-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_10371544-10658894

-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 snap_scaffold_9-snap.2095-T1
Valid prediction for Augustus_model.g15592.t1
Valid prediction for GeneMark_model.39877_t
Valid prediction for snap_scaffold_9-snap.2060-T1
Valid prediction for snap_scaffold_9-snap.2073-T1
Valid prediction for snap_scaffold_9-snap.2070-T1
Valid prediction for snap_scaffold_9-snap.2112-T1
Valid prediction for GlimmerHMM_glimmerT_23302-T1
Valid prediction for Augustus_model.g15596.t1
Valid prediction for snap_scaffold_9-snap.2065-T1
Valid prediction for snap_scaffold_9-snap.2062-T1
Valid prediction for snap_scaffold_9-snap.2061-T1
Valid prediction for GlimmerHMM_glimmerT_23295-T1
Valid prediction for GeneMark_model.39850_t
Valid prediction for GlimmerHMM_glimmerT_23297-T1
Valid prediction for Augustus_model.g15589.t1
Valid prediction for GeneMark_model.39870_t
Valid prediction for GeneMark_model.39838_t
Valid prediction for GeneMark_model.39847_t
Valid prediction for GlimmerHMM_glimmerT_23281-T1
Valid prediction for snap_scaffold_9-snap.2106-T1
Valid prediction for GeneMark_model.39893_t
Valid prediction for GlimmerHMM_glimmerT_23309-T1
Valid prediction for GlimmerHMM_glimmerT_23288-T1
Valid prediction for snap_scaffold_9-snap.2087-T1
Valid prediction for GeneMark_model.39856_t
Valid prediction for snap_scaffold_9-snap.2093-T1
Valid prediction for snap_scaffold_9-snap.2102-T1
Valid prediction for GeneMark_model.39884_t
Valid prediction for snap_scaffold_9-snap.2072-T1
Valid prediction for GeneMark_model.39878_t
Valid prediction for GeneMark_model.39849_t
Valid prediction for snap_scaffold_9-snap.2115-T1
Valid prediction for snap_scaffold_9-snap.2098-T1
Valid prediction for GeneMark_model.39876_t
Valid prediction for snap_scaffold_9-snap.2099-T1
Valid prediction for snap_scaffold_9-snap.2083-T1
Valid prediction for snap_scaffold_9-snap.2078-T1
Valid prediction for GeneMark_model.39872_t
Valid prediction for GeneMark_model.39855_t
Valid prediction for GeneMark_model.39851_t
Valid prediction for Augustus_model.g15594.t1
Valid prediction for snap_scaffold_9-snap.2091-T1
Valid prediction for snap_scaffold_9-snap.2089-T1
Valid prediction for snap_scaffold_9-snap.2074-T1
Valid prediction for GeneMark_model.39866_t
Valid prediction for snap_scaffold_9-snap.2114-T1
Couldn't classify 185458, 186096
Sorry, prediction pasa_asmbl_54275.p1 fails validation.
(GCC)	 TT	185458-186096	AC	CCA
Valid prediction for GeneMark_model.39869_t
Valid prediction for Augustus_model.g15595.t1
Valid prediction for GlimmerHMM_glimmerT_23299-T1
Valid prediction for GeneMark_model.39844_t
Valid prediction for GlimmerHMM_glimmerT_23284-T1
Valid prediction for Augustus_model.g15597.t1
Valid prediction for Augustus_model.g15593.t1
Valid prediction for snap_scaffold_9-snap.2075-T1
Valid prediction for Augustus_model.g15602.t1
Valid prediction for snap_scaffold_9-snap.2100-T1
Valid prediction for Augustus_model.g15600.t1
Valid prediction for snap_scaffold_9-snap.2104-T1
Valid prediction for snap_scaffold_9-snap.2081-T1
Valid prediction for GeneMark_model.39858_t
Valid prediction for snap_scaffold_9-snap.2096-T1
Valid prediction for GeneMark_model.39860_t
Valid prediction for GlimmerHMM_glimmerT_23290-T1
Valid prediction for GeneMark_model.39836_t
Valid prediction for snap_scaffold_9-snap.2064-T1
Valid prediction for GeneMark_model.39889_t
Valid prediction for GeneMark_model.39841_t
Valid prediction for GlimmerHMM_glimmerT_23301-T1
Valid prediction for snap_scaffold_9-snap.2059-T1
Valid prediction for snap_scaffold_9-snap.2107-T1
Valid prediction for GlimmerHMM_glimmerT_23300-T1
Valid prediction for GeneMark_model.39874_t
Valid prediction for GeneMark_model.39891_t
Valid prediction for GlimmerHMM_glimmerT_23292-T1
Valid prediction for GlimmerHMM_glimmerT_23310-T1
Valid prediction for snap_scaffold_9-snap.2069-T1
Valid prediction for GeneMark_model.39882_t
Valid prediction for GeneMark_model.39839_t

-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 GeneMark_model.39880_t
Valid prediction for Augustus_model.g15605.t1
Valid prediction for snap_scaffold_9-snap.2079-T1
Valid prediction for GlimmerHMM_glimmerT_23307-T1
Valid prediction for GeneMark_model.39875_t
Valid prediction for GeneMark_model.39865_t
Valid prediction for GeneMark_model.39854_t
Valid prediction for HiQ_model.g15606.t1
Valid prediction for snap_scaffold_9-snap.2094-T1
Valid prediction for GeneMark_model.39890_t
Valid prediction for snap_scaffold_9-snap.2082-T1
Valid prediction for Augustus_model.g15603.t1
Valid prediction for GlimmerHMM_glimmerT_23298-T1
Valid prediction for snap_scaffold_9-snap.2105-T1
Valid prediction for snap_scaffold_9-snap.2097-T1
Valid prediction for GeneMark_model.39846_t
Valid prediction for snap_scaffold_9-snap.2103-T1
Valid prediction for snap_scaffold_9-snap.2101-T1
Valid prediction for GeneMark_model.39871_t
Valid prediction for GeneMark_model.39894_t
Valid prediction for GeneMark_model.39859_t
Valid prediction for snap_scaffold_9-snap.2063-T1
Valid prediction for GeneMark_model.39867_t
Valid prediction for snap_scaffold_9-snap.2110-T1
Valid prediction for snap_scaffold_9-snap.2067-T1
Valid prediction for GeneMark_model.39879_t
Valid prediction for GlimmerHMM_glimmerT_23305-T1
Valid prediction for Augustus_model.g15598.t1
Valid prediction for GlimmerHMM_glimmerT_23289-T1
Valid prediction for GeneMark_model.39842_t
Valid prediction for snap_scaffold_9-snap.2071-T1
Valid prediction for GlimmerHMM_glimmerT_23287-T1
Valid prediction for snap_scaffold_9-snap.2086-T1
Valid prediction for snap_scaffold_9-snap.2111-T1
Valid prediction for snap_scaffold_9-snap.2085-T1
Valid prediction for GeneMark_model.39868_t
Valid prediction for GlimmerHMM_glimmerT_23306-T1
Valid prediction for GeneMark_model.39873_t
Valid prediction for snap_scaffold_9-snap.2084-T1
Valid prediction for GlimmerHMM_glimmerT_23283-T1
Valid prediction for GlimmerHMM_glimmerT_23279-T1
Valid prediction for GeneMark_model.39888_t
Valid prediction for snap_scaffold_9-snap.2076-T1
Valid prediction for GlimmerHMM_glimmerT_23294-T1
Valid prediction for GlimmerHMM_glimmerT_23303-T1
Valid prediction for snap_scaffold_9-snap.2080-T1
Valid prediction for Augustus_model.g15608.t1
Valid prediction for Augustus_model.g15601.t1
Valid prediction for GeneMark_model.39883_t
Valid prediction for Augustus_model.g15591.t1
Valid prediction for GlimmerHMM_glimmerT_23304-T1
Valid prediction for GeneMark_model.39886_t
Valid prediction for Augustus_model.g15607.t1
Valid prediction for snap_scaffold_9-snap.2088-T1
Couldn't classify 42198, 42445
Sorry, prediction pasa_asmbl_55219.p1 fails validation.
(CCG)	 TC	42198-42445	GT	AGG
(GAG)	 AG	43306-43573	GT	TTG
(ACG)	 AG	44758-44904	GT	AGG
(ATA)	 AG	46227-46303	GT	AGG
(GAA)	 AG	46502-46671	GT	AGG
(ATG)	 AG	47469-48073	GT	AGG
(GGC)	 AG	48329-48766	TT	AAT
add_exon() Sorry, pasa_asmbl_55219.p1 47469-48073-initial-1 is invalid.
-recovered pasa_asmbl_55219.p1, initial, 47469, 48073
-recovered pasa_asmbl_55219.p1, terminal, 48329, 48766
-recovered pasa_asmbl_55219.p1, internal, 43306, 43573
-recovered pasa_asmbl_55219.p1, internal, 44758, 44904
-recovered pasa_asmbl_55219.p1, internal, 46227, 46303
-recovered pasa_asmbl_55219.p1, internal, 46502, 46671
-recovered pasa_asmbl_55219.p1, internal, 47469, 48073
Valid prediction for GeneMark_model.39853_t
Valid prediction for GlimmerHMM_glimmerT_23293-T1
Valid prediction for GlimmerHMM_glimmerT_23291-T1
Valid prediction for GlimmerHMM_glimmerT_23285-T1
Valid prediction for snap_scaffold_9-snap.2077-T1
Valid prediction for Augustus_model.g15590.t1
Valid prediction for Augustus_model.g15604.t1
Valid prediction for snap_scaffold_9-snap.2068-T1
Valid prediction for snap_scaffold_9-snap.2092-T1
Valid prediction for GeneMark_model.39857_t
Valid prediction for snap_scaffold_9-snap.2066-T1
Valid prediction for GeneMark_model.39852_t
Valid prediction for GeneMark_model.39862_t
Valid prediction for snap_scaffold_9-snap.2108-T1
Valid prediction for GeneMark_model.39887_t
Valid prediction for snap_scaffold_9-snap.2109-T1
Valid prediction for GlimmerHMM_glimmerT_23280-T1
Valid prediction for Augustus_model.g15599.t1
Valid prediction for GeneMark_model.39848_t
Valid prediction for GlimmerHMM_glimmerT_23308-T1
Valid prediction for snap_scaffold_9-snap.2090-T1
Valid prediction for GeneMark_model.39837_t
Valid prediction for GeneMark_model.39845_t
Valid prediction for GeneMark_model.39861_t
Valid prediction for GeneMark_model.39864_t
Valid prediction for GlimmerHMM_glimmerT_23282-T1
Valid prediction for GeneMark_model.39892_t
Valid prediction for GlimmerHMM_glimmerT_23296-T1
Valid prediction for GeneMark_model.39840_t
Valid prediction for GlimmerHMM_glimmerT_23286-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28871, rend_intergenic: 26436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36821, rend_intergenic: 32800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48683, rend_intergenic: 37744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54869, rend_intergenic: 49501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58711, rend_intergenic: 54956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101933, rend_intergenic: 98814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107087, rend_intergenic: 102053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110061, rend_intergenic: 109972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128386, rend_intergenic: 123248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139034, rend_intergenic: 130026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147109, rend_intergenic: 139035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158359, rend_intergenic: 155731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166298, rend_intergenic: 165251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172265, rend_intergenic: 171900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182346, rend_intergenic: 181270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 267484, rend_intergenic: 266055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 287351
-exon list size: 684


building trellis

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92.7    
92.9    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 28871, rend_intergenic: 26436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36821, rend_intergenic: 32800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48683, rend_intergenic: 37744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54869, rend_intergenic: 49501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58711, rend_intergenic: 54956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101933, rend_intergenic: 98814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107087, rend_intergenic: 102053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110061, rend_intergenic: 109972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128386, rend_intergenic: 123248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139034, rend_intergenic: 130026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147109, rend_intergenic: 139035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158359, rend_intergenic: 155731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166298, rend_intergenic: 165251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172265, rend_intergenic: 171900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182346, rend_intergenic: 181270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 267484, rend_intergenic: 266055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support