-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_8/scaffold_8_2940066-3167117

-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 snap_scaffold_8-snap.585-T1
Valid prediction for GeneMark_model.33981_t
Valid prediction for Augustus_model.g13291.t1
Valid prediction for snap_scaffold_8-snap.573-T1
Valid prediction for GeneMark_model.33984_t
Valid prediction for GlimmerHMM_glimmerT_19885-T1
Valid prediction for snap_scaffold_8-snap.567-T1
Valid prediction for snap_scaffold_8-snap.599-T1
Valid prediction for GeneMark_model.33962_t
Valid prediction for snap_scaffold_8-snap.571-T1
Sorry, intron length (9) is less than minimum required (10)
Couldn't classify 115508, 115631
Couldn't classify 119420, 119446
Sorry, prediction pasa_asmbl_51734.p1 fails validation.
(TTC)	 TG	115508-115631	GT	AGG
(GCC)	 AG	117807-117960	GT	AAG
(GAA)	 AG	118421-118544	GT	TGG
(ACG)	 AG	118646-118749	GT	AGG
(GTT)	 AG	118882-118978	GT	GTG
(TGC)	 AG	119420-119446	AT	GCA
-recovered pasa_asmbl_51734.p1, internal, 117807, 117960
-recovered pasa_asmbl_51734.p1, internal, 118421, 118544
-recovered pasa_asmbl_51734.p1, internal, 118646, 118749
-recovered pasa_asmbl_51734.p1, internal, 118882, 118978
Valid prediction for GlimmerHMM_glimmerT_19867-T1
Valid prediction for CodingQuarry_transcript_59463-T1
Valid prediction for GeneMark_model.33939_t
Valid prediction for GlimmerHMM_glimmerT_19874-T1
Valid prediction for GeneMark_model.33941_t
Valid prediction for GlimmerHMM_glimmerT_19884-T1
Valid prediction for GlimmerHMM_glimmerT_19875-T1
Valid prediction for GlimmerHMM_glimmerT_19873-T1
Valid prediction for GeneMark_model.33948_t
Valid prediction for Augustus_model.g13292.t1
Valid prediction for GeneMark_model.33973_t
Valid prediction for snap_scaffold_8-snap.605-T1
Valid prediction for snap_scaffold_8-snap.572-T1
Valid prediction for snap_scaffold_8-snap.593-T1
Valid prediction for GeneMark_model.33979_t
Valid prediction for GeneMark_model.33971_t
Valid prediction for snap_scaffold_8-snap.597-T1
Valid prediction for GeneMark_model.33952_t
Valid prediction for GeneMark_model.33937_t
Valid prediction for GlimmerHMM_glimmerT_19878-T1
Valid prediction for GeneMark_model.33994_t
Valid prediction for GeneMark_model.33975_t
Valid prediction for snap_scaffold_8-snap.587-T1
Valid prediction for snap_scaffold_8-snap.570-T1
Valid prediction for snap_scaffold_8-snap.604-T1
Valid prediction for GeneMark_model.33991_t
Valid prediction for GeneMark_model.33966_t
Valid prediction for Augustus_model.g13283.t1
Valid prediction for GeneMark_model.33956_t
Valid prediction for GeneMark_model.33977_t
Valid prediction for GeneMark_model.33946_t
Valid prediction for GeneMark_model.33969_t
Valid prediction for snap_scaffold_8-snap.564-T1
Valid prediction for GeneMark_model.33990_t
Valid prediction for GeneMark_model.33954_t
Valid prediction for snap_scaffold_8-snap.566-T1
Valid prediction for GeneMark_model.33992_t
Valid prediction for GlimmerHMM_glimmerT_19865-T1
Valid prediction for Augustus_model.g13293.t1
Valid prediction for GlimmerHMM_glimmerT_19869-T1
Valid prediction for GeneMark_model.33964_t
Valid prediction for GeneMark_model.33944_t
Valid prediction for snap_scaffold_8-snap.601-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.33987_t
Valid prediction for snap_scaffold_8-snap.592-T1
Valid prediction for snap_scaffold_8-snap.569-T1
Couldn't classify 109034, 109175
Sorry, prediction pasa_asmbl_51731.p1 fails validation.
(ATG)	 TA	108175-108428	GT	GGG
(GTT)	 AG	109034-109175	AT	CCA
-recovered pasa_asmbl_51731.p1, initial, 108175, 108428
Valid prediction for GlimmerHMM_glimmerT_19868-T1
Valid prediction for GeneMark_model.33950_t
Valid prediction for GeneMark_model.33942_t
Valid prediction for GeneMark_model.33989_t
Valid prediction for GeneMark_model.33959_t
Valid prediction for snap_scaffold_8-snap.582-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: -)Couldn't classify 60882, 60918
Sorry, prediction pasa_asmbl_52721.p1 fails validation.
(GAG)	 AC	60882-60918	GT	AGG
(ATG)	 AG	61100-61278	GT	AGG
(AAC)	 AG	62033-62160	GT	GGG
(ATC)	 AG	62564-62667	GT	AGG
(CCT)	 AG	62805-62983	GT	AGG
(GAA)	 AG	63502-63778	GT	AGG
(ACC)	 AG	64228-64323	GT	AAG
(CAG)	 AG	64519-64631	GT	AGG
(CAG)	 AG	64984-65132	GT	AGG
(GTT)	 AG	65250-65277	AC	GAA
add_exon() Sorry, pasa_asmbl_52721.p1 61100-61278-initial-1 is invalid.
-recovered pasa_asmbl_52721.p1, initial, 61100, 61278
-recovered pasa_asmbl_52721.p1, terminal, 65250, 65277
-recovered pasa_asmbl_52721.p1, internal, 61100, 61278
-recovered pasa_asmbl_52721.p1, internal, 62033, 62160
-recovered pasa_asmbl_52721.p1, internal, 62564, 62667
-recovered pasa_asmbl_52721.p1, internal, 62805, 62983
-recovered pasa_asmbl_52721.p1, internal, 63502, 63778
-recovered pasa_asmbl_52721.p1, internal, 64228, 64323
-recovered pasa_asmbl_52721.p1, internal, 64519, 64631
-recovered pasa_asmbl_52721.p1, internal, 64984, 65132
Valid prediction for Augustus_model.g13297.t1
Valid prediction for Augustus_model.g13296.t1
Valid prediction for GeneMark_model.33983_t
Valid prediction for GeneMark_model.33963_t
Valid prediction for GlimmerHMM_glimmerT_19883-T1
Valid prediction for GeneMark_model.33945_t
Valid prediction for snap_scaffold_8-snap.581-T1
Valid prediction for GeneMark_model.33974_t
Valid prediction for snap_scaffold_8-snap.594-T1
Valid prediction for snap_scaffold_8-snap.600-T1
Valid prediction for GeneMark_model.33978_t
Valid prediction for snap_scaffold_8-snap.598-T1
Valid prediction for Augustus_model.g13288.t1
Valid prediction for GeneMark_model.33980_t
Valid prediction for GlimmerHMM_glimmerT_19870-T1
Valid prediction for snap_scaffold_8-snap.583-T1
Valid prediction for GlimmerHMM_glimmerT_19879-T1
Valid prediction for Augustus_model.g13295.t1
Valid prediction for snap_scaffold_8-snap.591-T1
Valid prediction for snap_scaffold_8-snap.565-T1
Couldn't classify 186401, 186547
Sorry, prediction GeneMark_model.33947_t fails validation.
(ATG)	 CA	186139-186173	GT	GGG
(AAG)	 AG	186401-186547	GT	CTG
-recovered GeneMark_model.33947_t, initial, 186139, 186173
-recovered GeneMark_model.33947_t, internal, 186401, 186547
Valid prediction for snap_scaffold_8-snap.562-T1
Valid prediction for Augustus_model.g13294.t1
Valid prediction for Augustus_model.g13290.t1
Valid prediction for GlimmerHMM_glimmerT_19871-T1
Valid prediction for snap_scaffold_8-snap.584-T1
Valid prediction for snap_scaffold_8-snap.580-T1
Valid prediction for GeneMark_model.33940_t
Valid prediction for GlimmerHMM_glimmerT_19872-T1
Valid prediction for GeneMark_model.33967_t
Valid prediction for snap_scaffold_8-snap.602-T1
Valid prediction for GeneMark_model.33988_t
Valid prediction for GeneMark_model.33953_t
Valid prediction for snap_scaffold_8-snap.578-T1
Valid prediction for Augustus_model.g13284.t1
Valid prediction for GeneMark_model.33976_t
Valid prediction for GeneMark_model.33982_t
Valid prediction for snap_scaffold_8-snap.606-T1
Valid prediction for Augustus_model.g13285.t1
Valid prediction for snap_scaffold_8-snap.577-T1
Valid prediction for GlimmerHMM_glimmerT_19880-T1
Valid prediction for snap_scaffold_8-snap.596-T1
Valid prediction for GlimmerHMM_glimmerT_19866-T1
Valid prediction for Augustus_model.g13286.t1
Valid prediction for GeneMark_model.33968_t
Valid prediction for snap_scaffold_8-snap.603-T1
Valid prediction for GeneMark_model.33960_t
Valid prediction for snap_scaffold_8-snap.579-T1
Valid prediction for GeneMark_model.33961_t
Valid prediction for GeneMark_model.33986_t
Valid prediction for GlimmerHMM_glimmerT_19876-T1
Valid prediction for GeneMark_model.33958_t
Valid prediction for snap_scaffold_8-snap.575-T1
Valid prediction for GeneMark_model.33985_t
Valid prediction for GeneMark_model.33970_t
Valid prediction for snap_scaffold_8-snap.586-T1
Valid prediction for snap_scaffold_8-snap.595-T1
Valid prediction for snap_scaffold_8-snap.588-T1
Valid prediction for snap_scaffold_8-snap.589-T1
Couldn't classify 96664, 96768
Sorry, prediction pasa_asmbl_53617.p1 fails validation.
(ATG)	 AG	96366-96575	GT	ACG
(GAT)	 AG	96664-96768	TT	TCT
-recovered pasa_asmbl_53617.p1, initial, 96366, 96575
-recovered pasa_asmbl_53617.p1, internal, 96366, 96575
Valid prediction for snap_scaffold_8-snap.568-T1
Valid prediction for GlimmerHMM_glimmerT_19881-T1
Valid prediction for GeneMark_model.33972_t
Valid prediction for snap_scaffold_8-snap.590-T1
Valid prediction for snap_scaffold_8-snap.576-T1
Valid prediction for GeneMark_model.33938_t
Valid prediction for GeneMark_model.33936_t
Valid prediction for snap_scaffold_8-snap.563-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.33943_t
Couldn't classify 56067, 56148
Couldn't classify 56972, 57118
Sorry, prediction pasa_asmbl_52725.p1 fails validation.
(AGC)	 CA	56067-56148	GT	AGG
(ACG)	 AG	56533-56667	GT	AGG
(GGT)	 AG	56760-56845	GT	AGG
(GAC)	 AG	56972-57118	GT	TGG
-recovered pasa_asmbl_52725.p1, internal, 56533, 56667
-recovered pasa_asmbl_52725.p1, internal, 56760, 56845
-recovered pasa_asmbl_52725.p1, internal, 56972, 57118
Valid prediction for GlimmerHMM_glimmerT_19882-T1
Valid prediction for GeneMark_model.33951_t
Valid prediction for snap_scaffold_8-snap.607-T1
Valid prediction for GeneMark_model.33993_t
Valid prediction for GlimmerHMM_glimmerT_19877-T1
Valid prediction for Augustus_model.g13287.t1
Valid prediction for Augustus_model.g13289.t1
Valid prediction for GeneMark_model.33965_t
Valid prediction for GeneMark_model.33949_t
Valid prediction for snap_scaffold_8-snap.574-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11440, rend_intergenic: 6260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12590, rend_intergenic: 12365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16940, rend_intergenic: 12723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23287, rend_intergenic: 17225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46491, rend_intergenic: 23553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91031, rend_intergenic: 88455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113464, rend_intergenic: 109887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116527, rend_intergenic: 114198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151966, rend_intergenic: 143959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169587, rend_intergenic: 164335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197220, rend_intergenic: 187451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215051, rend_intergenic: 197368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 227052
-exon list size: 867


building trellis

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69.6    
69.7    
69.9    
70.0    
70.1    
70.2    
70.3    
70.4    
70.5    
70.7    
70.8    
70.9    
71.0    
71.1    
71.2    
71.3    
71.5    
71.6    
71.7    
71.8    
71.9    
72.0    
72.2    
72.3    
72.4    
72.5    
72.6    
72.7    
72.8    
73.0    
73.1    
73.2    
73.3    
73.4    
73.5    
73.6    
73.8    
73.9    
74.0    
74.1    
74.2    
74.3    
74.5    
74.6    
74.7    
74.8    
74.9    
75.0    
75.1    
75.3    
75.4    
75.5    
75.6    
75.7    
75.8    
75.9    
76.1    
76.2    
76.3    
76.4    
76.5    
76.6    
76.8    
76.9    
77.0    
77.1    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
77.9    
78.0    
78.1    
78.3    
78.4    
78.5    
78.6    
78.7    
78.8    
78.9    
79.1    
79.2    
79.3    
79.4    
79.5    
79.6    
79.7    
79.9    
80.0    
80.1    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
80.9    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.7    
81.8    
81.9    
82.0    
82.2    
82.3    
82.4    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.2    
83.3    
83.4    
83.5    
83.7    
83.8    
83.9    
84.0    
84.1    
84.2    
84.3    
84.5    
84.6    
84.7    
84.8    
84.9    
85.0    
85.2    
85.3    
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    
87.2    
87.3    
87.5    
87.6    
87.7    
87.8    
87.9    
88.0    
88.1    
88.3    
88.4    
88.5    
88.6    
88.7    
88.8    
89.0    
89.1    
89.2    
89.3    
89.4    
89.5    
89.6    
89.8    
89.9    
90.0    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.6    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.1    
93.2    
93.3    
93.4    
93.6    
93.7    
93.8    
93.9    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.7    
94.8    
94.9    
95.1    
95.2    
95.3    
95.4    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.2    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.7    
97.8    
97.9    
98.0    
98.2    
98.3    
98.4    
98.5    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.7    
99.8    
99.9    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 11440, rend_intergenic: 6260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12590, rend_intergenic: 12365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16940, rend_intergenic: 12723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23287, rend_intergenic: 17225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46491, rend_intergenic: 23553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91031, rend_intergenic: 88455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113464, rend_intergenic: 109887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116527, rend_intergenic: 114198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151966, rend_intergenic: 143959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169587, rend_intergenic: 164335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197220, rend_intergenic: 187451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215051, rend_intergenic: 197368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support