-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_1799091-1970687

-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_14443-T1
Valid prediction for Augustus_model.g9636.t1
Valid prediction for Augustus_model.g9634.t1
Valid prediction for GeneMark_model.24290_t
Valid prediction for GeneMark_model.24332_t
Valid prediction for GeneMark_model.24270_t
Valid prediction for snap_scaffold_6-snap.424-T1
Valid prediction for GeneMark_model.24322_t
Valid prediction for snap_scaffold_6-snap.427-T1
Valid prediction for GlimmerHMM_glimmerT_14433-T1
Valid prediction for GeneMark_model.24273_t
Valid prediction for GeneMark_model.24302_t
Valid prediction for GeneMark_model.24281_t
Valid prediction for snap_scaffold_6-snap.445-T1
Valid prediction for GeneMark_model.24309_t
Valid prediction for snap_scaffold_6-snap.441-T1
Valid prediction for snap_scaffold_6-snap.444-T1
Valid prediction for GeneMark_model.24292_t
Valid prediction for snap_scaffold_6-snap.423-T1
Valid prediction for Augustus_model.g9630.t1
Valid prediction for snap_scaffold_6-snap.419-T1
Valid prediction for GeneMark_model.24295_t
Valid prediction for snap_scaffold_6-snap.434-T1
Valid prediction for GlimmerHMM_glimmerT_14431-T1
Couldn't classify 36676, 36740
Sorry, prediction CodingQuarry_transcript_54792-T1 fails validation.
(ATG)	 AC	36405-36459	GT	AGG
(GAT)	 AG	36676-36740	GG	GAG
(AAG)	 AG	36768-36860	AA	GAA
-recovered CodingQuarry_transcript_54792-T1, initial, 36405, 36459
-recovered CodingQuarry_transcript_54792-T1, terminal, 36768, 36860
Valid prediction for GeneMark_model.24279_t
Valid prediction for GeneMark_model.24304_t
Valid prediction for GeneMark_model.24286_t
Valid prediction for GeneMark_model.24315_t
Valid prediction for GlimmerHMM_glimmerT_14439-T1
Couldn't classify 47354, 47420
Sorry, prediction pasa_asmbl_46695.p1 fails validation.
(ATC)	 CC	47354-47420	GT	AGG
(CCT)	 AG	47514-47648	GT	AAG
(GAG)	 AG	47856-48139	TA	AGT
-recovered pasa_asmbl_46695.p1, terminal, 47856, 48139
-recovered pasa_asmbl_46695.p1, internal, 47514, 47648
Valid prediction for GeneMark_model.24313_t
Valid prediction for GeneMark_model.24274_t
Valid prediction for Augustus_model.g9624.t1
Valid prediction for GlimmerHMM_glimmerT_14438-T1
Valid prediction for GeneMark_model.24266_t
Valid prediction for GeneMark_model.24284_t
Valid prediction for GlimmerHMM_glimmerT_14449-T1
Valid prediction for GlimmerHMM_glimmerT_14432-T1
Valid prediction for CodingQuarry_transcript_54793-T1
Valid prediction for GeneMark_model.24319_t
Valid prediction for Augustus_model.g9629.t1
Valid prediction for snap_scaffold_6-snap.440-T1
Valid prediction for Augustus_model.g9642.t1
Valid prediction for GeneMark_model.24311_t
Valid prediction for GlimmerHMM_glimmerT_14436-T1
Valid prediction for GeneMark_model.24277_t
Couldn't classify 85704, 86273
Sorry, prediction pasa_asmbl_46697.p1 fails validation.
(GGT)	 GA	85704-86273	GA	TGG
Valid prediction for GeneMark_model.24287_t
Valid prediction for GeneMark_model.24276_t
Valid prediction for GlimmerHMM_glimmerT_14435-T1
Couldn't classify 37178, 37538
Sorry, prediction pasa_asmbl_46693.p1 fails validation.
(TCC)	 CC	37178-37538	GT	TGG
(TGG)	 AG	38662-38722	GT	AGG
(GGA)	 AG	39252-39365	GT	AGG
(CTT)	 AG	39697-39847	CC	GAC
-recovered pasa_asmbl_46693.p1, terminal, 39697, 39847
-recovered pasa_asmbl_46693.p1, internal, 38662, 38722
-recovered pasa_asmbl_46693.p1, internal, 39252, 39365
Valid prediction for snap_scaffold_6-snap.425-T1
Valid prediction for Augustus_model.g9631.t1
Valid prediction for GeneMark_model.24328_t
Valid prediction for GeneMark_model.24317_t
Valid prediction for GeneMark_model.24288_t
Valid prediction for snap_scaffold_6-snap.418-T1
Valid prediction for snap_scaffold_6-snap.429-T1
Couldn't classify 42521, 42610
Couldn't classify 46814, 46851
Sorry, prediction pasa_asmbl_46694.p1 fails validation.
(CAG)	 AC	42521-42610	GT	TGG
(GAT)	 AG	43689-43733	GT	TGG
(GGG)	 AG	43931-44040	GT	GAG
(TAT)	 AG	46447-46619	GT	CAG
(ATG)	 AG	46814-46851	AA	AGA
-recovered pasa_asmbl_46694.p1, internal, 43689, 43733
-recovered pasa_asmbl_46694.p1, internal, 43931, 44040
-recovered pasa_asmbl_46694.p1, internal, 46447, 46619
Valid prediction for snap_scaffold_6-snap.437-T1
Valid prediction for GlimmerHMM_glimmerT_14442-T1
Valid prediction for snap_scaffold_6-snap.430-T1
Valid prediction for snap_scaffold_6-snap.412-T1
Valid prediction for GlimmerHMM_glimmerT_14447-T1
Valid prediction for GeneMark_model.24300_t
Valid prediction for snap_scaffold_6-snap.416-T1
Valid prediction for GeneMark_model.24324_t
Valid prediction for GeneMark_model.24307_t
Valid prediction for snap_scaffold_6-snap.413-T1
Valid prediction for GlimmerHMM_glimmerT_14429-T1
Valid prediction for Augustus_model.g9626.t1
Valid prediction for Augustus_model.g9632.t1
Valid prediction for GlimmerHMM_glimmerT_14451-T1
Valid prediction for GeneMark_model.24326_t
Valid prediction for Augustus_model.g9625.t1
Couldn't classify 36676, 37093
Sorry, prediction pasa_asmbl_47931.p1 fails validation.
(ATG)	 AC	32951-33006	GT	AGG
(CCC)	 AG	33304-33462	GT	CGG
(TGG)	 AG	34117-34180	GT	CTG
(GGG)	 AG	34557-34640	GT	GTG
(GGC)	 AG	34749-34847	GT	AGG
(GTG)	 AG	36092-36144	GT	AGG
(CCC)	 AG	36358-36459	GT	AGG
(GAT)	 AG	36676-37093	CC	TGC
-recovered pasa_asmbl_47931.p1, initial, 32951, 33006
-recovered pasa_asmbl_47931.p1, internal, 33304, 33462
-recovered pasa_asmbl_47931.p1, internal, 34117, 34180
-recovered pasa_asmbl_47931.p1, internal, 34557, 34640
-recovered pasa_asmbl_47931.p1, internal, 34749, 34847
-recovered pasa_asmbl_47931.p1, internal, 36092, 36144
-recovered pasa_asmbl_47931.p1, internal, 36358, 36459
Valid prediction for Augustus_model.g9635.t1
Valid prediction for Augustus_model.g9633.t1
Valid prediction for Augustus_model.g9640.t1
Valid prediction for GlimmerHMM_glimmerT_14437-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 GeneMark_model.24318_t
Valid prediction for GlimmerHMM_glimmerT_14444-T1
Valid prediction for GeneMark_model.24272_t
Valid prediction for snap_scaffold_6-snap.428-T1
Valid prediction for GeneMark_model.24306_t
Valid prediction for GlimmerHMM_glimmerT_14434-T1
Valid prediction for GeneMark_model.24289_t
Valid prediction for GeneMark_model.24301_t
Valid prediction for GlimmerHMM_glimmerT_14445-T1
Valid prediction for GlimmerHMM_glimmerT_14448-T1
Valid prediction for GeneMark_model.24330_t
Valid prediction for snap_scaffold_6-snap.435-T1
Valid prediction for GeneMark_model.24310_t
Valid prediction for snap_scaffold_6-snap.414-T1
Valid prediction for Augustus_model.g9644.t1
Valid prediction for Augustus_model.g9641.t1
Valid prediction for GeneMark_model.24280_t
Valid prediction for GeneMark_model.24308_t
Valid prediction for GlimmerHMM_glimmerT_14430-T1
Valid prediction for snap_scaffold_6-snap.426-T1
Valid prediction for GeneMark_model.24299_t
Valid prediction for GeneMark_model.24269_t
Valid prediction for Augustus_model.g9627.t1
Valid prediction for GeneMark_model.24265_t
Valid prediction for GeneMark_model.24278_t
Valid prediction for snap_scaffold_6-snap.422-T1
Valid prediction for GeneMark_model.24275_t
Valid prediction for GeneMark_model.24327_t
Valid prediction for GeneMark_model.24267_t
Valid prediction for GeneMark_model.24283_t
Valid prediction for GeneMark_model.24329_t
Valid prediction for snap_scaffold_6-snap.421-T1
Valid prediction for GlimmerHMM_glimmerT_14440-T1
Valid prediction for GeneMark_model.24334_t
Valid prediction for Augustus_model.g9637.t1
Valid prediction for snap_scaffold_6-snap.443-T1
Valid prediction for GeneMark_model.24271_t
Valid prediction for GeneMark_model.24333_t
Valid prediction for snap_scaffold_6-snap.436-T1
Valid prediction for GeneMark_model.24325_t
Valid prediction for GeneMark_model.24297_t
Valid prediction for snap_scaffold_6-snap.439-T1
Valid prediction for GeneMark_model.24285_t
Valid prediction for GlimmerHMM_glimmerT_14441-T1
Valid prediction for snap_scaffold_6-snap.432-T1
Valid prediction for GeneMark_model.24282_t
Valid prediction for snap_scaffold_6-snap.411-T1
Valid prediction for Augustus_model.g9628.t1
Valid prediction for Augustus_model.g9639.t1
Valid prediction for snap_scaffold_6-snap.438-T1
Valid prediction for snap_scaffold_6-snap.433-T1
Valid prediction for GeneMark_model.24294_t
Valid prediction for snap_scaffold_6-snap.417-T1
Valid prediction for GeneMark_model.24321_t
Valid prediction for GeneMark_model.24314_t
Valid prediction for GeneMark_model.24291_t
Valid prediction for GeneMark_model.24293_t
Valid prediction for snap_scaffold_6-snap.431-T1
Valid prediction for GlimmerHMM_glimmerT_14452-T1
Valid prediction for GlimmerHMM_glimmerT_14450-T1
Valid prediction for GeneMark_model.24303_t
Valid prediction for snap_scaffold_6-snap.446-T1
Valid prediction for snap_scaffold_6-snap.420-T1
Valid prediction for Augustus_model.g9643.t1
Valid prediction for snap_scaffold_6-snap.442-T1
Valid prediction for GeneMark_model.24316_t
Valid prediction for Augustus_model.g9638.t1
Valid prediction for GeneMark_model.24312_t
Valid prediction for GlimmerHMM_glimmerT_14446-T1
Valid prediction for snap_scaffold_6-snap.415-T1
Valid prediction for GeneMark_model.24305_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4428, rend_intergenic: 3521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11425, rend_intergenic: 8309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14774, rend_intergenic: 12083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27612, rend_intergenic: 14865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32650, rend_intergenic: 28448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48139, rend_intergenic: 33279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59067, rend_intergenic: 56799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67033, rend_intergenic: 59121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73254, rend_intergenic: 67037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85777, rend_intergenic: 73566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115074, rend_intergenic: 91271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119121, rend_intergenic: 115088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124852, rend_intergenic: 119280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136665, rend_intergenic: 126877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139727, rend_intergenic: 137033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151803, rend_intergenic: 144269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159041, rend_intergenic: 152711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164035, rend_intergenic: 159177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165694, rend_intergenic: 164250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171597
-exon list size: 915


building trellis

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63.4    
63.5    
63.6    
63.7    
63.8    
63.9    
64.0    
64.1    
64.2    
64.3    
64.4    
64.6    
64.7    
64.8    
64.9    
65.0    
65.1    
65.2    
65.3    
65.4    
65.5    
65.6    
65.8    
65.9    
66.0    
66.1    
66.2    
66.3    
66.4    
66.5    
66.6    
66.7    
66.8    
67.0    
67.1    
67.2    
67.3    
67.4    
67.5    
67.6    
67.7    
67.8    
67.9    
68.0    
68.2    
68.3    
68.4    
68.5    
68.6    
68.7    
68.8    
68.9    
69.0    
69.1    
69.2    
69.4    
69.5    
69.6    
69.7    
69.8    
69.9    
70.0    
70.1    
70.2    
70.3    
70.4    
70.6    
70.7    
70.8    
70.9    
71.0    
71.1    
71.2    
71.3    
71.4    
71.5    
71.6    
71.8    
71.9    
72.0    
72.1    
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    
73.7    
73.8    
73.9    
74.0    
74.2    
74.3    
74.4    
74.5    
74.6    
74.7    
74.8    
74.9    
75.0    
75.1    
75.2    
75.4    
75.5    
75.6    
75.7    
75.8    
75.9    
76.0    
76.1    
76.2    
76.3    
76.4    
76.6    
76.7    
76.8    
76.9    
77.0    
77.1    
77.2    
77.3    
77.4    
77.5    
77.6    
77.8    
77.9    
78.0    
78.1    
78.2    
78.3    
78.4    
78.5    
78.6    
78.7    
78.8    
79.0    
79.1    
79.2    
79.3    
79.4    
79.5    
79.6    
79.7    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.5    
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    
82.1    
82.2    
82.3    
82.4    
82.6    
82.7    
82.8    
82.9    
83.0    
83.1    
83.2    
83.3    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.1    
84.2    
84.3    
84.4    
84.5    
84.6    
84.7    
84.8    
85.0    
85.1    
85.2    
85.3    
85.4    
85.5    
85.6    
85.7    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.5    
86.6    
86.7    
86.8    
86.9    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.7    
87.8    
87.9    
88.0    
88.1    
88.2    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.0    
89.1    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.2    
90.3    
90.4    
90.5    
90.6    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.4    
91.5    
91.6    
91.7    
91.8    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.6    
92.7    
92.8    
92.9    
93.0    
93.1    
93.2    
93.3    
93.5    
93.6    
93.7    
93.8    
93.9    
94.0    
94.1    
94.2    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.0    
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    
96.6    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.4    
97.5    
97.6    
97.7    
97.8    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.6    
98.7    
98.8    
98.9    
99.0    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.8    
99.9    
-found 44 predictions from path traversal
Error with prediction: snap lend_intergenic: 4428, rend_intergenic: 3521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11425, rend_intergenic: 8309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14774, rend_intergenic: 12083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27612, rend_intergenic: 14865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32650, rend_intergenic: 28448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48139, rend_intergenic: 33279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59067, rend_intergenic: 56799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67033, rend_intergenic: 59121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73254, rend_intergenic: 67037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85777, rend_intergenic: 73566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115074, rend_intergenic: 91271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119121, rend_intergenic: 115088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124852, rend_intergenic: 119280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136665, rend_intergenic: 126877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139727, rend_intergenic: 137033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151803, rend_intergenic: 144269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159041, rend_intergenic: 152711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164035, rend_intergenic: 159177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165694, rend_intergenic: 164250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support