-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_449026-786066

-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_21-snap.128-T1
Valid prediction for snap_scaffold_21-snap.117-T1
Valid prediction for Augustus_model.g31308.t1
Valid prediction for pasa_asmbl_28265.p1
Valid prediction for snap_scaffold_21-snap.89-T1
Valid prediction for Augustus_model.g31310.t1
Valid prediction for Augustus_model.g31298.t1
Valid prediction for snap_scaffold_21-snap.127-T1
Valid prediction for Augustus_model.g31305.t1
Valid prediction for GlimmerHMM_glimmerT_47000-T1
Valid prediction for snap_scaffold_21-snap.82-T1
Couldn't classify 245210, 245359
Sorry, prediction pasa_asmbl_28284.p1 fails validation.
(ATG)	 AG	241785-241841	GT	GGG
(GAG)	 AG	242848-242991	GT	AGG
(CCC)	 AG	245210-245359	GT	AGG
-recovered pasa_asmbl_28284.p1, initial, 241785, 241841
-recovered pasa_asmbl_28284.p1, internal, 241785, 241841
-recovered pasa_asmbl_28284.p1, internal, 242848, 242991
-recovered pasa_asmbl_28284.p1, internal, 245210, 245359
Valid prediction for GlimmerHMM_glimmerT_47028-T1
Valid prediction for GlimmerHMM_glimmerT_46999-T1
Valid prediction for GlimmerHMM_glimmerT_47002-T1
Valid prediction for snap_scaffold_21-snap.81-T1
Couldn't classify 155426, 155591
Sorry, prediction pasa_asmbl_28281.p1 fails validation.
(AGG)	 AC	155426-155591	GT	AGG
(ACC)	 AG	157640-157843	GT	GAG
(GAG)	 AG	160601-160672	GT	AGG
(ACT)	 AG	161170-161232	GT	AGG
(GTT)	 AG	161523-161579	GT	AGG
(ATC)	 AG	161670-161717	GT	AGG
(GCT)	 AG	161994-162514	AC	AGA
add_exon() Sorry, pasa_asmbl_28281.p1 161523-161579-terminal-1 is invalid.
-recovered pasa_asmbl_28281.p1, terminal, 161523, 161579
-recovered pasa_asmbl_28281.p1, terminal, 161994, 162514
-recovered pasa_asmbl_28281.p1, internal, 157640, 157843
-recovered pasa_asmbl_28281.p1, internal, 160601, 160672
-recovered pasa_asmbl_28281.p1, internal, 161170, 161232
-recovered pasa_asmbl_28281.p1, internal, 161523, 161579
-recovered pasa_asmbl_28281.p1, internal, 161670, 161717
Valid prediction for snap_scaffold_21-snap.95-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_32417-T1
Valid prediction for snap_scaffold_21-snap.97-T1
Valid prediction for HiQ_model.g31320.t1
Valid prediction for GlimmerHMM_glimmerT_47004-T1
Valid prediction for GlimmerHMM_glimmerT_47012-T1
Valid prediction for GlimmerHMM_glimmerT_47015-T1
Couldn't classify 249428, 249511
Sorry, prediction pasa_asmbl_28286.p1 fails validation.
(CAG)	 TC	249428-249511	GT	AGG
(CCA)	 AG	249727-249801	GT	AGG
(CGG)	 AG	249902-250052	GT	TGG
(GCT)	 AG	250664-250816	GT	TGG
(AGT)	 AG	251640-251722	AA	AGA
-recovered pasa_asmbl_28286.p1, terminal, 251640, 251722
-recovered pasa_asmbl_28286.p1, internal, 249727, 249801
-recovered pasa_asmbl_28286.p1, internal, 249902, 250052
-recovered pasa_asmbl_28286.p1, internal, 250664, 250816
Valid prediction for Augustus_model.g31314.t1
Valid prediction for pasa_asmbl_28302.p1
Valid prediction for GlimmerHMM_glimmerT_47006-T1
Valid prediction for snap_scaffold_21-snap.104-T1
Valid prediction for GlimmerHMM_glimmerT_47009-T1
Valid prediction for Augustus_model.g31294.t1
Valid prediction for snap_scaffold_21-snap.102-T1
Valid prediction for snap_scaffold_21-snap.110-T1
Valid prediction for snap_scaffold_21-snap.112-T1
Valid prediction for CodingQuarry_transcript_32421-T1
Valid prediction for HiQ_model.g31293.t1
Valid prediction for GlimmerHMM_glimmerT_47021-T1
Valid prediction for snap_scaffold_21-snap.93-T1
Valid prediction for HiQ_model.g31323.t1
Valid prediction for snap_scaffold_21-snap.86-T1
Valid prediction for pasa_asmbl_28267.p1
Valid prediction for snap_scaffold_21-snap.88-T1
Valid prediction for HiQ_model.g31317.t1
Valid prediction for GlimmerHMM_glimmerT_47011-T1
Valid prediction for snap_scaffold_21-snap.125-T1
Valid prediction for snap_scaffold_21-snap.96-T1
Valid prediction for snap_scaffold_21-snap.116-T1
Valid prediction for Augustus_model.g31324.t1
Valid prediction for snap_scaffold_21-snap.101-T1
Valid prediction for snap_scaffold_21-snap.114-T1
Valid prediction for snap_scaffold_21-snap.105-T1
Valid prediction for GlimmerHMM_glimmerT_47022-T1
Valid prediction for Augustus_model.g31300.t1
Valid prediction for snap_scaffold_21-snap.126-T1
Valid prediction for HiQ_model.g31326.t1
Valid prediction for CodingQuarry_transcript_32420-T1
Valid prediction for Augustus_model.g31325.t1
Valid prediction for GlimmerHMM_glimmerT_47031-T1
Valid prediction for snap_scaffold_21-snap.115-T1
Valid prediction for pasa_asmbl_28276.p1
Valid prediction for snap_scaffold_21-snap.98-T1
Valid prediction for snap_scaffold_21-snap.87-T1
Couldn't classify 287346, 287681
Couldn't classify 292035, 292139
Sorry, prediction pasa_asmbl_28295.p1 fails validation.
(GTT)	 AT	287346-287681	GT	AGG
(GTA)	 AG	289263-289425	GT	TTG
(CTG)	 AG	289778-290820	GT	AGG
(GTC)	 AG	290976-291155	GT	AGG
(ATC)	 AG	292035-292139	AC	GAA
-recovered pasa_asmbl_28295.p1, internal, 289263, 289425
-recovered pasa_asmbl_28295.p1, internal, 289778, 290820
-recovered pasa_asmbl_28295.p1, internal, 290976, 291155
Valid prediction for snap_scaffold_21-snap.103-T1
Valid prediction for snap_scaffold_21-snap.84-T1
Valid prediction for Augustus_model.g31315.t1
Valid prediction for GlimmerHMM_glimmerT_47024-T1
Valid prediction for snap_scaffold_21-snap.83-T1
Valid prediction for GlimmerHMM_glimmerT_47032-T1
Valid prediction for snap_scaffold_21-snap.99-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for HiQ_model.g31306.t1
Valid prediction for pasa_asmbl_28272.p1

-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 74374, 74406
Sorry, prediction pasa_asmbl_27354.p1 fails validation.
(GTC)	 TC	74374-74406	GT	ATG
(ACT)	 AG	74495-74551	GT	AGG
(AAC)	 AG	74645-74718	GT	TTG
(AAT)	 AG	74809-74964	GT	GAG
(CTA)	 AG	75096-75744	GT	AGG
(GCA)	 AG	75880-75948	GT	ATG
(GGG)	 AG	76094-76243	GT	AGG
(ATC)	 AG	76344-76483	GT	AGG
(TTT)	 AG	77277-77345	GC	AGG
(CAA)	 AG	78012-78108	GT	AGG
(GTT)	 AG	78333-78436	GT	AGG
(ATA)	 AG	78805-78889	GT	AGG
(GCT)	 AG	78979-79185	AG	AAA
add_exon() Sorry, pasa_asmbl_27354.p1 74809-74964-terminal-1 is invalid.
-recovered pasa_asmbl_27354.p1, terminal, 74809, 74964
-recovered pasa_asmbl_27354.p1, terminal, 78979, 79185
-recovered pasa_asmbl_27354.p1, internal, 74495, 74551
-recovered pasa_asmbl_27354.p1, internal, 74645, 74718
-recovered pasa_asmbl_27354.p1, internal, 74809, 74964
-recovered pasa_asmbl_27354.p1, internal, 75096, 75744
-recovered pasa_asmbl_27354.p1, internal, 75880, 75948
-recovered pasa_asmbl_27354.p1, internal, 76094, 76243
-recovered pasa_asmbl_27354.p1, internal, 76344, 76483
-recovered pasa_asmbl_27354.p1, internal, 77277, 77345
-recovered pasa_asmbl_27354.p1, internal, 78012, 78108
-recovered pasa_asmbl_27354.p1, internal, 78333, 78436
-recovered pasa_asmbl_27354.p1, internal, 78805, 78889
Valid prediction for snap_scaffold_21-snap.129-T1
Valid prediction for CodingQuarry_transcript_32419-T1
Valid prediction for snap_scaffold_21-snap.124-T1
Valid prediction for snap_scaffold_21-snap.108-T1
Valid prediction for GlimmerHMM_glimmerT_47005-T1
Valid prediction for HiQ_model.g31291.t1
Valid prediction for Augustus_model.g31322.t1
Valid prediction for Augustus_model.g31304.t1
Valid prediction for Augustus_model.g31312.t1
Valid prediction for GlimmerHMM_glimmerT_47016-T1
Valid prediction for GlimmerHMM_glimmerT_47025-T1
Valid prediction for snap_scaffold_21-snap.107-T1
Valid prediction for CodingQuarry_transcript_32414-T1
Valid prediction for HiQ_model.g31292.t1
Valid prediction for Augustus_model.g31327.t1
Valid prediction for snap_scaffold_21-snap.111-T1
Valid prediction for snap_scaffold_21-snap.109-T1
Valid prediction for GlimmerHMM_glimmerT_47030-T1
Valid prediction for Augustus_model.g31303.t1
Couldn't classify 321475, 321476
Couldn't classify 321869, 322013
Sorry, prediction CodingQuarry_transcript_32415-T1 fails validation.
(ATC)	 AT	321475-321476	CC	ATC
(GGA)	 AT	321869-322013	GC	TGG
(GTC)	 AG	322153-322288	GT	TGG
(GAT)	 AG	322390-322553	GT	ATG
(TGC)	 AG	322663-322910	GT	AAG
(GCC)	 AG	323114-323315	GT	AGG
(ATG)	 AG	323398-323549	GT	CGG
(CAC)	 AG	324188-324374	GC	AGG
(AGC)	 AG	324470-324613	GT	AGG
(AAC)	 AG	324864-325061	GT	AGG
(GCC)	 AG	325415-325576	GT	AGG
(AGG)	 AG	325739-325872	GT	CTG
(CTA)	 AG	326021-326223	GT	GGG
(TGG)	 AG	326393-326564	GT	AGG
(TGC)	 AG	326988-327210	GT	AGG
(TTG)	 AG	327511-327678	AC	AAA
-recovered CodingQuarry_transcript_32415-T1, initial, 323398, 323549
-recovered CodingQuarry_transcript_32415-T1, terminal, 327511, 327678
-recovered CodingQuarry_transcript_32415-T1, internal, 322153, 322288
-recovered CodingQuarry_transcript_32415-T1, internal, 322390, 322553
-recovered CodingQuarry_transcript_32415-T1, internal, 322663, 322910
-recovered CodingQuarry_transcript_32415-T1, internal, 323114, 323315
-recovered CodingQuarry_transcript_32415-T1, internal, 323398, 323549
-recovered CodingQuarry_transcript_32415-T1, internal, 324188, 324374
-recovered CodingQuarry_transcript_32415-T1, internal, 324470, 324613
-recovered CodingQuarry_transcript_32415-T1, internal, 324864, 325061
-recovered CodingQuarry_transcript_32415-T1, internal, 325415, 325576
-recovered CodingQuarry_transcript_32415-T1, internal, 325739, 325872
-recovered CodingQuarry_transcript_32415-T1, internal, 326021, 326223
-recovered CodingQuarry_transcript_32415-T1, internal, 326393, 326564
-recovered CodingQuarry_transcript_32415-T1, internal, 326988, 327210
Valid prediction for snap_scaffold_21-snap.80-T1
Valid prediction for CodingQuarry_transcript_32418-T1
Couldn't classify 60922, 60998
Sorry, prediction pasa_asmbl_27360.p1 fails validation.
(AGT)	 AA	60922-60998	GT	CAG
(CCC)	 AG	61152-61214	GT	CTG
(GAA)	 AG	61307-61361	GT	AGG
(GGT)	 AG	61782-61944	GT	AGG
(CTG)	 AG	63019-63058	GT	AGG
(ACC)	 AG	63316-63421	GT	AGG
(AAT)	 AG	63548-63584	GT	AAG
(TCT)	 AG	64309-64529	CG	GAC
-recovered pasa_asmbl_27360.p1, terminal, 64309, 64529
-recovered pasa_asmbl_27360.p1, internal, 61152, 61214
-recovered pasa_asmbl_27360.p1, internal, 61307, 61361
-recovered pasa_asmbl_27360.p1, internal, 61782, 61944
-recovered pasa_asmbl_27360.p1, internal, 63019, 63058
-recovered pasa_asmbl_27360.p1, internal, 63316, 63421
-recovered pasa_asmbl_27360.p1, internal, 63548, 63584
Valid prediction for snap_scaffold_21-snap.123-T1
Valid prediction for GlimmerHMM_glimmerT_46997-T1
Valid prediction for snap_scaffold_21-snap.79-T1
Valid prediction for Augustus_model.g31321.t1
Valid prediction for snap_scaffold_21-snap.78-T1
Couldn't classify 72401, 72418
Couldn't classify 73990, 74084
Sorry, prediction pasa_asmbl_27358.p1 fails validation.
(GGT)	 CA	72401-72418	GT	AGG
(TTT)	 AG	72506-72570	GT	AGG
(TGT)	 AG	72660-72799	GT	AAG
(ATC)	 AG	72963-73289	GT	CGG
(GCA)	 AG	73990-74084	AT	ACA
add_exon() Sorry, pasa_asmbl_27358.p1 72506-72570-terminal-2 is invalid.
-recovered pasa_asmbl_27358.p1, terminal, 72506, 72570
-recovered pasa_asmbl_27358.p1, internal, 72506, 72570
-recovered pasa_asmbl_27358.p1, internal, 72660, 72799
-recovered pasa_asmbl_27358.p1, internal, 72963, 73289
Valid prediction for GlimmerHMM_glimmerT_47010-T1
Valid prediction for snap_scaffold_21-snap.85-T1
Valid prediction for pasa_asmbl_27356.p1
Valid prediction for snap_scaffold_21-snap.91-T1
Valid prediction for Augustus_model.g31295.t1
Valid prediction for GlimmerHMM_glimmerT_47013-T1
Couldn't classify 69275, 69276
Couldn't classify 70908, 70961
Sorry, prediction pasa_asmbl_27359.p1 fails validation.
(ATG)	 GA	69275-69276	GT	ATG
(GGA)	 AG	69359-69449	GT	GGG
(CCG)	 AG	69763-69915	GT	AGG
(GAA)	 AG	70728-70808	GT	AGG
(GAA)	 AG	70908-70961	AC	GAA
-recovered pasa_asmbl_27359.p1, internal, 69359, 69449
-recovered pasa_asmbl_27359.p1, internal, 69763, 69915
-recovered pasa_asmbl_27359.p1, internal, 70728, 70808
Valid prediction for GlimmerHMM_glimmerT_47007-T1
Valid prediction for GlimmerHMM_glimmerT_47018-T1
Valid prediction for GlimmerHMM_glimmerT_47003-T1
Valid prediction for Augustus_model.g31296.t1
Valid prediction for Augustus_model.g31319.t1
Valid prediction for GlimmerHMM_glimmerT_47035-T1
Valid prediction for snap_scaffold_21-snap.94-T1
Valid prediction for GlimmerHMM_glimmerT_47023-T1
Couldn't classify 82020, 82327
Sorry, prediction pasa_asmbl_27346.p1 fails validation.
(CTA)	 AG	82020-82327	GT	AGG
(ACC)	 AG	82470-82596	GT	AGG
(AAT)	 AG	83501-83638	GT	CGG
(CTG)	 AG	83937-84029	GT	AGG
(TGT)	 AG	84184-84312	AC	AAA
-recovered pasa_asmbl_27346.p1, terminal, 84184, 84312
-recovered pasa_asmbl_27346.p1, internal, 82020, 82327
-recovered pasa_asmbl_27346.p1, internal, 82470, 82596
-recovered pasa_asmbl_27346.p1, internal, 83501, 83638
-recovered pasa_asmbl_27346.p1, internal, 83937, 84029
Valid prediction for CodingQuarry_transcript_32416-T1
Valid prediction for pasa_asmbl_27328.p1
Valid prediction for GlimmerHMM_glimmerT_47029-T1
Valid prediction for snap_scaffold_21-snap.90-T1
Valid prediction for GlimmerHMM_glimmerT_46998-T1
Valid prediction for snap_scaffold_21-snap.119-T1
Valid prediction for Augustus_model.g31297.t1
Valid prediction for snap_scaffold_21-snap.122-T1
Valid prediction for pasa_asmbl_27339.p1
Valid prediction for snap_scaffold_21-snap.113-T1
Valid prediction for GlimmerHMM_glimmerT_47017-T1
Valid prediction for Augustus_model.g31302.t1
Valid prediction for GlimmerHMM_glimmerT_47014-T1
Valid prediction for GlimmerHMM_glimmerT_47034-T1
Valid prediction for GlimmerHMM_glimmerT_47026-T1
Valid prediction for GlimmerHMM_glimmerT_47033-T1
Valid prediction for pasa_asmbl_27321.p1
Valid prediction for Augustus_model.g31313.t1
Valid prediction for GlimmerHMM_glimmerT_47001-T1
Valid prediction for HiQ_model.g31316.t1
Valid prediction for GlimmerHMM_glimmerT_47020-T1
Valid prediction for Augustus_model.g31301.t1
Valid prediction for snap_scaffold_21-snap.92-T1
Valid prediction for GlimmerHMM_glimmerT_47008-T1
Valid prediction for snap_scaffold_21-snap.106-T1
Valid prediction for snap_scaffold_21-snap.121-T1
Valid prediction for Augustus_model.g31307.t1
Valid prediction for pasa_asmbl_27326.p1
Valid prediction for snap_scaffold_21-snap.120-T1
Valid prediction for Augustus_model.g31318.t1
Couldn't classify 276380, 276929
Couldn't classify 277537, 277548
Sorry, prediction pasa_asmbl_27331.p1 fails validation.
(GCT)	 GA	276380-276929	GT	AGG
(CTG)	 AG	277126-277328	GT	AGG
(GTT)	 AG	277537-277548	GA	GTG
-recovered pasa_asmbl_27331.p1, internal, 277126, 277328
Valid prediction for snap_scaffold_21-snap.118-T1
Valid prediction for HiQ_model.g31299.t1
Valid prediction for HiQ_model.g31309.t1
Valid prediction for Augustus_model.g31311.t1
Valid prediction for GlimmerHMM_glimmerT_47027-T1
Valid prediction for GlimmerHMM_glimmerT_47019-T1
Valid prediction for snap_scaffold_21-snap.100-T1
Valid prediction for snap_scaffold_21-snap.130-T1
Valid prediction for pasa_asmbl_27335.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)
-building DP trellis

-building trellis in range 1 - 337041
-exon list size: 556


building trellis

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27.4    
27.6    
27.8    
28.0    
28.1    
28.3    
28.5    
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28.9    
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29.2    
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32.6    
32.8    
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34.6    
34.8    
34.9    
35.1    
35.3    
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35.8    
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45.9    
46.1    
46.2    
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    
48.7    
48.9    
49.1    
49.3    
49.5    
49.6    
49.8    
50.0    
50.2    
50.4    
50.5    
50.7    
50.9    
51.1    
51.3    
51.4    
51.6    
51.8    
52.0    
52.2    
52.3    
52.5    
52.7    
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    
57.5    
57.7    
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    
60.9    
61.1    
61.3    
61.5    
61.6    
61.8    
62.0    
62.2    
62.4    
62.5    
62.7    
62.9    
63.1    
63.3    
63.4    
63.6    
63.8    
64.0    
64.2    
64.3    
64.5    
64.7    
64.9    
65.1    
65.2    
65.4    
65.6    
65.8    
65.9    
66.1    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.4    
67.6    
67.7    
67.9    
68.1    
68.3    
68.5    
68.6    
68.8    
69.0    
69.2    
69.4    
69.5    
69.7    
69.9    
70.1    
70.3    
70.4    
70.6    
70.8    
71.0    
71.1    
71.3    
71.5    
71.7    
71.9    
72.0    
72.2    
72.4    
72.6    
72.8    
72.9    
73.1    
73.3    
73.5    
73.7    
73.8    
74.0    
74.2    
74.4    
74.6    
74.7    
74.9    
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 47 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 42 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 323896 - 337041
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

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