-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_15875338-16025878

-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 GlimmerHMM_glimmerT_24071-T1
Valid prediction for GlimmerHMM_glimmerT_24055-T1
Valid prediction for snap_scaffold_9-snap.3242-T1
Couldn't classify 138917, 139405
Sorry, prediction pasa_asmbl_54566.p1 fails validation.
(ATC)	 CC	138917-139405	GA	AGG
Valid prediction for GeneMark_model.41297_t
Valid prediction for snap_scaffold_9-snap.3246-T1
Valid prediction for GlimmerHMM_glimmerT_24058-T1
Valid prediction for GlimmerHMM_glimmerT_24054-T1
Valid prediction for GeneMark_model.41265_t
Valid prediction for GeneMark_model.41274_t
Valid prediction for GeneMark_model.41280_t
Valid prediction for snap_scaffold_9-snap.3243-T1
Valid prediction for GlimmerHMM_glimmerT_24056-T1
Valid prediction for snap_scaffold_9-snap.3231-T1
Valid prediction for GlimmerHMM_glimmerT_24062-T1
Valid prediction for GlimmerHMM_glimmerT_24051-T1
Valid prediction for Augustus_model.g16114.t1
Valid prediction for Augustus_model.g16109.t1
Valid prediction for GeneMark_model.41276_t
Valid prediction for GeneMark_model.41251_t
Valid prediction for snap_scaffold_9-snap.3261-T1
Valid prediction for snap_scaffold_9-snap.3238-T1
Valid prediction for GeneMark_model.41277_t
Valid prediction for snap_scaffold_9-snap.3248-T1
Valid prediction for snap_scaffold_9-snap.3256-T1
Valid prediction for GeneMark_model.41257_t
Valid prediction for Augustus_model.g16108.t1
Valid prediction for snap_scaffold_9-snap.3259-T1
Valid prediction for GeneMark_model.41292_t
Valid prediction for GeneMark_model.41272_t
Valid prediction for snap_scaffold_9-snap.3232-T1
Valid prediction for GlimmerHMM_glimmerT_24067-T1
Valid prediction for GeneMark_model.41293_t
Valid prediction for Augustus_model.g16111.t1
Valid prediction for snap_scaffold_9-snap.3228-T1
Valid prediction for GlimmerHMM_glimmerT_24050-T1
Valid prediction for GeneMark_model.41286_t
Valid prediction for GeneMark_model.41296_t
Valid prediction for snap_scaffold_9-snap.3257-T1
Valid prediction for Augustus_model.g16121.t1
Valid prediction for GeneMark_model.41266_t
Valid prediction for GeneMark_model.41262_t
Valid prediction for GlimmerHMM_glimmerT_24047-T1
Valid prediction for GeneMark_model.41260_t
Valid prediction for GeneMark_model.41259_t
Valid prediction for GlimmerHMM_glimmerT_24069-T1
Valid prediction for GeneMark_model.41289_t
Valid prediction for GeneMark_model.41283_t
Valid prediction for Augustus_model.g16115.t1
Valid prediction for snap_scaffold_9-snap.3240-T1
Valid prediction for Augustus_model.g16123.t1
Valid prediction for snap_scaffold_9-snap.3249-T1
Valid prediction for GlimmerHMM_glimmerT_24073-T1
Valid prediction for GlimmerHMM_glimmerT_24060-T1
Valid prediction for GlimmerHMM_glimmerT_24053-T1
Valid prediction for Augustus_model.g16116.t1
Valid prediction for GeneMark_model.41279_t
Couldn't classify 137959, 138091
Couldn't classify 138366, 138661
Sorry, prediction pasa_asmbl_54759.p1 fails validation.
(TCC)	 CC	137959-138091	GT	AGG
(GTG)	 AG	138366-138661	GG	ACG
Valid prediction for GlimmerHMM_glimmerT_24048-T1
Valid prediction for Augustus_model.g16122.t1
Valid prediction for GeneMark_model.41269_t
Valid prediction for Augustus_model.g16112.t1
Valid prediction for GeneMark_model.41271_t
Valid prediction for snap_scaffold_9-snap.3250-T1
Valid prediction for snap_scaffold_9-snap.3229-T1
Valid prediction for Augustus_model.g16110.t1
Valid prediction for GeneMark_model.41253_t
Valid prediction for GeneMark_model.41282_t
Valid prediction for GlimmerHMM_glimmerT_24063-T1
Valid prediction for snap_scaffold_9-snap.3235-T1
Valid prediction for GeneMark_model.41281_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_24061-T1
Valid prediction for GlimmerHMM_glimmerT_24070-T1
Valid prediction for GeneMark_model.41295_t
Valid prediction for GeneMark_model.41270_t
Valid prediction for snap_scaffold_9-snap.3253-T1
Valid prediction for GeneMark_model.41264_t
Valid prediction for snap_scaffold_9-snap.3236-T1
Valid prediction for snap_scaffold_9-snap.3237-T1
Couldn't classify 74066, 74503
Sorry, prediction pasa_asmbl_55521.p1 fails validation.
(ATC)	 GT	74066-74503	GG	ACG
Valid prediction for Augustus_model.g16113.t1
Valid prediction for Augustus_model.g16117.t1
Valid prediction for snap_scaffold_9-snap.3262-T1
Valid prediction for GlimmerHMM_glimmerT_24066-T1
Valid prediction for GlimmerHMM_glimmerT_24072-T1
Valid prediction for snap_scaffold_9-snap.3239-T1
Valid prediction for GlimmerHMM_glimmerT_24064-T1
Valid prediction for GeneMark_model.41256_t
Valid prediction for GeneMark_model.41278_t
Valid prediction for GeneMark_model.41290_t
Valid prediction for snap_scaffold_9-snap.3251-T1
Valid prediction for GeneMark_model.41284_t
Valid prediction for GeneMark_model.41267_t
Valid prediction for GeneMark_model.41255_t
Valid prediction for snap_scaffold_9-snap.3234-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g16120.t1
Valid prediction for GeneMark_model.41294_t
Couldn't classify 39969, 40068
Sorry, prediction pasa_asmbl_55525.p2 fails validation.
(ATG)	 GA	34478-34518	GT	GGG
(GTG)	 AG	36925-37089	GT	AAG
(GTT)	 AG	38153-38230	GT	AGG
(AGC)	 AG	39969-40068	GG	CAG
-recovered pasa_asmbl_55525.p2, initial, 34478, 34518
-recovered pasa_asmbl_55525.p2, internal, 36925, 37089
-recovered pasa_asmbl_55525.p2, internal, 38153, 38230
Valid prediction for snap_scaffold_9-snap.3244-T1
Valid prediction for GeneMark_model.41261_t
Valid prediction for GeneMark_model.41258_t
Couldn't classify 23465, 23782
Sorry, prediction pasa_asmbl_54565.p2 fails validation.
(CCC)	 AT	23465-23782	CT	AGC
Valid prediction for GeneMark_model.41268_t
Valid prediction for snap_scaffold_9-snap.3241-T1
Valid prediction for snap_scaffold_9-snap.3254-T1
Valid prediction for snap_scaffold_9-snap.3230-T1
Valid prediction for GeneMark_model.41249_t
Valid prediction for snap_scaffold_9-snap.3252-T1
Couldn't classify 42526, 42817
Sorry, prediction pasa_asmbl_55524.p2 fails validation.
(AGG)	 CC	42526-42817	GT	CGG
(AAG)	 AG	43174-43367	CC	AAC
-recovered pasa_asmbl_55524.p2, terminal, 43174, 43367
Valid prediction for GlimmerHMM_glimmerT_24057-T1
Valid prediction for GeneMark_model.41291_t
Valid prediction for GeneMark_model.41285_t
Valid prediction for GlimmerHMM_glimmerT_24065-T1
Valid prediction for GlimmerHMM_glimmerT_24049-T1
Valid prediction for snap_scaffold_9-snap.3255-T1
Valid prediction for GeneMark_model.41263_t
Valid prediction for GlimmerHMM_glimmerT_24068-T1
Valid prediction for GeneMark_model.41288_t
Valid prediction for Augustus_model.g16119.t1
Valid prediction for snap_scaffold_9-snap.3247-T1
Valid prediction for GlimmerHMM_glimmerT_24052-T1
Valid prediction for snap_scaffold_9-snap.3245-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.41287_t
Valid prediction for Augustus_model.g16118.t1
Valid prediction for GlimmerHMM_glimmerT_24059-T1
Valid prediction for GeneMark_model.41275_t
Valid prediction for snap_scaffold_9-snap.3233-T1
Valid prediction for snap_scaffold_9-snap.3258-T1
Valid prediction for GeneMark_model.41273_t
Valid prediction for GeneMark_model.41250_t
Valid prediction for GeneMark_model.41254_t
Valid prediction for snap_scaffold_9-snap.3260-T1
Valid prediction for GeneMark_model.41252_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8074, rend_intergenic: 4355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18140, rend_intergenic: 12445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36273, rend_intergenic: 19703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40489, rend_intergenic: 38006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41470, rend_intergenic: 40592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45022, rend_intergenic: 43357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56368, rend_intergenic: 50483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87797, rend_intergenic: 67396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113929, rend_intergenic: 109153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129207, rend_intergenic: 125696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136378, rend_intergenic: 130015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146283, rend_intergenic: 141121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 150541
-exon list size: 556


building trellis

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28.3    
28.5    
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30.1    
30.3    
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30.8    
31.0    
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31.9    
32.1    
32.3    
32.4    
32.6    
32.8    
33.0    
33.2    
33.3    
33.5    
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33.9    
34.1    
34.2    
34.4    
34.6    
34.8    
34.9    
35.1    
35.3    
35.5    
35.7    
35.8    
36.0    
36.2    
36.4    
36.6    
36.7    
36.9    
37.1    
37.3    
37.5    
37.6    
37.8    
38.0    
38.2    
38.4    
38.5    
38.7    
38.9    
39.1    
39.2    
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39.6    
39.8    
40.0    
40.1    
40.3    
40.5    
40.7    
40.9    
41.0    
41.2    
41.4    
41.6    
41.8    
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42.1    
42.3    
42.5    
42.7    
42.8    
43.0    
43.2    
43.4    
43.5    
43.7    
43.9    
44.1    
44.3    
44.4    
44.6    
44.8    
45.0    
45.2    
45.3    
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46.1    
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46.4    
46.6    
46.8    
47.0    
47.1    
47.3    
47.5    
47.7    
47.8    
48.0    
48.2    
48.4    
48.6    
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49.1    
49.3    
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50.0    
50.2    
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50.5    
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51.1    
51.3    
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51.6    
51.8    
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52.3    
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52.9    
53.0    
53.2    
53.4    
53.6    
53.8    
53.9    
54.1    
54.3    
54.5    
54.7    
54.8    
55.0    
55.2    
55.4    
55.6    
55.7    
55.9    
56.1    
56.3    
56.5    
56.6    
56.8    
57.0    
57.2    
57.3    
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57.9    
58.1    
58.2    
58.4    
58.6    
58.8    
59.0    
59.1    
59.3    
59.5    
59.7    
59.9    
60.0    
60.2    
60.4    
60.6    
60.8    
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61.1    
61.3    
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62.0    
62.2    
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63.1    
63.3    
63.4    
63.6    
63.8    
64.0    
64.2    
64.3    
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65.2    
65.4    
65.6    
65.8    
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66.1    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.4    
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68.1    
68.3    
68.5    
68.6    
68.8    
69.0    
69.2    
69.4    
69.5    
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70.3    
70.4    
70.6    
70.8    
71.0    
71.1    
71.3    
71.5    
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71.9    
72.0    
72.2    
72.4    
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72.9    
73.1    
73.3    
73.5    
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73.8    
74.0    
74.2    
74.4    
74.6    
74.7    
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75.1    
75.3    
75.4    
75.6    
75.8    
76.0    
76.2    
76.3    
76.5    
76.7    
76.9    
77.1    
77.2    
77.4    
77.6    
77.8    
78.0    
78.1    
78.3    
78.5    
78.7    
78.9    
79.0    
79.2    
79.4    
79.6    
79.7    
79.9    
80.1    
80.3    
80.5    
80.6    
80.8    
81.0    
81.2    
81.4    
81.5    
81.7    
81.9    
82.1    
82.3    
82.4    
82.6    
82.8    
83.0    
83.2    
83.3    
83.5    
83.7    
83.9    
84.1    
84.2    
84.4    
84.6    
84.8    
84.9    
85.1    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.4    
88.5    
88.7    
88.9    
89.1    
89.2    
89.4    
89.6    
89.8    
90.0    
90.1    
90.3    
90.5    
90.7    
90.9    
91.0    
91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 8074, rend_intergenic: 4355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18140, rend_intergenic: 12445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36273, rend_intergenic: 19703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40489, rend_intergenic: 38006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41470, rend_intergenic: 40592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45022, rend_intergenic: 43357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56368, rend_intergenic: 50483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87797, rend_intergenic: 67396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113929, rend_intergenic: 109153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129207, rend_intergenic: 125696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136378, rend_intergenic: 130015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146283, rend_intergenic: 141121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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