-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_14864517-15047223

-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.41034_t
Valid prediction for GeneMark_model.41045_t
Valid prediction for snap_scaffold_9-snap.3061-T1
Valid prediction for snap_scaffold_9-snap.3041-T1
Valid prediction for GeneMark_model.41056_t
Valid prediction for GeneMark_model.41053_t
Valid prediction for GeneMark_model.41024_t
Valid prediction for Augustus_model.g16024.t1
Valid prediction for snap_scaffold_9-snap.3033-T1
Valid prediction for GeneMark_model.41050_t
Valid prediction for GeneMark_model.41026_t
Valid prediction for snap_scaffold_9-snap.3055-T1
Valid prediction for snap_scaffold_9-snap.3062-T1
Valid prediction for GeneMark_model.41052_t
Valid prediction for GeneMark_model.41025_t
Valid prediction for snap_scaffold_9-snap.3063-T1
Valid prediction for GlimmerHMM_glimmerT_23909-T1
Valid prediction for GeneMark_model.41021_t
Valid prediction for GlimmerHMM_glimmerT_23915-T1
Valid prediction for GlimmerHMM_glimmerT_23903-T1
Valid prediction for GeneMark_model.41060_t
Valid prediction for GeneMark_model.41037_t
Valid prediction for snap_scaffold_9-snap.3046-T1
Valid prediction for snap_scaffold_9-snap.3057-T1
Valid prediction for GeneMark_model.41023_t
Couldn't classify 113386, 113412
Sorry, prediction GeneMark_model.41048_t fails validation.
(GGG)	 AG	113386-113412	GT	ACG
(AGC)	 AG	113594-113641	GT	GAG
(ATG)	 AG	113673-113731	GT	CGG
(GCG)	 AG	114328-114562	GT	GAG
(AGA)	 AG	114583-114627	GT	GTG
(CGA)	 AG	114702-114762	TC	GAT
add_exon() Sorry, GeneMark_model.41048_t 113673-113731-initial-1 is invalid.
-recovered GeneMark_model.41048_t, initial, 113673, 113731
-recovered GeneMark_model.41048_t, terminal, 114702, 114762
-recovered GeneMark_model.41048_t, internal, 113386, 113412
-recovered GeneMark_model.41048_t, internal, 113594, 113641
-recovered GeneMark_model.41048_t, internal, 113673, 113731
-recovered GeneMark_model.41048_t, internal, 114328, 114562
-recovered GeneMark_model.41048_t, internal, 114583, 114627
Valid prediction for GlimmerHMM_glimmerT_23913-T1
Valid prediction for GeneMark_model.41042_t
Valid prediction for GeneMark_model.41015_t
Valid prediction for snap_scaffold_9-snap.3040-T1
Valid prediction for GlimmerHMM_glimmerT_23896-T1
Valid prediction for GeneMark_model.41039_t
Valid prediction for snap_scaffold_9-snap.3053-T1
Valid prediction for Augustus_model.g16012.t1
Valid prediction for GeneMark_model.41030_t
Valid prediction for snap_scaffold_9-snap.3043-T1
Valid prediction for GeneMark_model.41022_t
Valid prediction for snap_scaffold_9-snap.3064-T1
Valid prediction for GeneMark_model.41019_t
Valid prediction for snap_scaffold_9-snap.3038-T1
Valid prediction for snap_scaffold_9-snap.3067-T1
Valid prediction for snap_scaffold_9-snap.3034-T1
Valid prediction for GlimmerHMM_glimmerT_23908-T1
Valid prediction for GeneMark_model.41043_t
Valid prediction for snap_scaffold_9-snap.3042-T1
Valid prediction for snap_scaffold_9-snap.3037-T1
Valid prediction for GlimmerHMM_glimmerT_23901-T1
Valid prediction for GeneMark_model.41035_t
Valid prediction for GeneMark_model.41028_t
Valid prediction for snap_scaffold_9-snap.3058-T1
Valid prediction for snap_scaffold_9-snap.3045-T1
Valid prediction for Augustus_model.g16014.t1
Valid prediction for snap_scaffold_9-snap.3060-T1
Valid prediction for GeneMark_model.41017_t
Valid prediction for Augustus_model.g16013.t1
Valid prediction for GlimmerHMM_glimmerT_23919-T1
Valid prediction for Augustus_model.g16023.t1
Valid prediction for GlimmerHMM_glimmerT_23916-T1
Couldn't classify 112778, 112846
Sorry, prediction GeneMark_model.41047_t fails validation.
(ATG)	 TG	107890-107909	GT	GGG
(GAG)	 AG	108016-108042	GT	AGG
(GGT)	 AG	108462-108491	GT	GAG
(ACA)	 AG	109163-109201	GT	AAG
(AGA)	 AG	109847-109960	GT	AGG
(GAG)	 AG	110197-110250	GT	AGG
(TGT)	 AG	110546-110683	GT	GAG
(GAG)	 AG	111660-111674	GT	GAG
(GGA)	 AG	111984-111998	GT	TTG
(GAG)	 AG	112410-112431	GT	CAG
(GTG)	 AG	112778-112846	GT	CTG
-recovered GeneMark_model.41047_t, initial, 107890, 107909
add_exon() Sorry, GeneMark_model.41047_t 108016-108042-terminal-1 is invalid.
-recovered GeneMark_model.41047_t, terminal, 108016, 108042
-recovered GeneMark_model.41047_t, internal, 108016, 108042
-recovered GeneMark_model.41047_t, internal, 108462, 108491
-recovered GeneMark_model.41047_t, internal, 109163, 109201
-recovered GeneMark_model.41047_t, internal, 109847, 109960
-recovered GeneMark_model.41047_t, internal, 110197, 110250
-recovered GeneMark_model.41047_t, internal, 110546, 110683
-recovered GeneMark_model.41047_t, internal, 111660, 111674
-recovered GeneMark_model.41047_t, internal, 111984, 111998
-recovered GeneMark_model.41047_t, internal, 112410, 112431
-recovered GeneMark_model.41047_t, internal, 112778, 112846
Valid prediction for Augustus_model.g16019.t1
Valid prediction for GeneMark_model.41058_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 GlimmerHMM_glimmerT_23897-T1
Valid prediction for GlimmerHMM_glimmerT_23911-T1
Valid prediction for snap_scaffold_9-snap.3068-T1
Valid prediction for snap_scaffold_9-snap.3032-T1
Valid prediction for GeneMark_model.41040_t
Valid prediction for GeneMark_model.41036_t
Valid prediction for GeneMark_model.41027_t
Valid prediction for Augustus_model.g16025.t1
Valid prediction for GlimmerHMM_glimmerT_23906-T1
Valid prediction for GlimmerHMM_glimmerT_23910-T1
Valid prediction for Augustus_model.g16026.t1
Valid prediction for GeneMark_model.41032_t
Valid prediction for GeneMark_model.41061_t
Valid prediction for GeneMark_model.41057_t
Valid prediction for snap_scaffold_9-snap.3047-T1
Valid prediction for snap_scaffold_9-snap.3066-T1
Valid prediction for GlimmerHMM_glimmerT_23905-T1
Valid prediction for snap_scaffold_9-snap.3070-T1
Valid prediction for GeneMark_model.41033_t
Valid prediction for snap_scaffold_9-snap.3069-T1
Valid prediction for HiQ_model.g16021.t1
Valid prediction for Augustus_model.g16020.t1
Valid prediction for GeneMark_model.41038_t
Valid prediction for snap_scaffold_9-snap.3056-T1
Valid prediction for GeneMark_model.41014_t
Valid prediction for GlimmerHMM_glimmerT_23917-T1
Valid prediction for snap_scaffold_9-snap.3049-T1
Valid prediction for GlimmerHMM_glimmerT_23900-T1
Valid prediction for snap_scaffold_9-snap.3035-T1
Valid prediction for GeneMark_model.41046_t
Valid prediction for GlimmerHMM_glimmerT_23918-T1
Valid prediction for GlimmerHMM_glimmerT_23920-T1
Valid prediction for snap_scaffold_9-snap.3048-T1
Valid prediction for GeneMark_model.41054_t
Valid prediction for snap_scaffold_9-snap.3050-T1
Valid prediction for Augustus_model.g16018.t1
Valid prediction for GeneMark_model.41018_t
Valid prediction for pasa_asmbl_55471.p1
Valid prediction for snap_scaffold_9-snap.3039-T1
Valid prediction for snap_scaffold_9-snap.3051-T1
Valid prediction for GlimmerHMM_glimmerT_23914-T1
Valid prediction for Augustus_model.g16015.t1
Valid prediction for GeneMark_model.41055_t
Valid prediction for snap_scaffold_9-snap.3059-T1
Valid prediction for snap_scaffold_9-snap.3054-T1
Valid prediction for GlimmerHMM_glimmerT_23921-T1
Valid prediction for GeneMark_model.41020_t
Valid prediction for snap_scaffold_9-snap.3052-T1
Valid prediction for GeneMark_model.41041_t
Valid prediction for snap_scaffold_9-snap.3044-T1
Valid prediction for GeneMark_model.41016_t
Valid prediction for GlimmerHMM_glimmerT_23902-T1
Couldn't classify 74718, 74748
Sorry, prediction pasa_asmbl_55772.p1 fails validation.
(AGC)	 TT	74718-74748	GT	AGG
(AGG)	 AG	75331-75460	GT	GTG
(GTA)	 AG	75846-75995	GT	TGG
(CTT)	 AG	76908-76977	GT	AGG
(CTG)	 AG	77268-77378	GT	CTG
(AAC)	 AG	77626-77721	GT	AGG
(TGC)	 AG	77876-78010	GT	AGG
(AAA)	 AG	78164-78263	GT	AGG
(GCG)	 AG	78679-78833	GT	AGG
(GTG)	 AG	78930-79055	GT	AGG
(GGT)	 AG	79200-79331	GT	AGG
(GAT)	 AG	79556-79623	GT	AGG
(GTG)	 AG	79789-79877	GT	AGG
(ATG)	 AG	80053-80150	GT	CTG
(GGT)	 AG	80424-80511	GT	CTG
(GGG)	 AG	80864-80959	GT	CGG
(GGG)	 AG	81235-81365	GT	GGG
(GCC)	 AG	81718-81843	CA	AGC
add_exon() Sorry, pasa_asmbl_55772.p1 80053-80150-initial-1 is invalid.
-recovered pasa_asmbl_55772.p1, initial, 80053, 80150
-recovered pasa_asmbl_55772.p1, terminal, 81718, 81843
-recovered pasa_asmbl_55772.p1, internal, 75331, 75460
-recovered pasa_asmbl_55772.p1, internal, 75846, 75995
-recovered pasa_asmbl_55772.p1, internal, 76908, 76977
-recovered pasa_asmbl_55772.p1, internal, 77268, 77378
-recovered pasa_asmbl_55772.p1, internal, 77626, 77721
-recovered pasa_asmbl_55772.p1, internal, 77876, 78010
-recovered pasa_asmbl_55772.p1, internal, 78164, 78263
-recovered pasa_asmbl_55772.p1, internal, 78679, 78833
-recovered pasa_asmbl_55772.p1, internal, 78930, 79055
-recovered pasa_asmbl_55772.p1, internal, 79200, 79331
-recovered pasa_asmbl_55772.p1, internal, 79556, 79623
-recovered pasa_asmbl_55772.p1, internal, 79789, 79877
-recovered pasa_asmbl_55772.p1, internal, 80053, 80150
-recovered pasa_asmbl_55772.p1, internal, 80424, 80511
-recovered pasa_asmbl_55772.p1, internal, 80864, 80959
-recovered pasa_asmbl_55772.p1, internal, 81235, 81365
Valid prediction for GeneMark_model.41031_t
Valid prediction for GeneMark_model.41044_t
Valid prediction for GlimmerHMM_glimmerT_23899-T1
Valid prediction for Augustus_model.g16022.t1
Valid prediction for GeneMark_model.41049_t
Valid prediction for GlimmerHMM_glimmerT_23907-T1
Valid prediction for GlimmerHMM_glimmerT_23904-T1
Valid prediction for GeneMark_model.41059_t
Valid prediction for GlimmerHMM_glimmerT_23912-T1
Valid prediction for GeneMark_model.41051_t
Valid prediction for HiQ_model.g16017.t1
Valid prediction for snap_scaffold_9-snap.3036-T1
Valid prediction for GeneMark_model.41013_t
Valid prediction for GeneMark_model.41029_t
Valid prediction for GlimmerHMM_glimmerT_23898-T1
Valid prediction for CodingQuarry_transcript_62246-T1
Valid prediction for snap_scaffold_9-snap.3065-T1
Valid prediction for Augustus_model.g16016.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10999, rend_intergenic: 9068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15641, rend_intergenic: 11099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22347, rend_intergenic: 21609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26886, rend_intergenic: 25231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44400, rend_intergenic: 27046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65477, rend_intergenic: 60980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100375, rend_intergenic: 91664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102374, rend_intergenic: 100865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112833, rend_intergenic: 104409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133288, rend_intergenic: 128098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159398, rend_intergenic: 152822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162128, rend_intergenic: 160082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 182707
-exon list size: 686


building trellis

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80.5    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.8    
83.0    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.0    
84.2    
84.3    
84.4    
84.6    
84.7    
84.9    
85.0    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.6    
87.8    
87.9    
88.1    
88.2    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.4    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.7    
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 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 10999, rend_intergenic: 9068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15641, rend_intergenic: 11099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22347, rend_intergenic: 21609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26886, rend_intergenic: 25231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44400, rend_intergenic: 27046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65477, rend_intergenic: 60980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100375, rend_intergenic: 91664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102374, rend_intergenic: 100865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112833, rend_intergenic: 104409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133288, rend_intergenic: 128098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159398, rend_intergenic: 152822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162128, rend_intergenic: 160082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support