-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_8992179-9152457

-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 GeneMark_model.88902_t
Valid prediction for Augustus_model.g34334.t1
Valid prediction for GlimmerHMM_glimmerT_51203-T1
Valid prediction for GeneMark_model.88890_t
Valid prediction for GlimmerHMM_glimmerT_51190-T1
Valid prediction for GeneMark_model.88856_t
Valid prediction for Augustus_model.g34330.t1
Valid prediction for snap_scaffold_22-snap.1896-T1
Valid prediction for snap_scaffold_22-snap.1881-T1
Valid prediction for GeneMark_model.88874_t
Valid prediction for GlimmerHMM_glimmerT_51200-T1
Valid prediction for GeneMark_model.88899_t
Valid prediction for snap_scaffold_22-snap.1884-T1
Valid prediction for GeneMark_model.88861_t
Valid prediction for GeneMark_model.88876_t
Valid prediction for GeneMark_model.88851_t
Valid prediction for GlimmerHMM_glimmerT_51206-T1
Valid prediction for GeneMark_model.88884_t
Valid prediction for GlimmerHMM_glimmerT_51207-T1
Valid prediction for snap_scaffold_22-snap.1879-T1
Valid prediction for GeneMark_model.88870_t
Valid prediction for GeneMark_model.88897_t
Valid prediction for Augustus_model.g34336.t1
Valid prediction for snap_scaffold_22-snap.1888-T1
Valid prediction for snap_scaffold_22-snap.1893-T1
Valid prediction for snap_scaffold_22-snap.1878-T1
Valid prediction for GeneMark_model.88877_t
Valid prediction for GeneMark_model.88847_t
Valid prediction for GeneMark_model.88886_t
Valid prediction for GeneMark_model.88855_t
Valid prediction for GeneMark_model.88864_t
Valid prediction for GeneMark_model.88857_t
Valid prediction for snap_scaffold_22-snap.1890-T1
Valid prediction for snap_scaffold_22-snap.1899-T1
Valid prediction for snap_scaffold_22-snap.1883-T1
Valid prediction for GeneMark_model.88846_t
Valid prediction for GeneMark_model.88900_t
Valid prediction for GeneMark_model.88888_t
Valid prediction for snap_scaffold_22-snap.1886-T1
Valid prediction for GeneMark_model.88853_t
Valid prediction for GeneMark_model.88892_t
Valid prediction for GeneMark_model.88894_t
Valid prediction for GeneMark_model.88896_t
Valid prediction for GeneMark_model.88859_t
Valid prediction for GeneMark_model.88849_t
Valid prediction for GeneMark_model.88904_t
Valid prediction for GeneMark_model.88867_t
Valid prediction for GeneMark_model.88872_t
Valid prediction for GlimmerHMM_glimmerT_51196-T1
Valid prediction for GeneMark_model.88879_t
Valid prediction for snap_scaffold_22-snap.1901-T1
Valid prediction for snap_scaffold_22-snap.1882-T1
Valid prediction for GeneMark_model.88869_t
Valid prediction for Augustus_model.g34333.t1
Valid prediction for GlimmerHMM_glimmerT_51191-T1
Valid prediction for GeneMark_model.88863_t
Valid prediction for GeneMark_model.88881_t
Couldn't classify 148047, 148128
Sorry, prediction pasa_asmbl_29582.p1 fails validation.
(GCT)	 CA	148047-148128	GT	AGG
(ATA)	 AG	148613-148663	GT	AGG
(GTG)	 AG	149801-149872	GT	AGG
(GTG)	 AG	150259-150306	GT	TAG
(ACA)	 AG	150786-150905	GT	GCG
(AGA)	 AG	151450-151515	GT	AGG
(TCC)	 AG	153233-153294	CC	AAC
-recovered pasa_asmbl_29582.p1, terminal, 153233, 153294
-recovered pasa_asmbl_29582.p1, internal, 148613, 148663
-recovered pasa_asmbl_29582.p1, internal, 149801, 149872
-recovered pasa_asmbl_29582.p1, internal, 150259, 150306
-recovered pasa_asmbl_29582.p1, internal, 150786, 150905
-recovered pasa_asmbl_29582.p1, internal, 151450, 151515

-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.88850_t
Valid prediction for GeneMark_model.88865_t
Couldn't classify 100700, 100735
Sorry, prediction GeneMark_model.88875_t fails validation.
(ATG)	 TC	95108-95130	GT	GAG
(AGA)	 AG	95302-95475	GT	AGG
(GGA)	 AG	95670-95711	GT	GAG
(AGG)	 AG	95735-95812	GT	GAG
(AGA)	 AG	95836-95922	GT	GTG
(ATC)	 AG	96351-96446	GT	GAG
(ATT)	 AG	96467-96481	GT	GGG
(TAA)	 AG	96505-96513	GT	GGG
(TAA)	 AG	96543-96554	GT	GGG
(TAA)	 AG	96580-96615	GT	AAG
(TGA)	 AG	96647-96655	GT	GGG
(GGT)	 AG	96681-96761	GT	AGG
(TGA)	 AG	96797-96820	GT	GAG
(AGA)	 AG	96911-96931	GT	GGG
(AGG)	 AG	96956-97003	GT	GAG
(GAC)	 AG	97040-97045	GT	GGG
(TGA)	 AG	97068-97076	GT	GGG
(CGT)	 AG	97097-97105	GT	AAG
(TGA)	 AG	97170-97205	GT	AAG
(TGA)	 AG	97237-97245	GT	GGG
(TGA)	 AG	97267-97275	GT	GGG
(TGA)	 AG	97297-97323	GT	GAG
(TGA)	 AG	97357-97379	GT	GAG
(ACT)	 AG	97590-97732	GT	AGG
(GTG)	 AG	98735-98784	GT	GAG
(GAG)	 AG	98870-99076	GC	AGG
(GAG)	 AG	99099-99267	GT	ATG
(AGA)	 AG	99296-99330	GT	GAG
(AGA)	 AG	99419-99433	GT	GAG
(AGG)	 AG	99463-99525	GC	GAG
(AGG)	 AG	99553-99588	GC	GAG
(GAG)	 AG	99612-99647	GT	GGG
(GTG)	 AG	99668-99712	GT	AAG
(GGA)	 AG	100079-100162	GT	GTG
(GGG)	 AG	100700-100735	GT	GAG
-recovered GeneMark_model.88875_t, initial, 95108, 95130
add_exon() Sorry, GeneMark_model.88875_t 95302-95475-terminal-1 is invalid.
-recovered GeneMark_model.88875_t, terminal, 95302, 95475
add_exon() Sorry, GeneMark_model.88875_t 96580-96615-terminal-1 is invalid.
-recovered GeneMark_model.88875_t, terminal, 96580, 96615
-recovered GeneMark_model.88875_t, terminal, 97097, 97105
add_exon() Sorry, GeneMark_model.88875_t 97170-97205-terminal-1 is invalid.
-recovered GeneMark_model.88875_t, terminal, 97170, 97205
-recovered GeneMark_model.88875_t, internal, 95302, 95475
-recovered GeneMark_model.88875_t, internal, 95670, 95711
-recovered GeneMark_model.88875_t, internal, 95735, 95812
-recovered GeneMark_model.88875_t, internal, 95836, 95922
-recovered GeneMark_model.88875_t, internal, 96351, 96446
-recovered GeneMark_model.88875_t, internal, 96467, 96481
-recovered GeneMark_model.88875_t, internal, 96505, 96513
-recovered GeneMark_model.88875_t, internal, 96543, 96554
-recovered GeneMark_model.88875_t, internal, 96580, 96615
-recovered GeneMark_model.88875_t, internal, 96647, 96655
-recovered GeneMark_model.88875_t, internal, 96681, 96761
-recovered GeneMark_model.88875_t, internal, 96797, 96820
-recovered GeneMark_model.88875_t, internal, 96911, 96931
-recovered GeneMark_model.88875_t, internal, 96956, 97003
-recovered GeneMark_model.88875_t, internal, 97040, 97045
-recovered GeneMark_model.88875_t, internal, 97068, 97076
-recovered GeneMark_model.88875_t, internal, 97097, 97105
-recovered GeneMark_model.88875_t, internal, 97170, 97205
-recovered GeneMark_model.88875_t, internal, 97237, 97245
-recovered GeneMark_model.88875_t, internal, 97267, 97275
-recovered GeneMark_model.88875_t, internal, 97297, 97323
-recovered GeneMark_model.88875_t, internal, 97357, 97379
-recovered GeneMark_model.88875_t, internal, 97590, 97732
-recovered GeneMark_model.88875_t, internal, 98735, 98784
-recovered GeneMark_model.88875_t, internal, 98870, 99076
-recovered GeneMark_model.88875_t, internal, 99099, 99267
-recovered GeneMark_model.88875_t, internal, 99296, 99330
-recovered GeneMark_model.88875_t, internal, 99419, 99433
-recovered GeneMark_model.88875_t, internal, 99463, 99525
-recovered GeneMark_model.88875_t, internal, 99553, 99588
-recovered GeneMark_model.88875_t, internal, 99612, 99647
-recovered GeneMark_model.88875_t, internal, 99668, 99712
-recovered GeneMark_model.88875_t, internal, 100079, 100162
-recovered GeneMark_model.88875_t, internal, 100700, 100735
Valid prediction for GeneMark_model.88885_t
Valid prediction for snap_scaffold_22-snap.1895-T1
Valid prediction for snap_scaffold_22-snap.1885-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g34328.t1
Valid prediction for GeneMark_model.88883_t
Valid prediction for GeneMark_model.88887_t
Valid prediction for GlimmerHMM_glimmerT_51193-T1
Valid prediction for snap_scaffold_22-snap.1877-T1
Valid prediction for Augustus_model.g34326.t1
Valid prediction for GlimmerHMM_glimmerT_51201-T1
Valid prediction for GlimmerHMM_glimmerT_51198-T1
Valid prediction for snap_scaffold_22-snap.1898-T1
Valid prediction for snap_scaffold_22-snap.1891-T1
Valid prediction for GeneMark_model.88845_t
Valid prediction for snap_scaffold_22-snap.1892-T1
Valid prediction for GeneMark_model.88903_t
Valid prediction for GeneMark_model.88848_t
Valid prediction for snap_scaffold_22-snap.1889-T1
Valid prediction for GeneMark_model.88882_t
Valid prediction for GeneMark_model.88895_t
Valid prediction for GeneMark_model.88898_t
Valid prediction for HiQ_model.g34331.t1
Valid prediction for GeneMark_model.88878_t
Couldn't classify 66188, 66286
Sorry, prediction pasa_asmbl_30550.p1 fails validation.
(GAG)	 AG	66188-66286	GT	GGG
(GCT)	 AG	66658-66796	GT	CAG
(ACA)	 AG	67556-67635	TG	AAT
-recovered pasa_asmbl_30550.p1, terminal, 67556, 67635
-recovered pasa_asmbl_30550.p1, internal, 66188, 66286
-recovered pasa_asmbl_30550.p1, internal, 66658, 66796
Valid prediction for GeneMark_model.88858_t
Valid prediction for snap_scaffold_22-snap.1897-T1
Valid prediction for Augustus_model.g34329.t1
Valid prediction for snap_scaffold_22-snap.1900-T1
Valid prediction for GlimmerHMM_glimmerT_51197-T1
Valid prediction for HiQ_model.g34332.t1
Valid prediction for snap_scaffold_22-snap.1887-T1
Valid prediction for Augustus_model.g34327.t1
Valid prediction for Augustus_model.g34324.t1
Valid prediction for snap_scaffold_22-snap.1880-T1
Couldn't classify 110869, 110946
Couldn't classify 115067, 115190
Sorry, prediction pasa_asmbl_30276.p1 fails validation.
(TGT)	 AG	110869-110946	GT	AGG
(CAA)	 AG	112071-112112	GT	AGG
(GCT)	 AG	114625-114710	GT	AGG
(GGC)	 AG	115067-115190	GT	AGG
-recovered pasa_asmbl_30276.p1, internal, 110869, 110946
-recovered pasa_asmbl_30276.p1, internal, 112071, 112112
-recovered pasa_asmbl_30276.p1, internal, 114625, 114710
-recovered pasa_asmbl_30276.p1, internal, 115067, 115190
Valid prediction for GeneMark_model.88866_t
Valid prediction for GeneMark_model.88860_t
Valid prediction for GeneMark_model.88862_t
Valid prediction for GeneMark_model.88891_t
Valid prediction for GlimmerHMM_glimmerT_51195-T1
Valid prediction for GeneMark_model.88893_t
Valid prediction for GeneMark_model.88868_t
Valid prediction for GeneMark_model.88889_t
Valid prediction for GeneMark_model.88873_t
Valid prediction for GlimmerHMM_glimmerT_51205-T1
Valid prediction for GlimmerHMM_glimmerT_51194-T1
Valid prediction for Augustus_model.g34335.t1
Valid prediction for Augustus_model.g34325.t1
Valid prediction for GlimmerHMM_glimmerT_51192-T1
Valid prediction for GlimmerHMM_glimmerT_51189-T1
Valid prediction for GeneMark_model.88880_t
Valid prediction for GeneMark_model.88871_t
Valid prediction for GlimmerHMM_glimmerT_51199-T1
Valid prediction for GeneMark_model.88854_t
Valid prediction for GeneMark_model.88901_t
Valid prediction for GlimmerHMM_glimmerT_51202-T1
Valid prediction for GeneMark_model.88852_t
Valid prediction for snap_scaffold_22-snap.1894-T1
Valid prediction for GlimmerHMM_glimmerT_51204-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23886, rend_intergenic: 13267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49084, rend_intergenic: 25399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70221, rend_intergenic: 49456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82156, rend_intergenic: 77445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90555, rend_intergenic: 90126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106441, rend_intergenic: 103366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126743, rend_intergenic: 114892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134152, rend_intergenic: 129249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150922, rend_intergenic: 141442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151465, rend_intergenic: 150943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153542, rend_intergenic: 151467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 160279
-exon list size: 688


building trellis

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73.0    
73.2    
73.3    
73.5    
73.6    
73.8    
73.9    
74.1    
74.2    
74.3    
74.5    
74.6    
74.8    
74.9    
75.1    
75.2    
75.4    
75.5    
75.7    
75.8    
75.9    
76.1    
76.2    
76.4    
76.5    
76.7    
76.8    
77.0    
77.1    
77.2    
77.4    
77.5    
77.7    
77.8    
78.0    
78.1    
78.3    
78.4    
78.6    
78.7    
78.8    
79.0    
79.1    
79.3    
79.4    
79.6    
79.7    
79.9    
80.0    
80.1    
80.3    
80.4    
80.6    
80.7    
80.9    
81.0    
81.2    
81.3    
81.4    
81.6    
81.7    
81.9    
82.0    
82.2    
82.3    
82.5    
82.6    
82.8    
82.9    
83.0    
83.2    
83.3    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
87.0    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.8    
89.0    
89.1    
89.3    
89.4    
89.6    
89.7    
89.9    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 23886, rend_intergenic: 13267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49084, rend_intergenic: 25399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70221, rend_intergenic: 49456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82156, rend_intergenic: 77445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90555, rend_intergenic: 90126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106441, rend_intergenic: 103366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126743, rend_intergenic: 114892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134152, rend_intergenic: 129249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150922, rend_intergenic: 141442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151465, rend_intergenic: 150943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153542, rend_intergenic: 151467  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