-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_7927770-8115992

-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 GlimmerHMM_glimmerT_28041-T1
Valid prediction for snap_scaffold_11-snap.1839-T1
Valid prediction for GeneMark_model.48476_t
Valid prediction for GlimmerHMM_glimmerT_28029-T1
Valid prediction for Augustus_model.g18691.t1
Couldn't classify 165082, 165555
Couldn't classify 165661, 165869
Sorry, prediction CodingQuarry_transcript_8119-T1 fails validation.
(ATG)	 AA	160144-163779	GT	AGG
(CTC)	 AG	164012-164169	GT	GGG
(GTA)	 AG	164546-164721	GT	AGG
(GAA)	 AG	164839-164937	GT	CGG
(ATG)	 AG	165082-165555	AC	TTA
(ACC)	 GC	165661-165869	GT	TGG
(GAT)	 AG	166079-166504	GC	AGG
-recovered CodingQuarry_transcript_8119-T1, initial, 160144, 163779
-recovered CodingQuarry_transcript_8119-T1, terminal, 166079, 166504
-recovered CodingQuarry_transcript_8119-T1, internal, 164012, 164169
-recovered CodingQuarry_transcript_8119-T1, internal, 164546, 164721
-recovered CodingQuarry_transcript_8119-T1, internal, 164839, 164937
-recovered CodingQuarry_transcript_8119-T1, internal, 166079, 166504
Valid prediction for Augustus_model.g18698.t1
Valid prediction for pasa_asmbl_5682.p1
Valid prediction for pasa_asmbl_5679.p1
Valid prediction for GlimmerHMM_glimmerT_28056-T1
Couldn't classify 37571, 38218
Sorry, prediction pasa_asmbl_5669.p1 fails validation.
(AGA)	 AC	37571-38218	GT	AAG
Valid prediction for snap_scaffold_11-snap.1850-T1
Valid prediction for CodingQuarry_transcript_8112-T1
Couldn't classify 176783, 177110
Sorry, prediction pasa_asmbl_5700.p1 fails validation.
(TCT)	 CC	176783-177110	GT	GGG
(ACC)	 AG	177247-177355	GT	AGG
(GAA)	 AG	177641-177753	GT	TGG
(GTG)	 AG	178016-178115	GT	TGG
(GAA)	 AG	178275-178344	AA	AGA
-recovered pasa_asmbl_5700.p1, terminal, 178275, 178344
-recovered pasa_asmbl_5700.p1, internal, 177247, 177355
-recovered pasa_asmbl_5700.p1, internal, 177641, 177753
-recovered pasa_asmbl_5700.p1, internal, 178016, 178115
Couldn't classify 32105, 32422
Sorry, prediction pasa_asmbl_5668.p1 fails validation.
(ATG)	 TA	32105-32422	CA	CCC
Valid prediction for snap_scaffold_11-snap.1862-T1
Valid prediction for GeneMark_model.48485_t
Valid prediction for snap_scaffold_11-snap.1837-T1
Valid prediction for GlimmerHMM_glimmerT_28028-T1
Valid prediction for pasa_asmbl_5699.p1
Valid prediction for GeneMark_model.48487_t
Valid prediction for snap_scaffold_11-snap.1847-T1
Valid prediction for snap_scaffold_11-snap.1843-T1
Valid prediction for snap_scaffold_11-snap.1826-T1
Valid prediction for CodingQuarry_transcript_8121-T1
Valid prediction for GeneMark_model.48488_t
Valid prediction for CodingQuarry_transcript_8111-T1
Valid prediction for GeneMark_model.48482_t
Valid prediction for GlimmerHMM_glimmerT_28047-T1
Valid prediction for CodingQuarry_transcript_8110-T1
Valid prediction for GlimmerHMM_glimmerT_28049-T1
Valid prediction for GeneMark_model.48472_t
Valid prediction for snap_scaffold_11-snap.1849-T1
Valid prediction for GlimmerHMM_glimmerT_28038-T1
Valid prediction for GlimmerHMM_glimmerT_28044-T1
Valid prediction for HiQ_model.g18705.t1
Valid prediction for Augustus_model.g18700.t1
Valid prediction for GlimmerHMM_glimmerT_28030-T1
Valid prediction for GlimmerHMM_glimmerT_28046-T1
Valid prediction for snap_scaffold_11-snap.1852-T1
Valid prediction for GlimmerHMM_glimmerT_28040-T1
Valid prediction for pasa_asmbl_5674.p1
Valid prediction for HiQ_model.g18706.t1
Valid prediction for Augustus_model.g18697.t1
Valid prediction for pasa_asmbl_5686.p1
Valid prediction for GlimmerHMM_glimmerT_28054-T1
Valid prediction for snap_scaffold_11-snap.1854-T1
Valid prediction for GeneMark_model.48469_t
Couldn't classify 123450, 123618
Sorry, prediction pasa_asmbl_5677.p1 fails validation.
(AGT)	 CC	123450-123618	GT	AGG
(GTA)	 AG	123761-123957	GT	AGG
(TAT)	 AG	124222-124293	GG	AAG
-recovered pasa_asmbl_5677.p1, terminal, 124222, 124293
-recovered pasa_asmbl_5677.p1, internal, 123761, 123957
Valid prediction for CodingQuarry_transcript_8120-T1
Valid prediction for GeneMark_model.48483_t
Valid prediction for snap_scaffold_11-snap.1857-T1
Valid prediction for HiQ_model.g18696.t1
Valid prediction for HiQ_model.g18704.t1
Valid prediction for snap_scaffold_11-snap.1828-T1
Couldn't classify 22806, 22928
Couldn't classify 25224, 25423
Sorry, prediction pasa_asmbl_5666.p1 fails validation.
(ATA)	 AG	22806-22928	GT	GGG
(GTG)	 AG	23014-23175	GT	AGG
(AGA)	 AG	23909-24038	GT	TGG
(GCT)	 AG	25224-25423	AA	ACA
-recovered pasa_asmbl_5666.p1, internal, 22806, 22928
-recovered pasa_asmbl_5666.p1, internal, 23014, 23175
-recovered pasa_asmbl_5666.p1, internal, 23909, 24038
Valid prediction for CodingQuarry_transcript_8117-T1
Valid prediction for snap_scaffold_11-snap.1848-T1
Valid prediction for GeneMark_model.48480_t
Valid prediction for GeneMark_model.48489_t
Valid prediction for snap_scaffold_11-snap.1853-T1
Valid prediction for GlimmerHMM_glimmerT_28048-T1
Valid prediction for snap_scaffold_11-snap.1851-T1
Valid prediction for GlimmerHMM_glimmerT_28035-T1
Valid prediction for GeneMark_model.48484_t
Valid prediction for HiQ_model.g18693.t1
Valid prediction for GlimmerHMM_glimmerT_28057-T1
Valid prediction for pasa_asmbl_5671.p1
Valid prediction for HiQ_model.g18703.t1
Valid prediction for Augustus_model.g18686.t1
Valid prediction for snap_scaffold_11-snap.1860-T1
Valid prediction for GlimmerHMM_glimmerT_28031-T1
Valid prediction for GlimmerHMM_glimmerT_28055-T1
Valid prediction for GeneMark_model.48468_t
Valid prediction for snap_scaffold_11-snap.1861-T1
Valid prediction for snap_scaffold_11-snap.1858-T1
Valid prediction for GeneMark_model.48475_t
Valid prediction for HiQ_model.g18685.t1
Valid prediction for GlimmerHMM_glimmerT_28039-T1
Valid prediction for GeneMark_model.48492_t
Valid prediction for CodingQuarry_transcript_8118-T1
Valid prediction for Augustus_model.g18690.t1
Couldn't classify 77509, 77716
Couldn't classify 78175, 78291
Sorry, prediction pasa_asmbl_5670.p1 fails validation.
(ACG)	 AA	77509-77716	GT	TGG
(GTT)	 AG	77939-78084	GT	ATG
(GAG)	 AG	78175-78291	AA	CCA
-recovered pasa_asmbl_5670.p1, internal, 77939, 78084
Valid prediction for Augustus_model.g18699.t1
Valid prediction for GlimmerHMM_glimmerT_28036-T1
Valid prediction for GlimmerHMM_glimmerT_28050-T1
Valid prediction for GeneMark_model.48490_t
Valid prediction for snap_scaffold_11-snap.1859-T1
Valid prediction for snap_scaffold_11-snap.1838-T1
Valid prediction for snap_scaffold_11-snap.1827-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: -)Couldn't classify 183956, 184122
Sorry, prediction pasa_asmbl_6788.p1 fails validation.
(ACC)	 GC	183956-184122	GT	AGG
(GTT)	 AG	184229-184286	GT	CAG
(CTG)	 AG	184909-185085	GT	ACG
(GTC)	 AG	185189-185341	GT	GAG
-recovered pasa_asmbl_6788.p1, terminal, 185189, 185341
-recovered pasa_asmbl_6788.p1, internal, 184229, 184286
-recovered pasa_asmbl_6788.p1, internal, 184909, 185085
-recovered pasa_asmbl_6788.p1, internal, 185189, 185341
Valid prediction for CodingQuarry_transcript_8114-T1
Valid prediction for GeneMark_model.48478_t
Valid prediction for GeneMark_model.48470_t
Valid prediction for snap_scaffold_11-snap.1841-T1
Valid prediction for GeneMark_model.48473_t
Valid prediction for CodingQuarry_transcript_8109-T1
Valid prediction for GlimmerHMM_glimmerT_28034-T1
Valid prediction for GlimmerHMM_glimmerT_28027-T1
Valid prediction for CodingQuarry_transcript_8115-T1
Valid prediction for CodingQuarry_transcript_8113-T1
Valid prediction for CodingQuarry_transcript_8106-T1
Valid prediction for snap_scaffold_11-snap.1830-T1
Valid prediction for pasa_asmbl_6809.p1
Valid prediction for snap_scaffold_11-snap.1842-T1
Valid prediction for GlimmerHMM_glimmerT_28052-T1
Valid prediction for snap_scaffold_11-snap.1831-T1
Valid prediction for GlimmerHMM_glimmerT_28042-T1
Valid prediction for snap_scaffold_11-snap.1833-T1
Valid prediction for snap_scaffold_11-snap.1845-T1
Valid prediction for GeneMark_model.48491_t
Valid prediction for pasa_asmbl_6811.p1
Valid prediction for GeneMark_model.48481_t
Valid prediction for GeneMark_model.48479_t
Valid prediction for snap_scaffold_11-snap.1855-T1
Couldn't classify 114839, 114953
Sorry, prediction pasa_asmbl_6790.p1 fails validation.
(ACG)	 CG	114839-114953	GT	AGG
(GTT)	 AG	115313-115512	GT	AGG
(TTC)	 AG	115591-115642	GT	AGG
(GTA)	 AG	115775-115876	GT	TAG
(GAA)	 AG	116051-116181	GT	AAG
(GTC)	 AG	116297-116396	GT	AGG
(ATT)	 AG	116511-116569	GT	AGG
(TCA)	 AG	116720-116802	GT	CTG
(CAC)	 AG	116930-117000	GT	CAG
(TCA)	 AG	117199-117299	GT	GGG
(CCC)	 AG	117546-117686	GT	AGG
(GTG)	 AG	117832-117942	GT	GGG
(GAT)	 AG	118111-118239	CA	AAC
-recovered pasa_asmbl_6790.p1, terminal, 115591, 115642
-recovered pasa_asmbl_6790.p1, terminal, 118111, 118239
-recovered pasa_asmbl_6790.p1, internal, 115313, 115512
-recovered pasa_asmbl_6790.p1, internal, 115591, 115642
-recovered pasa_asmbl_6790.p1, internal, 115775, 115876
-recovered pasa_asmbl_6790.p1, internal, 116051, 116181
-recovered pasa_asmbl_6790.p1, internal, 116297, 116396
-recovered pasa_asmbl_6790.p1, internal, 116511, 116569
-recovered pasa_asmbl_6790.p1, internal, 116720, 116802
-recovered pasa_asmbl_6790.p1, internal, 116930, 117000
-recovered pasa_asmbl_6790.p1, internal, 117199, 117299
-recovered pasa_asmbl_6790.p1, internal, 117546, 117686
-recovered pasa_asmbl_6790.p1, internal, 117832, 117942
Valid prediction for GeneMark_model.48467_t
Valid prediction for GlimmerHMM_glimmerT_28045-T1
Valid prediction for Augustus_model.g18684.t1
Couldn't classify 95667, 95687
Sorry, prediction pasa_asmbl_6792.p1 fails validation.
(AGT)	 AA	95667-95687	GT	AGG
(TTC)	 AG	95769-95870	GT	AGG
(TGT)	 AG	96018-96137	GT	TGG
(GTC)	 AG	96322-96417	GT	AGG
(GAA)	 AG	96740-96886	GT	AGG
(GTG)	 AG	97022-97110	GT	ATG
(AGG)	 AG	97218-97388	GT	AGG
(ACT)	 AG	97618-97796	GT	AGG
(GGG)	 AG	97877-98078	GT	CGG
(TGG)	 AG	98270-98384	GT	AAG
(GAG)	 AG	98504-98664	GT	CGG
(CAT)	 AG	98751-98886	GT	TGG
(GCT)	 AG	99061-99141	GT	TGG
(GAA)	 AG	99237-99407	GT	AGG
(GAA)	 AG	99647-99784	GT	AGG
(GAA)	 AG	99901-100046	GT	AGG
(GGA)	 AG	100861-100986	GT	AGG
(GTC)	 AG	101085-101190	GT	CGG
(GTT)	 AG	101511-101663	GT	TGG
(GAT)	 AG	101847-101944	GT	AGG
(TAA)	 AG	102156-102246	CT	AAC
add_exon() Sorry, pasa_asmbl_6792.p1 97618-97796-terminal-2 is invalid.
-recovered pasa_asmbl_6792.p1, terminal, 97618, 97796
-recovered pasa_asmbl_6792.p1, terminal, 102156, 102246
-recovered pasa_asmbl_6792.p1, internal, 95769, 95870
-recovered pasa_asmbl_6792.p1, internal, 96018, 96137
-recovered pasa_asmbl_6792.p1, internal, 96322, 96417
-recovered pasa_asmbl_6792.p1, internal, 96740, 96886
-recovered pasa_asmbl_6792.p1, internal, 97022, 97110
-recovered pasa_asmbl_6792.p1, internal, 97218, 97388
-recovered pasa_asmbl_6792.p1, internal, 97618, 97796
-recovered pasa_asmbl_6792.p1, internal, 97877, 98078
-recovered pasa_asmbl_6792.p1, internal, 98270, 98384
-recovered pasa_asmbl_6792.p1, internal, 98504, 98664
-recovered pasa_asmbl_6792.p1, internal, 98751, 98886
-recovered pasa_asmbl_6792.p1, internal, 99061, 99141
-recovered pasa_asmbl_6792.p1, internal, 99237, 99407
-recovered pasa_asmbl_6792.p1, internal, 99647, 99784
-recovered pasa_asmbl_6792.p1, internal, 99901, 100046
-recovered pasa_asmbl_6792.p1, internal, 100861, 100986
-recovered pasa_asmbl_6792.p1, internal, 101085, 101190
-recovered pasa_asmbl_6792.p1, internal, 101511, 101663
-recovered pasa_asmbl_6792.p1, internal, 101847, 101944
Valid prediction for snap_scaffold_11-snap.1844-T1
Valid prediction for snap_scaffold_11-snap.1835-T1
Valid prediction for HiQ_model.g18702.t1
Valid prediction for snap_scaffold_11-snap.1856-T1
Valid prediction for GlimmerHMM_glimmerT_28043-T1
Valid prediction for snap_scaffold_11-snap.1824-T1
Valid prediction for Augustus_model.g18688.t1
Valid prediction for Augustus_model.g18692.t1
Valid prediction for snap_scaffold_11-snap.1840-T1
Valid prediction for GlimmerHMM_glimmerT_28053-T1
Valid prediction for pasa_asmbl_6794.p1
Couldn't classify 125103, 125948
Sorry, prediction pasa_asmbl_6789.p1 fails validation.
(TCT)	 TC	125103-125948	AG	GAA
Valid prediction for GlimmerHMM_glimmerT_28033-T1
Valid prediction for GlimmerHMM_glimmerT_28037-T1
Valid prediction for snap_scaffold_11-snap.1846-T1
Valid prediction for HiQ_model.g18701.t1
Valid prediction for GeneMark_model.48471_t
Valid prediction for Augustus_model.g18695.t1
Valid prediction for GlimmerHMM_glimmerT_28051-T1
Valid prediction for snap_scaffold_11-snap.1836-T1
Couldn't classify 143506, 143583
Couldn't classify 144370, 144434
Sorry, prediction pasa_asmbl_7273.p1 fails validation.
(GAG)	 AG	143506-143583	GT	AGG
(AGC)	 AG	143814-144023	GT	AGG
(TTG)	 AG	144154-144274	GT	AGG
(GGC)	 AG	144370-144434	GG	CAG
-recovered pasa_asmbl_7273.p1, internal, 143506, 143583
-recovered pasa_asmbl_7273.p1, internal, 143814, 144023
-recovered pasa_asmbl_7273.p1, internal, 144154, 144274
Valid prediction for GeneMark_model.48477_t
Valid prediction for Augustus_model.g18694.t1
Valid prediction for GlimmerHMM_glimmerT_28032-T1
Valid prediction for snap_scaffold_11-snap.1832-T1
Valid prediction for snap_scaffold_11-snap.1829-T1
Valid prediction for Augustus_model.g18687.t1
Valid prediction for snap_scaffold_11-snap.1825-T1
Valid prediction for Augustus_model.g18683.t1
Valid prediction for HiQ_model.g18689.t1
Valid prediction for GeneMark_model.48486_t
Valid prediction for GeneMark_model.48474_t
Valid prediction for pasa_asmbl_6800.p2
Valid prediction for CodingQuarry_transcript_8116-T1
Couldn't classify 71185, 71370
Couldn't classify 74064, 74150
Sorry, prediction pasa_asmbl_6796.p1 fails validation.
(CCT)	 TG	71185-71370	GT	AGG
(TAT)	 AG	71528-71593	GT	TGG
(GTT)	 AG	71747-71798	GT	TGG
(TTA)	 AG	71894-71961	GT	TGG
(GGT)	 AG	72097-72251	GT	GAG
(CCT)	 AG	72533-72673	GT	ATG
(GTC)	 AG	72764-72893	GT	CGG
(ATG)	 AG	73353-73441	GT	AGG
(TTC)	 AG	73706-73818	GT	GGG
(CCT)	 AG	73911-73981	GT	AGG
(GTG)	 AG	74064-74150	GT	GTG
-recovered pasa_asmbl_6796.p1, initial, 73353, 73441
-recovered pasa_asmbl_6796.p1, internal, 71528, 71593
-recovered pasa_asmbl_6796.p1, internal, 71747, 71798
-recovered pasa_asmbl_6796.p1, internal, 71894, 71961
-recovered pasa_asmbl_6796.p1, internal, 72097, 72251
-recovered pasa_asmbl_6796.p1, internal, 72533, 72673
-recovered pasa_asmbl_6796.p1, internal, 72764, 72893
-recovered pasa_asmbl_6796.p1, internal, 73353, 73441
-recovered pasa_asmbl_6796.p1, internal, 73706, 73818
-recovered pasa_asmbl_6796.p1, internal, 73911, 73981
-recovered pasa_asmbl_6796.p1, internal, 74064, 74150
Valid prediction for snap_scaffold_11-snap.1834-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 117201, rend_intergenic: 113502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 188223
-exon list size: 535


building trellis

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50.5    
50.7    
50.8    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.1    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.4    
53.6    
53.8    
54.0    
54.2    
54.4    
54.6    
54.7    
54.9    
55.1    
55.3    
55.5    
55.7    
55.9    
56.1    
56.2    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.5    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.6    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.4    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.2    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.6    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.6    
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 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 117201, rend_intergenic: 113502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support