034, rend_intergenic: 57098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76439, rend_intergenic: 59059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91787, rend_intergenic: 76462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108769, rend_intergenic: 92087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120072, rend_intergenic: 109094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 123493
-exon list size: 589


building trellis

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86.3    
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87.0    
87.1    
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87.6    
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88.0    
88.2    
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88.7    
88.8    
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90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
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93.9    
94.1    
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94.8    
94.9    
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95.4    
95.6    
95.8    
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96.1    
96.3    
96.4    
96.6    
96.8    
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97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 17996, rend_intergenic: 17009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28655, rend_intergenic: 18046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38904, rend_intergenic: 36681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55650, rend_intergenic: 48418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59034, rend_intergenic: 57098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76439, rend_intergenic: 59059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91787, rend_intergenic: 76462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108769, rend_intergenic: 92087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120072, rend_intergenic: 109094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 5 predictions persist after filtering for low support