-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_12881484-13157533

-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_5-snap.2404-T1
Valid prediction for CodingQuarry_transcript_52168-T1
Valid prediction for HiQ_model.g8773.t1
Valid prediction for GlimmerHMM_glimmerT_13156-T1
Valid prediction for GlimmerHMM_glimmerT_13159-T1
Valid prediction for snap_scaffold_5-snap.2420-T1
Valid prediction for pasa_asmbl_44509.p1
Valid prediction for HiQ_model.g8779.t1
Valid prediction for GlimmerHMM_glimmerT_13171-T1
Valid prediction for Augustus_model.g8783.t1
Valid prediction for pasa_asmbl_44504.p1
Valid prediction for snap_scaffold_5-snap.2424-T1
Valid prediction for GeneMark_model.22185_t
Valid prediction for Augustus_model.g8786.t1
Valid prediction for GlimmerHMM_glimmerT_13166-T1
Valid prediction for snap_scaffold_5-snap.2421-T1
Valid prediction for GlimmerHMM_glimmerT_13136-T1
Valid prediction for GlimmerHMM_glimmerT_13169-T1
Valid prediction for pasa_asmbl_44517.p1
Valid prediction for CodingQuarry_transcript_52186-T1
Valid prediction for snap_scaffold_5-snap.2426-T1
Valid prediction for snap_scaffold_5-snap.2402-T1
Valid prediction for GeneMark_model.22168_t
Valid prediction for GlimmerHMM_glimmerT_13155-T1
Valid prediction for HiQ_model.g8771.t1
Couldn't classify 197978, 198104
Couldn't classify 198244, 198413
Sorry, prediction pasa_asmbl_44522.p1 fails validation.
(AAC)	 TC	197978-198104	GT	TGG
(GTG)	 AG	198244-198413	GC	CCG
-recovered pasa_asmbl_44522.p1, internal, 198244, 198413
Valid prediction for GeneMark_model.22177_t
Valid prediction for GeneMark_model.22176_t
Valid prediction for GeneMark_model.22187_t
Valid prediction for snap_scaffold_5-snap.2429-T1
Valid prediction for CodingQuarry_transcript_52184-T1
Valid prediction for CodingQuarry_transcript_52167-T1
Valid prediction for GlimmerHMM_glimmerT_13162-T1
Valid prediction for Augustus_model.g8777.t1
Valid prediction for CodingQuarry_transcript_52166-T1
Valid prediction for GeneMark_model.22180_t
Valid prediction for Augustus_model.g8775.t1
Valid prediction for pasa_asmbl_44508.p1
Valid prediction for HiQ_model.g8791.t1
Valid prediction for snap_scaffold_5-snap.2434-T1
Valid prediction for HiQ_model.g8763.t1
Valid prediction for pasa_asmbl_44527.p1
Valid prediction for GlimmerHMM_glimmerT_13164-T1
Valid prediction for CodingQuarry_transcript_52169-T1
Valid prediction for CodingQuarry_transcript_52176-T1
Valid prediction for snap_scaffold_5-snap.2417-T1
Valid prediction for snap_scaffold_5-snap.2427-T1
Valid prediction for snap_scaffold_5-snap.2422-T1
Valid prediction for snap_scaffold_5-snap.2399-T1
Valid prediction for GeneMark_model.22175_t
Valid prediction for pasa_asmbl_44507.p1
Valid prediction for GlimmerHMM_glimmerT_13150-T1
Valid prediction for CodingQuarry_transcript_52179-T1
Valid prediction for GeneMark_model.22162_t
Valid prediction for GeneMark_model.22195_t
Valid prediction for GlimmerHMM_glimmerT_13157-T1
Valid prediction for CodingQuarry_transcript_52177-T1
Valid prediction for Augustus_model.g8776.t1
Couldn't classify 216096, 216115
Sorry, prediction pasa_asmbl_44525.p1 fails validation.
(TTT)	 GA	216096-216115	GT	AGG
(GAT)	 AG	217015-217189	GT	TGG
(GTG)	 AG	217310-217461	GT	CTG
(GTA)	 AG	217712-217847	TA	GAT
-recovered pasa_asmbl_44525.p1, terminal, 217712, 217847
-recovered pasa_asmbl_44525.p1, internal, 217015, 217189
-recovered pasa_asmbl_44525.p1, internal, 217310, 217461
Valid prediction for HiQ_model.g8784.t1
Valid prediction for snap_scaffold_5-snap.2403-T1
Valid prediction for snap_scaffold_5-snap.2431-T1
Valid prediction for CodingQuarry_transcript_52180-T1
Valid prediction for GlimmerHMM_glimmerT_13153-T1
Valid prediction for snap_scaffold_5-snap.2415-T1
Valid prediction for pasa_asmbl_44510.p1
Valid prediction for GlimmerHMM_glimmerT_13161-T1
Valid prediction for GeneMark_model.22181_t
Valid prediction for Augustus_model.g8782.t1
Valid prediction for GlimmerHMM_glimmerT_13139-T1
Valid prediction for snap_scaffold_5-snap.2416-T1
Valid prediction for snap_scaffold_5-snap.2425-T1
Valid prediction for snap_scaffold_5-snap.2418-T1
Valid prediction for GlimmerHMM_glimmerT_13151-T1
Valid prediction for snap_scaffold_5-snap.2413-T1
Valid prediction for CodingQuarry_transcript_52181-T1
Valid prediction for GlimmerHMM_glimmerT_13148-T1
Valid prediction for pasa_asmbl_44502.p1
Valid prediction for CodingQuarry_transcript_52174-T1
Valid prediction for HiQ_model.g8761.t1
Valid prediction for Augustus_model.g8788.t1
Valid prediction for pasa_asmbl_44519.p1
Valid prediction for CodingQuarry_transcript_52178-T1
Valid prediction for GeneMark_model.22192_t
Valid prediction for GlimmerHMM_glimmerT_13137-T1
Valid prediction for HiQ_model.g8780.t1
Couldn't classify 198582, 198676
Sorry, prediction pasa_asmbl_44523.p1 fails validation.
(ACT)	 GT	198582-198676	GT	TGG
(TCT)	 AG	199184-199242	GT	TAG
(TGG)	 AG	199921-200030	GT	AGG
(CAC)	 AG	200122-200224	GT	AGG
(TGT)	 AG	200410-200558	GT	AGG
(ATT)	 AG	200704-200967	CA	GAC
-recovered pasa_asmbl_44523.p1, terminal, 200704, 200967
-recovered pasa_asmbl_44523.p1, internal, 199184, 199242
-recovered pasa_asmbl_44523.p1, internal, 199921, 200030
-recovered pasa_asmbl_44523.p1, internal, 200122, 200224
-recovered pasa_asmbl_44523.p1, internal, 200410, 200558
Valid prediction for GeneMark_model.22166_t
Valid prediction for GlimmerHMM_glimmerT_13152-T1
Valid prediction for GeneMark_model.22184_t
Valid prediction for HiQ_model.g8778.t1
Valid prediction for HiQ_model.g8774.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_5-snap.2409-T1
Valid prediction for snap_scaffold_5-snap.2400-T1
Valid prediction for GeneMark_model.22172_t
Valid prediction for snap_scaffold_5-snap.2406-T1
Valid prediction for GeneMark_model.22167_t
Valid prediction for GlimmerHMM_glimmerT_13146-T1
Valid prediction for snap_scaffold_5-snap.2412-T1
Valid prediction for CodingQuarry_transcript_52173-T1
Valid prediction for snap_scaffold_5-snap.2405-T1
Valid prediction for GlimmerHMM_glimmerT_13165-T1
Valid prediction for snap_scaffold_5-snap.2423-T1
Valid prediction for Augustus_model.g8762.t1
Valid prediction for snap_scaffold_5-snap.2410-T1
Valid prediction for GlimmerHMM_glimmerT_13168-T1
Valid prediction for HiQ_model.g8785.t1
Valid prediction for GlimmerHMM_glimmerT_13160-T1
Valid prediction for Augustus_model.g8790.t1
Valid prediction for GeneMark_model.22183_t
Valid prediction for snap_scaffold_5-snap.2433-T1
Valid prediction for GeneMark_model.22170_t
Valid prediction for pasa_asmbl_45900.p1
Valid prediction for GeneMark_model.22194_t
Valid prediction for CodingQuarry_transcript_52188-T1
Valid prediction for CodingQuarry_transcript_52185-T1
Valid prediction for pasa_asmbl_45896.p1
Valid prediction for pasa_asmbl_45878.p1
Valid prediction for pasa_asmbl_45903.p1
Valid prediction for GlimmerHMM_glimmerT_13172-T1
Couldn't classify 207574, 207744
Sorry, prediction pasa_asmbl_45880.p1 fails validation.
(ATG)	 CG	205147-205299	GT	CGG
(GAC)	 AG	206712-206789	GT	AGG
(GCA)	 AG	207184-207306	GT	AGG
(CTG)	 AG	207574-207744	GT	TGG
-recovered pasa_asmbl_45880.p1, initial, 205147, 205299
-recovered pasa_asmbl_45880.p1, internal, 206712, 206789
-recovered pasa_asmbl_45880.p1, internal, 207184, 207306
-recovered pasa_asmbl_45880.p1, internal, 207574, 207744
Valid prediction for snap_scaffold_5-snap.2408-T1
Valid prediction for HiQ_model.g8768.t1
Valid prediction for GlimmerHMM_glimmerT_13170-T1
Valid prediction for snap_scaffold_5-snap.2438-T1
Valid prediction for HiQ_model.g8767.t1
Valid prediction for pasa_asmbl_45886.p1
Valid prediction for GeneMark_model.22182_t
Valid prediction for CodingQuarry_transcript_52182-T1
Valid prediction for GeneMark_model.22193_t
Valid prediction for Augustus_model.g8765.t1
Valid prediction for snap_scaffold_5-snap.2437-T1
Couldn't classify 69752, 69799
Sorry, prediction pasa_asmbl_45887.p1 fails validation.
(TTT)	 GC	69752-69799	GC	TGG
(GTG)	 AG	69941-70034	GT	GGG
(ACC)	 AG	70202-70405	GT	AAG
(GTA)	 AG	70500-70534	GC	GAG
-recovered pasa_asmbl_45887.p1, terminal, 70500, 70534
-recovered pasa_asmbl_45887.p1, internal, 69941, 70034
-recovered pasa_asmbl_45887.p1, internal, 70202, 70405
-recovered pasa_asmbl_45887.p1, internal, 70500, 70534
Valid prediction for snap_scaffold_5-snap.2401-T1
Valid prediction for GeneMark_model.22189_t
Valid prediction for snap_scaffold_5-snap.2414-T1
Valid prediction for pasa_asmbl_45901.p1
Valid prediction for GlimmerHMM_glimmerT_13147-T1
Valid prediction for HiQ_model.g8795.t1
Valid prediction for GlimmerHMM_glimmerT_13145-T1
Valid prediction for CodingQuarry_transcript_52172-T1
Valid prediction for snap_scaffold_5-snap.2428-T1
Valid prediction for Augustus_model.g8764.t1
Valid prediction for pasa_asmbl_45881.p1
Valid prediction for GeneMark_model.22190_t
Valid prediction for GeneMark_model.22165_t
Valid prediction for GlimmerHMM_glimmerT_13140-T1
Valid prediction for snap_scaffold_5-snap.2432-T1
Valid prediction for GeneMark_model.22174_t
Valid prediction for CodingQuarry_transcript_52187-T1
Valid prediction for GeneMark_model.22188_t
Valid prediction for GlimmerHMM_glimmerT_13144-T1
Valid prediction for GlimmerHMM_glimmerT_13154-T1
Couldn't classify 207610, 207744
Sorry, prediction pasa_asmbl_45879.p1 fails validation.
(AGA)	 GT	207610-207744	GT	TGG
(TCT)	 AG	209055-209246	GT	CAG
(TCG)	 AG	209462-209555	GT	AGG
(AGA)	 AG	209723-209835	GT	CGG
(GTT)	 AG	210040-210198	GT	AGG
(GAA)	 AG	210493-210612	GT	ATG
(ATG)	 AG	210698-210856	GT	AGG
(AAG)	 AG	210970-211151	GT	TGG
(GGG)	 AG	211285-211447	GT	CCG
(ATT)	 AG	211587-211706	GT	GGG
(ATG)	 AG	211840-212034	GT	TGG
(GGA)	 AG	212363-212544	GT	AAG
(TTA)	 AG	212714-212838	GT	AGG
(GCC)	 AG	212929-213079	GT	AGG
(GTA)	 AG	213231-213345	GT	AGG
(GAG)	 AG	213487-213842	GT	AGG
(GCC)	 AG	215008-215146	GT	AGG
(GTT)	 AG	215250-215429	GT	AGG
(GTC)	 AG	215517-215675	GT	CTG
(ATG)	 AG	215823-216308	GT	AGG
(GCT)	 AG	216430-216514	GT	GGG
(GTT)	 AG	216644-216849	GT	AGG
(AAG)	 AG	217019-217291	GT	AGG
(GTG)	 AG	217585-217719	GG	GAG
-recovered pasa_asmbl_45879.p1, initial, 210698, 210856
-recovered pasa_asmbl_45879.p1, initial, 211840, 212034
-recovered pasa_asmbl_45879.p1, initial, 215823, 216308
-recovered pasa_asmbl_45879.p1, terminal, 217585, 217719
-recovered pasa_asmbl_45879.p1, internal, 209055, 209246
-recovered pasa_asmbl_45879.p1, internal, 209462, 209555
-recovered pasa_asmbl_45879.p1, internal, 209723, 209835
-recovered pasa_asmbl_45879.p1, internal, 210040, 210198
-recovered pasa_asmbl_45879.p1, internal, 210493, 210612
-recovered pasa_asmbl_45879.p1, internal, 210698, 210856
-recovered pasa_asmbl_45879.p1, internal, 210970, 211151
-recovered pasa_asmbl_45879.p1, internal, 211285, 211447
-recovered pasa_asmbl_45879.p1, internal, 211587, 211706
-recovered pasa_asmbl_45879.p1, internal, 211840, 212034
-recovered pasa_asmbl_45879.p1, internal, 212363, 212544
-recovered pasa_asmbl_45879.p1, internal, 212714, 212838
-recovered pasa_asmbl_45879.p1, internal, 212929, 213079
-recovered pasa_asmbl_45879.p1, internal, 213231, 213345
-recovered pasa_asmbl_45879.p1, internal, 213487, 213842
-recovered pasa_asmbl_45879.p1, internal, 215008, 215146
-recovered pasa_asmbl_45879.p1, internal, 215250, 215429
-recovered pasa_asmbl_45879.p1, internal, 215517, 215675
-recovered pasa_asmbl_45879.p1, internal, 215823, 216308
-recovered pasa_asmbl_45879.p1, internal, 216430, 216514
-recovered pasa_asmbl_45879.p1, internal, 216644, 216849
-recovered pasa_asmbl_45879.p1, internal, 217019, 217291
Valid prediction for snap_scaffold_5-snap.2435-T1
Valid prediction for Augustus_model.g8766.t1
Valid prediction for GeneMark_model.22169_t
Valid prediction for pasa_asmbl_45874.p1
Valid prediction for CodingQuarry_transcript_52170-T1
Valid prediction for Augustus_model.g8789.t1
Valid prediction for GlimmerHMM_glimmerT_13149-T1
Valid prediction for snap_scaffold_5-snap.2411-T1
Valid prediction for GeneMark_model.22163_t
Valid prediction for GlimmerHMM_glimmerT_13173-T1
Valid prediction for Augustus_model.g8793.t1
Valid prediction for snap_scaffold_5-snap.2430-T1
Valid prediction for GlimmerHMM_glimmerT_13142-T1
Valid prediction for CodingQuarry_transcript_52183-T1
Valid prediction for HiQ_model.g8770.t1
Valid prediction for GlimmerHMM_glimmerT_13167-T1
Couldn't classify 67144, 67279
Couldn't classify 67791, 67820
Sorry, prediction pasa_asmbl_45890.p1 fails validation.
(TCA)	 CG	67144-67279	GT	CGG
(ATA)	 AG	67368-67474	GT	CAG
(GTG)	 AG	67569-67667	GT	AGG
(TAT)	 AG	67791-67820	GC	AGG
-recovered pasa_asmbl_45890.p1, internal, 67368, 67474
-recovered pasa_asmbl_45890.p1, internal, 67569, 67667
-recovered pasa_asmbl_45890.p1, internal, 67791, 67820
Valid prediction for Augustus_model.g8769.t1
Valid prediction for snap_scaffold_5-snap.2419-T1
Valid prediction for Augustus_model.g8787.t1
Valid prediction for GlimmerHMM_glimmerT_13143-T1
Valid prediction for HiQ_model.g8794.t1
Valid prediction for GeneMark_model.22178_t
Valid prediction for snap_scaffold_5-snap.2407-T1
Valid prediction for GeneMark_model.22171_t
Valid prediction for GlimmerHMM_glimmerT_13163-T1
Valid prediction for snap_scaffold_5-snap.2436-T1
Valid prediction for GlimmerHMM_glimmerT_13141-T1
Valid prediction for GeneMark_model.22191_t
Valid prediction for GeneMark_model.22179_t
Couldn't classify 239531, 240063
Sorry, prediction pasa_asmbl_45872.p1 fails validation.
(AGA)	 GT	239531-240063	GT	AGG
(ATC)	 AG	240557-240649	GT	AGG
(TGA)	 AG	242064-242163	GT	AGG
(ACG)	 AG	242275-242443	GT	AAG
(GTA)	 AG	242518-242615	GT	TGG
(ACG)	 AG	243023-243129	GT	AGG
(TCT)	 AG	243336-243540	GT	ATG
(AAG)	 AG	243773-243913	TG	AGT
-recovered pasa_asmbl_45872.p1, terminal, 243773, 243913
-recovered pasa_asmbl_45872.p1, internal, 240557, 240649
-recovered pasa_asmbl_45872.p1, internal, 242064, 242163
-recovered pasa_asmbl_45872.p1, internal, 242275, 242443
-recovered pasa_asmbl_45872.p1, internal, 242518, 242615
-recovered pasa_asmbl_45872.p1, internal, 243023, 243129
-recovered pasa_asmbl_45872.p1, internal, 243336, 243540
Valid prediction for Augustus_model.g8772.t1
Valid prediction for GeneMark_model.22173_t
Valid prediction for HiQ_model.g8792.t1
Valid prediction for CodingQuarry_transcript_52171-T1
Valid prediction for GlimmerHMM_glimmerT_13138-T1
Couldn't classify 52408, 52434
Sorry, prediction pasa_asmbl_45893.p1 fails validation.
(TTC)	 TC	52408-52434	GT	AGG
(AAA)	 AG	52520-52634	GT	GGG
(GCT)	 AG	52765-52990	GT	CGG
(TAA)	 AG	53070-53246	GT	AGG
(ATT)	 AG	53434-53620	AT	AAA
-recovered pasa_asmbl_45893.p1, terminal, 53434, 53620
-recovered pasa_asmbl_45893.p1, internal, 52520, 52634
-recovered pasa_asmbl_45893.p1, internal, 52765, 52990
-recovered pasa_asmbl_45893.p1, internal, 53070, 53246
Valid prediction for pasa_asmbl_45870.p1
Valid prediction for GlimmerHMM_glimmerT_13158-T1
Valid prediction for Augustus_model.g8781.t1

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

-building trellis in range 1 - 276050
-exon list size: 590


building trellis

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27.4    
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33.6    
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34.1    
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34.6    
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48.1    
48.3    
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48.6    
48.8    
49.0    
49.2    
49.3    
49.5    
49.7    
49.8    
50.0    
50.2    
50.3    
50.5    
50.7    
50.8    
51.0    
51.2    
51.4    
51.5    
51.7    
51.9    
52.0    
52.2    
52.4    
52.5    
52.7    
52.9    
53.0    
53.2    
53.4    
53.5    
53.7    
53.9    
54.1    
54.2    
54.4    
54.6    
54.7    
54.9    
55.1    
55.2    
55.4    
55.6    
55.7    
55.9    
56.1    
56.2    
56.4    
56.6    
56.8    
56.9    
57.1    
57.3    
57.4    
57.6    
57.8    
57.9    
58.1    
58.3    
58.4    
58.6    
58.8    
59.0    
59.1    
59.3    
59.5    
59.6    
59.8    
60.0    
60.1    
60.3    
60.5    
60.6    
60.8    
61.0    
61.1    
61.3    
61.5    
61.7    
61.8    
62.0    
62.2    
62.3    
62.5    
62.7    
62.8    
63.0    
63.2    
63.3    
63.5    
63.7    
63.9    
64.0    
64.2    
64.4    
64.5    
64.7    
64.9    
65.0    
65.2    
65.4    
65.5    
65.7    
65.9    
66.0    
66.2    
66.4    
66.6    
66.7    
66.9    
67.1    
67.2    
67.4    
67.6    
67.7    
67.9    
68.1    
68.2    
68.4    
68.6    
68.8    
68.9    
69.1    
69.3    
69.4    
69.6    
69.8    
69.9    
70.1    
70.3    
70.4    
70.6    
70.8    
70.9    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.1    
72.3    
72.5    
72.6    
72.8    
73.0    
73.1    
73.3    
73.5    
73.6    
73.8    
74.0    
74.2    
74.3    
74.5    
74.7    
74.8    
75.0    
75.2    
75.3    
75.5    
75.7    
75.8    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.0    
77.2    
77.4    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.1    
79.2    
79.4    
79.6    
79.7    
79.9    
80.1    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.8    
81.9    
82.1    
82.3    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.4    
83.6    
83.8    
84.0    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.6    
85.8    
86.0    
86.1    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.3    
87.5    
87.7    
87.8    
88.0    
88.2    
88.3    
88.5    
88.7    
88.9    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 40 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 40 predictions persist after filtering for low support