-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_15221625-15407160

-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.41110_t
Valid prediction for HiQ_model.g16072.t1
Valid prediction for GeneMark_model.41097_t
Valid prediction for snap_scaffold_9-snap.3115-T1
Valid prediction for snap_scaffold_9-snap.3113-T1
Valid prediction for GlimmerHMM_glimmerT_23951-T1
Valid prediction for GeneMark_model.41124_t
Valid prediction for GlimmerHMM_glimmerT_23977-T1
Valid prediction for snap_scaffold_9-snap.3124-T1
Valid prediction for GlimmerHMM_glimmerT_23983-T1
Valid prediction for snap_scaffold_9-snap.3114-T1
Valid prediction for snap_scaffold_9-snap.3149-T1
Valid prediction for GlimmerHMM_glimmerT_23954-T1
Valid prediction for Augustus_model.g16050.t1
Valid prediction for CodingQuarry_transcript_62257-T1
Valid prediction for GlimmerHMM_glimmerT_23985-T1
Valid prediction for GlimmerHMM_glimmerT_23966-T1
Valid prediction for GlimmerHMM_glimmerT_23956-T1
Valid prediction for GeneMark_model.41098_t
Valid prediction for snap_scaffold_9-snap.3128-T1
Valid prediction for GeneMark_model.41129_t
Valid prediction for Augustus_model.g16073.t1
Valid prediction for pasa_asmbl_54538.p1
Valid prediction for GeneMark_model.41126_t
Valid prediction for GeneMark_model.41118_t
Valid prediction for Augustus_model.g16071.t1
Valid prediction for Augustus_model.g16054.t1
Valid prediction for Augustus_model.g16058.t1
Valid prediction for snap_scaffold_9-snap.3116-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_23982-T1
Valid prediction for GlimmerHMM_glimmerT_23953-T1
Valid prediction for snap_scaffold_9-snap.3118-T1
Valid prediction for GeneMark_model.41120_t
Valid prediction for Augustus_model.g16051.t1
Valid prediction for GeneMark_model.41112_t
Valid prediction for snap_scaffold_9-snap.3153-T1
Valid prediction for snap_scaffold_9-snap.3151-T1
Valid prediction for pasa_asmbl_54533.p1
Valid prediction for GeneMark_model.41122_t
Valid prediction for GlimmerHMM_glimmerT_23961-T1
Valid prediction for snap_scaffold_9-snap.3147-T1
Valid prediction for snap_scaffold_9-snap.3139-T1
Valid prediction for GlimmerHMM_glimmerT_23962-T1
Valid prediction for GlimmerHMM_glimmerT_23964-T1
Couldn't classify 30525, 30604
Couldn't classify 33487, 33592
Sorry, prediction pasa_asmbl_54528.p1 fails validation.
(GTG)	 CT	30525-30604	GT	CAG
(AGA)	 AG	30821-30935	GT	AGG
(ATT)	 AG	31101-31175	GT	AGG
(GAG)	 AG	31292-31415	GT	AGG
(CTG)	 AG	32497-32603	GT	CTG
(GAT)	 AG	32925-33011	GT	TGG
(GCC)	 AG	33128-33208	GT	AGG
(TTC)	 AG	33297-33370	GT	GGG
(TGA)	 AG	33487-33592	GG	GAG
-recovered pasa_asmbl_54528.p1, internal, 30821, 30935
-recovered pasa_asmbl_54528.p1, internal, 31101, 31175
-recovered pasa_asmbl_54528.p1, internal, 31292, 31415
-recovered pasa_asmbl_54528.p1, internal, 32497, 32603
-recovered pasa_asmbl_54528.p1, internal, 32925, 33011
-recovered pasa_asmbl_54528.p1, internal, 33128, 33208
-recovered pasa_asmbl_54528.p1, internal, 33297, 33370
Valid prediction for GeneMark_model.41106_t
Valid prediction for snap_scaffold_9-snap.3130-T1
Valid prediction for snap_scaffold_9-snap.3148-T1
Couldn't classify 37016, 37099
Sorry, prediction pasa_asmbl_54662.p1 fails validation.
(GGG)	 CA	37016-37099	GT	ACG
(ATG)	 AG	37307-37512	GT	CCG
(AAC)	 AG	37685-37788	GT	GGG
(ATG)	 AG	37907-38087	GT	CAG
(GGA)	 AG	38230-38260	TC	AAT
-recovered pasa_asmbl_54662.p1, initial, 37307, 37512
add_exon() Sorry, pasa_asmbl_54662.p1 37907-38087-initial-1 is invalid.
-recovered pasa_asmbl_54662.p1, initial, 37907, 38087
-recovered pasa_asmbl_54662.p1, terminal, 38230, 38260
-recovered pasa_asmbl_54662.p1, internal, 37307, 37512
-recovered pasa_asmbl_54662.p1, internal, 37685, 37788
-recovered pasa_asmbl_54662.p1, internal, 37907, 38087
Valid prediction for GlimmerHMM_glimmerT_23952-T1
Valid prediction for GlimmerHMM_glimmerT_23972-T1
Valid prediction for CodingQuarry_transcript_62256-T1
Valid prediction for Augustus_model.g16061.t1
Valid prediction for Augustus_model.g16052.t1
Valid prediction for GeneMark_model.41128_t
Valid prediction for snap_scaffold_9-snap.3143-T1
Valid prediction for Augustus_model.g16057.t1
Valid prediction for GlimmerHMM_glimmerT_23973-T1
Valid prediction for snap_scaffold_9-snap.3150-T1
Valid prediction for GlimmerHMM_glimmerT_23958-T1
Valid prediction for GeneMark_model.41102_t
Valid prediction for snap_scaffold_9-snap.3152-T1
Valid prediction for snap_scaffold_9-snap.3140-T1
Valid prediction for snap_scaffold_9-snap.3123-T1
Valid prediction for GeneMark_model.41099_t
Valid prediction for Augustus_model.g16063.t1
Valid prediction for GeneMark_model.41130_t
Valid prediction for GeneMark_model.41104_t
Valid prediction for snap_scaffold_9-snap.3142-T1
Valid prediction for snap_scaffold_9-snap.3126-T1
Valid prediction for GeneMark_model.41109_t
Valid prediction for pasa_asmbl_54543.p1
Valid prediction for Augustus_model.g16074.t1
Valid prediction for GeneMark_model.41101_t
Valid prediction for GlimmerHMM_glimmerT_23980-T1
Valid prediction for HiQ_model.g16068.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_23978-T1
Couldn't classify 87172, 87231
Couldn't classify 89130, 89237
Sorry, prediction pasa_asmbl_55484.p1 fails validation.
(GAC)	 TG	87172-87231	GT	TGG
(TTG)	 AG	87880-88075	GT	GAG
(GTG)	 AG	88220-88341	GT	AGG
(GTC)	 AG	88456-88653	GT	AGG
(TTC)	 AG	88748-88924	GT	AGG
(AAA)	 AG	89130-89237	CG	GCC
add_exon() Sorry, pasa_asmbl_55484.p1 87880-88075-terminal-3 is invalid.
-recovered pasa_asmbl_55484.p1, terminal, 87880, 88075
-recovered pasa_asmbl_55484.p1, internal, 87880, 88075
-recovered pasa_asmbl_55484.p1, internal, 88220, 88341
-recovered pasa_asmbl_55484.p1, internal, 88456, 88653
-recovered pasa_asmbl_55484.p1, internal, 88748, 88924
Valid prediction for snap_scaffold_9-snap.3127-T1
Valid prediction for GlimmerHMM_glimmerT_23981-T1
Valid prediction for snap_scaffold_9-snap.3141-T1
Valid prediction for Augustus_model.g16062.t1
Valid prediction for Augustus_model.g16053.t1
Valid prediction for CodingQuarry_transcript_62255-T1
Valid prediction for GlimmerHMM_glimmerT_23976-T1
Valid prediction for GlimmerHMM_glimmerT_23975-T1
Valid prediction for snap_scaffold_9-snap.3132-T1
Valid prediction for snap_scaffold_9-snap.3135-T1
Valid prediction for CodingQuarry_transcript_62253-T1
Valid prediction for pasa_asmbl_55489.p1
Valid prediction for snap_scaffold_9-snap.3136-T1
Valid prediction for GlimmerHMM_glimmerT_23967-T1
Valid prediction for Augustus_model.g16066.t1
Couldn't classify 90339, 90594
Couldn't classify 91459, 91484
Sorry, prediction pasa_asmbl_55483.p1 fails validation.
(CTC)	 CG	90339-90594	GT	GGG
(AGC)	 AG	90934-91072	GT	AGG
(GTA)	 AG	91221-91366	GT	GGG
(GTG)	 AG	91459-91484	GA	AGG
-recovered pasa_asmbl_55483.p1, internal, 90934, 91072
-recovered pasa_asmbl_55483.p1, internal, 91221, 91366
Valid prediction for HiQ_model.g16065.t1
Valid prediction for snap_scaffold_9-snap.3146-T1
Valid prediction for GlimmerHMM_glimmerT_23963-T1
Valid prediction for Augustus_model.g16055.t1
Valid prediction for snap_scaffold_9-snap.3131-T1
Valid prediction for snap_scaffold_9-snap.3144-T1
Valid prediction for GlimmerHMM_glimmerT_23970-T1
Valid prediction for snap_scaffold_9-snap.3129-T1
Valid prediction for Augustus_model.g16064.t1
Valid prediction for snap_scaffold_9-snap.3133-T1
Couldn't classify 92062, 92067
Sorry, prediction pasa_asmbl_55482.p1 fails validation.
(AAC)	 AA	92062-92067	GT	AGG
(CTG)	 AG	92220-92408	GT	GGG
(GTG)	 AG	92498-92645	GT	AGG
(AGG)	 AG	92924-93068	GT	AGG
(AAA)	 AG	93263-93375	GT	CTG
(TAA)	 AG	93767-93912	GT	TGG
(GTA)	 AG	94101-94207	GT	AGG
(AGA)	 AG	94317-94989	AG	GAA
-recovered pasa_asmbl_55482.p1, terminal, 94317, 94989
-recovered pasa_asmbl_55482.p1, internal, 92220, 92408
-recovered pasa_asmbl_55482.p1, internal, 92498, 92645
-recovered pasa_asmbl_55482.p1, internal, 92924, 93068
-recovered pasa_asmbl_55482.p1, internal, 93263, 93375
-recovered pasa_asmbl_55482.p1, internal, 93767, 93912
-recovered pasa_asmbl_55482.p1, internal, 94101, 94207
Valid prediction for GeneMark_model.41125_t
Valid prediction for GlimmerHMM_glimmerT_23971-T1
Valid prediction for GeneMark_model.41105_t
Valid prediction for GeneMark_model.41113_t
Valid prediction for Augustus_model.g16069.t1
Valid prediction for GeneMark_model.41127_t
Valid prediction for GlimmerHMM_glimmerT_23968-T1
Valid prediction for GlimmerHMM_glimmerT_23984-T1
Valid prediction for snap_scaffold_9-snap.3121-T1
Valid prediction for snap_scaffold_9-snap.3119-T1
Valid prediction for GeneMark_model.41121_t
Valid prediction for snap_scaffold_9-snap.3145-T1
Valid prediction for snap_scaffold_9-snap.3134-T1
Valid prediction for Augustus_model.g16059.t1
Valid prediction for Augustus_model.g16060.t1
Valid prediction for Augustus_model.g16056.t1
Valid prediction for snap_scaffold_9-snap.3122-T1
Valid prediction for GeneMark_model.41116_t
Valid prediction for snap_scaffold_9-snap.3120-T1
Valid prediction for pasa_asmbl_55485.p1
Valid prediction for GeneMark_model.41111_t
Valid prediction for CodingQuarry_transcript_62251-T1
Valid prediction for GeneMark_model.41100_t
Valid prediction for HiQ_model.g16070.t1
Valid prediction for snap_scaffold_9-snap.3137-T1
Valid prediction for GeneMark_model.41108_t
Valid prediction for snap_scaffold_9-snap.3125-T1
Valid prediction for GlimmerHMM_glimmerT_23974-T1
Valid prediction for GeneMark_model.41103_t
Valid prediction for GlimmerHMM_glimmerT_23960-T1
Valid prediction for GlimmerHMM_glimmerT_23955-T1
Valid prediction for GlimmerHMM_glimmerT_23959-T1
Valid prediction for GlimmerHMM_glimmerT_23965-T1
Valid prediction for CodingQuarry_transcript_62254-T1
Valid prediction for GeneMark_model.41123_t
Valid prediction for Augustus_model.g16067.t1
Valid prediction for GeneMark_model.41107_t
Valid prediction for snap_scaffold_9-snap.3117-T1
Valid prediction for GlimmerHMM_glimmerT_23979-T1
Valid prediction for GlimmerHMM_glimmerT_23957-T1
Valid prediction for GeneMark_model.41117_t
Valid prediction for snap_scaffold_9-snap.3138-T1
Valid prediction for pasa_asmbl_55487.p2
Valid prediction for GeneMark_model.41119_t
Valid prediction for GeneMark_model.41115_t
Valid prediction for GlimmerHMM_glimmerT_23969-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 33766, rend_intergenic: 23155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63392, rend_intergenic: 59515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75084, rend_intergenic: 72408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89621, rend_intergenic: 85427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126455, rend_intergenic: 121457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134538, rend_intergenic: 126690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 185536
-exon list size: 744


building trellis

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77.1    
77.2    
77.3    
77.5    
77.6    
77.7    
77.9    
78.0    
78.2    
78.3    
78.4    
78.6    
78.7    
78.8    
79.0    
79.1    
79.2    
79.4    
79.5    
79.6    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.8    
81.9    
82.0    
82.2    
82.3    
82.4    
82.6    
82.7    
82.8    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.5    
86.6    
86.7    
86.9    
87.0    
87.1    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 33766, rend_intergenic: 23155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63392, rend_intergenic: 59515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75084, rend_intergenic: 72408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89621, rend_intergenic: 85427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126455, rend_intergenic: 121457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134538, rend_intergenic: 126690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support