-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_26/scaffold_26_743674-950102

-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: +)Couldn't classify 155318, 155770
Sorry, prediction pasa_asmbl_34707.p1 fails validation.
(GTT)	 CA	155318-155770	GC	AGG
Valid prediction for GlimmerHMM_glimmerT_55034-T1
Valid prediction for CodingQuarry_transcript_40243-T1
Valid prediction for pasa_asmbl_34702.p1
Couldn't classify 33735, 33921
Sorry, prediction pasa_asmbl_34696.p1 fails validation.
(ATG)	 AG	29839-29886	GT	AGG
(TTC)	 AG	32220-32406	GT	AGG
(GAG)	 AG	32754-32830	GT	AGG
(ACC)	 AG	33338-33381	GT	AGG
(GAA)	 AG	33735-33921	GT	CTG
-recovered pasa_asmbl_34696.p1, initial, 29839, 29886
add_exon() Sorry, pasa_asmbl_34696.p1 32220-32406-terminal-3 is invalid.
-recovered pasa_asmbl_34696.p1, terminal, 32220, 32406
-recovered pasa_asmbl_34696.p1, internal, 29839, 29886
-recovered pasa_asmbl_34696.p1, internal, 32220, 32406
-recovered pasa_asmbl_34696.p1, internal, 32754, 32830
-recovered pasa_asmbl_34696.p1, internal, 33338, 33381
-recovered pasa_asmbl_34696.p1, internal, 33735, 33921
Valid prediction for GlimmerHMM_glimmerT_55030-T1
Valid prediction for GlimmerHMM_glimmerT_55016-T1
Valid prediction for Augustus_model.g36496.t1
Valid prediction for HiQ_model.g36493.t1
Valid prediction for GlimmerHMM_glimmerT_55012-T1
Valid prediction for GlimmerHMM_glimmerT_55020-T1
Valid prediction for Augustus_model.g36489.t1
Valid prediction for snap_scaffold_26-snap.177-T1
Valid prediction for snap_scaffold_26-snap.193-T1
Valid prediction for snap_scaffold_26-snap.175-T1
Valid prediction for snap_scaffold_26-snap.188-T1
Valid prediction for snap_scaffold_26-snap.164-T1
Valid prediction for snap_scaffold_26-snap.173-T1
Valid prediction for snap_scaffold_26-snap.196-T1
Valid prediction for GlimmerHMM_glimmerT_55024-T1
Valid prediction for pasa_asmbl_34710.p1
Valid prediction for HiQ_model.g36485.t1
Valid prediction for snap_scaffold_26-snap.166-T1
Valid prediction for Augustus_model.g36492.t1
Valid prediction for snap_scaffold_26-snap.187-T1
Valid prediction for GlimmerHMM_glimmerT_55010-T1
Valid prediction for GlimmerHMM_glimmerT_55025-T1
Valid prediction for GlimmerHMM_glimmerT_55011-T1
Couldn't classify 72282, 72444
Sorry, prediction pasa_asmbl_34699.p1 fails validation.
(ATG)	 TC	68221-68322	GT	AGG
(ATG)	 AG	70053-70137	GT	AGG
(GTA)	 AG	70940-70970	GT	AGG
(GGT)	 AG	71711-71757	GT	CAG
(TCA)	 AG	71831-71902	GT	CGG
(AGA)	 AG	72117-72174	GT	GAG
(GCA)	 AG	72282-72444	GT	AGG
-recovered pasa_asmbl_34699.p1, initial, 68221, 68322
-recovered pasa_asmbl_34699.p1, initial, 70053, 70137
-recovered pasa_asmbl_34699.p1, terminal, 72117, 72174
-recovered pasa_asmbl_34699.p1, internal, 70053, 70137
-recovered pasa_asmbl_34699.p1, internal, 70940, 70970
-recovered pasa_asmbl_34699.p1, internal, 71711, 71757
-recovered pasa_asmbl_34699.p1, internal, 71831, 71902
-recovered pasa_asmbl_34699.p1, internal, 72117, 72174
-recovered pasa_asmbl_34699.p1, internal, 72282, 72444
Valid prediction for Augustus_model.g36488.t1
Couldn't classify 74081, 74144
Couldn't classify 77229, 77389
Sorry, prediction pasa_asmbl_35335.p1 fails validation.
(AGG)	 CC	74081-74144	GT	AGG
(ACG)	 AG	74423-74523	GT	AGG
(GAC)	 AG	74875-75016	GT	AGG
(GAG)	 AG	77229-77389	GT	GGG
-recovered pasa_asmbl_35335.p1, internal, 74423, 74523
-recovered pasa_asmbl_35335.p1, internal, 74875, 75016
-recovered pasa_asmbl_35335.p1, internal, 77229, 77389
Valid prediction for snap_scaffold_26-snap.172-T1
Valid prediction for snap_scaffold_26-snap.185-T1
Valid prediction for snap_scaffold_26-snap.182-T1
Valid prediction for GlimmerHMM_glimmerT_55033-T1
Couldn't classify 148442, 148843
Sorry, prediction pasa_asmbl_34706.p1 fails validation.
(ATG)	 AG	148442-148843	TG	GCT
Valid prediction for GlimmerHMM_glimmerT_55021-T1
Valid prediction for CodingQuarry_transcript_40246-T1
Valid prediction for Augustus_model.g36494.t1
Valid prediction for Augustus_model.g36490.t1
Valid prediction for GlimmerHMM_glimmerT_55023-T1
Valid prediction for GlimmerHMM_glimmerT_55013-T1
Valid prediction for snap_scaffold_26-snap.159-T1
Valid prediction for Augustus_model.g36484.t1
Valid prediction for Augustus_model.g36482.t1
Valid prediction for Augustus_model.g36487.t1
Valid prediction for snap_scaffold_26-snap.178-T1
Valid prediction for CodingQuarry_transcript_40248-T1
Valid prediction for snap_scaffold_26-snap.160-T1
Valid prediction for snap_scaffold_26-snap.194-T1
Valid prediction for snap_scaffold_26-snap.191-T1
Valid prediction for Augustus_model.g36491.t1
Valid prediction for snap_scaffold_26-snap.169-T1
Valid prediction for GlimmerHMM_glimmerT_55028-T1
Valid prediction for GlimmerHMM_glimmerT_55019-T1
Valid prediction for GlimmerHMM_glimmerT_55029-T1
Valid prediction for snap_scaffold_26-snap.186-T1
Valid prediction for GlimmerHMM_glimmerT_55022-T1
Valid prediction for snap_scaffold_26-snap.162-T1
Valid prediction for snap_scaffold_26-snap.197-T1
Valid prediction for GlimmerHMM_glimmerT_55017-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_26-snap.180-T1
Valid prediction for snap_scaffold_26-snap.161-T1
Valid prediction for GlimmerHMM_glimmerT_55009-T1
Valid prediction for snap_scaffold_26-snap.190-T1
Valid prediction for GlimmerHMM_glimmerT_55026-T1
Valid prediction for GlimmerHMM_glimmerT_55014-T1
Valid prediction for GlimmerHMM_glimmerT_55032-T1
Valid prediction for snap_scaffold_26-snap.183-T1
Valid prediction for Augustus_model.g36486.t1
Valid prediction for snap_scaffold_26-snap.181-T1
Couldn't classify 192616, 192840
Couldn't classify 193574, 193723
Sorry, prediction pasa_asmbl_35909.p1 fails validation.
(GTT)	 GA	192616-192840	GT	AGG
(GAT)	 AG	193574-193723	GG	CAG
Valid prediction for snap_scaffold_26-snap.171-T1
Valid prediction for snap_scaffold_26-snap.168-T1
Valid prediction for snap_scaffold_26-snap.192-T1
Valid prediction for GlimmerHMM_glimmerT_55008-T1
Valid prediction for snap_scaffold_26-snap.158-T1
Valid prediction for snap_scaffold_26-snap.163-T1
Valid prediction for snap_scaffold_26-snap.184-T1
Valid prediction for snap_scaffold_26-snap.167-T1
Valid prediction for snap_scaffold_26-snap.176-T1
Valid prediction for snap_scaffold_26-snap.189-T1
Valid prediction for GlimmerHMM_glimmerT_55015-T1
Valid prediction for snap_scaffold_26-snap.174-T1
Valid prediction for GlimmerHMM_glimmerT_55027-T1
Valid prediction for GlimmerHMM_glimmerT_55035-T1
Valid prediction for GlimmerHMM_glimmerT_55031-T1
Valid prediction for Augustus_model.g36483.t1
Valid prediction for snap_scaffold_26-snap.198-T1
Valid prediction for snap_scaffold_26-snap.165-T1
Valid prediction for snap_scaffold_26-snap.170-T1
Valid prediction for snap_scaffold_26-snap.195-T1
Valid prediction for snap_scaffold_26-snap.179-T1
Valid prediction for GlimmerHMM_glimmerT_55018-T1
Valid prediction for Augustus_model.g36495.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5495, rend_intergenic: 3105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12932, rend_intergenic: 9945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29358, rend_intergenic: 25133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35944, rend_intergenic: 29839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42496, rend_intergenic: 39760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49529, rend_intergenic: 42815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59854, rend_intergenic: 51751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68288, rend_intergenic: 59872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79022, rend_intergenic: 70065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94116, rend_intergenic: 92996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94914, rend_intergenic: 94132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120594, rend_intergenic: 102546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127965, rend_intergenic: 121628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140334, rend_intergenic: 133595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155770, rend_intergenic: 150235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167849, rend_intergenic: 161509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168864, rend_intergenic: 168311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181150, rend_intergenic: 169487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181344, rend_intergenic: 181182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200075, rend_intergenic: 188244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200280, rend_intergenic: 200199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 206429
-exon list size: 370


building trellis

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26.3    
26.6    
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27.4    
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28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.6    
29.8    
30.1    
30.4    
30.6    
30.9    
31.2    
31.5    
31.7    
32.0    
32.3    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.7    
34.9    
35.2    
35.5    
35.8    
36.0    
36.3    
36.6    
36.8    
37.1    
37.4    
37.6    
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38.2    
38.4    
38.7    
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39.2    
39.5    
39.8    
40.1    
40.3    
40.6    
40.9    
41.1    
41.4    
41.7    
41.9    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.1    
44.4    
44.6    
44.9    
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45.4    
45.7    
46.0    
46.2    
46.5    
46.8    
47.0    
47.3    
47.6    
47.8    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
52.2    
52.4    
52.7    
53.0    
53.2    
53.5    
53.8    
54.0    
54.3    
54.6    
54.8    
55.1    
55.4    
55.6    
55.9    
56.2    
56.5    
56.7    
57.0    
57.3    
57.5    
57.8    
58.1    
58.3    
58.6    
58.9    
59.1    
59.4    
59.7    
59.9    
60.2    
60.5    
60.8    
61.0    
61.3    
61.6    
61.8    
62.1    
62.4    
62.6    
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63.2    
63.4    
63.7    
64.0    
64.2    
64.5    
64.8    
65.1    
65.3    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
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68.0    
68.3    
68.5    
68.8    
69.1    
69.4    
69.6    
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72.3    
72.6    
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73.7    
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75.0    
75.3    
75.5    
75.8    
76.1    
76.3    
76.6    
76.9    
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78.0    
78.2    
78.5    
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79.3    
79.6    
79.8    
80.1    
80.4    
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81.2    
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82.0    
82.3    
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83.1    
83.3    
83.6    
83.9    
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84.4    
84.7    
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85.5    
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86.0    
86.3    
86.6    
86.8    
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87.4    
87.6    
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88.2    
88.4    
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89.2    
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90.1    
90.3    
90.6    
90.9    
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91.4    
91.7    
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92.5    
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93.3    
93.5    
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94.6    
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95.4    
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96.2    
96.5    
96.8    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 5495, rend_intergenic: 3105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12932, rend_intergenic: 9945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29358, rend_intergenic: 25133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35944, rend_intergenic: 29839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42496, rend_intergenic: 39760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49529, rend_intergenic: 42815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59854, rend_intergenic: 51751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68288, rend_intergenic: 59872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79022, rend_intergenic: 70065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94116, rend_intergenic: 92996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94914, rend_intergenic: 94132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120594, rend_intergenic: 102546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127965, rend_intergenic: 121628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140334, rend_intergenic: 133595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155770, rend_intergenic: 150235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167849, rend_intergenic: 161509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168864, rend_intergenic: 168311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181150, rend_intergenic: 169487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181344, rend_intergenic: 181182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200075, rend_intergenic: 188244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200280, rend_intergenic: 200199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support