-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_12818492-13038529

-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_16-snap.2485-T1
Valid prediction for GeneMark_model.68859_t
Valid prediction for GeneMark_model.68845_t
Valid prediction for snap_scaffold_16-snap.2469-T1
Valid prediction for snap_scaffold_16-snap.2449-T1
Valid prediction for snap_scaffold_16-snap.2490-T1
Valid prediction for GeneMark_model.68839_t
Valid prediction for snap_scaffold_16-snap.2448-T1
Valid prediction for GeneMark_model.68835_t
Valid prediction for GeneMark_model.68872_t
Valid prediction for snap_scaffold_16-snap.2454-T1
Valid prediction for GeneMark_model.68849_t
Valid prediction for GeneMark_model.68852_t
Valid prediction for snap_scaffold_16-snap.2465-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.68881_t
Valid prediction for snap_scaffold_16-snap.2489-T1
Valid prediction for snap_scaffold_16-snap.2482-T1
Valid prediction for snap_scaffold_16-snap.2451-T1
Valid prediction for snap_scaffold_16-snap.2480-T1
Valid prediction for GlimmerHMM_glimmerT_40123-T1
Valid prediction for snap_scaffold_16-snap.2491-T1
Valid prediction for GeneMark_model.68861_t
Valid prediction for Augustus_model.g26945.t1
Valid prediction for GlimmerHMM_glimmerT_40127-T1
Valid prediction for GeneMark_model.68857_t
Valid prediction for Augustus_model.g26952.t1
Valid prediction for snap_scaffold_16-snap.2467-T1
Valid prediction for GeneMark_model.68891_t
Valid prediction for GlimmerHMM_glimmerT_40129-T1
Valid prediction for GeneMark_model.68885_t
Valid prediction for GeneMark_model.68855_t
Valid prediction for snap_scaffold_16-snap.2492-T1
Valid prediction for GlimmerHMM_glimmerT_40115-T1
Valid prediction for GeneMark_model.68897_t
Valid prediction for snap_scaffold_16-snap.2462-T1
Valid prediction for Augustus_model.g26953.t1
Valid prediction for GlimmerHMM_glimmerT_40148-T1
Valid prediction for GeneMark_model.68883_t
Valid prediction for GlimmerHMM_glimmerT_40146-T1
Valid prediction for snap_scaffold_16-snap.2455-T1
Valid prediction for Augustus_model.g26951.t1
Valid prediction for GeneMark_model.68837_t
Valid prediction for snap_scaffold_16-snap.2452-T1
Valid prediction for GeneMark_model.68879_t
Valid prediction for GlimmerHMM_glimmerT_40113-T1
Valid prediction for GeneMark_model.68865_t
Valid prediction for GeneMark_model.68867_t
Valid prediction for GeneMark_model.68893_t
Valid prediction for snap_scaffold_16-snap.2459-T1
Valid prediction for snap_scaffold_16-snap.2446-T1
Valid prediction for snap_scaffold_16-snap.2486-T1
Valid prediction for GlimmerHMM_glimmerT_40139-T1
Valid prediction for GeneMark_model.68846_t
Valid prediction for GeneMark_model.68877_t
Valid prediction for snap_scaffold_16-snap.2442-T1
Valid prediction for GeneMark_model.68889_t
Valid prediction for GlimmerHMM_glimmerT_40114-T1
Valid prediction for GlimmerHMM_glimmerT_40125-T1
Valid prediction for GlimmerHMM_glimmerT_40126-T1
Valid prediction for GeneMark_model.68831_t
Valid prediction for GlimmerHMM_glimmerT_40128-T1
Valid prediction for GeneMark_model.68833_t
Valid prediction for GlimmerHMM_glimmerT_40137-T1
Valid prediction for snap_scaffold_16-snap.2466-T1
Valid prediction for GlimmerHMM_glimmerT_40122-T1
Valid prediction for GeneMark_model.68843_t
Valid prediction for GlimmerHMM_glimmerT_40136-T1
Valid prediction for Augustus_model.g26954.t1
Valid prediction for Augustus_model.g26946.t1
Valid prediction for Augustus_model.g26948.t1
Valid prediction for GlimmerHMM_glimmerT_40130-T1
Valid prediction for GeneMark_model.68847_t
Valid prediction for GeneMark_model.68854_t
Valid prediction for GeneMark_model.68863_t
Valid prediction for GeneMark_model.68841_t
Valid prediction for Augustus_model.g26950.t1
Valid prediction for snap_scaffold_16-snap.2461-T1
Valid prediction for GeneMark_model.68888_t
Valid prediction for GeneMark_model.68829_t
Valid prediction for snap_scaffold_16-snap.2487-T1
Valid prediction for GlimmerHMM_glimmerT_40140-T1
Valid prediction for snap_scaffold_16-snap.2476-T1
Valid prediction for GlimmerHMM_glimmerT_40120-T1
Valid prediction for GeneMark_model.68895_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 GlimmerHMM_glimmerT_40138-T1
Valid prediction for snap_scaffold_16-snap.2481-T1
Valid prediction for snap_scaffold_16-snap.2443-T1
Valid prediction for GeneMark_model.68892_t
Valid prediction for GlimmerHMM_glimmerT_40131-T1
Valid prediction for GlimmerHMM_glimmerT_40116-T1
Valid prediction for snap_scaffold_16-snap.2456-T1
Valid prediction for snap_scaffold_16-snap.2468-T1
Valid prediction for GlimmerHMM_glimmerT_40143-T1
Valid prediction for snap_scaffold_16-snap.2494-T1
Valid prediction for GeneMark_model.68853_t
Valid prediction for GeneMark_model.68880_t
Valid prediction for snap_scaffold_16-snap.2460-T1
Valid prediction for Augustus_model.g26949.t1
Valid prediction for snap_scaffold_16-snap.2457-T1
Valid prediction for GeneMark_model.68866_t
Valid prediction for GlimmerHMM_glimmerT_40124-T1
Valid prediction for Augustus_model.g26958.t1
Valid prediction for snap_scaffold_16-snap.2483-T1
Valid prediction for GlimmerHMM_glimmerT_40135-T1
Valid prediction for snap_scaffold_16-snap.2447-T1
Valid prediction for GeneMark_model.68860_t
Valid prediction for GeneMark_model.68862_t
Valid prediction for GeneMark_model.68894_t
Valid prediction for GeneMark_model.68848_t
Valid prediction for GeneMark_model.68868_t
Valid prediction for snap_scaffold_16-snap.2463-T1
Valid prediction for GeneMark_model.68875_t
Valid prediction for snap_scaffold_16-snap.2464-T1
Valid prediction for GlimmerHMM_glimmerT_40117-T1
Valid prediction for snap_scaffold_16-snap.2479-T1
Valid prediction for GeneMark_model.68864_t
Valid prediction for GeneMark_model.68871_t
Valid prediction for GlimmerHMM_glimmerT_40119-T1
Valid prediction for Augustus_model.g26947.t1
Valid prediction for snap_scaffold_16-snap.2475-T1
Valid prediction for snap_scaffold_16-snap.2473-T1
Valid prediction for snap_scaffold_16-snap.2472-T1
Valid prediction for GeneMark_model.68886_t
Valid prediction for snap_scaffold_16-snap.2477-T1
Valid prediction for snap_scaffold_16-snap.2458-T1
Valid prediction for GeneMark_model.68869_t
Valid prediction for snap_scaffold_16-snap.2444-T1
Valid prediction for snap_scaffold_16-snap.2471-T1
Valid prediction for GeneMark_model.68890_t
Valid prediction for GlimmerHMM_glimmerT_40121-T1
Valid prediction for Augustus_model.g26956.t1
Valid prediction for GlimmerHMM_glimmerT_40141-T1
Valid prediction for Augustus_model.g26955.t1
Valid prediction for snap_scaffold_16-snap.2493-T1
Valid prediction for GeneMark_model.68882_t
Valid prediction for GeneMark_model.68838_t
Valid prediction for GeneMark_model.68870_t
Valid prediction for GeneMark_model.68840_t
Valid prediction for GlimmerHMM_glimmerT_40112-T1
Valid prediction for GlimmerHMM_glimmerT_40118-T1
Valid prediction for snap_scaffold_16-snap.2450-T1
Valid prediction for snap_scaffold_16-snap.2488-T1
Valid prediction for snap_scaffold_16-snap.2470-T1
Valid prediction for GlimmerHMM_glimmerT_40132-T1
Valid prediction for GeneMark_model.68858_t
Valid prediction for snap_scaffold_16-snap.2474-T1
Valid prediction for snap_scaffold_16-snap.2453-T1
Valid prediction for GeneMark_model.68896_t
Valid prediction for GeneMark_model.68834_t
Valid prediction for GeneMark_model.68844_t
Valid prediction for GeneMark_model.68878_t
Valid prediction for GeneMark_model.68874_t
Valid prediction for GlimmerHMM_glimmerT_40145-T1
Valid prediction for GeneMark_model.68884_t
Valid prediction for snap_scaffold_16-snap.2478-T1
Valid prediction for GeneMark_model.68836_t
Valid prediction for GeneMark_model.68850_t
Valid prediction for GlimmerHMM_glimmerT_40134-T1
Valid prediction for Augustus_model.g26957.t1
Valid prediction for GlimmerHMM_glimmerT_40142-T1
Valid prediction for GlimmerHMM_glimmerT_40147-T1
Valid prediction for GeneMark_model.68856_t
Valid prediction for GeneMark_model.68832_t
Valid prediction for GeneMark_model.68876_t
Valid prediction for GlimmerHMM_glimmerT_40133-T1
Valid prediction for GeneMark_model.68873_t
Valid prediction for GlimmerHMM_glimmerT_40144-T1
Valid prediction for GeneMark_model.68830_t
Valid prediction for snap_scaffold_16-snap.2445-T1
Valid prediction for snap_scaffold_16-snap.2484-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 64669, rend_intergenic: 64666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6194, rend_intergenic: 3282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12309, rend_intergenic: 7531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14559, rend_intergenic: 12407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37336, rend_intergenic: 15337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38996, rend_intergenic: 38004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40920, rend_intergenic: 39305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45420, rend_intergenic: 43154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63925, rend_intergenic: 59397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70905, rend_intergenic: 65062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80157, rend_intergenic: 75744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92088, rend_intergenic: 80620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110477, rend_intergenic: 92600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110813, rend_intergenic: 110488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144324, rend_intergenic: 111119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161860, rend_intergenic: 145513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163972, rend_intergenic: 161963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182127, rend_intergenic: 172442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211862, rend_intergenic: 194407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 220038
-exon list size: 968


building trellis

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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    
69.4    
69.5    
69.6    
69.7    
69.8    
69.9    
70.0    
70.1    
70.2    
70.3    
70.4    
70.5    
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    
72.9    
73.0    
73.1    
73.2    
73.3    
73.4    
73.5    
73.6    
73.7    
73.8    
73.9    
74.0    
74.1    
74.2    
74.3    
74.4    
74.5    
74.6    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.4    
75.5    
75.6    
75.7    
75.8    
75.9    
76.0    
76.1    
76.2    
76.3    
76.4    
76.5    
76.6    
76.7    
76.8    
76.9    
77.0    
77.1    
77.2    
77.3    
77.4    
77.5    
77.6    
77.7    
77.8    
77.9    
78.0    
78.1    
78.2    
78.4    
78.5    
78.6    
78.7    
78.8    
78.9    
79.0    
79.1    
79.2    
79.3    
79.4    
79.5    
79.6    
79.7    
79.8    
79.9    
80.0    
80.1    
80.2    
80.3    
80.4    
80.5    
80.6    
80.7    
80.8    
80.9    
81.0    
81.1    
81.2    
81.3    
81.4    
81.5    
81.6    
81.8    
81.9    
82.0    
82.1    
82.2    
82.3    
82.4    
82.5    
82.6    
82.7    
82.8    
82.9    
83.0    
83.1    
83.2    
83.3    
83.4    
83.5    
83.6    
83.7    
83.8    
83.9    
84.0    
84.1    
84.2    
84.3    
84.4    
84.5    
84.6    
84.7    
84.8    
84.9    
85.1    
85.2    
85.3    
85.4    
85.5    
85.6    
85.7    
85.8    
85.9    
86.0    
86.1    
86.2    
86.3    
86.4    
86.5    
86.6    
86.7    
86.8    
86.9    
87.0    
87.1    
87.2    
87.3    
87.4    
87.5    
87.6    
87.7    
87.8    
87.9    
88.0    
88.1    
88.2    
88.4    
88.5    
88.6    
88.7    
88.8    
88.9    
89.0    
89.1    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.8    
89.9    
90.0    
90.1    
90.2    
90.3    
90.4    
90.5    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.2    
91.3    
91.4    
91.5    
91.6    
91.8    
91.9    
92.0    
92.1    
92.2    
92.3    
92.4    
92.5    
92.6    
92.7    
92.8    
92.9    
93.0    
93.1    
93.2    
93.3    
93.4    
93.5    
93.6    
93.7    
93.8    
93.9    
94.0    
94.1    
94.2    
94.3    
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    
95.8    
95.9    
96.0    
96.1    
96.2    
96.3    
96.4    
96.5    
96.6    
96.7    
96.8    
96.9    
97.0    
97.1    
97.2    
97.3    
97.4    
97.5    
97.6    
97.7    
97.8    
97.9    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.7    
98.8    
98.9    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.6    
99.7    
99.8    
99.9    
-found 58 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 64669, rend_intergenic: 64666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6194, rend_intergenic: 3282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12309, rend_intergenic: 7531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14559, rend_intergenic: 12407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37336, rend_intergenic: 15337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38996, rend_intergenic: 38004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40920, rend_intergenic: 39305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45420, rend_intergenic: 43154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63925, rend_intergenic: 59397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70905, rend_intergenic: 65062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80157, rend_intergenic: 75744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92088, rend_intergenic: 80620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110477, rend_intergenic: 92600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110813, rend_intergenic: 110488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144324, rend_intergenic: 111119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161860, rend_intergenic: 145513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163972, rend_intergenic: 161963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182127, rend_intergenic: 172442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211862, rend_intergenic: 194407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 208044 - 220038
-exon list size: 34


building trellis

2.8    
5.6    
8.3    
11.1    
13.9    
16.7    
19.4    
22.2    
25.0    
27.8    
30.6    
33.3    
36.1    
38.9    
41.7    
44.4    
47.2    
50.0    
52.8    
55.6    
58.3    
61.1    
63.9    
66.7    
69.4    
72.2    
75.0    
77.8    
80.6    
83.3    
86.1    
88.9    
91.7    
94.4    
97.2    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support