-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_18473195-18655994

-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_6-snap.3970-T1
Valid prediction for Augustus_model.g11103.t1
Valid prediction for snap_scaffold_6-snap.3947-T1
Valid prediction for snap_scaffold_6-snap.3965-T1
Valid prediction for snap_scaffold_6-snap.3952-T1
Valid prediction for snap_scaffold_6-snap.3969-T1
Valid prediction for snap_scaffold_6-snap.3980-T1
Valid prediction for Augustus_model.g11102.t1
Valid prediction for GlimmerHMM_glimmerT_16587-T1
Couldn't classify 150104, 150373
Sorry, prediction pasa_asmbl_47830.p1 fails validation.
(ATG)	 GA	148484-148691	GT	AGG
(TGC)	 AG	149607-149734	GT	AGG
(GTA)	 AG	150104-150373	GC	AGG
-recovered pasa_asmbl_47830.p1, initial, 148484, 148691
-recovered pasa_asmbl_47830.p1, internal, 149607, 149734
-recovered pasa_asmbl_47830.p1, internal, 150104, 150373
Valid prediction for snap_scaffold_6-snap.3961-T1
Valid prediction for snap_scaffold_6-snap.3981-T1
Valid prediction for snap_scaffold_6-snap.3977-T1
Valid prediction for GlimmerHMM_glimmerT_16598-T1
Couldn't classify 101569, 101651
Sorry, prediction pasa_asmbl_47829.p1 fails validation.
(TGT)	 CG	101569-101651	GT	AGG
(GGA)	 AG	101960-102032	GT	AGG
(GTA)	 AG	102299-102390	GT	AGG
(TCT)	 AG	102827-102997	GT	GTG
(GTT)	 AG	103145-103207	GT	CGG
(AGA)	 AG	103690-103766	GT	AGG
(GTA)	 AG	104154-104296	GT	AGG
(TCT)	 AG	104849-104956	GT	GGG
(CTG)	 AG	106067-106147	GT	AGG
(GGT)	 AG	106779-106982	GG	AAG
-recovered pasa_asmbl_47829.p1, terminal, 106779, 106982
-recovered pasa_asmbl_47829.p1, internal, 101960, 102032
-recovered pasa_asmbl_47829.p1, internal, 102299, 102390
-recovered pasa_asmbl_47829.p1, internal, 102827, 102997
-recovered pasa_asmbl_47829.p1, internal, 103145, 103207
-recovered pasa_asmbl_47829.p1, internal, 103690, 103766
-recovered pasa_asmbl_47829.p1, internal, 104154, 104296
-recovered pasa_asmbl_47829.p1, internal, 104849, 104956
-recovered pasa_asmbl_47829.p1, internal, 106067, 106147
Valid prediction for snap_scaffold_6-snap.3957-T1
Valid prediction for snap_scaffold_6-snap.3983-T1
Valid prediction for snap_scaffold_6-snap.3972-T1
Valid prediction for GlimmerHMM_glimmerT_16595-T1
Valid prediction for snap_scaffold_6-snap.3964-T1
Couldn't classify 165822, 166088
Sorry, prediction pasa_asmbl_47952.p1 fails validation.
(ATG)	 AG	165822-166088	CA	CAC
Valid prediction for snap_scaffold_6-snap.3943-T1
Valid prediction for Augustus_model.g11109.t1
Valid prediction for GlimmerHMM_glimmerT_16592-T1
Valid prediction for GlimmerHMM_glimmerT_16578-T1
Valid prediction for snap_scaffold_6-snap.3973-T1
Valid prediction for GlimmerHMM_glimmerT_16585-T1
Valid prediction for snap_scaffold_6-snap.3968-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_16589-T1
Valid prediction for Augustus_model.g11104.t1
Valid prediction for snap_scaffold_6-snap.3951-T1
Valid prediction for snap_scaffold_6-snap.3945-T1
Couldn't classify 151351, 151392
Sorry, prediction pasa_asmbl_47832.p1 fails validation.
(AGT)	 GA	151351-151392	GT	ACG
(CCC)	 AG	151563-151694	GT	AGG
(GTG)	 AG	152116-152225	GT	AGG
(GTT)	 AG	152312-152456	GT	GGG
(GTG)	 AG	152977-153124	GT	CAG
(TTG)	 AG	153425-153441	GT	GAG
-recovered pasa_asmbl_47832.p1, terminal, 153425, 153441
-recovered pasa_asmbl_47832.p1, internal, 151563, 151694
-recovered pasa_asmbl_47832.p1, internal, 152116, 152225
-recovered pasa_asmbl_47832.p1, internal, 152312, 152456
-recovered pasa_asmbl_47832.p1, internal, 152977, 153124
-recovered pasa_asmbl_47832.p1, internal, 153425, 153441
Valid prediction for GlimmerHMM_glimmerT_16576-T1
Valid prediction for snap_scaffold_6-snap.3954-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_16584-T1
Valid prediction for GlimmerHMM_glimmerT_16588-T1
Valid prediction for Augustus_model.g11101.t1
Valid prediction for GlimmerHMM_glimmerT_16586-T1
Valid prediction for Augustus_model.g11108.t1
Valid prediction for snap_scaffold_6-snap.3959-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_55433-T1
Valid prediction for snap_scaffold_6-snap.3974-T1
Valid prediction for Augustus_model.g11106.t1
Valid prediction for GlimmerHMM_glimmerT_16594-T1
Valid prediction for GlimmerHMM_glimmerT_16596-T1
Valid prediction for snap_scaffold_6-snap.3950-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: -)Couldn't classify 175248, 175261
Couldn't classify 175944, 176090
Sorry, prediction pasa_asmbl_49256.p1 fails validation.
(ACA)	 GG	175248-175261	GT	AGG
(CGA)	 AG	175430-175610	GT	AGG
(GCC)	 AG	175944-176090	GG	GAG
-recovered pasa_asmbl_49256.p1, internal, 175430, 175610
Valid prediction for pasa_asmbl_49266.p1
Valid prediction for GlimmerHMM_glimmerT_16597-T1
Valid prediction for GlimmerHMM_glimmerT_16583-T1
Valid prediction for snap_scaffold_6-snap.3966-T1
Valid prediction for Augustus_model.g11098.t1
Valid prediction for GlimmerHMM_glimmerT_16590-T1
Valid prediction for snap_scaffold_6-snap.3962-T1
Valid prediction for GlimmerHMM_glimmerT_16579-T1
Valid prediction for GlimmerHMM_glimmerT_16593-T1
Couldn't classify 123568, 123987
Sorry, prediction pasa_asmbl_49264.p1 fails validation.
(GTG)	 CA	123568-123987	CC	ACC
Valid prediction for GlimmerHMM_glimmerT_16591-T1
Valid prediction for GlimmerHMM_glimmerT_16575-T1
Valid prediction for snap_scaffold_6-snap.3971-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g11107.t1
Valid prediction for snap_scaffold_6-snap.3963-T1
Valid prediction for snap_scaffold_6-snap.3958-T1
Valid prediction for snap_scaffold_6-snap.3979-T1
Valid prediction for Augustus_model.g11110.t1
Valid prediction for GlimmerHMM_glimmerT_16582-T1
Valid prediction for snap_scaffold_6-snap.3967-T1
Couldn't classify 125002, 125661
Sorry, prediction pasa_asmbl_49262.p1 fails validation.
(AGC)	 CC	125002-125661	GG	CAG
Valid prediction for snap_scaffold_6-snap.3955-T1
Valid prediction for Augustus_model.g11100.t1
Couldn't classify 168643, 168960
Sorry, prediction pasa_asmbl_49259.p1 fails validation.
(ATG)	 CG	168643-168960	CA	CCC
Valid prediction for snap_scaffold_6-snap.3982-T1
Valid prediction for GlimmerHMM_glimmerT_16573-T1
Valid prediction for snap_scaffold_6-snap.3976-T1
Valid prediction for Augustus_model.g11105.t1
Valid prediction for snap_scaffold_6-snap.3948-T1
Valid prediction for GlimmerHMM_glimmerT_16574-T1
Valid prediction for snap_scaffold_6-snap.3984-T1
Valid prediction for snap_scaffold_6-snap.3960-T1
Valid prediction for Augustus_model.g11099.t1
Valid prediction for GlimmerHMM_glimmerT_16580-T1
Valid prediction for snap_scaffold_6-snap.3975-T1
Valid prediction for snap_scaffold_6-snap.3949-T1
Valid prediction for snap_scaffold_6-snap.3953-T1
Valid prediction for GlimmerHMM_glimmerT_16577-T1
Valid prediction for snap_scaffold_6-snap.3956-T1
Valid prediction for snap_scaffold_6-snap.3942-T1
Valid prediction for snap_scaffold_6-snap.3978-T1
Valid prediction for snap_scaffold_6-snap.3944-T1
Couldn't classify 124192, 124494
Sorry, prediction pasa_asmbl_49263.p1 fails validation.
(GAT)	 AT	124192-124494	GA	AGG
Valid prediction for snap_scaffold_6-snap.3946-T1
Valid prediction for GlimmerHMM_glimmerT_16581-T1
Valid prediction for Augustus_model.g11097.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5948, rend_intergenic: 2325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6828, rend_intergenic: 6056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14323, rend_intergenic: 11725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19894, rend_intergenic: 19355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42059, rend_intergenic: 24619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46630, rend_intergenic: 44013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48747, rend_intergenic: 46643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54401, rend_intergenic: 52636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67696, rend_intergenic: 56938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78940, rend_intergenic: 72583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85792, rend_intergenic: 80166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95729, rend_intergenic: 89401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119023, rend_intergenic: 95777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124320, rend_intergenic: 119958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136559, rend_intergenic: 125148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145539, rend_intergenic: 139700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153399, rend_intergenic: 149603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160759, rend_intergenic: 154998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166610, rend_intergenic: 165672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174338, rend_intergenic: 167359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 154901, rend_intergenic: 154898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 182800
-exon list size: 412


building trellis

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29.2    
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30.9    
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32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
37.0    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.5    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.2    
43.5    
43.7    
44.0    
44.2    
44.4    
44.7    
44.9    
45.2    
45.4    
45.7    
45.9    
46.1    
46.4    
46.6    
46.9    
47.1    
47.3    
47.6    
47.8    
48.1    
48.3    
48.6    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
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51.7    
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53.4    
53.6    
53.9    
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54.3    
54.6    
54.8    
55.1    
55.3    
55.6    
55.8    
56.0    
56.3    
56.5    
56.8    
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57.2    
57.5    
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58.0    
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58.7    
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60.1    
60.4    
60.6    
60.9    
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61.4    
61.6    
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62.3    
62.6    
62.8    
63.0    
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63.5    
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64.0    
64.3    
64.5    
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65.0    
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65.9    
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67.1    
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67.6    
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68.1    
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68.8    
69.1    
69.3    
69.6    
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70.0    
70.3    
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71.3    
71.5    
71.7    
72.0    
72.2    
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76.1    
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77.1    
77.3    
77.5    
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78.0    
78.3    
78.5    
78.7    
79.0    
79.2    
79.5    
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80.0    
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80.4    
80.7    
80.9    
81.2    
81.4    
81.6    
81.9    
82.1    
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82.6    
82.9    
83.1    
83.3    
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83.8    
84.1    
84.3    
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85.3    
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86.0    
86.2    
86.5    
86.7    
87.0    
87.2    
87.4    
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87.9    
88.2    
88.4    
88.6    
88.9    
89.1    
89.4    
89.6    
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90.1    
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90.6    
90.8    
91.1    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.8    
93.0    
93.2    
93.5    
93.7    
94.0    
94.2    
94.4    
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94.9    
95.2    
95.4    
95.7    
95.9    
96.1    
96.4    
96.6    
96.9    
97.1    
97.3    
97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 5948, rend_intergenic: 2325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6828, rend_intergenic: 6056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14323, rend_intergenic: 11725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19894, rend_intergenic: 19355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42059, rend_intergenic: 24619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46630, rend_intergenic: 44013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48747, rend_intergenic: 46643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54401, rend_intergenic: 52636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67696, rend_intergenic: 56938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78940, rend_intergenic: 72583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85792, rend_intergenic: 80166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95729, rend_intergenic: 89401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119023, rend_intergenic: 95777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124320, rend_intergenic: 119958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136559, rend_intergenic: 125148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145539, rend_intergenic: 139700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153399, rend_intergenic: 149603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160759, rend_intergenic: 154998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166610, rend_intergenic: 165672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174338, rend_intergenic: 167359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 154901, rend_intergenic: 154898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 166091 - 182800
-exon list size: 15


building trellis

5.9    
11.8    
17.6    
23.5    
29.4    
35.3    
41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-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