-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_17255778-17459013

-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_7-snap.3328-T1
Valid prediction for snap_scaffold_7-snap.3318-T1
Valid prediction for snap_scaffold_7-snap.3331-T1
Valid prediction for snap_scaffold_7-snap.3327-T1
Valid prediction for snap_scaffold_7-snap.3325-T1
Valid prediction for GeneMark_model.32596_t
Valid prediction for GeneMark_model.32574_t
Valid prediction for GlimmerHMM_glimmerT_19242-T1
Valid prediction for Augustus_model.g12997.t1
Valid prediction for snap_scaffold_7-snap.3362-T1
Valid prediction for snap_scaffold_7-snap.3347-T1
Valid prediction for snap_scaffold_7-snap.3342-T1
Valid prediction for GeneMark_model.32548_t
Valid prediction for GeneMark_model.32554_t
Valid prediction for snap_scaffold_7-snap.3344-T1
Valid prediction for snap_scaffold_7-snap.3354-T1
Valid prediction for snap_scaffold_7-snap.3330-T1
Valid prediction for snap_scaffold_7-snap.3335-T1
Valid prediction for GeneMark_model.32539_t
Valid prediction for GeneMark_model.32543_t
Valid prediction for GlimmerHMM_glimmerT_19257-T1
Valid prediction for GeneMark_model.32586_t
Valid prediction for GeneMark_model.32579_t
Valid prediction for GeneMark_model.32577_t
Valid prediction for GeneMark_model.32582_t
Valid prediction for GeneMark_model.32534_t
Valid prediction for snap_scaffold_7-snap.3340-T1
Valid prediction for snap_scaffold_7-snap.3349-T1
Valid prediction for GeneMark_model.32556_t
Valid prediction for GeneMark_model.32576_t
Valid prediction for snap_scaffold_7-snap.3332-T1
Valid prediction for snap_scaffold_7-snap.3356-T1
Valid prediction for GlimmerHMM_glimmerT_19251-T1
Valid prediction for snap_scaffold_7-snap.3337-T1
Valid prediction for snap_scaffold_7-snap.3322-T1
Valid prediction for GlimmerHMM_glimmerT_19256-T1
Valid prediction for GeneMark_model.32562_t
Valid prediction for GeneMark_model.32572_t
Valid prediction for GeneMark_model.32581_t
Valid prediction for GlimmerHMM_glimmerT_19255-T1
Valid prediction for snap_scaffold_7-snap.3314-T1
Valid prediction for GeneMark_model.32589_t
Valid prediction for GeneMark_model.32580_t
Valid prediction for GeneMark_model.32559_t
Valid prediction for GeneMark_model.32549_t
Valid prediction for GeneMark_model.32564_t
Valid prediction for GlimmerHMM_glimmerT_19248-T1
Valid prediction for GeneMark_model.32569_t
Valid prediction for GeneMark_model.32546_t
Valid prediction for snap_scaffold_7-snap.3317-T1
Valid prediction for Augustus_model.g12998.t1
Valid prediction for GlimmerHMM_glimmerT_19252-T1
Valid prediction for snap_scaffold_7-snap.3357-T1
Valid prediction for snap_scaffold_7-snap.3339-T1
Valid prediction for GeneMark_model.32537_t
Valid prediction for GlimmerHMM_glimmerT_19265-T1
Valid prediction for GeneMark_model.32551_t
Valid prediction for GeneMark_model.32590_t
Valid prediction for GeneMark_model.32588_t
Valid prediction for snap_scaffold_7-snap.3363-T1
Valid prediction for snap_scaffold_7-snap.3351-T1
Valid prediction for GeneMark_model.32570_t
Couldn't classify 63824, 63930
Sorry, prediction pasa_asmbl_51362.p1 fails validation.
(ATG)	 GG	58500-58635	GT	AGG
(GGG)	 AG	59116-59183	GT	GGG
(GCG)	 AG	60003-60071	GT	AGG
(GAC)	 AG	60230-60350	GT	TGG
(GAA)	 AG	60832-60916	GT	TGG
(CTT)	 AG	61007-61086	GT	CAG
(AGT)	 AG	63824-63930	GT	ACG
-recovered pasa_asmbl_51362.p1, initial, 58500, 58635
-recovered pasa_asmbl_51362.p1, internal, 59116, 59183
-recovered pasa_asmbl_51362.p1, internal, 60003, 60071
-recovered pasa_asmbl_51362.p1, internal, 60230, 60350
-recovered pasa_asmbl_51362.p1, internal, 60832, 60916
-recovered pasa_asmbl_51362.p1, internal, 61007, 61086
-recovered pasa_asmbl_51362.p1, internal, 63824, 63930
Valid prediction for snap_scaffold_7-snap.3360-T1
Valid prediction for GeneMark_model.32565_t
Valid prediction for GlimmerHMM_glimmerT_19246-T1
Valid prediction for Augustus_model.g13002.t1
Valid prediction for GeneMark_model.32536_t
Valid prediction for GlimmerHMM_glimmerT_19263-T1
Valid prediction for GeneMark_model.32567_t
Valid prediction for Augustus_model.g13003.t1
Valid prediction for GlimmerHMM_glimmerT_19266-T1
Valid prediction for snap_scaffold_7-snap.3320-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 Augustus_model.g12995.t1
Valid prediction for snap_scaffold_7-snap.3334-T1
Valid prediction for GlimmerHMM_glimmerT_19244-T1
Valid prediction for Augustus_model.g12996.t1
Valid prediction for GeneMark_model.32593_t
Valid prediction for GlimmerHMM_glimmerT_19247-T1
Valid prediction for snap_scaffold_7-snap.3345-T1
Valid prediction for GlimmerHMM_glimmerT_19249-T1
Valid prediction for GeneMark_model.32533_t
Valid prediction for GeneMark_model.32550_t
Valid prediction for GlimmerHMM_glimmerT_19245-T1
Valid prediction for GeneMark_model.32560_t
Valid prediction for GeneMark_model.32563_t
Valid prediction for GeneMark_model.32573_t
Valid prediction for snap_scaffold_7-snap.3321-T1
Valid prediction for GeneMark_model.32594_t
Valid prediction for snap_scaffold_7-snap.3315-T1
Valid prediction for snap_scaffold_7-snap.3350-T1
Valid prediction for snap_scaffold_7-snap.3359-T1
Valid prediction for GlimmerHMM_glimmerT_19253-T1
Valid prediction for GlimmerHMM_glimmerT_19268-T1
Valid prediction for GeneMark_model.32540_t
Valid prediction for snap_scaffold_7-snap.3338-T1
Valid prediction for GeneMark_model.32568_t
Valid prediction for GlimmerHMM_glimmerT_19264-T1
Valid prediction for snap_scaffold_7-snap.3348-T1
Valid prediction for Augustus_model.g13001.t1
Valid prediction for GeneMark_model.32553_t
Valid prediction for GeneMark_model.32538_t
Valid prediction for snap_scaffold_7-snap.3352-T1
Valid prediction for GeneMark_model.32561_t
Valid prediction for GeneMark_model.32552_t
Valid prediction for GeneMark_model.32558_t
Valid prediction for GeneMark_model.32575_t
Valid prediction for GeneMark_model.32535_t
Valid prediction for GeneMark_model.32592_t
Valid prediction for snap_scaffold_7-snap.3329-T1
Valid prediction for GeneMark_model.32583_t
Valid prediction for GlimmerHMM_glimmerT_19262-T1
Valid prediction for snap_scaffold_7-snap.3323-T1
Valid prediction for GeneMark_model.32571_t
Valid prediction for GeneMark_model.32578_t
Valid prediction for GlimmerHMM_glimmerT_19258-T1
Valid prediction for GeneMark_model.32545_t
Valid prediction for GeneMark_model.32587_t
Valid prediction for snap_scaffold_7-snap.3326-T1
Valid prediction for snap_scaffold_7-snap.3319-T1
Valid prediction for snap_scaffold_7-snap.3324-T1
Valid prediction for snap_scaffold_7-snap.3343-T1
Valid prediction for GlimmerHMM_glimmerT_19243-T1
Valid prediction for snap_scaffold_7-snap.3358-T1
Valid prediction for Augustus_model.g13004.t1
Valid prediction for GlimmerHMM_glimmerT_19254-T1
Valid prediction for Augustus_model.g12999.t1
Valid prediction for GlimmerHMM_glimmerT_19261-T1
Valid prediction for GlimmerHMM_glimmerT_19267-T1
Valid prediction for snap_scaffold_7-snap.3364-T1
Valid prediction for GeneMark_model.32585_t
Valid prediction for snap_scaffold_7-snap.3333-T1
Valid prediction for GeneMark_model.32584_t
Valid prediction for snap_scaffold_7-snap.3316-T1
Valid prediction for GeneMark_model.32541_t
Valid prediction for snap_scaffold_7-snap.3346-T1
Valid prediction for snap_scaffold_7-snap.3355-T1
Valid prediction for Augustus_model.g13000.t1
Valid prediction for GeneMark_model.32557_t
Valid prediction for GlimmerHMM_glimmerT_19260-T1
Valid prediction for GlimmerHMM_glimmerT_19269-T1
Valid prediction for GeneMark_model.32542_t
Valid prediction for GeneMark_model.32591_t
Valid prediction for snap_scaffold_7-snap.3341-T1
Valid prediction for GlimmerHMM_glimmerT_19250-T1
Valid prediction for GeneMark_model.32595_t
Valid prediction for GeneMark_model.32547_t
Valid prediction for snap_scaffold_7-snap.3353-T1
Valid prediction for GeneMark_model.32555_t
Valid prediction for GlimmerHMM_glimmerT_19259-T1
Valid prediction for snap_scaffold_7-snap.3361-T1
Valid prediction for snap_scaffold_7-snap.3336-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13422, rend_intergenic: 8164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17933, rend_intergenic: 16910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24315, rend_intergenic: 19735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29218, rend_intergenic: 26251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32093, rend_intergenic: 29333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37007, rend_intergenic: 33493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42073, rend_intergenic: 37135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49098, rend_intergenic: 43114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84194, rend_intergenic: 70952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90417, rend_intergenic: 88310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92198, rend_intergenic: 90510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105146, rend_intergenic: 95999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115434, rend_intergenic: 113805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119933, rend_intergenic: 117959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136865, rend_intergenic: 122773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146302, rend_intergenic: 144836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148841, rend_intergenic: 146725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151387, rend_intergenic: 150366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154699, rend_intergenic: 151463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164333, rend_intergenic: 160468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168743, rend_intergenic: 167047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172256, rend_intergenic: 169423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181416, rend_intergenic: 176435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183633, rend_intergenic: 181427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186383, rend_intergenic: 184863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 203236
-exon list size: 866


building trellis

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70.7    
70.9    
71.0    
71.1    
71.2    
71.3    
71.4    
71.5    
71.7    
71.8    
71.9    
72.0    
72.1    
72.2    
72.4    
72.5    
72.6    
72.7    
72.8    
72.9    
73.0    
73.2    
73.3    
73.4    
73.5    
73.6    
73.7    
73.8    
74.0    
74.1    
74.2    
74.3    
74.4    
74.5    
74.7    
74.8    
74.9    
75.0    
75.1    
75.2    
75.3    
75.5    
75.6    
75.7    
75.8    
75.9    
76.0    
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    
77.8    
77.9    
78.0    
78.1    
78.2    
78.3    
78.5    
78.6    
78.7    
78.8    
78.9    
79.0    
79.1    
79.3    
79.4    
79.5    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.3    
80.4    
80.5    
80.6    
80.8    
80.9    
81.0    
81.1    
81.2    
81.3    
81.5    
81.6    
81.7    
81.8    
81.9    
82.0    
82.1    
82.3    
82.4    
82.5    
82.6    
82.7    
82.8    
82.9    
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    
84.6    
84.7    
84.8    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.6    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.1    
87.2    
87.3    
87.4    
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    
89.1    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.2    
91.4    
91.5    
91.6    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.4    
92.5    
92.6    
92.7    
92.9    
93.0    
93.1    
93.2    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.7    
94.8    
94.9    
95.0    
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    
96.7    
96.8    
96.9    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.7    
97.8    
97.9    
98.0    
98.2    
98.3    
98.4    
98.5    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.7    
99.8    
99.9    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 13422, rend_intergenic: 8164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17933, rend_intergenic: 16910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24315, rend_intergenic: 19735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29218, rend_intergenic: 26251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32093, rend_intergenic: 29333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37007, rend_intergenic: 33493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42073, rend_intergenic: 37135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49098, rend_intergenic: 43114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84194, rend_intergenic: 70952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90417, rend_intergenic: 88310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92198, rend_intergenic: 90510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105146, rend_intergenic: 95999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115434, rend_intergenic: 113805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119933, rend_intergenic: 117959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136865, rend_intergenic: 122773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146302, rend_intergenic: 144836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148841, rend_intergenic: 146725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151387, rend_intergenic: 150366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154699, rend_intergenic: 151463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164333, rend_intergenic: 160468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168743, rend_intergenic: 167047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172256, rend_intergenic: 169423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181416, rend_intergenic: 176435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183633, rend_intergenic: 181427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186383, rend_intergenic: 184863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support