-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_17120072-17304548

-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 GeneMark_model.3374_t
Valid prediction for Augustus_model.g1711.t1
Valid prediction for GeneMark_model.3418_t
Valid prediction for GeneMark_model.3389_t
Valid prediction for GeneMark_model.3388_t
Valid prediction for Augustus_model.g1713.t1
Valid prediction for GeneMark_model.3401_t
Valid prediction for snap_scaffold_1-snap.3118-T1
Valid prediction for GeneMark_model.3409_t
Valid prediction for GlimmerHMM_glimmerT_2345-T1
Valid prediction for Augustus_model.g1710.t1
Valid prediction for snap_scaffold_1-snap.3098-T1
Valid prediction for GeneMark_model.3406_t
Valid prediction for snap_scaffold_1-snap.3093-T1
Valid prediction for GeneMark_model.3362_t
Valid prediction for snap_scaffold_1-snap.3094-T1
Valid prediction for snap_scaffold_1-snap.3082-T1
Valid prediction for GlimmerHMM_glimmerT_2358-T1
Valid prediction for snap_scaffold_1-snap.3102-T1
Valid prediction for GlimmerHMM_glimmerT_2353-T1
Valid prediction for GeneMark_model.3367_t
Valid prediction for pasa_asmbl_2503.p1
Valid prediction for snap_scaffold_1-snap.3130-T1
Valid prediction for GeneMark_model.3391_t
Valid prediction for GlimmerHMM_glimmerT_2332-T1
Valid prediction for GlimmerHMM_glimmerT_2348-T1
Valid prediction for GlimmerHMM_glimmerT_2347-T1
Valid prediction for snap_scaffold_1-snap.3127-T1
Valid prediction for GeneMark_model.3394_t
Valid prediction for snap_scaffold_1-snap.3125-T1
Valid prediction for GlimmerHMM_glimmerT_2354-T1
Valid prediction for snap_scaffold_1-snap.3080-T1
Valid prediction for GeneMark_model.3404_t
Valid prediction for GeneMark_model.3396_t
Valid prediction for snap_scaffold_1-snap.3116-T1
Valid prediction for snap_scaffold_1-snap.3112-T1
Valid prediction for GeneMark_model.3379_t
Valid prediction for snap_scaffold_1-snap.3103-T1
Valid prediction for Augustus_model.g1714.t1
Valid prediction for snap_scaffold_1-snap.3120-T1
Valid prediction for GeneMark_model.3423_t
Valid prediction for GlimmerHMM_glimmerT_2359-T1
Valid prediction for GlimmerHMM_glimmerT_2349-T1
Valid prediction for Augustus_model.g1707.t1
Valid prediction for GeneMark_model.3364_t
Valid prediction for GeneMark_model.3415_t
Valid prediction for GeneMark_model.3411_t
Valid prediction for GlimmerHMM_glimmerT_2340-T1
Valid prediction for snap_scaffold_1-snap.3078-T1
Valid prediction for Augustus_model.g1712.t1
Valid prediction for GeneMark_model.3372_t
Valid prediction for GeneMark_model.3381_t
Valid prediction for GeneMark_model.3399_t
Valid prediction for GeneMark_model.3419_t
Valid prediction for GeneMark_model.3370_t
Valid prediction for Augustus_model.g1708.t1
Valid prediction for snap_scaffold_1-snap.3115-T1
Valid prediction for snap_scaffold_1-snap.3088-T1
Valid prediction for GeneMark_model.3420_t
Valid prediction for GeneMark_model.3421_t
Valid prediction for snap_scaffold_1-snap.3121-T1
Valid prediction for snap_scaffold_1-snap.3108-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 snap_scaffold_1-snap.3083-T1
Valid prediction for GeneMark_model.3383_t
Valid prediction for GeneMark_model.3416_t
Valid prediction for snap_scaffold_1-snap.3107-T1
Valid prediction for GeneMark_model.3422_t
Valid prediction for GeneMark_model.3384_t
Valid prediction for GlimmerHMM_glimmerT_2344-T1
Valid prediction for snap_scaffold_1-snap.3131-T1
Valid prediction for GeneMark_model.3369_t
Valid prediction for snap_scaffold_1-snap.3095-T1
Valid prediction for snap_scaffold_1-snap.3089-T1
Valid prediction for snap_scaffold_1-snap.3132-T1
Valid prediction for GlimmerHMM_glimmerT_2351-T1
Valid prediction for snap_scaffold_1-snap.3081-T1
Valid prediction for Augustus_model.g1704.t1
Valid prediction for snap_scaffold_1-snap.3106-T1
Valid prediction for snap_scaffold_1-snap.3092-T1
Valid prediction for GeneMark_model.3371_t
Valid prediction for GeneMark_model.3405_t
Valid prediction for GeneMark_model.3402_t
Valid prediction for GeneMark_model.3412_t
Valid prediction for GeneMark_model.3386_t
Valid prediction for GeneMark_model.3361_t
Valid prediction for snap_scaffold_1-snap.3099-T1
Valid prediction for GeneMark_model.3393_t
Valid prediction for snap_scaffold_1-snap.3129-T1
Valid prediction for snap_scaffold_1-snap.3119-T1
Valid prediction for GeneMark_model.3366_t
Valid prediction for GlimmerHMM_glimmerT_2342-T1
Valid prediction for GlimmerHMM_glimmerT_2338-T1
Valid prediction for GeneMark_model.3385_t
Valid prediction for snap_scaffold_1-snap.3111-T1
Valid prediction for snap_scaffold_1-snap.3113-T1
Valid prediction for snap_scaffold_1-snap.3124-T1
Couldn't classify 61339, 61713
Sorry, prediction pasa_asmbl_2502.p1 fails validation.
(CAT)	 GC	61339-61713	TG	CCT
Valid prediction for GeneMark_model.3373_t
Valid prediction for snap_scaffold_1-snap.3101-T1
Valid prediction for GeneMark_model.3397_t
Valid prediction for snap_scaffold_1-snap.3100-T1
Valid prediction for GeneMark_model.3392_t
Valid prediction for snap_scaffold_1-snap.3097-T1
Valid prediction for snap_scaffold_1-snap.3114-T1
Valid prediction for snap_scaffold_1-snap.3077-T1
Valid prediction for snap_scaffold_1-snap.3091-T1
Valid prediction for GlimmerHMM_glimmerT_2333-T1
Valid prediction for GeneMark_model.3414_t
Valid prediction for GeneMark_model.3365_t
Valid prediction for GeneMark_model.3376_t
Valid prediction for snap_scaffold_1-snap.3090-T1
Valid prediction for GlimmerHMM_glimmerT_2341-T1
Valid prediction for GeneMark_model.3368_t
Valid prediction for GeneMark_model.3413_t
Valid prediction for GlimmerHMM_glimmerT_2339-T1
Valid prediction for GeneMark_model.3378_t
Valid prediction for GeneMark_model.3375_t
Valid prediction for GeneMark_model.3407_t
Valid prediction for GeneMark_model.3410_t
Valid prediction for snap_scaffold_1-snap.3105-T1
Valid prediction for GlimmerHMM_glimmerT_2350-T1
Valid prediction for GeneMark_model.3400_t
Valid prediction for GlimmerHMM_glimmerT_2336-T1
Valid prediction for GeneMark_model.3417_t
Valid prediction for Augustus_model.g1705.t1
Valid prediction for GlimmerHMM_glimmerT_2356-T1
Valid prediction for snap_scaffold_1-snap.3084-T1
Valid prediction for snap_scaffold_1-snap.3076-T1
Valid prediction for GlimmerHMM_glimmerT_2352-T1
Valid prediction for GlimmerHMM_glimmerT_2337-T1
Valid prediction for GeneMark_model.3380_t
Valid prediction for GeneMark_model.3363_t
Valid prediction for snap_scaffold_1-snap.3096-T1
Valid prediction for GlimmerHMM_glimmerT_2360-T1
Valid prediction for GlimmerHMM_glimmerT_2355-T1
Valid prediction for snap_scaffold_1-snap.3117-T1
Valid prediction for snap_scaffold_1-snap.3128-T1
Valid prediction for GlimmerHMM_glimmerT_2343-T1
Valid prediction for GlimmerHMM_glimmerT_2346-T1
Valid prediction for GeneMark_model.3387_t
Valid prediction for Augustus_model.g1703.t1
Valid prediction for snap_scaffold_1-snap.3122-T1
Valid prediction for GeneMark_model.3398_t
Valid prediction for GeneMark_model.3403_t
Valid prediction for snap_scaffold_1-snap.3123-T1
Valid prediction for snap_scaffold_1-snap.3104-T1
Valid prediction for GeneMark_model.3390_t
Valid prediction for snap_scaffold_1-snap.3126-T1
Valid prediction for GeneMark_model.3382_t
Valid prediction for snap_scaffold_1-snap.3086-T1
Valid prediction for GeneMark_model.3395_t
Valid prediction for GlimmerHMM_glimmerT_2357-T1
Valid prediction for snap_scaffold_1-snap.3087-T1
Valid prediction for snap_scaffold_1-snap.3085-T1
Valid prediction for snap_scaffold_1-snap.3110-T1
Valid prediction for snap_scaffold_1-snap.3079-T1
Valid prediction for GeneMark_model.3408_t
Valid prediction for GlimmerHMM_glimmerT_2335-T1
Valid prediction for GlimmerHMM_glimmerT_2334-T1
Valid prediction for Augustus_model.g1706.t1
Valid prediction for Augustus_model.g1709.t1
Valid prediction for snap_scaffold_1-snap.3109-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 134298, rend_intergenic: 134295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11525, rend_intergenic: 8258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13235, rend_intergenic: 12055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17854, rend_intergenic: 14674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41731, rend_intergenic: 18872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47999, rend_intergenic: 43580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54986, rend_intergenic: 51575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68822, rend_intergenic: 59121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73716, rend_intergenic: 70810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81374, rend_intergenic: 73788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94065, rend_intergenic: 86583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100001, rend_intergenic: 94424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111222, rend_intergenic: 107120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123022, rend_intergenic: 111951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131379, rend_intergenic: 124207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140455, rend_intergenic: 138121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144727, rend_intergenic: 142852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152350, rend_intergenic: 149947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155003, rend_intergenic: 152948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157125, rend_intergenic: 155912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168871, rend_intergenic: 166663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 184477
-exon list size: 867


building trellis

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76.3    
76.4    
76.5    
76.6    
76.8    
76.9    
77.0    
77.1    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
77.9    
78.0    
78.1    
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    
79.9    
80.0    
80.1    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
80.9    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.7    
81.8    
81.9    
82.0    
82.2    
82.3    
82.4    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.2    
83.3    
83.4    
83.5    
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    
85.2    
85.3    
85.4    
85.5    
85.6    
85.7    
85.8    
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    
87.5    
87.6    
87.7    
87.8    
87.9    
88.0    
88.1    
88.3    
88.4    
88.5    
88.6    
88.7    
88.8    
89.0    
89.1    
89.2    
89.3    
89.4    
89.5    
89.6    
89.8    
89.9    
90.0    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.6    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.1    
93.2    
93.3    
93.4    
93.6    
93.7    
93.8    
93.9    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.7    
94.8    
94.9    
95.1    
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 50 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 134298, rend_intergenic: 134295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11525, rend_intergenic: 8258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13235, rend_intergenic: 12055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17854, rend_intergenic: 14674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41731, rend_intergenic: 18872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47999, rend_intergenic: 43580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54986, rend_intergenic: 51575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68822, rend_intergenic: 59121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73716, rend_intergenic: 70810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81374, rend_intergenic: 73788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94065, rend_intergenic: 86583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100001, rend_intergenic: 94424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111222, rend_intergenic: 107120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123022, rend_intergenic: 111951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131379, rend_intergenic: 124207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140455, rend_intergenic: 138121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144727, rend_intergenic: 142852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152350, rend_intergenic: 149947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155003, rend_intergenic: 152948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157125, rend_intergenic: 155912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168871, rend_intergenic: 166663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10361
-exon list size: 30


building trellis

3.1    
6.2    
9.4    
12.5    
15.6    
18.8    
21.9    
25.0    
28.1    
31.2    
34.4    
37.5    
40.6    
43.8    
46.9    
50.0    
53.1    
56.2    
59.4    
62.5    
65.6    
68.8    
71.9    
75.0    
78.1    
81.2    
84.4    
87.5    
90.6    
93.8    
96.9    
-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

-building DP trellis

-building trellis in range 1 - 10214
-exon list size: 29


building trellis

3.2    
6.5    
9.7    
12.9    
16.1    
19.4    
22.6    
25.8    
29.0    
32.3    
35.5    
38.7    
41.9    
45.2    
48.4    
51.6    
54.8    
58.1    
61.3    
64.5    
67.7    
71.0    
74.2    
77.4    
80.6    
83.9    
87.1    
90.3    
93.5    
96.8    
-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