-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_2410894-2612505

-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_4-snap.573-T1
Valid prediction for Augustus_model.g5915.t1
Valid prediction for snap_scaffold_4-snap.568-T1
Valid prediction for snap_scaffold_4-snap.545-T1
Valid prediction for GlimmerHMM_glimmerT_9098-T1
Valid prediction for GeneMark_model.14963_t
Valid prediction for snap_scaffold_4-snap.557-T1
Valid prediction for GeneMark_model.14973_t
Valid prediction for GeneMark_model.14940_t
Valid prediction for GeneMark_model.14972_t
Valid prediction for Augustus_model.g5905.t1
Valid prediction for GlimmerHMM_glimmerT_9111-T1
Valid prediction for snap_scaffold_4-snap.571-T1
Valid prediction for GlimmerHMM_glimmerT_9095-T1
Valid prediction for GeneMark_model.14984_t
Valid prediction for GlimmerHMM_glimmerT_9099-T1
Valid prediction for GeneMark_model.15004_t
Valid prediction for Augustus_model.g5908.t1
Valid prediction for GeneMark_model.15002_t
Valid prediction for GlimmerHMM_glimmerT_9109-T1
Valid prediction for GlimmerHMM_glimmerT_9094-T1
Valid prediction for GeneMark_model.14948_t
Valid prediction for GeneMark_model.14978_t
Valid prediction for GeneMark_model.14953_t
Valid prediction for GeneMark_model.15001_t
Valid prediction for GlimmerHMM_glimmerT_9108-T1
Valid prediction for GeneMark_model.14994_t
Valid prediction for GeneMark_model.14945_t
Valid prediction for GeneMark_model.14937_t
Valid prediction for snap_scaffold_4-snap.547-T1
Valid prediction for GlimmerHMM_glimmerT_9089-T1
Valid prediction for GeneMark_model.14990_t
Valid prediction for GeneMark_model.14950_t
Valid prediction for GeneMark_model.15009_t
Valid prediction for GeneMark_model.14999_t
Valid prediction for snap_scaffold_4-snap.541-T1
Valid prediction for GlimmerHMM_glimmerT_9091-T1
Valid prediction for GeneMark_model.14977_t
Valid prediction for snap_scaffold_4-snap.570-T1
Valid prediction for snap_scaffold_4-snap.561-T1
Valid prediction for snap_scaffold_4-snap.567-T1
Valid prediction for GlimmerHMM_glimmerT_9106-T1
Valid prediction for GeneMark_model.14958_t
Valid prediction for GeneMark_model.14996_t
Valid prediction for GeneMark_model.14970_t
Valid prediction for GeneMark_model.15007_t
Valid prediction for snap_scaffold_4-snap.576-T1
Valid prediction for snap_scaffold_4-snap.574-T1
Valid prediction for Augustus_model.g5906.t1
Valid prediction for snap_scaffold_4-snap.549-T1
Valid prediction for GeneMark_model.14988_t
Valid prediction for GlimmerHMM_glimmerT_9104-T1
Valid prediction for snap_scaffold_4-snap.554-T1
Valid prediction for Augustus_model.g5909.t1
Valid prediction for snap_scaffold_4-snap.539-T1
Valid prediction for Augustus_model.g5910.t1
Valid prediction for GeneMark_model.14967_t
Valid prediction for Augustus_model.g5907.t1
Valid prediction for GeneMark_model.14956_t
Valid prediction for GeneMark_model.14968_t
Valid prediction for GeneMark_model.14983_t
Valid prediction for Augustus_model.g5913.t1
Valid prediction for snap_scaffold_4-snap.543-T1
Valid prediction for snap_scaffold_4-snap.565-T1
Valid prediction for snap_scaffold_4-snap.551-T1
Valid prediction for GeneMark_model.14981_t
Valid prediction for GlimmerHMM_glimmerT_9107-T1
Valid prediction for GlimmerHMM_glimmerT_9092-T1
Valid prediction for GeneMark_model.14961_t
Valid prediction for Augustus_model.g5912.t1
Valid prediction for GeneMark_model.14935_t
Valid prediction for GlimmerHMM_glimmerT_9105-T1
Valid prediction for GeneMark_model.14942_t
Valid prediction for GeneMark_model.14992_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_4-snap.553-T1
Valid prediction for snap_scaffold_4-snap.558-T1
Valid prediction for Augustus_model.g5914.t1
Valid prediction for GeneMark_model.14959_t
Valid prediction for snap_scaffold_4-snap.544-T1
Valid prediction for snap_scaffold_4-snap.552-T1
Valid prediction for snap_scaffold_4-snap.556-T1
Valid prediction for GeneMark_model.14969_t
Valid prediction for GeneMark_model.14936_t
Valid prediction for snap_scaffold_4-snap.555-T1
Valid prediction for GeneMark_model.14971_t
Valid prediction for GeneMark_model.15010_t
Valid prediction for GeneMark_model.14980_t
Valid prediction for GeneMark_model.14987_t
Valid prediction for GeneMark_model.14966_t
Valid prediction for GeneMark_model.14941_t
Valid prediction for GeneMark_model.14960_t
Valid prediction for GeneMark_model.15012_t
Valid prediction for GeneMark_model.14957_t
Valid prediction for snap_scaffold_4-snap.577-T1
Valid prediction for GeneMark_model.14976_t
Valid prediction for snap_scaffold_4-snap.562-T1
Valid prediction for GeneMark_model.14949_t
Valid prediction for GeneMark_model.14998_t
Valid prediction for snap_scaffold_4-snap.550-T1
Valid prediction for snap_scaffold_4-snap.546-T1
Valid prediction for GeneMark_model.14951_t
Valid prediction for GeneMark_model.14938_t
Valid prediction for snap_scaffold_4-snap.548-T1
Valid prediction for GeneMark_model.14934_t
Valid prediction for snap_scaffold_4-snap.559-T1
Valid prediction for GlimmerHMM_glimmerT_9112-T1
Valid prediction for GeneMark_model.14944_t
Valid prediction for GlimmerHMM_glimmerT_9101-T1
Valid prediction for GeneMark_model.14946_t
Valid prediction for snap_scaffold_4-snap.578-T1
Valid prediction for Augustus_model.g5911.t1
Valid prediction for GeneMark_model.14964_t
Valid prediction for GeneMark_model.14943_t
Valid prediction for snap_scaffold_4-snap.572-T1
Valid prediction for GeneMark_model.14993_t
Valid prediction for GeneMark_model.14954_t
Valid prediction for GeneMark_model.14947_t
Valid prediction for GlimmerHMM_glimmerT_9100-T1
Valid prediction for GeneMark_model.15003_t
Valid prediction for snap_scaffold_4-snap.566-T1
Valid prediction for GeneMark_model.15006_t
Valid prediction for GeneMark_model.14995_t
Valid prediction for GeneMark_model.14986_t
Valid prediction for GlimmerHMM_glimmerT_9097-T1
Valid prediction for snap_scaffold_4-snap.564-T1
Valid prediction for GeneMark_model.15011_t
Valid prediction for GlimmerHMM_glimmerT_9090-T1
Valid prediction for GeneMark_model.14965_t
Valid prediction for GlimmerHMM_glimmerT_9110-T1
Valid prediction for GeneMark_model.14979_t
Valid prediction for GlimmerHMM_glimmerT_9096-T1
Valid prediction for snap_scaffold_4-snap.563-T1
Valid prediction for GeneMark_model.14989_t
Valid prediction for GeneMark_model.14952_t
Valid prediction for snap_scaffold_4-snap.569-T1
Valid prediction for GlimmerHMM_glimmerT_9103-T1
Valid prediction for GeneMark_model.14962_t
Valid prediction for GeneMark_model.15000_t
Valid prediction for GeneMark_model.14997_t
Valid prediction for GlimmerHMM_glimmerT_9102-T1
Valid prediction for GeneMark_model.15005_t
Valid prediction for snap_scaffold_4-snap.540-T1
Valid prediction for Augustus_model.g5916.t1
Valid prediction for GlimmerHMM_glimmerT_9113-T1
Valid prediction for GeneMark_model.14939_t
Valid prediction for GeneMark_model.14985_t
Valid prediction for GeneMark_model.15008_t
Valid prediction for GeneMark_model.14974_t
Valid prediction for snap_scaffold_4-snap.560-T1
Valid prediction for snap_scaffold_4-snap.542-T1
Valid prediction for snap_scaffold_4-snap.575-T1
Valid prediction for GeneMark_model.14982_t
Valid prediction for GeneMark_model.14991_t
Valid prediction for GeneMark_model.14955_t
Valid prediction for GlimmerHMM_glimmerT_9088-T1
Valid prediction for GlimmerHMM_glimmerT_9093-T1
Valid prediction for snap_scaffold_4-snap.538-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10444, rend_intergenic: 3441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12365, rend_intergenic: 11678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18550, rend_intergenic: 13318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20992, rend_intergenic: 19262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25612, rend_intergenic: 21002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41445, rend_intergenic: 25722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45062, rend_intergenic: 41815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67764, rend_intergenic: 45521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72798, rend_intergenic: 69711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79832, rend_intergenic: 77776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84227, rend_intergenic: 80392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94970, rend_intergenic: 85836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105853, rend_intergenic: 97000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120836, rend_intergenic: 115873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126931, rend_intergenic: 125462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146590, rend_intergenic: 146390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149473, rend_intergenic: 146728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154224, rend_intergenic: 150590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166265, rend_intergenic: 159035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172001, rend_intergenic: 168424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181131, rend_intergenic: 173269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188957, rend_intergenic: 181812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199869, rend_intergenic: 194179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 201612
-exon list size: 997


building trellis

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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    
71.7    
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    
75.0    
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    
78.3    
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    
81.7    
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    
85.0    
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    
88.3    
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    
91.7    
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    
95.0    
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    
98.3    
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 50 predictions from path traversal
Error with prediction: snap lend_intergenic: 10444, rend_intergenic: 3441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12365, rend_intergenic: 11678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18550, rend_intergenic: 13318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20992, rend_intergenic: 19262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25612, rend_intergenic: 21002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41445, rend_intergenic: 25722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45062, rend_intergenic: 41815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67764, rend_intergenic: 45521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72798, rend_intergenic: 69711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79832, rend_intergenic: 77776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84227, rend_intergenic: 80392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94970, rend_intergenic: 85836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105853, rend_intergenic: 97000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120836, rend_intergenic: 115873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126931, rend_intergenic: 125462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146590, rend_intergenic: 146390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149473, rend_intergenic: 146728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154224, rend_intergenic: 150590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166265, rend_intergenic: 159035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172001, rend_intergenic: 168424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181131, rend_intergenic: 173269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188957, rend_intergenic: 181812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199869, rend_intergenic: 194179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support