-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_1652692-1849998

-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 HiQ_model.g27258.t1
Valid prediction for CodingQuarry_transcript_21824-T1
Valid prediction for GlimmerHMM_glimmerT_40680-T1
Valid prediction for GeneMark_model.70068_t
Valid prediction for CodingQuarry_transcript_21823-T1
Valid prediction for Augustus_model.g27261.t1
Valid prediction for CodingQuarry_transcript_21826-T1
Valid prediction for GlimmerHMM_glimmerT_40693-T1
Valid prediction for CodingQuarry_transcript_21821-T1
Couldn't classify 154164, 154269
Sorry, prediction pasa_asmbl_17758.p1 fails validation.
(ATG)	 GG	152381-152457	GT	CGG
(GGT)	 AG	152662-152817	GT	AGG
(GCA)	 AG	153009-153105	GT	AGG
(GTC)	 AG	153247-153350	GT	AGG
(ATT)	 AG	153516-153694	GT	TGG
(GAC)	 AG	153836-153995	GT	AGG
(GTA)	 AG	154164-154269	GC	CCG
-recovered pasa_asmbl_17758.p1, initial, 152381, 152457
-recovered pasa_asmbl_17758.p1, terminal, 152662, 152817
-recovered pasa_asmbl_17758.p1, internal, 152662, 152817
-recovered pasa_asmbl_17758.p1, internal, 153009, 153105
-recovered pasa_asmbl_17758.p1, internal, 153247, 153350
-recovered pasa_asmbl_17758.p1, internal, 153516, 153694
-recovered pasa_asmbl_17758.p1, internal, 153836, 153995
-recovered pasa_asmbl_17758.p1, internal, 154164, 154269
Valid prediction for GeneMark_model.70079_t
Valid prediction for GlimmerHMM_glimmerT_40695-T1
Valid prediction for GeneMark_model.70077_t
Valid prediction for GeneMark_model.70052_t
Valid prediction for GeneMark_model.70087_t
Valid prediction for GlimmerHMM_glimmerT_40705-T1
Valid prediction for snap_scaffold_17-snap.368-T1
Valid prediction for GeneMark_model.70046_t
Valid prediction for GeneMark_model.70067_t
Valid prediction for Augustus_model.g27262.t1
Valid prediction for GlimmerHMM_glimmerT_40691-T1
Valid prediction for GeneMark_model.70048_t
Valid prediction for snap_scaffold_17-snap.367-T1
Valid prediction for snap_scaffold_17-snap.371-T1
Valid prediction for GeneMark_model.70083_t
Valid prediction for Augustus_model.g27264.t1
Valid prediction for GeneMark_model.70085_t
Valid prediction for HiQ_model.g27252.t1
Valid prediction for GeneMark_model.70055_t
Valid prediction for GeneMark_model.70062_t
Valid prediction for HiQ_model.g27267.t1
Valid prediction for GlimmerHMM_glimmerT_40682-T1
Valid prediction for pasa_asmbl_17753.p1
Valid prediction for GlimmerHMM_glimmerT_40699-T1
Valid prediction for GlimmerHMM_glimmerT_40702-T1
Couldn't classify 154504, 154537
Couldn't classify 161363, 161488
Sorry, prediction pasa_asmbl_17760.p1 fails validation.
(ACC)	 GC	154504-154537	GT	AGG
(GCC)	 AG	156506-156765	GT	AGG
(GAG)	 AG	156955-157125	GT	AGG
(GAC)	 AG	157544-157673	GT	AGG
(TGC)	 AG	158149-158256	GT	AGG
(GCC)	 AG	159159-159298	GT	TGG
(AAC)	 AG	160223-160383	GT	AGG
(CCC)	 AG	160833-160972	GT	CTG
(GTG)	 AG	161137-161255	GT	AGG
(CTG)	 AG	161363-161488	GT	GGG
-recovered pasa_asmbl_17760.p1, internal, 156506, 156765
-recovered pasa_asmbl_17760.p1, internal, 156955, 157125
-recovered pasa_asmbl_17760.p1, internal, 157544, 157673
-recovered pasa_asmbl_17760.p1, internal, 158149, 158256
-recovered pasa_asmbl_17760.p1, internal, 159159, 159298
-recovered pasa_asmbl_17760.p1, internal, 160223, 160383
-recovered pasa_asmbl_17760.p1, internal, 160833, 160972
-recovered pasa_asmbl_17760.p1, internal, 161137, 161255
-recovered pasa_asmbl_17760.p1, internal, 161363, 161488
Valid prediction for GlimmerHMM_glimmerT_40685-T1
Valid prediction for CodingQuarry_transcript_21825-T1
Valid prediction for snap_scaffold_17-snap.379-T1
Valid prediction for snap_scaffold_17-snap.372-T1
Valid prediction for snap_scaffold_17-snap.381-T1
Valid prediction for GeneMark_model.70058_t
Valid prediction for snap_scaffold_17-snap.359-T1
Valid prediction for GlimmerHMM_glimmerT_40678-T1
Valid prediction for snap_scaffold_17-snap.369-T1
Valid prediction for GeneMark_model.70060_t
Valid prediction for snap_scaffold_17-snap.358-T1
Valid prediction for snap_scaffold_17-snap.383-T1
Valid prediction for CodingQuarry_transcript_21827-T1
Valid prediction for GlimmerHMM_glimmerT_40688-T1
Valid prediction for GeneMark_model.70073_t
Valid prediction for pasa_asmbl_17749.p1
Valid prediction for GeneMark_model.70071_t
Valid prediction for snap_scaffold_17-snap.375-T1
Valid prediction for GlimmerHMM_glimmerT_40692-T1
Valid prediction for snap_scaffold_17-snap.349-T1
Valid prediction for HiQ_model.g27266.t1
Valid prediction for snap_scaffold_17-snap.364-T1
Valid prediction for snap_scaffold_17-snap.354-T1
Valid prediction for snap_scaffold_17-snap.361-T1
Valid prediction for Augustus_model.g27260.t1
Valid prediction for GlimmerHMM_glimmerT_40704-T1
Valid prediction for GeneMark_model.70043_t
Valid prediction for GeneMark_model.70064_t
Valid prediction for GlimmerHMM_glimmerT_40689-T1
Valid prediction for GeneMark_model.70066_t
Valid prediction for CodingQuarry_transcript_21828-T1
Valid prediction for snap_scaffold_17-snap.352-T1
Valid prediction for Augustus_model.g27265.t1
Valid prediction for GeneMark_model.70075_t

-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_17-snap.380-T1
Valid prediction for snap_scaffold_17-snap.357-T1
Valid prediction for GeneMark_model.70061_t
Valid prediction for GeneMark_model.70084_t
Couldn't classify 81874, 82179
Sorry, prediction pasa_asmbl_18777.p1 fails validation.
(AAC)	 CC	81874-82179	GT	CGG
(GCT)	 AG	82498-82597	GT	TGG
(CCA)	 AG	82924-83135	GT	AGG
(TAC)	 AG	83235-83618	TT	GAT
-recovered pasa_asmbl_18777.p1, terminal, 83235, 83618
-recovered pasa_asmbl_18777.p1, internal, 82498, 82597
-recovered pasa_asmbl_18777.p1, internal, 82924, 83135
Valid prediction for snap_scaffold_17-snap.350-T1
Valid prediction for GeneMark_model.70053_t
Valid prediction for snap_scaffold_17-snap.374-T1
Valid prediction for GlimmerHMM_glimmerT_40686-T1
Valid prediction for GeneMark_model.70056_t
Valid prediction for GlimmerHMM_glimmerT_40700-T1
Valid prediction for Augustus_model.g27254.t1
Valid prediction for GeneMark_model.70081_t
Valid prediction for snap_scaffold_17-snap.378-T1
Valid prediction for CodingQuarry_transcript_21822-T1
Valid prediction for Augustus_model.g27253.t1
Valid prediction for GeneMark_model.70065_t
Valid prediction for Augustus_model.g27263.t1
Valid prediction for snap_scaffold_17-snap.356-T1
Valid prediction for snap_scaffold_17-snap.355-T1
Valid prediction for GeneMark_model.70076_t
Couldn't classify 67417, 67734
Sorry, prediction pasa_asmbl_18779.p2 fails validation.
(ATG)	 GC	67417-67734	CC	AAC
Valid prediction for GeneMark_model.70082_t
Valid prediction for GeneMark_model.70074_t
Valid prediction for GlimmerHMM_glimmerT_40696-T1
Valid prediction for GeneMark_model.70041_t
Valid prediction for snap_scaffold_17-snap.365-T1
Valid prediction for GeneMark_model.70057_t
Valid prediction for GeneMark_model.70063_t
Valid prediction for GlimmerHMM_glimmerT_40703-T1
Valid prediction for Augustus_model.g27256.t1
Valid prediction for GeneMark_model.70050_t
Valid prediction for GlimmerHMM_glimmerT_40677-T1
Valid prediction for GeneMark_model.70054_t
Valid prediction for HiQ_model.g27259.t1
Valid prediction for GlimmerHMM_glimmerT_40683-T1
Valid prediction for snap_scaffold_17-snap.382-T1
Valid prediction for GeneMark_model.70080_t
Valid prediction for GlimmerHMM_glimmerT_40681-T1
Couldn't classify 78356, 78536
Couldn't classify 81053, 81690
Sorry, prediction pasa_asmbl_18778.p1 fails validation.
(GAG)	 CA	78356-78536	GT	TGG
(GGC)	 AG	80707-80886	GT	TGG
(GTT)	 AG	81053-81690	GC	TCG
-recovered pasa_asmbl_18778.p1, internal, 80707, 80886
-recovered pasa_asmbl_18778.p1, internal, 81053, 81690
Valid prediction for snap_scaffold_17-snap.377-T1
Valid prediction for snap_scaffold_17-snap.376-T1
Valid prediction for GeneMark_model.70051_t
Valid prediction for snap_scaffold_17-snap.384-T1
Valid prediction for HiQ_model.g27257.t1
Valid prediction for GeneMark_model.70086_t
Couldn't classify 132627, 132742
Sorry, prediction pasa_asmbl_18772.p2 fails validation.
(ATG)	 AG	131331-131495	GT	AGG
(AAG)	 AG	131749-131820	GT	AGG
(GGA)	 AG	131985-132120	GT	CGG
(GTG)	 AG	132269-132391	GT	AGG
(ACA)	 AG	132627-132742	AT	AGA
-recovered pasa_asmbl_18772.p2, initial, 131331, 131495
-recovered pasa_asmbl_18772.p2, internal, 131331, 131495
-recovered pasa_asmbl_18772.p2, internal, 131749, 131820
-recovered pasa_asmbl_18772.p2, internal, 131985, 132120
-recovered pasa_asmbl_18772.p2, internal, 132269, 132391
Valid prediction for GeneMark_model.70042_t
Valid prediction for GlimmerHMM_glimmerT_40679-T1
Valid prediction for GeneMark_model.70078_t
Valid prediction for snap_scaffold_17-snap.347-T1
Valid prediction for GeneMark_model.70070_t
Valid prediction for GlimmerHMM_glimmerT_40698-T1
Valid prediction for snap_scaffold_17-snap.370-T1
Valid prediction for GeneMark_model.70045_t
Valid prediction for GlimmerHMM_glimmerT_40697-T1
Valid prediction for snap_scaffold_17-snap.360-T1
Valid prediction for GlimmerHMM_glimmerT_40701-T1
Valid prediction for GeneMark_model.70072_t
Valid prediction for GeneMark_model.70047_t
Valid prediction for GlimmerHMM_glimmerT_40684-T1
Valid prediction for snap_scaffold_17-snap.366-T1
Couldn't classify 132847, 132989
Sorry, prediction pasa_asmbl_19577.p1 fails validation.
(TTC)	 CT	132847-132989	GT	GTG
(GAA)	 AG	133157-133321	GT	GAG
(GAT)	 AG	134292-134409	GT	AGG
(CCA)	 AG	135845-135949	GT	TGG
(GGG)	 AG	136182-136215	GT	AAG
(GTA)	 AG	136873-136919	TG	GAT
-recovered pasa_asmbl_19577.p1, terminal, 136873, 136919
-recovered pasa_asmbl_19577.p1, internal, 133157, 133321
-recovered pasa_asmbl_19577.p1, internal, 134292, 134409
-recovered pasa_asmbl_19577.p1, internal, 135845, 135949
-recovered pasa_asmbl_19577.p1, internal, 136182, 136215
Valid prediction for snap_scaffold_17-snap.351-T1
Valid prediction for snap_scaffold_17-snap.348-T1
Valid prediction for GeneMark_model.70044_t
Valid prediction for GlimmerHMM_glimmerT_40687-T1
Valid prediction for Augustus_model.g27255.t1
Valid prediction for GeneMark_model.70049_t
Valid prediction for GeneMark_model.70059_t
Valid prediction for GlimmerHMM_glimmerT_40690-T1
Valid prediction for snap_scaffold_17-snap.353-T1
Valid prediction for snap_scaffold_17-snap.363-T1
Valid prediction for pasa_asmbl_18775.p1
Valid prediction for snap_scaffold_17-snap.362-T1
Valid prediction for snap_scaffold_17-snap.373-T1
Valid prediction for GlimmerHMM_glimmerT_40694-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19608, rend_intergenic: 12625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26645, rend_intergenic: 23637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63937, rend_intergenic: 53177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79772, rend_intergenic: 67502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84315, rend_intergenic: 81917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96105, rend_intergenic: 85170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116199, rend_intergenic: 113690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122560, rend_intergenic: 116316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133480, rend_intergenic: 130006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161982, rend_intergenic: 147690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175451, rend_intergenic: 166053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182193, rend_intergenic: 176415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184556, rend_intergenic: 182301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196164, rend_intergenic: 186185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 197307
-exon list size: 715


building trellis

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70.4    
70.6    
70.7    
70.9    
71.0    
71.1    
71.3    
71.4    
71.5    
71.7    
71.8    
72.0    
72.1    
72.2    
72.4    
72.5    
72.7    
72.8    
72.9    
73.1    
73.2    
73.4    
73.5    
73.6    
73.8    
73.9    
74.1    
74.2    
74.3    
74.5    
74.6    
74.8    
74.9    
75.0    
75.2    
75.3    
75.5    
75.6    
75.7    
75.9    
76.0    
76.2    
76.3    
76.4    
76.6    
76.7    
76.8    
77.0    
77.1    
77.3    
77.4    
77.5    
77.7    
77.8    
78.0    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
78.9    
79.1    
79.2    
79.4    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.0    
81.2    
81.3    
81.5    
81.6    
81.7    
81.9    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.8    
83.0    
83.1    
83.3    
83.4    
83.5    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.6    
85.8    
85.9    
86.1    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.8    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 19608, rend_intergenic: 12625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26645, rend_intergenic: 23637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63937, rend_intergenic: 53177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79772, rend_intergenic: 67502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84315, rend_intergenic: 81917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96105, rend_intergenic: 85170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116199, rend_intergenic: 113690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122560, rend_intergenic: 116316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133480, rend_intergenic: 130006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161982, rend_intergenic: 147690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175451, rend_intergenic: 166053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182193, rend_intergenic: 176415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184556, rend_intergenic: 182301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196164, rend_intergenic: 186185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support