-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_4013730-4320876

-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.966-T1
Valid prediction for snap_scaffold_7-snap.972-T1
Valid prediction for Augustus_model.g11538.t1
Valid prediction for Augustus_model.g11516.t1
Valid prediction for GlimmerHMM_glimmerT_17275-T1
Couldn't classify 9704, 9728
Sorry, prediction pasa_asmbl_49710.p1 fails validation.
(AGT)	 AA	9704-9728	GT	AGG
(GAC)	 AG	12178-12339	GT	AGG
(AAT)	 AG	14928-15051	GT	CAG
(GCT)	 AG	15302-15527	GT	GAG
-recovered pasa_asmbl_49710.p1, terminal, 15302, 15527
-recovered pasa_asmbl_49710.p1, internal, 12178, 12339
-recovered pasa_asmbl_49710.p1, internal, 14928, 15051
-recovered pasa_asmbl_49710.p1, internal, 15302, 15527
Valid prediction for snap_scaffold_7-snap.975-T1
Valid prediction for GlimmerHMM_glimmerT_17272-T1
Valid prediction for CodingQuarry_transcript_57487-T1
Valid prediction for snap_scaffold_7-snap.950-T1
Valid prediction for GlimmerHMM_glimmerT_17259-T1
Couldn't classify 39651, 39708
Sorry, prediction pasa_asmbl_49717.p1 fails validation.
(GCC)	 AG	39651-39708	GT	AGG
(CGA)	 AG	39859-39946	GT	TTG
(CTT)	 AG	40902-41032	GT	AGG
(TGC)	 AG	41230-41344	GT	AGG
(AGA)	 AG	41622-41740	GT	TGG
(GTG)	 AG	41847-41937	GT	AGG
(GTA)	 AG	44072-44167	GT	AGG
(AGG)	 AG	44297-44390	GT	AGG
(AGG)	 AG	44735-44892	GT	AAG
(ACC)	 AG	45023-45131	GA	AGG
-recovered pasa_asmbl_49717.p1, terminal, 45023, 45131
-recovered pasa_asmbl_49717.p1, internal, 39651, 39708
-recovered pasa_asmbl_49717.p1, internal, 39859, 39946
-recovered pasa_asmbl_49717.p1, internal, 40902, 41032
-recovered pasa_asmbl_49717.p1, internal, 41230, 41344
-recovered pasa_asmbl_49717.p1, internal, 41622, 41740
-recovered pasa_asmbl_49717.p1, internal, 41847, 41937
-recovered pasa_asmbl_49717.p1, internal, 44072, 44167
-recovered pasa_asmbl_49717.p1, internal, 44297, 44390
-recovered pasa_asmbl_49717.p1, internal, 44735, 44892
Valid prediction for Augustus_model.g11523.t1
Valid prediction for GlimmerHMM_glimmerT_17261-T1
Valid prediction for CodingQuarry_transcript_57488-T1
Valid prediction for snap_scaffold_7-snap.951-T1
Valid prediction for HiQ_model.g11519.t1
Valid prediction for snap_scaffold_7-snap.940-T1
Valid prediction for Augustus_model.g11528.t1
Valid prediction for GlimmerHMM_glimmerT_17264-T1
Valid prediction for Augustus_model.g11525.t1
Valid prediction for pasa_asmbl_49726.p1
Valid prediction for Augustus_model.g11532.t1
Valid prediction for CodingQuarry_transcript_57489-T1
Valid prediction for snap_scaffold_7-snap.967-T1
Valid prediction for Augustus_model.g11524.t1
Valid prediction for GlimmerHMM_glimmerT_17280-T1
Valid prediction for GlimmerHMM_glimmerT_17258-T1
Valid prediction for snap_scaffold_7-snap.941-T1
Valid prediction for Augustus_model.g11536.t1
Couldn't classify 81814, 81898
Sorry, prediction pasa_asmbl_49722.p1 fails validation.
(ATG)	 CG	74097-74171	GT	CGG
(GTC)	 AG	75225-75281	GT	CAG
(GAA)	 AG	75393-75502	GT	CTG
(CCA)	 AG	75605-76643	GT	AGG
(GGT)	 AG	76775-76874	GT	AGG
(AAG)	 AG	76949-77119	GT	CTG
(TGC)	 AG	77210-77307	GT	CAG
(GTC)	 AG	77598-77778	GT	AGG
(GGC)	 AG	80268-80391	GT	AGG
(TGT)	 AG	81814-81898	CC	CAC
-recovered pasa_asmbl_49722.p1, initial, 74097, 74171
-recovered pasa_asmbl_49722.p1, internal, 75225, 75281
-recovered pasa_asmbl_49722.p1, internal, 75393, 75502
-recovered pasa_asmbl_49722.p1, internal, 75605, 76643
-recovered pasa_asmbl_49722.p1, internal, 76775, 76874
-recovered pasa_asmbl_49722.p1, internal, 76949, 77119
-recovered pasa_asmbl_49722.p1, internal, 77210, 77307
-recovered pasa_asmbl_49722.p1, internal, 77598, 77778
-recovered pasa_asmbl_49722.p1, internal, 80268, 80391
Valid prediction for snap_scaffold_7-snap.971-T1
Valid prediction for GlimmerHMM_glimmerT_17251-T1
Valid prediction for snap_scaffold_7-snap.956-T1
Valid prediction for GlimmerHMM_glimmerT_17250-T1
Valid prediction for HiQ_model.g11534.t1
Valid prediction for snap_scaffold_7-snap.982-T1
Valid prediction for snap_scaffold_7-snap.979-T1
Valid prediction for GlimmerHMM_glimmerT_17254-T1
Valid prediction for snap_scaffold_7-snap.974-T1
Valid prediction for snap_scaffold_7-snap.957-T1
Valid prediction for GlimmerHMM_glimmerT_17277-T1
Valid prediction for GlimmerHMM_glimmerT_17263-T1
Valid prediction for snap_scaffold_7-snap.980-T1
Valid prediction for CodingQuarry_transcript_57480-T1
Valid prediction for snap_scaffold_7-snap.949-T1
Valid prediction for snap_scaffold_7-snap.978-T1
Valid prediction for snap_scaffold_7-snap.952-T1
Valid prediction for HiQ_model.g11517.t1
Valid prediction for GlimmerHMM_glimmerT_17270-T1
Valid prediction for snap_scaffold_7-snap.969-T1
Valid prediction for GlimmerHMM_glimmerT_17267-T1
Valid prediction for snap_scaffold_7-snap.946-T1
Valid prediction for HiQ_model.g11530.t1
Couldn't classify 207425, 207833
Sorry, prediction pasa_asmbl_49729.p1 fails validation.
(GTC)	 CA	207425-207833	GT	ACG
(GAA)	 AG	208032-208082	GT	TGG
(CTT)	 AG	208332-208442	GT	ACG
(GTG)	 AG	208627-208654	GT	AGG
(CGA)	 AG	208960-209135	GT	AAG
(ATC)	 AG	211267-211304	GG	GAG
-recovered pasa_asmbl_49729.p1, terminal, 211267, 211304
-recovered pasa_asmbl_49729.p1, internal, 208032, 208082
-recovered pasa_asmbl_49729.p1, internal, 208332, 208442
-recovered pasa_asmbl_49729.p1, internal, 208627, 208654
-recovered pasa_asmbl_49729.p1, internal, 208960, 209135

-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_17260-T1
Valid prediction for Augustus_model.g11541.t1
Valid prediction for GlimmerHMM_glimmerT_17257-T1
Valid prediction for snap_scaffold_7-snap.981-T1
Valid prediction for GlimmerHMM_glimmerT_17266-T1
Valid prediction for snap_scaffold_7-snap.939-T1
Valid prediction for Augustus_model.g11531.t1
Valid prediction for pasa_asmbl_50856.p1
Valid prediction for snap_scaffold_7-snap.944-T1
Valid prediction for snap_scaffold_7-snap.964-T1
Valid prediction for CodingQuarry_transcript_57486-T1
Valid prediction for snap_scaffold_7-snap.938-T1
Valid prediction for snap_scaffold_7-snap.973-T1
Valid prediction for CodingQuarry_transcript_57483-T1
Valid prediction for snap_scaffold_7-snap.943-T1
Valid prediction for Augustus_model.g11526.t1
Valid prediction for Augustus_model.g11529.t1
Valid prediction for snap_scaffold_7-snap.945-T1
Valid prediction for snap_scaffold_7-snap.953-T1
Valid prediction for snap_scaffold_7-snap.965-T1
Valid prediction for GlimmerHMM_glimmerT_17271-T1
Valid prediction for snap_scaffold_7-snap.968-T1
Valid prediction for snap_scaffold_7-snap.942-T1
Valid prediction for Augustus_model.g11542.t1
Valid prediction for snap_scaffold_7-snap.954-T1
Valid prediction for snap_scaffold_7-snap.958-T1
Couldn't classify 276238, 276321
Sorry, prediction pasa_asmbl_50845.p1 fails validation.
(TAC)	 TC	276238-276321	GC	AGG
(AAT)	 AG	276457-276624	GT	AGG
(GCG)	 AG	276710-277084	GT	AGG
(GAG)	 AG	277176-277366	GT	AGG
(GTA)	 AG	277549-277691	GT	AGG
(GGA)	 AG	279614-279724	GT	TGG
(GTT)	 AG	279948-280052	GT	AAG
(ATT)	 AG	280207-280358	TG	AGT
-recovered pasa_asmbl_50845.p1, terminal, 280207, 280358
-recovered pasa_asmbl_50845.p1, internal, 276457, 276624
-recovered pasa_asmbl_50845.p1, internal, 276710, 277084
-recovered pasa_asmbl_50845.p1, internal, 277176, 277366
-recovered pasa_asmbl_50845.p1, internal, 277549, 277691
-recovered pasa_asmbl_50845.p1, internal, 279614, 279724
-recovered pasa_asmbl_50845.p1, internal, 279948, 280052
Valid prediction for snap_scaffold_7-snap.959-T1
Valid prediction for GlimmerHMM_glimmerT_17256-T1
Valid prediction for snap_scaffold_7-snap.955-T1
Valid prediction for snap_scaffold_7-snap.947-T1
Valid prediction for GlimmerHMM_glimmerT_17265-T1
Valid prediction for GlimmerHMM_glimmerT_17278-T1
Valid prediction for GlimmerHMM_glimmerT_17268-T1
Couldn't classify 275699, 275832
Sorry, prediction pasa_asmbl_50850.p1 fails validation.
(ATG)	 CC	273972-274072	GT	AAG
(GAT)	 AG	274487-274541	GT	AAG
(TCT)	 AG	275327-275448	GT	AGG
(GAC)	 AG	275545-275624	GT	TGG
(GAT)	 AG	275699-275832	TG	GGT
-recovered pasa_asmbl_50850.p1, initial, 273972, 274072
-recovered pasa_asmbl_50850.p1, internal, 274487, 274541
-recovered pasa_asmbl_50850.p1, internal, 275327, 275448
-recovered pasa_asmbl_50850.p1, internal, 275545, 275624
Valid prediction for GlimmerHMM_glimmerT_17276-T1
Valid prediction for Augustus_model.g11539.t1
Valid prediction for snap_scaffold_7-snap.963-T1
Valid prediction for Augustus_model.g11537.t1
Valid prediction for GlimmerHMM_glimmerT_17252-T1
Valid prediction for GlimmerHMM_glimmerT_17255-T1
Valid prediction for snap_scaffold_7-snap.976-T1
Valid prediction for pasa_asmbl_50855.p1
Couldn't classify 157264, 157302
Couldn't classify 164519, 164600
Sorry, prediction pasa_asmbl_50857.p1 fails validation.
(TTT)	 TG	157264-157302	GT	AGG
(GTG)	 AG	157753-157852	GT	AGG
(GGA)	 AG	158433-158477	GT	AGG
(ATG)	 AG	161171-161221	GT	AGG
(ACA)	 AG	161330-161404	GT	ATG
(CCT)	 AG	162890-163076	GT	AGG
(ATA)	 AG	164519-164600	GG	AAG
-recovered pasa_asmbl_50857.p1, initial, 161171, 161221
-recovered pasa_asmbl_50857.p1, internal, 157753, 157852
-recovered pasa_asmbl_50857.p1, internal, 158433, 158477
-recovered pasa_asmbl_50857.p1, internal, 161171, 161221
-recovered pasa_asmbl_50857.p1, internal, 161330, 161404
-recovered pasa_asmbl_50857.p1, internal, 162890, 163076
Valid prediction for Augustus_model.g11540.t1
Valid prediction for Augustus_model.g11533.t1
Valid prediction for snap_scaffold_7-snap.962-T1
Valid prediction for Augustus_model.g11518.t1
Valid prediction for snap_scaffold_7-snap.977-T1
Valid prediction for snap_scaffold_7-snap.960-T1
Valid prediction for Augustus_model.g11522.t1
Valid prediction for pasa_asmbl_50851.p1
Valid prediction for CodingQuarry_transcript_57485-T1
Valid prediction for GlimmerHMM_glimmerT_17273-T1
Valid prediction for snap_scaffold_7-snap.970-T1
Valid prediction for GlimmerHMM_glimmerT_17269-T1
Valid prediction for GlimmerHMM_glimmerT_17274-T1
Valid prediction for snap_scaffold_7-snap.948-T1
Valid prediction for snap_scaffold_7-snap.961-T1
Valid prediction for HiQ_model.g11521.t1
Valid prediction for GlimmerHMM_glimmerT_17262-T1
Valid prediction for Augustus_model.g11520.t1
Valid prediction for Augustus_model.g11527.t1
Valid prediction for Augustus_model.g11535.t1
Valid prediction for CodingQuarry_transcript_57484-T1
Valid prediction for GlimmerHMM_glimmerT_17279-T1
Valid prediction for CodingQuarry_transcript_57482-T1
Valid prediction for GlimmerHMM_glimmerT_17253-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 207811, rend_intergenic: 205184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222189, rend_intergenic: 220669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223324, rend_intergenic: 222757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 292864, rend_intergenic: 288368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 307147
-exon list size: 442


building trellis

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11.9    
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13.5    
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14.9    
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15.5    
15.8    
16.0    
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16.4    
16.7    
16.9    
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17.6    
17.8    
18.0    
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18.5    
18.7    
18.9    
19.1    
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19.6    
19.8    
20.0    
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20.5    
20.7    
20.9    
21.2    
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21.6    
21.8    
22.1    
22.3    
22.5    
22.7    
23.0    
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23.6    
23.9    
24.1    
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25.9    
26.1    
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26.8    
27.0    
27.3    
27.5    
27.7    
27.9    
28.2    
28.4    
28.6    
28.8    
29.1    
29.3    
29.5    
29.7    
30.0    
30.2    
30.4    
30.6    
30.9    
31.1    
31.3    
31.5    
31.8    
32.0    
32.2    
32.4    
32.7    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.5    
34.7    
34.9    
35.1    
35.4    
35.6    
35.8    
36.0    
36.3    
36.5    
36.7    
36.9    
37.2    
37.4    
37.6    
37.8    
38.1    
38.3    
38.5    
38.7    
39.0    
39.2    
39.4    
39.6    
39.9    
40.1    
40.3    
40.5    
40.8    
41.0    
41.2    
41.4    
41.7    
41.9    
42.1    
42.3    
42.6    
42.8    
43.0    
43.2    
43.5    
43.7    
43.9    
44.1    
44.4    
44.6    
44.8    
45.0    
45.3    
45.5    
45.7    
45.9    
46.2    
46.4    
46.6    
46.8    
47.1    
47.3    
47.5    
47.7    
48.0    
48.2    
48.4    
48.6    
48.9    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.1    
51.4    
51.6    
51.8    
52.0    
52.3    
52.5    
52.7    
52.9    
53.2    
53.4    
53.6    
53.8    
54.1    
54.3    
54.5    
54.7    
55.0    
55.2    
55.4    
55.6    
55.9    
56.1    
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56.5    
56.8    
57.0    
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57.4    
57.7    
57.9    
58.1    
58.3    
58.6    
58.8    
59.0    
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59.5    
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59.9    
60.1    
60.4    
60.6    
60.8    
61.0    
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61.5    
61.7    
61.9    
62.2    
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62.6    
62.8    
63.1    
63.3    
63.5    
63.7    
64.0    
64.2    
64.4    
64.6    
64.9    
65.1    
65.3    
65.5    
65.8    
66.0    
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66.4    
66.7    
66.9    
67.1    
67.3    
67.6    
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68.0    
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68.9    
69.1    
69.4    
69.6    
69.8    
70.0    
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70.7    
70.9    
71.2    
71.4    
71.6    
71.8    
72.1    
72.3    
72.5    
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73.0    
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73.4    
73.6    
73.9    
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74.3    
74.5    
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75.9    
76.1    
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76.8    
77.0    
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77.9    
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78.8    
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80.0    
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80.9    
81.1    
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81.8    
82.0    
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82.9    
83.1    
83.3    
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84.9    
85.1    
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85.8    
86.0    
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86.9    
87.2    
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87.6    
87.8    
88.1    
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88.7    
89.0    
89.2    
89.4    
89.6    
89.9    
90.1    
90.3    
90.5    
90.8    
91.0    
91.2    
91.4    
91.7    
91.9    
92.1    
92.3    
92.6    
92.8    
93.0    
93.2    
93.5    
93.7    
93.9    
94.1    
94.4    
94.6    
94.8    
95.0    
95.3    
95.5    
95.7    
95.9    
96.2    
96.4    
96.6    
96.8    
97.1    
97.3    
97.5    
97.7    
98.0    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 207811, rend_intergenic: 205184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222189, rend_intergenic: 220669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223324, rend_intergenic: 222757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 292864, rend_intergenic: 288368  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 35 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 292242 - 307147
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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 292621 - 307147
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support