-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_9353674-9532743

-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.48825_t
Valid prediction for GeneMark_model.48863_t
Valid prediction for snap_scaffold_11-snap.2144-T1
Valid prediction for GeneMark_model.48818_t
Valid prediction for GlimmerHMM_glimmerT_28284-T1
Valid prediction for GeneMark_model.48835_t
Valid prediction for GeneMark_model.48838_t
Valid prediction for GeneMark_model.48823_t
Valid prediction for GeneMark_model.48855_t
Valid prediction for GeneMark_model.48824_t
Valid prediction for GeneMark_model.48821_t
Valid prediction for GeneMark_model.48827_t
Valid prediction for snap_scaffold_11-snap.2139-T1
Valid prediction for snap_scaffold_11-snap.2150-T1
Valid prediction for snap_scaffold_11-snap.2163-T1
Valid prediction for GeneMark_model.48843_t
Valid prediction for GeneMark_model.48845_t
Valid prediction for snap_scaffold_11-snap.2155-T1
Valid prediction for GeneMark_model.48859_t
Valid prediction for snap_scaffold_11-snap.2124-T1
Valid prediction for snap_scaffold_11-snap.2156-T1
Valid prediction for GeneMark_model.48866_t
Valid prediction for GeneMark_model.48853_t
Valid prediction for Augustus_model.g18877.t1
Couldn't classify 149317, 149499
Sorry, prediction pasa_asmbl_5849.p1 fails validation.
(GGG)	 TG	149317-149499	GT	AGG
(CTG)	 AG	150178-150292	GT	CGG
(AGT)	 AG	150908-151025	GT	AGG
(GGA)	 AG	151165-151356	GT	AGG
(GAT)	 AG	151448-151638	GT	TGG
(AGG)	 AG	151734-153070	CA	AGC
-recovered pasa_asmbl_5849.p1, terminal, 151734, 153070
-recovered pasa_asmbl_5849.p1, internal, 150178, 150292
-recovered pasa_asmbl_5849.p1, internal, 150908, 151025
-recovered pasa_asmbl_5849.p1, internal, 151165, 151356
-recovered pasa_asmbl_5849.p1, internal, 151448, 151638
Valid prediction for GeneMark_model.48841_t
Valid prediction for snap_scaffold_11-snap.2147-T1
Couldn't classify 156663, 157160
Sorry, prediction pasa_asmbl_6918.p1 fails validation.
(AAT)	 CG	156663-157160	TA	AAT
Valid prediction for GlimmerHMM_glimmerT_28276-T1
Valid prediction for GlimmerHMM_glimmerT_28274-T1
Valid prediction for Augustus_model.g18863.t1
Valid prediction for snap_scaffold_11-snap.2128-T1
Couldn't classify 148921, 149220
Sorry, prediction pasa_asmbl_5848.p1 fails validation.
(ATG)	 TG	148921-149220	AG	CCA
Valid prediction for GlimmerHMM_glimmerT_28291-T1
Valid prediction for GeneMark_model.48833_t
Valid prediction for snap_scaffold_11-snap.2160-T1
Valid prediction for GeneMark_model.48819_t
Valid prediction for snap_scaffold_11-snap.2142-T1
Valid prediction for GeneMark_model.48828_t
Valid prediction for GeneMark_model.48849_t
Valid prediction for GlimmerHMM_glimmerT_28292-T1
Valid prediction for GeneMark_model.48837_t
Valid prediction for snap_scaffold_11-snap.2130-T1
Valid prediction for snap_scaffold_11-snap.2136-T1
Valid prediction for GlimmerHMM_glimmerT_28290-T1
Valid prediction for snap_scaffold_11-snap.2135-T1
Valid prediction for snap_scaffold_11-snap.2154-T1
Valid prediction for GeneMark_model.48860_t
Valid prediction for GeneMark_model.48851_t
Valid prediction for GeneMark_model.48830_t
Valid prediction for GeneMark_model.48861_t
Valid prediction for GeneMark_model.48816_t
Valid prediction for snap_scaffold_11-snap.2149-T1
Valid prediction for snap_scaffold_11-snap.2157-T1
Valid prediction for GeneMark_model.48847_t
Valid prediction for Augustus_model.g18876.t1
Valid prediction for GlimmerHMM_glimmerT_28279-T1
Valid prediction for GeneMark_model.48864_t
Valid prediction for GeneMark_model.48840_t
Valid prediction for snap_scaffold_11-snap.2152-T1
Valid prediction for snap_scaffold_11-snap.2131-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 Augustus_model.g18871.t1
Couldn't classify 87517, 87647
Couldn't classify 88312, 88419
Sorry, prediction pasa_asmbl_6914.p1 fails validation.
(CTG)	 AG	87517-87647	GT	AAG
(GTG)	 AG	87798-88044	GT	AGG
(TTC)	 AG	88312-88419	GA	AGG
-recovered pasa_asmbl_6914.p1, internal, 87517, 87647
-recovered pasa_asmbl_6914.p1, internal, 87798, 88044
Valid prediction for GeneMark_model.48865_t
Valid prediction for snap_scaffold_11-snap.2138-T1
Valid prediction for snap_scaffold_11-snap.2162-T1
Valid prediction for snap_scaffold_11-snap.2140-T1
Valid prediction for Augustus_model.g18867.t1
Valid prediction for Augustus_model.g18864.t1
Valid prediction for GlimmerHMM_glimmerT_28280-T1
Valid prediction for GlimmerHMM_glimmerT_28273-T1
Valid prediction for snap_scaffold_11-snap.2159-T1
Valid prediction for snap_scaffold_11-snap.2134-T1
Valid prediction for GlimmerHMM_glimmerT_28272-T1
Valid prediction for GeneMark_model.48862_t
Valid prediction for GeneMark_model.48817_t
Valid prediction for snap_scaffold_11-snap.2126-T1
Valid prediction for snap_scaffold_11-snap.2133-T1
Valid prediction for GlimmerHMM_glimmerT_28277-T1
Valid prediction for GeneMark_model.48850_t
Valid prediction for GlimmerHMM_glimmerT_28289-T1
Valid prediction for GeneMark_model.48836_t
Valid prediction for pasa_asmbl_6915.p1
Valid prediction for CodingQuarry_transcript_8176-T1
Valid prediction for Augustus_model.g18865.t1
Valid prediction for snap_scaffold_11-snap.2127-T1
Couldn't classify 16347, 16372
Sorry, prediction pasa_asmbl_6919.p1 fails validation.
(CTC)	 TC	16347-16372	GT	CGG
(GAA)	 AG	16666-16752	GT	TGG
(GTG)	 AG	17501-17607	GT	AGG
(CGT)	 AG	17853-17927	GT	TGG
(ACT)	 AG	19035-19225	GT	AGG
(AAG)	 AG	19976-20041	GT	ATG
(GTG)	 AG	20615-20708	GT	TCG
(GCA)	 AG	20846-20955	GG	AGG
-recovered pasa_asmbl_6919.p1, terminal, 20846, 20955
-recovered pasa_asmbl_6919.p1, internal, 16666, 16752
-recovered pasa_asmbl_6919.p1, internal, 17501, 17607
-recovered pasa_asmbl_6919.p1, internal, 17853, 17927
-recovered pasa_asmbl_6919.p1, internal, 19035, 19225
-recovered pasa_asmbl_6919.p1, internal, 19976, 20041
-recovered pasa_asmbl_6919.p1, internal, 20615, 20708
Valid prediction for GeneMark_model.48857_t
Valid prediction for Augustus_model.g18862.t1
Valid prediction for snap_scaffold_11-snap.2129-T1
Valid prediction for Augustus_model.g18875.t1
Valid prediction for GeneMark_model.48831_t
Valid prediction for GlimmerHMM_glimmerT_28293-T1
Valid prediction for snap_scaffold_11-snap.2161-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.48858_t
Valid prediction for Augustus_model.g18868.t1
Valid prediction for snap_scaffold_11-snap.2125-T1
Couldn't classify 115737, 115752
Couldn't classify 118126, 118283
Sorry, prediction pasa_asmbl_6911.p1 fails validation.
(CTG)	 CT	115737-115752	GT	TCG
(CTG)	 AG	116021-116266	GT	AGG
(CAT)	 AG	116478-116615	GT	ACG
(CCT)	 AG	116901-116994	GT	CTG
(GTG)	 AG	117254-117306	GT	CTG
(ACA)	 AG	117679-117773	GT	AGG
(CAA)	 AG	117886-117964	GT	AGG
(CGG)	 AG	118126-118283	GT	AAG
-recovered pasa_asmbl_6911.p1, internal, 116021, 116266
-recovered pasa_asmbl_6911.p1, internal, 116478, 116615
-recovered pasa_asmbl_6911.p1, internal, 116901, 116994
-recovered pasa_asmbl_6911.p1, internal, 117254, 117306
-recovered pasa_asmbl_6911.p1, internal, 117679, 117773
-recovered pasa_asmbl_6911.p1, internal, 117886, 117964
-recovered pasa_asmbl_6911.p1, internal, 118126, 118283
Valid prediction for GeneMark_model.48842_t
Valid prediction for GeneMark_model.48856_t
Couldn't classify 12943, 13022
Couldn't classify 13629, 13722
Sorry, prediction pasa_asmbl_6921.p1 fails validation.
(CAC)	 TC	12943-13022	GT	ATG
(GTT)	 AG	13125-13242	GT	AGG
(GTG)	 AG	13432-13520	GT	AGG
(GTG)	 AG	13629-13722	GG	GAG
-recovered pasa_asmbl_6921.p1, internal, 13125, 13242
-recovered pasa_asmbl_6921.p1, internal, 13432, 13520
Valid prediction for GeneMark_model.48839_t
Valid prediction for snap_scaffold_11-snap.2146-T1
Valid prediction for HiQ_model.g18870.t1
Valid prediction for GeneMark_model.48848_t
Valid prediction for snap_scaffold_11-snap.2145-T1
Valid prediction for GeneMark_model.48832_t
Valid prediction for snap_scaffold_11-snap.2148-T1
Valid prediction for GlimmerHMM_glimmerT_28288-T1
Valid prediction for GeneMark_model.48867_t
Valid prediction for snap_scaffold_11-snap.2158-T1
Valid prediction for GlimmerHMM_glimmerT_28287-T1
Valid prediction for GlimmerHMM_glimmerT_28281-T1
Valid prediction for Augustus_model.g18866.t1
Valid prediction for Augustus_model.g18874.t1
Valid prediction for GeneMark_model.48844_t
Valid prediction for GlimmerHMM_glimmerT_28285-T1
Valid prediction for snap_scaffold_11-snap.2153-T1
Valid prediction for snap_scaffold_11-snap.2141-T1
Valid prediction for GlimmerHMM_glimmerT_28275-T1
Valid prediction for GeneMark_model.48829_t
Valid prediction for Augustus_model.g18878.t1
Valid prediction for snap_scaffold_11-snap.2151-T1
Valid prediction for GlimmerHMM_glimmerT_28286-T1
Valid prediction for snap_scaffold_11-snap.2132-T1
Valid prediction for GeneMark_model.48846_t
Valid prediction for GlimmerHMM_glimmerT_28283-T1
Valid prediction for Augustus_model.g18873.t1
Valid prediction for GeneMark_model.48852_t
Valid prediction for snap_scaffold_11-snap.2137-T1
Valid prediction for GeneMark_model.48826_t
Valid prediction for GeneMark_model.48822_t
Valid prediction for GeneMark_model.48854_t
Valid prediction for GlimmerHMM_glimmerT_28294-T1
Valid prediction for GeneMark_model.48834_t
Couldn't classify 112754, 112781
Couldn't classify 115238, 115414
Sorry, prediction pasa_asmbl_6912.p2 fails validation.
(CGC)	 CC	112754-112781	GT	AGG
(AGA)	 AG	113741-113925	GT	TGG
(TAC)	 AG	115238-115414	AA	ACA
-recovered pasa_asmbl_6912.p2, internal, 113741, 113925
Valid prediction for Augustus_model.g18872.t1
Valid prediction for Augustus_model.g18869.t1
Valid prediction for GlimmerHMM_glimmerT_28282-T1
Valid prediction for GlimmerHMM_glimmerT_28278-T1
Valid prediction for snap_scaffold_11-snap.2143-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25287, rend_intergenic: 23554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28682, rend_intergenic: 25287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36050, rend_intergenic: 31421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43799, rend_intergenic: 41434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52550, rend_intergenic: 45815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63821, rend_intergenic: 59113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72170, rend_intergenic: 65156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81965, rend_intergenic: 80437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102431, rend_intergenic: 91402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115664, rend_intergenic: 112604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133060, rend_intergenic: 119091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141540, rend_intergenic: 133359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153070, rend_intergenic: 148234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174192, rend_intergenic: 164375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179070
-exon list size: 781


building trellis

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71.5    
71.6    
71.8    
71.9    
72.0    
72.2    
72.3    
72.4    
72.5    
72.7    
72.8    
72.9    
73.1    
73.2    
73.3    
73.4    
73.6    
73.7    
73.8    
73.9    
74.1    
74.2    
74.3    
74.5    
74.6    
74.7    
74.8    
75.0    
75.1    
75.2    
75.4    
75.5    
75.6    
75.7    
75.9    
76.0    
76.1    
76.2    
76.4    
76.5    
76.6    
76.8    
76.9    
77.0    
77.1    
77.3    
77.4    
77.5    
77.7    
77.8    
77.9    
78.0    
78.2    
78.3    
78.4    
78.5    
78.7    
78.8    
78.9    
79.1    
79.2    
79.3    
79.4    
79.6    
79.7    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.7    
81.9    
82.0    
82.1    
82.2    
82.4    
82.5    
82.6    
82.8    
82.9    
83.0    
83.1    
83.3    
83.4    
83.5    
83.7    
83.8    
83.9    
84.0    
84.2    
84.3    
84.4    
84.5    
84.7    
84.8    
84.9    
85.1    
85.2    
85.3    
85.4    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.3    
86.5    
86.6    
86.7    
86.8    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.7    
87.9    
88.0    
88.1    
88.3    
88.4    
88.5    
88.6    
88.8    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.0    
90.2    
90.3    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.7    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 25287, rend_intergenic: 23554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28682, rend_intergenic: 25287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36050, rend_intergenic: 31421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43799, rend_intergenic: 41434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52550, rend_intergenic: 45815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63821, rend_intergenic: 59113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72170, rend_intergenic: 65156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81965, rend_intergenic: 80437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102431, rend_intergenic: 91402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115664, rend_intergenic: 112604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133060, rend_intergenic: 119091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141540, rend_intergenic: 133359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153070, rend_intergenic: 148234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174192, rend_intergenic: 164375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support