-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_1844668-2054661

-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_17-snap.416-T1
Valid prediction for GeneMark_model.70154_t
Valid prediction for GlimmerHMM_glimmerT_40708-T1
Valid prediction for GlimmerHMM_glimmerT_40718-T1
Valid prediction for Augustus_model.g27277.t1
Valid prediction for GeneMark_model.70165_t
Valid prediction for GlimmerHMM_glimmerT_40722-T1
Valid prediction for GlimmerHMM_glimmerT_40729-T1
Valid prediction for GeneMark_model.70115_t
Valid prediction for snap_scaffold_17-snap.404-T1
Valid prediction for GeneMark_model.70095_t
Valid prediction for GeneMark_model.70132_t
Valid prediction for GeneMark_model.70162_t
Valid prediction for GeneMark_model.70106_t
Valid prediction for GeneMark_model.70149_t
Valid prediction for snap_scaffold_17-snap.407-T1
Valid prediction for snap_scaffold_17-snap.390-T1
Valid prediction for snap_scaffold_17-snap.422-T1
Valid prediction for GeneMark_model.70153_t
Valid prediction for GeneMark_model.70136_t
Valid prediction for GlimmerHMM_glimmerT_40724-T1
Valid prediction for GeneMark_model.70138_t
Valid prediction for snap_scaffold_17-snap.419-T1
Valid prediction for GeneMark_model.70143_t
Valid prediction for GeneMark_model.70120_t
Valid prediction for snap_scaffold_17-snap.398-T1
Valid prediction for snap_scaffold_17-snap.397-T1
Valid prediction for snap_scaffold_17-snap.413-T1
Valid prediction for snap_scaffold_17-snap.387-T1
Valid prediction for GeneMark_model.70161_t
Valid prediction for snap_scaffold_17-snap.393-T1
Valid prediction for GeneMark_model.70113_t
Valid prediction for GeneMark_model.70142_t
Valid prediction for GeneMark_model.70166_t
Valid prediction for snap_scaffold_17-snap.406-T1
Valid prediction for GeneMark_model.70098_t
Valid prediction for GeneMark_model.70163_t
Valid prediction for snap_scaffold_17-snap.411-T1
Valid prediction for GeneMark_model.70134_t
Valid prediction for snap_scaffold_17-snap.423-T1
Valid prediction for snap_scaffold_17-snap.389-T1
Valid prediction for GlimmerHMM_glimmerT_40720-T1
Valid prediction for GeneMark_model.70089_t
Valid prediction for GlimmerHMM_glimmerT_40710-T1
Valid prediction for GeneMark_model.70116_t
Valid prediction for snap_scaffold_17-snap.409-T1
Valid prediction for GeneMark_model.70167_t
Valid prediction for GeneMark_model.70091_t
Valid prediction for GeneMark_model.70102_t
Valid prediction for GeneMark_model.70100_t
Valid prediction for GeneMark_model.70104_t
Valid prediction for GeneMark_model.70157_t
Valid prediction for GeneMark_model.70168_t
Valid prediction for GeneMark_model.70140_t
Valid prediction for GeneMark_model.70128_t
Valid prediction for GeneMark_model.70147_t
Valid prediction for snap_scaffold_17-snap.394-T1
Valid prediction for GeneMark_model.70122_t
Valid prediction for GeneMark_model.70124_t
Valid prediction for GlimmerHMM_glimmerT_40727-T1
Valid prediction for GeneMark_model.70130_t
Valid prediction for GlimmerHMM_glimmerT_40726-T1
Valid prediction for GeneMark_model.70118_t
Valid prediction for GeneMark_model.70093_t
Valid prediction for GeneMark_model.70159_t
Valid prediction for GeneMark_model.70096_t
Valid prediction for GeneMark_model.70144_t
Valid prediction for GeneMark_model.70127_t
Valid prediction for snap_scaffold_17-snap.425-T1
Valid prediction for GeneMark_model.70114_t
Valid prediction for GeneMark_model.70109_t
Valid prediction for snap_scaffold_17-snap.402-T1
Valid prediction for GlimmerHMM_glimmerT_40715-T1
Valid prediction for GeneMark_model.70111_t
Valid prediction for snap_scaffold_17-snap.399-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.70099_t
Valid prediction for GeneMark_model.70158_t
Valid prediction for GlimmerHMM_glimmerT_40711-T1
Valid prediction for snap_scaffold_17-snap.421-T1
Valid prediction for GeneMark_model.70108_t
Valid prediction for snap_scaffold_17-snap.396-T1
Valid prediction for GlimmerHMM_glimmerT_40721-T1
Valid prediction for GlimmerHMM_glimmerT_40728-T1
Valid prediction for GlimmerHMM_glimmerT_40709-T1
Valid prediction for GeneMark_model.70151_t
Valid prediction for CodingQuarry_transcript_21830-T1
Valid prediction for Augustus_model.g27278.t1
Valid prediction for CodingQuarry_transcript_21829-T1
Valid prediction for snap_scaffold_17-snap.386-T1
Valid prediction for snap_scaffold_17-snap.408-T1
Valid prediction for snap_scaffold_17-snap.392-T1
Valid prediction for pasa_asmbl_18780.p2
Valid prediction for GlimmerHMM_glimmerT_40706-T1
Valid prediction for GeneMark_model.70129_t
Valid prediction for Augustus_model.g27280.t1
Valid prediction for snap_scaffold_17-snap.400-T1
Valid prediction for GeneMark_model.70107_t
Valid prediction for Augustus_model.g27271.t1
Valid prediction for GlimmerHMM_glimmerT_40723-T1
Valid prediction for snap_scaffold_17-snap.412-T1
Valid prediction for GeneMark_model.70126_t
Valid prediction for GeneMark_model.70097_t
Valid prediction for GlimmerHMM_glimmerT_40717-T1
Valid prediction for snap_scaffold_17-snap.385-T1
Valid prediction for snap_scaffold_17-snap.424-T1
Valid prediction for GeneMark_model.70135_t
Valid prediction for GeneMark_model.70110_t
Valid prediction for Augustus_model.g27273.t1
Valid prediction for Augustus_model.g27269.t1
Valid prediction for snap_scaffold_17-snap.401-T1
Valid prediction for GeneMark_model.70088_t
Valid prediction for GeneMark_model.70150_t
Valid prediction for Augustus_model.g27276.t1
Valid prediction for GeneMark_model.70137_t
Valid prediction for GeneMark_model.70145_t
Valid prediction for snap_scaffold_17-snap.426-T1
Valid prediction for snap_scaffold_17-snap.417-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.70146_t
Valid prediction for GeneMark_model.70139_t
Valid prediction for GeneMark_model.70164_t
Valid prediction for GlimmerHMM_glimmerT_40725-T1
Valid prediction for Augustus_model.g27274.t1
Valid prediction for GeneMark_model.70125_t
Couldn't classify 109244, 109330
Sorry, prediction Augustus_model.g27275.t1 fails validation.
(TGC)	 AG	109244-109330	GT	AGG
(ATC)	 AG	109890-110046	GT	CAG
(GTA)	 AG	110175-110207	GT	AGG
(GTT)	 AG	111034-111225	GT	AGG
(CTG)	 AG	113391-113517	GT	AGG
(TCT)	 AG	114917-115119	GT	CAG
(GTT)	 AG	115223-115414	GT	AGG
(CTC)	 AG	115717-115855	GT	AGG
(CTT)	 AG	119944-120131	GT	AGG
(CCA)	 AG	120250-120444	GT	GGG
(CTC)	 AG	120999-121115	GT	TGG
(GTC)	 AG	121470-121534	AA	AGA
add_exon() Sorry, Augustus_model.g27275.t1 111034-111225-terminal-1 is invalid.
-recovered Augustus_model.g27275.t1, terminal, 111034, 111225
add_exon() Sorry, Augustus_model.g27275.t1 115223-115414-terminal-1 is invalid.
-recovered Augustus_model.g27275.t1, terminal, 115223, 115414
-recovered Augustus_model.g27275.t1, terminal, 121470, 121534
-recovered Augustus_model.g27275.t1, internal, 109244, 109330
-recovered Augustus_model.g27275.t1, internal, 109890, 110046
-recovered Augustus_model.g27275.t1, internal, 110175, 110207
-recovered Augustus_model.g27275.t1, internal, 111034, 111225
-recovered Augustus_model.g27275.t1, internal, 113391, 113517
-recovered Augustus_model.g27275.t1, internal, 114917, 115119
-recovered Augustus_model.g27275.t1, internal, 115223, 115414
-recovered Augustus_model.g27275.t1, internal, 115717, 115855
-recovered Augustus_model.g27275.t1, internal, 119944, 120131
-recovered Augustus_model.g27275.t1, internal, 120250, 120444
-recovered Augustus_model.g27275.t1, internal, 120999, 121115
Valid prediction for GeneMark_model.70105_t
Valid prediction for GeneMark_model.70133_t
Valid prediction for snap_scaffold_17-snap.403-T1
Valid prediction for GeneMark_model.70155_t
Valid prediction for GeneMark_model.70092_t
Valid prediction for snap_scaffold_17-snap.415-T1
Valid prediction for GlimmerHMM_glimmerT_40714-T1
Valid prediction for GeneMark_model.70101_t
Valid prediction for GlimmerHMM_glimmerT_40707-T1
Valid prediction for snap_scaffold_17-snap.414-T1
Valid prediction for GeneMark_model.70119_t
Valid prediction for GeneMark_model.70112_t
Valid prediction for GlimmerHMM_glimmerT_40712-T1
Valid prediction for snap_scaffold_17-snap.410-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g27272.t1
Valid prediction for GeneMark_model.70117_t
Valid prediction for GeneMark_model.70094_t
Valid prediction for GlimmerHMM_glimmerT_40716-T1
Valid prediction for GlimmerHMM_glimmerT_40713-T1
Valid prediction for snap_scaffold_17-snap.395-T1
Valid prediction for GeneMark_model.70160_t
Valid prediction for GeneMark_model.70148_t
Valid prediction for GeneMark_model.70090_t
Valid prediction for GeneMark_model.70121_t
Valid prediction for snap_scaffold_17-snap.418-T1
Valid prediction for Augustus_model.g27281.t1
Valid prediction for snap_scaffold_17-snap.391-T1
Valid prediction for snap_scaffold_17-snap.405-T1
Valid prediction for snap_scaffold_17-snap.388-T1
Valid prediction for Augustus_model.g27279.t1
Valid prediction for GeneMark_model.70156_t
Valid prediction for snap_scaffold_17-snap.420-T1
Valid prediction for GeneMark_model.70131_t
Valid prediction for HiQ_model.g27270.t1
Valid prediction for GeneMark_model.70123_t
Valid prediction for GlimmerHMM_glimmerT_40719-T1
Valid prediction for GeneMark_model.70103_t
Valid prediction for GeneMark_model.70141_t
Valid prediction for HiQ_model.g27268.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12178, rend_intergenic: 10488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16590, rend_intergenic: 12194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20610, rend_intergenic: 17176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31298, rend_intergenic: 26784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37901, rend_intergenic: 31627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42223, rend_intergenic: 37935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56609, rend_intergenic: 46247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62532, rend_intergenic: 57733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65575, rend_intergenic: 63566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75957, rend_intergenic: 68068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82560, rend_intergenic: 77709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95549, rend_intergenic: 82582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102266, rend_intergenic: 96484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108818, rend_intergenic: 102894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113806, rend_intergenic: 112060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124500, rend_intergenic: 115417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145747, rend_intergenic: 127731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162229, rend_intergenic: 147588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179748, rend_intergenic: 165293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189814, rend_intergenic: 180571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192898, rend_intergenic: 189934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199756, rend_intergenic: 193021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202636, rend_intergenic: 200021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 209994
-exon list size: 905


building trellis

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62.1    
62.2    
62.3    
62.4    
62.5    
62.6    
62.7    
62.8    
63.0    
63.1    
63.2    
63.3    
63.4    
63.5    
63.6    
63.7    
63.8    
63.9    
64.1    
64.2    
64.3    
64.4    
64.5    
64.6    
64.7    
64.8    
64.9    
65.0    
65.2    
65.3    
65.4    
65.5    
65.6    
65.7    
65.8    
65.9    
66.0    
66.2    
66.3    
66.4    
66.5    
66.6    
66.7    
66.8    
66.9    
67.0    
67.1    
67.3    
67.4    
67.5    
67.6    
67.7    
67.8    
67.9    
68.0    
68.1    
68.2    
68.4    
68.5    
68.6    
68.7    
68.8    
68.9    
69.0    
69.1    
69.2    
69.3    
69.5    
69.6    
69.7    
69.8    
69.9    
70.0    
70.1    
70.2    
70.3    
70.5    
70.6    
70.7    
70.8    
70.9    
71.0    
71.1    
71.2    
71.3    
71.4    
71.6    
71.7    
71.8    
71.9    
72.0    
72.1    
72.2    
72.3    
72.4    
72.5    
72.7    
72.8    
72.9    
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    
74.4    
74.5    
74.6    
74.8    
74.9    
75.0    
75.1    
75.2    
75.3    
75.4    
75.5    
75.6    
75.7    
75.9    
76.0    
76.1    
76.2    
76.3    
76.4    
76.5    
76.6    
76.7    
76.8    
77.0    
77.1    
77.2    
77.3    
77.4    
77.5    
77.6    
77.7    
77.8    
77.9    
78.1    
78.2    
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    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.5    
80.6    
80.7    
80.8    
80.9    
81.0    
81.1    
81.3    
81.4    
81.5    
81.6    
81.7    
81.8    
81.9    
82.0    
82.1    
82.2    
82.4    
82.5    
82.6    
82.7    
82.8    
82.9    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
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    
85.1    
85.2    
85.3    
85.4    
85.6    
85.7    
85.8    
85.9    
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    
87.4    
87.5    
87.7    
87.8    
87.9    
88.0    
88.1    
88.2    
88.3    
88.4    
88.5    
88.6    
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    
91.0    
91.1    
91.2    
91.3    
91.4    
91.5    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.3    
92.4    
92.5    
92.6    
92.7    
92.8    
92.9    
93.1    
93.2    
93.3    
93.4    
93.5    
93.6    
93.7    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.5    
94.6    
94.7    
94.8    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.6    
95.7    
95.8    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.6    
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    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.8    
98.9    
99.0    
99.1    
99.2    
99.3    
99.4    
99.6    
99.7    
99.8    
99.9    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 12178, rend_intergenic: 10488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16590, rend_intergenic: 12194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20610, rend_intergenic: 17176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31298, rend_intergenic: 26784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37901, rend_intergenic: 31627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42223, rend_intergenic: 37935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56609, rend_intergenic: 46247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62532, rend_intergenic: 57733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65575, rend_intergenic: 63566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75957, rend_intergenic: 68068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82560, rend_intergenic: 77709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95549, rend_intergenic: 82582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102266, rend_intergenic: 96484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108818, rend_intergenic: 102894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113806, rend_intergenic: 112060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124500, rend_intergenic: 115417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145747, rend_intergenic: 127731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162229, rend_intergenic: 147588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179748, rend_intergenic: 165293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189814, rend_intergenic: 180571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192898, rend_intergenic: 189934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199756, rend_intergenic: 193021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202636, rend_intergenic: 200021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support