-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_1862917-2090504

-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 GlimmerHMM_glimmerT_54985-T1
Valid prediction for snap_scaffold_25-snap.422-T1
Valid prediction for GeneMark_model.95835_t
Valid prediction for GlimmerHMM_glimmerT_54969-T1
Valid prediction for GeneMark_model.95833_t
Valid prediction for GlimmerHMM_glimmerT_54982-T1
Valid prediction for snap_scaffold_25-snap.402-T1
Valid prediction for snap_scaffold_25-snap.417-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.95856_t
Valid prediction for snap_scaffold_25-snap.397-T1
Valid prediction for snap_scaffold_25-snap.412-T1
Valid prediction for snap_scaffold_25-snap.393-T1
Valid prediction for GeneMark_model.95863_t
Valid prediction for GeneMark_model.95846_t
Valid prediction for snap_scaffold_25-snap.405-T1
Valid prediction for snap_scaffold_25-snap.387-T1
Couldn't classify 123485, 123689
Sorry, prediction GeneMark_model.95858_t fails validation.
(ACC)	 AG	123485-123689	GT	GAG
(ATA)	 AG	125300-125312	AG	AAA
-recovered GeneMark_model.95858_t, terminal, 125300, 125312
-recovered GeneMark_model.95858_t, internal, 123485, 123689
Valid prediction for GlimmerHMM_glimmerT_54981-T1
Valid prediction for GlimmerHMM_glimmerT_54965-T1
Valid prediction for GeneMark_model.95844_t
Valid prediction for GeneMark_model.95852_t
Valid prediction for snap_scaffold_25-snap.395-T1
Valid prediction for GeneMark_model.95880_t
Valid prediction for GeneMark_model.95854_t
Valid prediction for snap_scaffold_25-snap.391-T1
Valid prediction for GlimmerHMM_glimmerT_54977-T1
Valid prediction for GeneMark_model.95871_t
Valid prediction for GeneMark_model.95840_t
Valid prediction for snap_scaffold_25-snap.409-T1
Valid prediction for GeneMark_model.95872_t
Valid prediction for snap_scaffold_25-snap.418-T1
Valid prediction for GlimmerHMM_glimmerT_54959-T1
Valid prediction for snap_scaffold_25-snap.377-T1
Valid prediction for GeneMark_model.95861_t
Valid prediction for GeneMark_model.95866_t
Valid prediction for snap_scaffold_25-snap.384-T1
Valid prediction for snap_scaffold_25-snap.374-T1
Valid prediction for snap_scaffold_25-snap.389-T1
Valid prediction for GlimmerHMM_glimmerT_54968-T1
Valid prediction for snap_scaffold_25-snap.383-T1
Valid prediction for GlimmerHMM_glimmerT_54984-T1
Valid prediction for snap_scaffold_25-snap.420-T1
Valid prediction for GeneMark_model.95830_t
Valid prediction for GeneMark_model.95870_t
Valid prediction for snap_scaffold_25-snap.381-T1
Valid prediction for GeneMark_model.95877_t
Valid prediction for snap_scaffold_25-snap.378-T1
Valid prediction for GlimmerHMM_glimmerT_54973-T1
Valid prediction for GeneMark_model.95879_t
Couldn't classify 114019, 114043
Sorry, prediction GeneMark_model.95857_t fails validation.
(ATG)	 AT	112464-112476	GT	GGG
(GAA)	 AG	112666-112705	GT	GAG
(GGA)	 AG	112807-112815	GT	CTG
(GAG)	 AG	112841-112858	GT	CTG
(GTG)	 AG	112884-112901	GT	CTG
(GAA)	 AG	113016-113033	GT	CTG
(AAG)	 AG	113059-113076	GT	CTG
(GGA)	 AG	113763-113771	GT	GTG
(GGA)	 AG	113795-113917	GT	GAG
(AGG)	 AG	113946-113993	GT	GGG
(AAG)	 AG	114019-114043	GT	ATG
-recovered GeneMark_model.95857_t, initial, 112464, 112476
-recovered GeneMark_model.95857_t, internal, 112666, 112705
-recovered GeneMark_model.95857_t, internal, 112807, 112815
-recovered GeneMark_model.95857_t, internal, 112841, 112858
-recovered GeneMark_model.95857_t, internal, 112884, 112901
-recovered GeneMark_model.95857_t, internal, 113016, 113033
-recovered GeneMark_model.95857_t, internal, 113059, 113076
-recovered GeneMark_model.95857_t, internal, 113763, 113771
-recovered GeneMark_model.95857_t, internal, 113795, 113917
-recovered GeneMark_model.95857_t, internal, 113946, 113993
-recovered GeneMark_model.95857_t, internal, 114019, 114043
Valid prediction for GeneMark_model.95873_t
Valid prediction for snap_scaffold_25-snap.379-T1
Valid prediction for GlimmerHMM_glimmerT_54966-T1
Valid prediction for GeneMark_model.95847_t
Valid prediction for snap_scaffold_25-snap.408-T1
Valid prediction for snap_scaffold_25-snap.373-T1
Valid prediction for GeneMark_model.95867_t
Valid prediction for Augustus_model.g36708.t1
Valid prediction for GlimmerHMM_glimmerT_54971-T1
Valid prediction for GeneMark_model.95838_t
Valid prediction for snap_scaffold_25-snap.390-T1
Valid prediction for snap_scaffold_25-snap.423-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 snap_scaffold_25-snap.416-T1
Valid prediction for snap_scaffold_25-snap.380-T1
Valid prediction for snap_scaffold_25-snap.382-T1
Valid prediction for GeneMark_model.95876_t
Valid prediction for GlimmerHMM_glimmerT_54976-T1
Valid prediction for GeneMark_model.95869_t
Valid prediction for GeneMark_model.95882_t
Valid prediction for GlimmerHMM_glimmerT_54983-T1
Valid prediction for GeneMark_model.95831_t
Valid prediction for GeneMark_model.95837_t
Valid prediction for snap_scaffold_25-snap.386-T1
Valid prediction for snap_scaffold_25-snap.415-T1
Valid prediction for snap_scaffold_25-snap.411-T1
Valid prediction for snap_scaffold_25-snap.385-T1
Valid prediction for snap_scaffold_25-snap.396-T1
Valid prediction for snap_scaffold_25-snap.414-T1
Valid prediction for GeneMark_model.95843_t
Valid prediction for GeneMark_model.95853_t
Valid prediction for GeneMark_model.95836_t
Valid prediction for GeneMark_model.95881_t
Couldn't classify 217573, 217666
Couldn't classify 220402, 220557
Sorry, prediction pasa_asmbl_34034.p1 fails validation.
(GGG)	 AA	217573-217666	GT	TGG
(ACA)	 AG	218067-218179	GT	AGG
(AAG)	 AG	218710-218870	GT	AGG
(GGC)	 AG	219105-219238	GT	AGG
(AGA)	 AG	219974-220122	GT	AGG
(GCC)	 AG	220402-220557	CT	GCC
-recovered pasa_asmbl_34034.p1, internal, 218067, 218179
-recovered pasa_asmbl_34034.p1, internal, 218710, 218870
-recovered pasa_asmbl_34034.p1, internal, 219105, 219238
-recovered pasa_asmbl_34034.p1, internal, 219974, 220122
Valid prediction for GeneMark_model.95848_t
Valid prediction for snap_scaffold_25-snap.401-T1
Valid prediction for GeneMark_model.95839_t
Valid prediction for Augustus_model.g36705.t1
Valid prediction for GlimmerHMM_glimmerT_54974-T1
Valid prediction for GeneMark_model.95829_t
Valid prediction for snap_scaffold_25-snap.399-T1
Valid prediction for GeneMark_model.95865_t
Valid prediction for GlimmerHMM_glimmerT_54967-T1
Valid prediction for GeneMark_model.95855_t
Valid prediction for GeneMark_model.95862_t
Valid prediction for GlimmerHMM_glimmerT_54960-T1
Valid prediction for snap_scaffold_25-snap.419-T1
Valid prediction for snap_scaffold_25-snap.424-T1
Valid prediction for snap_scaffold_25-snap.400-T1
Valid prediction for snap_scaffold_25-snap.388-T1
Valid prediction for GeneMark_model.95828_t
Valid prediction for snap_scaffold_25-snap.425-T1
Valid prediction for snap_scaffold_25-snap.406-T1
Valid prediction for GlimmerHMM_glimmerT_54958-T1
Valid prediction for snap_scaffold_25-snap.394-T1
Valid prediction for GlimmerHMM_glimmerT_54964-T1
Valid prediction for GlimmerHMM_glimmerT_54970-T1
Valid prediction for snap_scaffold_25-snap.404-T1
Valid prediction for GlimmerHMM_glimmerT_54961-T1
Valid prediction for Augustus_model.g36706.t1
Valid prediction for GeneMark_model.95832_t
Valid prediction for snap_scaffold_25-snap.407-T1
Valid prediction for snap_scaffold_25-snap.403-T1
Valid prediction for GeneMark_model.95851_t
Valid prediction for Augustus_model.g36704.t1
Valid prediction for pasa_asmbl_34037.p2
Valid prediction for GlimmerHMM_glimmerT_54978-T1
Valid prediction for Augustus_model.g36707.t1
Valid prediction for GeneMark_model.95849_t
Valid prediction for GlimmerHMM_glimmerT_54963-T1
Valid prediction for snap_scaffold_25-snap.398-T1
Valid prediction for GeneMark_model.95834_t
Valid prediction for snap_scaffold_25-snap.413-T1
Valid prediction for Augustus_model.g36709.t1
Valid prediction for GeneMark_model.95874_t
Valid prediction for GeneMark_model.95841_t
Valid prediction for snap_scaffold_25-snap.375-T1
Valid prediction for snap_scaffold_25-snap.376-T1
Valid prediction for GeneMark_model.95864_t
Valid prediction for GeneMark_model.95845_t
Valid prediction for GlimmerHMM_glimmerT_54979-T1
Valid prediction for GeneMark_model.95859_t
Valid prediction for GlimmerHMM_glimmerT_54975-T1
Valid prediction for GeneMark_model.95860_t
Valid prediction for GeneMark_model.95850_t
Valid prediction for GeneMark_model.95868_t
Valid prediction for snap_scaffold_25-snap.392-T1
Valid prediction for GlimmerHMM_glimmerT_54986-T1
Valid prediction for snap_scaffold_25-snap.372-T1
Valid prediction for GeneMark_model.95842_t
Valid prediction for GeneMark_model.95875_t
Valid prediction for GlimmerHMM_glimmerT_54980-T1
Valid prediction for snap_scaffold_25-snap.421-T1
Valid prediction for snap_scaffold_25-snap.410-T1
Valid prediction for GeneMark_model.95878_t
Valid prediction for GlimmerHMM_glimmerT_54972-T1
Valid prediction for GlimmerHMM_glimmerT_54962-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7646, rend_intergenic: 3755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15877, rend_intergenic: 8328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27732, rend_intergenic: 27323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30986, rend_intergenic: 28331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34108, rend_intergenic: 32745  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41437, rend_intergenic: 35891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54247, rend_intergenic: 42880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78087, rend_intergenic: 76841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78256, rend_intergenic: 78230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81069, rend_intergenic: 78278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83499, rend_intergenic: 82859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131930, rend_intergenic: 84312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154842, rend_intergenic: 135030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159145, rend_intergenic: 158887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163423, rend_intergenic: 162669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172539, rend_intergenic: 172416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177630, rend_intergenic: 175754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203373, rend_intergenic: 202168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223234, rend_intergenic: 214637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 227588
-exon list size: 838


building trellis

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71.2    
71.3    
71.4    
71.5    
71.7    
71.8    
71.9    
72.0    
72.1    
72.3    
72.4    
72.5    
72.6    
72.7    
72.9    
73.0    
73.1    
73.2    
73.3    
73.5    
73.6    
73.7    
73.8    
73.9    
74.0    
74.2    
74.3    
74.4    
74.5    
74.6    
74.8    
74.9    
75.0    
75.1    
75.2    
75.4    
75.5    
75.6    
75.7    
75.8    
76.0    
76.1    
76.2    
76.3    
76.4    
76.5    
76.7    
76.8    
76.9    
77.0    
77.1    
77.3    
77.4    
77.5    
77.6    
77.7    
77.9    
78.0    
78.1    
78.2    
78.3    
78.5    
78.6    
78.7    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.5    
79.6    
79.8    
79.9    
80.0    
80.1    
80.2    
80.4    
80.5    
80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.3    
81.4    
81.5    
81.7    
81.8    
81.9    
82.0    
82.1    
82.3    
82.4    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.8    
83.9    
84.0    
84.2    
84.3    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.1    
85.2    
85.4    
85.5    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.3    
86.4    
86.5    
86.7    
86.8    
86.9    
87.0    
87.1    
87.3    
87.4    
87.5    
87.6    
87.7    
87.9    
88.0    
88.1    
88.2    
88.3    
88.5    
88.6    
88.7    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.6    
89.8    
89.9    
90.0    
90.1    
90.2    
90.4    
90.5    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.6    
92.7    
92.9    
93.0    
93.1    
93.2    
93.3    
93.5    
93.6    
93.7    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 7646, rend_intergenic: 3755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15877, rend_intergenic: 8328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27732, rend_intergenic: 27323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30986, rend_intergenic: 28331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34108, rend_intergenic: 32745  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41437, rend_intergenic: 35891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54247, rend_intergenic: 42880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78087, rend_intergenic: 76841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78256, rend_intergenic: 78230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81069, rend_intergenic: 78278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83499, rend_intergenic: 82859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131930, rend_intergenic: 84312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154842, rend_intergenic: 135030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159145, rend_intergenic: 158887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163423, rend_intergenic: 162669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172539, rend_intergenic: 172416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177630, rend_intergenic: 175754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203373, rend_intergenic: 202168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223234, rend_intergenic: 214637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support