-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_7292273-7459596

-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.1545-T1
Valid prediction for CodingQuarry_transcript_32564-T1
Valid prediction for pasa_asmbl_28744.p1
Valid prediction for GlimmerHMM_glimmerT_49244-T1
Valid prediction for HiQ_model.g33002.t1
Valid prediction for Augustus_model.g33025.t1
Valid prediction for GeneMark_model.85292_t
Valid prediction for GeneMark_model.85280_t
Valid prediction for GeneMark_model.85294_t
Couldn't classify 151456, 151500
Sorry, prediction pasa_asmbl_28752.p3 fails validation.
(TAC)	 AA	151456-151500	GT	AGG
(GTC)	 AG	151657-151947	GA	GAG
-recovered pasa_asmbl_28752.p3, terminal, 151657, 151947
Valid prediction for GlimmerHMM_glimmerT_49255-T1
Couldn't classify 15060, 15152
Sorry, prediction pasa_asmbl_28737.p1 fails validation.
(GTT)	 GC	15060-15152	GT	AGG
(GGT)	 AG	15311-15431	GT	AGG
(CGT)	 AG	15645-15733	GT	GGG
(GTC)	 AG	16013-16102	GA	GAG
add_exon() Sorry, pasa_asmbl_28737.p1 15311-15431-terminal-3 is invalid.
-recovered pasa_asmbl_28737.p1, terminal, 15311, 15431
-recovered pasa_asmbl_28737.p1, terminal, 16013, 16102
-recovered pasa_asmbl_28737.p1, internal, 15311, 15431
-recovered pasa_asmbl_28737.p1, internal, 15645, 15733
Valid prediction for GlimmerHMM_glimmerT_49245-T1
Valid prediction for snap_scaffold_21-snap.1564-T1
Valid prediction for Augustus_model.g33006.t1
Valid prediction for GeneMark_model.85285_t
Valid prediction for GlimmerHMM_glimmerT_49250-T1
Couldn't classify 60577, 60645
Couldn't classify 61417, 61440
Sorry, prediction pasa_asmbl_28979.p1 fails validation.
(ATA)	 AG	60577-60645	GT	TGG
(TTA)	 AG	60842-60968	GT	AGG
(CTG)	 AG	61053-61130	GT	TGG
(GTC)	 AG	61233-61312	GT	AGG
(ACT)	 AG	61417-61440	AT	AGA
-recovered pasa_asmbl_28979.p1, internal, 60577, 60645
-recovered pasa_asmbl_28979.p1, internal, 60842, 60968
-recovered pasa_asmbl_28979.p1, internal, 61053, 61130
-recovered pasa_asmbl_28979.p1, internal, 61233, 61312
Valid prediction for pasa_asmbl_28753.p1
Valid prediction for GlimmerHMM_glimmerT_49241-T1
Valid prediction for snap_scaffold_21-snap.1536-T1
Valid prediction for GlimmerHMM_glimmerT_49226-T1
Valid prediction for GlimmerHMM_glimmerT_49231-T1
Valid prediction for snap_scaffold_21-snap.1539-T1
Couldn't classify 121876, 122079
Couldn't classify 122219, 122323
Sorry, prediction pasa_asmbl_29042.p1 fails validation.
(GCC)	 AG	121876-122079	GT	AGG
(AGG)	 AG	122219-122323	GC	GGG
-recovered pasa_asmbl_29042.p1, internal, 121876, 122079
-recovered pasa_asmbl_29042.p1, internal, 122219, 122323
Valid prediction for snap_scaffold_21-snap.1530-T1
Valid prediction for Augustus_model.g33012.t1
Valid prediction for snap_scaffold_21-snap.1531-T1
Valid prediction for pasa_asmbl_28747.p1
Valid prediction for GlimmerHMM_glimmerT_49249-T1
Valid prediction for HiQ_model.g33015.t1
Valid prediction for snap_scaffold_21-snap.1548-T1
Couldn't classify 91479, 91649
Sorry, prediction pasa_asmbl_28746.p1 fails validation.
(TAT)	 CT	91479-91649	GT	AGG
(CTG)	 AG	91829-91897	GT	AGG
(AAA)	 AG	92016-92066	GT	CTG
(GTG)	 AG	92156-92257	CC	AAC
-recovered pasa_asmbl_28746.p1, terminal, 92156, 92257
-recovered pasa_asmbl_28746.p1, internal, 91829, 91897
-recovered pasa_asmbl_28746.p1, internal, 92016, 92066
Valid prediction for GeneMark_model.85295_t
Valid prediction for CodingQuarry_transcript_32560-T1
Valid prediction for GeneMark_model.85277_t
Valid prediction for snap_scaffold_21-snap.1528-T1
Valid prediction for GlimmerHMM_glimmerT_49256-T1
Valid prediction for pasa_asmbl_28738.p1
Couldn't classify 22695, 22818
Sorry, prediction pasa_asmbl_28739.p1 fails validation.
(GTT)	 GG	22695-22818	GT	AGG
(CGC)	 AG	23120-23232	GT	AGG
(ACA)	 AG	23530-23623	GT	AGG
(ACG)	 AG	23831-23976	GT	CCG
(AAT)	 AG	24188-24281	GT	AGG
(ATG)	 AG	24426-24487	GT	TTG
(AGA)	 AG	24831-24999	GT	AGG
(CTT)	 AG	25153-25341	GT	AGG
(AAC)	 AG	25460-25633	GT	AGG
(GTG)	 AG	25795-25887	GT	AGG
(AGA)	 AG	26031-26164	GT	AAG
add_exon() Sorry, pasa_asmbl_28739.p1 24426-24487-initial-1 is invalid.
-recovered pasa_asmbl_28739.p1, initial, 24426, 24487
-recovered pasa_asmbl_28739.p1, terminal, 26031, 26164
-recovered pasa_asmbl_28739.p1, internal, 23120, 23232
-recovered pasa_asmbl_28739.p1, internal, 23530, 23623
-recovered pasa_asmbl_28739.p1, internal, 23831, 23976
-recovered pasa_asmbl_28739.p1, internal, 24188, 24281
-recovered pasa_asmbl_28739.p1, internal, 24426, 24487
-recovered pasa_asmbl_28739.p1, internal, 24831, 24999
-recovered pasa_asmbl_28739.p1, internal, 25153, 25341
-recovered pasa_asmbl_28739.p1, internal, 25460, 25633
-recovered pasa_asmbl_28739.p1, internal, 25795, 25887
-recovered pasa_asmbl_28739.p1, internal, 26031, 26164
Valid prediction for GeneMark_model.85281_t
Valid prediction for Augustus_model.g33000.t1
Valid prediction for HiQ_model.g33001.t1
Valid prediction for CodingQuarry_transcript_32553-T1
Valid prediction for snap_scaffold_21-snap.1547-T1
Valid prediction for GlimmerHMM_glimmerT_49235-T1
Valid prediction for CodingQuarry_transcript_32559-T1
Valid prediction for snap_scaffold_21-snap.1540-T1
Couldn't classify 151309, 151329
Sorry, prediction pasa_asmbl_28751.p1 fails validation.
(ATG)	 CT	147929-148084	GT	AGG
(GAT)	 AG	148287-148373	GT	AGG
(CCG)	 AG	148497-148650	GT	AGG
(CTC)	 AG	148881-148937	GT	TGG
(CCC)	 AG	149023-149142	GT	AGG
(GTA)	 AG	149369-149490	GT	CTG
(GAG)	 AG	149630-149707	GT	GGG
(GTG)	 AG	149832-149933	GT	ACG
(CTG)	 AG	150114-150296	GT	AGG
(AGC)	 AG	150426-150500	GT	ACG
(GTC)	 AG	150589-150714	GT	TGG
(AAA)	 AG	151016-151189	GT	AGG
(CCC)	 AG	151309-151329	AC	TGA
-recovered pasa_asmbl_28751.p1, initial, 147929, 148084
-recovered pasa_asmbl_28751.p1, internal, 148287, 148373
-recovered pasa_asmbl_28751.p1, internal, 148497, 148650
-recovered pasa_asmbl_28751.p1, internal, 148881, 148937
-recovered pasa_asmbl_28751.p1, internal, 149023, 149142
-recovered pasa_asmbl_28751.p1, internal, 149369, 149490
-recovered pasa_asmbl_28751.p1, internal, 149630, 149707
-recovered pasa_asmbl_28751.p1, internal, 149832, 149933
-recovered pasa_asmbl_28751.p1, internal, 150114, 150296
-recovered pasa_asmbl_28751.p1, internal, 150426, 150500
-recovered pasa_asmbl_28751.p1, internal, 150589, 150714
-recovered pasa_asmbl_28751.p1, internal, 151016, 151189
Valid prediction for GeneMark_model.85297_t
Valid prediction for HiQ_model.g33014.t1
Valid prediction for Augustus_model.g33004.t1
Valid prediction for snap_scaffold_21-snap.1561-T1
Valid prediction for GlimmerHMM_glimmerT_49229-T1
Valid prediction for GlimmerHMM_glimmerT_49224-T1
Valid prediction for CodingQuarry_transcript_32555-T1
Valid prediction for Augustus_model.g33017.t1
Valid prediction for snap_scaffold_21-snap.1552-T1
Valid prediction for snap_scaffold_21-snap.1560-T1
Valid prediction for GlimmerHMM_glimmerT_49233-T1
Valid prediction for GlimmerHMM_glimmerT_49242-T1
Valid prediction for Augustus_model.g33018.t1
Valid prediction for CodingQuarry_transcript_32554-T1
Valid prediction for GlimmerHMM_glimmerT_49227-T1
Valid prediction for GlimmerHMM_glimmerT_49225-T1
Valid prediction for Augustus_model.g33007.t1
Valid prediction for HiQ_model.g33023.t1
Valid prediction for snap_scaffold_21-snap.1533-T1
Valid prediction for snap_scaffold_21-snap.1532-T1
Valid prediction for HiQ_model.g33022.t1
Couldn't classify 64948, 65271
Sorry, prediction pasa_asmbl_28743.p1 fails validation.
(ACT)	 TC	64948-65271	GT	CGG
(GGC)	 AG	65444-65550	GT	AAG
(CAT)	 AG	65666-65801	GT	AGG
(GTG)	 AG	65908-66042	GG	GAG
-recovered pasa_asmbl_28743.p1, terminal, 65908, 66042
-recovered pasa_asmbl_28743.p1, internal, 65444, 65550
-recovered pasa_asmbl_28743.p1, internal, 65666, 65801
Valid prediction for GeneMark_model.85286_t
Valid prediction for GeneMark_model.85290_t
Valid prediction for GlimmerHMM_glimmerT_49247-T1
Couldn't classify 126236, 126280
Couldn't classify 126873, 126935
Sorry, prediction pasa_asmbl_28974.p1 fails validation.
(GGC)	 CT	126236-126280	GT	AGG
(GGC)	 AG	126429-126527	GT	CGG
(ATC)	 AG	126624-126734	GT	AGG
(ATT)	 AG	126873-126935	TC	CCT
-recovered pasa_asmbl_28974.p1, internal, 126429, 126527
-recovered pasa_asmbl_28974.p1, internal, 126624, 126734
Valid prediction for snap_scaffold_21-snap.1534-T1
Valid prediction for snap_scaffold_21-snap.1538-T1
Valid prediction for snap_scaffold_21-snap.1555-T1
Valid prediction for snap_scaffold_21-snap.1550-T1
Valid prediction for Augustus_model.g32999.t1
Valid prediction for snap_scaffold_21-snap.1551-T1
Valid prediction for snap_scaffold_21-snap.1562-T1
Valid prediction for GlimmerHMM_glimmerT_49234-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_21-snap.1549-T1
Valid prediction for GlimmerHMM_glimmerT_49243-T1
Valid prediction for Augustus_model.g33021.t1
Valid prediction for GeneMark_model.85289_t
Valid prediction for GlimmerHMM_glimmerT_49248-T1
Valid prediction for snap_scaffold_21-snap.1543-T1
Valid prediction for GlimmerHMM_glimmerT_49246-T1
Valid prediction for GlimmerHMM_glimmerT_49254-T1
Valid prediction for Augustus_model.g33008.t1
Valid prediction for GeneMark_model.85282_t
Valid prediction for pasa_asmbl_27819.p1
Valid prediction for Augustus_model.g33005.t1
Valid prediction for GeneMark_model.85287_t
Valid prediction for Augustus_model.g33019.t1
Valid prediction for GlimmerHMM_glimmerT_49238-T1
Valid prediction for snap_scaffold_21-snap.1537-T1
Valid prediction for GeneMark_model.85279_t
Valid prediction for GlimmerHMM_glimmerT_49240-T1
Valid prediction for CodingQuarry_transcript_32558-T1
Valid prediction for GlimmerHMM_glimmerT_49228-T1
Valid prediction for snap_scaffold_21-snap.1557-T1
Valid prediction for CodingQuarry_transcript_32561-T1
Couldn't classify 24143, 24423
Sorry, prediction pasa_asmbl_28249.p1 fails validation.
(ATG)	 AT	23616-23658	GT	AGG
(GCA)	 AG	23736-23792	GT	AGG
(AAC)	 AG	23893-23931	GT	AGG
(AAA)	 AG	24013-24069	GT	TGG
(GAC)	 AG	24143-24423	CA	ATC
-recovered pasa_asmbl_28249.p1, initial, 23616, 23658
-recovered pasa_asmbl_28249.p1, internal, 23736, 23792
-recovered pasa_asmbl_28249.p1, internal, 23893, 23931
-recovered pasa_asmbl_28249.p1, internal, 24013, 24069
Valid prediction for snap_scaffold_21-snap.1544-T1
Valid prediction for CodingQuarry_transcript_32556-T1
Valid prediction for CodingQuarry_transcript_32562-T1
Valid prediction for GlimmerHMM_glimmerT_49232-T1
Valid prediction for snap_scaffold_21-snap.1558-T1
Valid prediction for Augustus_model.g33026.t1
Valid prediction for snap_scaffold_21-snap.1565-T1
Valid prediction for Augustus_model.g33011.t1
Valid prediction for GlimmerHMM_glimmerT_49230-T1
Valid prediction for Augustus_model.g33016.t1
Valid prediction for GeneMark_model.85296_t
Valid prediction for GeneMark_model.85299_t
Valid prediction for HiQ_model.g33003.t1
Valid prediction for Augustus_model.g33024.t1
Valid prediction for snap_scaffold_21-snap.1541-T1
Couldn't classify 27915, 27930
Couldn't classify 28896, 28972
Sorry, prediction pasa_asmbl_27837.p1 fails validation.
(AGC)	 AG	27915-27930	GT	TGG
(GCC)	 AG	28029-28155	GT	AGG
(GTT)	 AG	28317-28407	GT	GGG
(GCT)	 AG	28617-28686	GT	GGG
(AGA)	 AG	28896-28972	AT	CCA
-recovered pasa_asmbl_27837.p1, internal, 27915, 27930
-recovered pasa_asmbl_27837.p1, internal, 28029, 28155
-recovered pasa_asmbl_27837.p1, internal, 28317, 28407
-recovered pasa_asmbl_27837.p1, internal, 28617, 28686
Valid prediction for snap_scaffold_21-snap.1535-T1
Valid prediction for Augustus_model.g33010.t1
Valid prediction for Augustus_model.g33013.t1
Valid prediction for snap_scaffold_21-snap.1563-T1
Valid prediction for pasa_asmbl_27830.p1
Valid prediction for snap_scaffold_21-snap.1542-T1
Valid prediction for snap_scaffold_21-snap.1559-T1
Valid prediction for GeneMark_model.85293_t
Valid prediction for snap_scaffold_21-snap.1529-T1
Valid prediction for GlimmerHMM_glimmerT_49239-T1
Valid prediction for GlimmerHMM_glimmerT_49237-T1
Valid prediction for GlimmerHMM_glimmerT_49252-T1
Valid prediction for snap_scaffold_21-snap.1553-T1
Valid prediction for GeneMark_model.85284_t
Valid prediction for snap_scaffold_21-snap.1554-T1
Valid prediction for snap_scaffold_21-snap.1546-T1
Valid prediction for Augustus_model.g33020.t1
Valid prediction for GlimmerHMM_glimmerT_49236-T1
Valid prediction for GlimmerHMM_glimmerT_49253-T1
Valid prediction for GeneMark_model.85278_t
Valid prediction for Augustus_model.g33009.t1
Couldn't classify 79699, 80607
Sorry, prediction pasa_asmbl_27827.p1 fails validation.
(CCG)	 CC	79699-80607	GA	AGG
Valid prediction for snap_scaffold_21-snap.1556-T1
Couldn't classify 29691, 29820
Couldn't classify 30775, 30923
Sorry, prediction pasa_asmbl_27835.p1 fails validation.
(CCC)	 AG	29691-29820	GT	ACG
(GGT)	 AG	29918-30049	GT	AGG
(GCT)	 AG	30205-30381	GT	TTG
(ACA)	 AG	30478-30696	GT	AGG
(GGA)	 AG	30775-30923	CA	AGC
add_exon() Sorry, pasa_asmbl_27835.p1 29918-30049-terminal-1 is invalid.
-recovered pasa_asmbl_27835.p1, terminal, 29918, 30049
-recovered pasa_asmbl_27835.p1, internal, 29691, 29820
-recovered pasa_asmbl_27835.p1, internal, 29918, 30049
-recovered pasa_asmbl_27835.p1, internal, 30205, 30381
-recovered pasa_asmbl_27835.p1, internal, 30478, 30696
Valid prediction for GlimmerHMM_glimmerT_49251-T1

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

-building trellis in range 1 - 167324
-exon list size: 537


building trellis

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33.8    
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71.8    
72.0    
72.2    
72.4    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 35 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support