-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_10163059-10376078

-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: +)Couldn't classify 114535, 114666
Sorry, prediction pasa_asmbl_54271.p1 fails validation.
(GTC)	 AT	114535-114666	GT	TGG
(AGT)	 AG	114971-115241	GT	TGG
(GAC)	 AG	115318-115751	GA	AGG
-recovered pasa_asmbl_54271.p1, terminal, 115318, 115751
-recovered pasa_asmbl_54271.p1, internal, 114971, 115241
Valid prediction for GeneMark_model.39810_t
Valid prediction for snap_scaffold_9-snap.2051-T1
Valid prediction for snap_scaffold_9-snap.2038-T1
Valid prediction for GlimmerHMM_glimmerT_23275-T1
Valid prediction for pasa_asmbl_54266.p1
Valid prediction for GeneMark_model.39832_t
Valid prediction for GlimmerHMM_glimmerT_23255-T1
Valid prediction for GeneMark_model.39827_t
Valid prediction for GlimmerHMM_glimmerT_23265-T1
Valid prediction for GlimmerHMM_glimmerT_23261-T1
Valid prediction for snap_scaffold_9-snap.2047-T1
Valid prediction for snap_scaffold_9-snap.2028-T1
Valid prediction for CodingQuarry_transcript_62133-T1
Valid prediction for GlimmerHMM_glimmerT_23268-T1
Valid prediction for snap_scaffold_9-snap.2030-T1
Valid prediction for snap_scaffold_9-snap.2037-T1
Valid prediction for snap_scaffold_9-snap.2050-T1
Valid prediction for snap_scaffold_9-snap.2055-T1
Valid prediction for GeneMark_model.39824_t
Valid prediction for GeneMark_model.39803_t
Valid prediction for GlimmerHMM_glimmerT_23270-T1
Valid prediction for GlimmerHMM_glimmerT_23273-T1
Valid prediction for GeneMark_model.39818_t
Valid prediction for GlimmerHMM_glimmerT_23274-T1
Valid prediction for CodingQuarry_transcript_62132-T1
Valid prediction for snap_scaffold_9-snap.2053-T1
Valid prediction for GeneMark_model.39800_t
Couldn't classify 110617, 110800
Sorry, prediction pasa_asmbl_54268.p1 fails validation.
(AGA)	 AC	110617-110800	GT	TGG
(GTA)	 AG	111051-111169	GT	TGG
(GAG)	 AG	111284-111407	GT	AGG
(GGG)	 AG	111482-111808	GT	AGG
(GTG)	 AG	111995-112251	GA	GAG
-recovered pasa_asmbl_54268.p1, terminal, 111995, 112251
-recovered pasa_asmbl_54268.p1, internal, 111051, 111169
-recovered pasa_asmbl_54268.p1, internal, 111284, 111407
-recovered pasa_asmbl_54268.p1, internal, 111482, 111808
Valid prediction for GeneMark_model.39819_t
Valid prediction for Augustus_model.g15586.t1
Valid prediction for GeneMark_model.39826_t
Valid prediction for snap_scaffold_9-snap.2032-T1
Valid prediction for GeneMark_model.39820_t
Valid prediction for Augustus_model.g15580.t1
Valid prediction for GlimmerHMM_glimmerT_23257-T1
Valid prediction for HiQ_model.g15582.t1
Valid prediction for GlimmerHMM_glimmerT_23267-T1
Couldn't classify 117517, 117637
Couldn't classify 117760, 118085
Sorry, prediction pasa_asmbl_54273.p1 fails validation.
(AGT)	 AG	117517-117637	GT	AGG
(GAA)	 AG	117760-118085	GG	CAG
-recovered pasa_asmbl_54273.p1, internal, 117517, 117637
Valid prediction for snap_scaffold_9-snap.2042-T1
Valid prediction for GlimmerHMM_glimmerT_23251-T1
Valid prediction for snap_scaffold_9-snap.2043-T1
Valid prediction for snap_scaffold_9-snap.2044-T1
Valid prediction for Augustus_model.g15588.t1
Valid prediction for Augustus_model.g15579.t1
Valid prediction for GeneMark_model.39834_t
Valid prediction for GeneMark_model.39821_t
Valid prediction for snap_scaffold_9-snap.2039-T1
Valid prediction for HiQ_model.g15585.t1
Valid prediction for GeneMark_model.39795_t
Valid prediction for GeneMark_model.39836_t
Valid prediction for GeneMark_model.39798_t
Valid prediction for snap_scaffold_9-snap.2023-T1
Valid prediction for GeneMark_model.39804_t
Valid prediction for GlimmerHMM_glimmerT_23256-T1
Valid prediction for HiQ_model.g15584.t1
Valid prediction for GeneMark_model.39813_t
Valid prediction for snap_scaffold_9-snap.2049-T1
Valid prediction for Augustus_model.g15587.t1
Valid prediction for GeneMark_model.39812_t
Valid prediction for snap_scaffold_9-snap.2041-T1
Valid prediction for GeneMark_model.39806_t
Valid prediction for GlimmerHMM_glimmerT_23250-T1
Valid prediction for GlimmerHMM_glimmerT_23266-T1
Valid prediction for snap_scaffold_9-snap.2027-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_23258-T1
Valid prediction for GlimmerHMM_glimmerT_23254-T1
Valid prediction for GeneMark_model.39793_t
Valid prediction for snap_scaffold_9-snap.2025-T1
Valid prediction for GeneMark_model.39794_t
Valid prediction for snap_scaffold_9-snap.2036-T1
Valid prediction for GlimmerHMM_glimmerT_23269-T1
Valid prediction for GeneMark_model.39825_t
Valid prediction for GlimmerHMM_glimmerT_23277-T1
Valid prediction for snap_scaffold_9-snap.2054-T1
Valid prediction for GeneMark_model.39792_t
Valid prediction for GeneMark_model.39799_t
Valid prediction for snap_scaffold_9-snap.2056-T1
Valid prediction for GlimmerHMM_glimmerT_23259-T1
Valid prediction for GeneMark_model.39802_t
Valid prediction for GeneMark_model.39829_t
Valid prediction for GeneMark_model.39828_t
Valid prediction for GlimmerHMM_glimmerT_23276-T1
Valid prediction for snap_scaffold_9-snap.2024-T1
Valid prediction for snap_scaffold_9-snap.2046-T1
Valid prediction for snap_scaffold_9-snap.2048-T1
Valid prediction for GlimmerHMM_glimmerT_23263-T1
Valid prediction for CodingQuarry_transcript_62131-T1
Valid prediction for pasa_asmbl_55218.p1
Valid prediction for snap_scaffold_9-snap.2045-T1
Valid prediction for GlimmerHMM_glimmerT_23271-T1
Valid prediction for GlimmerHMM_glimmerT_23262-T1
Valid prediction for snap_scaffold_9-snap.2052-T1
Valid prediction for GeneMark_model.39833_t
Valid prediction for GlimmerHMM_glimmerT_23260-T1
Valid prediction for snap_scaffold_9-snap.2034-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.39801_t
Valid prediction for GlimmerHMM_glimmerT_23272-T1
Valid prediction for GeneMark_model.39809_t
Valid prediction for snap_scaffold_9-snap.2035-T1
Valid prediction for GeneMark_model.39817_t
Valid prediction for GeneMark_model.39830_t
Valid prediction for snap_scaffold_9-snap.2031-T1
Valid prediction for GeneMark_model.39815_t
Valid prediction for GlimmerHMM_glimmerT_23253-T1
Valid prediction for snap_scaffold_9-snap.2026-T1
Valid prediction for GeneMark_model.39807_t
Valid prediction for GeneMark_model.39797_t
Valid prediction for GeneMark_model.39835_t
Valid prediction for snap_scaffold_9-snap.2029-T1
Valid prediction for GeneMark_model.39811_t
Valid prediction for HiQ_model.g15583.t1
Valid prediction for Augustus_model.g15581.t1
Valid prediction for GlimmerHMM_glimmerT_23264-T1
Valid prediction for GeneMark_model.39822_t
Valid prediction for GlimmerHMM_glimmerT_23252-T1
Valid prediction for snap_scaffold_9-snap.2033-T1
Valid prediction for GeneMark_model.39823_t
Valid prediction for GeneMark_model.39814_t
Valid prediction for GeneMark_model.39831_t
Valid prediction for GeneMark_model.39816_t
Valid prediction for GeneMark_model.39796_t
Valid prediction for GeneMark_model.39808_t
Valid prediction for GeneMark_model.39805_t
Valid prediction for snap_scaffold_9-snap.2058-T1
Valid prediction for snap_scaffold_9-snap.2040-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13122, rend_intergenic: 6433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18809, rend_intergenic: 16393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27988, rend_intergenic: 25749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29884, rend_intergenic: 29032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54960, rend_intergenic: 37269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144042, rend_intergenic: 139107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191029, rend_intergenic: 184033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197057, rend_intergenic: 195258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198495, rend_intergenic: 197398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 213020
-exon list size: 548


building trellis

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98.2    
98.4    
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98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 13122, rend_intergenic: 6433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18809, rend_intergenic: 16393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27988, rend_intergenic: 25749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29884, rend_intergenic: 29032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54960, rend_intergenic: 37269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144042, rend_intergenic: 139107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191029, rend_intergenic: 184033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197057, rend_intergenic: 195258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198495, rend_intergenic: 197398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 200959 - 213020
-exon list size: 21


building trellis

4.3    
8.7    
13.0    
17.4    
21.7    
26.1    
30.4    
34.8    
39.1    
43.5    
47.8    
52.2    
56.5    
60.9    
65.2    
69.6    
73.9    
78.3    
82.6    
87.0    
91.3    
95.7    
-found 1 predictions from path traversal

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