-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_7670905-7965546

-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 GeneMark_model.39450_t
Valid prediction for snap_scaffold_9-snap.1633-T1
Valid prediction for snap_scaffold_9-snap.1646-T1
Valid prediction for pasa_asmbl_54126.p1
Valid prediction for GlimmerHMM_glimmerT_23004-T1
Couldn't classify 200013, 200248
Couldn't classify 200897, 200920
Sorry, prediction pasa_asmbl_54133.p1 fails validation.
(AAT)	 AG	200013-200248	GT	CGG
(CTT)	 AG	200372-200542	GT	TGG
(GTC)	 AG	200627-200786	GT	AGG
(GTG)	 AG	200897-200920	GT	GAG
-recovered pasa_asmbl_54133.p1, internal, 200013, 200248
-recovered pasa_asmbl_54133.p1, internal, 200372, 200542
-recovered pasa_asmbl_54133.p1, internal, 200627, 200786
-recovered pasa_asmbl_54133.p1, internal, 200897, 200920
Valid prediction for snap_scaffold_9-snap.1635-T1
Valid prediction for snap_scaffold_9-snap.1629-T1
Valid prediction for GlimmerHMM_glimmerT_23021-T1
Valid prediction for snap_scaffold_9-snap.1632-T1
Valid prediction for Augustus_model.g15385.t1
Valid prediction for GlimmerHMM_glimmerT_23000-T1
Valid prediction for GeneMark_model.39429_t
Valid prediction for snap_scaffold_9-snap.1642-T1
Valid prediction for Augustus_model.g15390.t1
Valid prediction for GeneMark_model.39454_t
Valid prediction for CodingQuarry_transcript_62073-T1
Couldn't classify 127664, 127786
Sorry, prediction pasa_asmbl_54127.p1 fails validation.
(ATA)	 AA	127664-127786	GT	CTG
(TGG)	 AG	127869-127952	GT	AGG
(CAA)	 AG	129093-129203	GT	AGG
(CTA)	 AG	129398-129684	GT	AGG
(GAG)	 AG	129791-130052	CA	GAC
-recovered pasa_asmbl_54127.p1, terminal, 129791, 130052
-recovered pasa_asmbl_54127.p1, internal, 127869, 127952
-recovered pasa_asmbl_54127.p1, internal, 129093, 129203
-recovered pasa_asmbl_54127.p1, internal, 129398, 129684
Valid prediction for GlimmerHMM_glimmerT_23022-T1
Valid prediction for GeneMark_model.39455_t
Valid prediction for GlimmerHMM_glimmerT_23019-T1
Valid prediction for snap_scaffold_9-snap.1671-T1
Valid prediction for GlimmerHMM_glimmerT_23015-T1
Valid prediction for Augustus_model.g15391.t1
Valid prediction for snap_scaffold_9-snap.1656-T1
Valid prediction for GlimmerHMM_glimmerT_23008-T1
Valid prediction for GlimmerHMM_glimmerT_23007-T1
Valid prediction for pasa_asmbl_54132.p1
Valid prediction for CodingQuarry_transcript_62074-T1
Valid prediction for Augustus_model.g15397.t1
Valid prediction for snap_scaffold_9-snap.1639-T1
Valid prediction for GlimmerHMM_glimmerT_23012-T1
Valid prediction for GlimmerHMM_glimmerT_22998-T1
Valid prediction for snap_scaffold_9-snap.1637-T1
Valid prediction for snap_scaffold_9-snap.1649-T1
Valid prediction for snap_scaffold_9-snap.1643-T1
Valid prediction for snap_scaffold_9-snap.1669-T1
Valid prediction for GlimmerHMM_glimmerT_23005-T1
Couldn't classify 201229, 201416
Sorry, prediction pasa_asmbl_54134.p1 fails validation.
(GCC)	 AG	201229-201416	GT	AGG
(GGC)	 AG	201840-201954	GT	AGG
(ATC)	 AG	202064-202285	GT	AGG
(GTA)	 AG	202452-202669	GT	AGG
(GAC)	 AG	202792-202968	GT	AAG
(AGG)	 AG	203122-203239	CA	GAC
-recovered pasa_asmbl_54134.p1, terminal, 203122, 203239
-recovered pasa_asmbl_54134.p1, internal, 201229, 201416
-recovered pasa_asmbl_54134.p1, internal, 201840, 201954
-recovered pasa_asmbl_54134.p1, internal, 202064, 202285
-recovered pasa_asmbl_54134.p1, internal, 202452, 202669
-recovered pasa_asmbl_54134.p1, internal, 202792, 202968
Valid prediction for snap_scaffold_9-snap.1666-T1
Valid prediction for Augustus_model.g15384.t1
Valid prediction for GlimmerHMM_glimmerT_23020-T1
Valid prediction for GeneMark_model.39444_t
Valid prediction for GeneMark_model.39445_t
Valid prediction for Augustus_model.g15383.t1
Valid prediction for GlimmerHMM_glimmerT_23013-T1
Valid prediction for snap_scaffold_9-snap.1659-T1
Valid prediction for GlimmerHMM_glimmerT_23010-T1
Valid prediction for GlimmerHMM_glimmerT_22996-T1
Valid prediction for snap_scaffold_9-snap.1651-T1
Valid prediction for snap_scaffold_9-snap.1660-T1
Valid prediction for GeneMark_model.39437_t
Valid prediction for HiQ_model.g15388.t1
Valid prediction for GeneMark_model.39431_t
Valid prediction for Augustus_model.g15399.t1
Valid prediction for snap_scaffold_9-snap.1655-T1
Valid prediction for GlimmerHMM_glimmerT_23016-T1
Valid prediction for GlimmerHMM_glimmerT_23024-T1
Valid prediction for GlimmerHMM_glimmerT_22997-T1
Valid prediction for snap_scaffold_9-snap.1645-T1
Valid prediction for snap_scaffold_9-snap.1647-T1
Valid prediction for snap_scaffold_9-snap.1641-T1
Valid prediction for GlimmerHMM_glimmerT_23003-T1
Valid prediction for GeneMark_model.39428_t
Valid prediction for snap_scaffold_9-snap.1668-T1
Valid prediction for GeneMark_model.39434_t
Valid prediction for snap_scaffold_9-snap.1653-T1
Valid prediction for snap_scaffold_9-snap.1634-T1
Valid prediction for Augustus_model.g15398.t1
Valid prediction for snap_scaffold_9-snap.1640-T1
Valid prediction for snap_scaffold_9-snap.1667-T1
Valid prediction for GeneMark_model.39452_t
Valid prediction for snap_scaffold_9-snap.1644-T1
Valid prediction for snap_scaffold_9-snap.1662-T1
Valid prediction for snap_scaffold_9-snap.1654-T1
Couldn't classify 124355, 124645
Couldn't classify 127869, 127949
Sorry, prediction pasa_asmbl_54122.p1 fails validation.
(GTC)	 CT	124355-124645	GT	TTG
(ATT)	 AG	125614-125751	GT	GGG
(CTG)	 AG	126541-126701	GT	AGG
(TCT)	 AG	126914-127121	GT	AGG
(AAT)	 AG	127448-127597	GT	CAG
(ATC)	 AG	127688-127786	GT	CTG
(TGG)	 AG	127869-127949	AA	ACA
-recovered pasa_asmbl_54122.p1, internal, 125614, 125751
-recovered pasa_asmbl_54122.p1, internal, 126541, 126701
-recovered pasa_asmbl_54122.p1, internal, 126914, 127121
-recovered pasa_asmbl_54122.p1, internal, 127448, 127597
-recovered pasa_asmbl_54122.p1, internal, 127688, 127786
Valid prediction for Augustus_model.g15396.t1
Valid prediction for snap_scaffold_9-snap.1630-T1
Valid prediction for GeneMark_model.39433_t
Valid prediction for GeneMark_model.39426_t
Valid prediction for pasa_asmbl_54121.p1
Couldn't classify 74554, 74595
Sorry, prediction pasa_asmbl_54119.p1 fails validation.
(CGG)	 GA	74554-74595	GT	TGG
(GGT)	 AG	76802-76878	GT	CAG
(CTT)	 AG	77457-77568	GT	AGG
(GAG)	 AG	79153-79289	GT	AGG
(ACT)	 AG	79378-79441	GT	AGG
(ATT)	 AG	80034-80162	GT	GTG
(GGT)	 AG	80861-80930	GT	ACG
(TCC)	 AG	81837-81950	GT	AGG
(GAC)	 AG	83039-83138	GT	AGG
(TCT)	 AG	83397-83516	GT	GGG
(CAT)	 AG	83622-83766	GT	AGG
(GCA)	 AG	83966-84130	AG	AAA
-recovered pasa_asmbl_54119.p1, terminal, 83966, 84130
-recovered pasa_asmbl_54119.p1, internal, 76802, 76878
-recovered pasa_asmbl_54119.p1, internal, 77457, 77568
-recovered pasa_asmbl_54119.p1, internal, 79153, 79289
-recovered pasa_asmbl_54119.p1, internal, 79378, 79441
-recovered pasa_asmbl_54119.p1, internal, 80034, 80162
-recovered pasa_asmbl_54119.p1, internal, 80861, 80930
-recovered pasa_asmbl_54119.p1, internal, 81837, 81950
-recovered pasa_asmbl_54119.p1, internal, 83039, 83138
-recovered pasa_asmbl_54119.p1, internal, 83397, 83516
-recovered pasa_asmbl_54119.p1, internal, 83622, 83766
Valid prediction for GeneMark_model.39435_t
Valid prediction for GlimmerHMM_glimmerT_23006-T1
Valid prediction for GeneMark_model.39440_t
Valid prediction for Augustus_model.g15386.t1
Valid prediction for GlimmerHMM_glimmerT_23011-T1
Valid prediction for GeneMark_model.39459_t
Valid prediction for snap_scaffold_9-snap.1670-T1
Valid prediction for Augustus_model.g15394.t1
Valid prediction for snap_scaffold_9-snap.1657-T1
Valid prediction for Augustus_model.g15395.t1
Valid prediction for GlimmerHMM_glimmerT_23002-T1
Valid prediction for GeneMark_model.39448_t
Valid prediction for GlimmerHMM_glimmerT_23001-T1
Valid prediction for snap_scaffold_9-snap.1650-T1
Valid prediction for GlimmerHMM_glimmerT_22995-T1
Valid prediction for Augustus_model.g15389.t1
Valid prediction for snap_scaffold_9-snap.1631-T1
Valid prediction for GeneMark_model.39441_t

-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 GlimmerHMM_glimmerT_23018-T1
Valid prediction for GeneMark_model.39446_t
Valid prediction for GeneMark_model.39425_t
Valid prediction for GeneMark_model.39432_t
Valid prediction for GeneMark_model.39451_t
Valid prediction for GeneMark_model.39458_t
Valid prediction for GeneMark_model.39449_t
Valid prediction for GlimmerHMM_glimmerT_23009-T1
Valid prediction for GeneMark_model.39442_t
Valid prediction for Augustus_model.g15392.t1
Valid prediction for GeneMark_model.39457_t
Valid prediction for CodingQuarry_transcript_62072-T1
Valid prediction for snap_scaffold_9-snap.1665-T1
Valid prediction for GeneMark_model.39439_t
Valid prediction for snap_scaffold_9-snap.1664-T1
Valid prediction for GeneMark_model.39438_t
Valid prediction for snap_scaffold_9-snap.1658-T1
Valid prediction for GlimmerHMM_glimmerT_23014-T1
Valid prediction for Augustus_model.g15380.t1
Valid prediction for CodingQuarry_transcript_62075-T1
Valid prediction for GeneMark_model.39427_t
Valid prediction for snap_scaffold_9-snap.1638-T1
Valid prediction for snap_scaffold_9-snap.1663-T1
Valid prediction for GeneMark_model.39430_t
Valid prediction for GlimmerHMM_glimmerT_22994-T1
Valid prediction for snap_scaffold_9-snap.1672-T1
Valid prediction for snap_scaffold_9-snap.1652-T1
Valid prediction for snap_scaffold_9-snap.1628-T1
Valid prediction for GeneMark_model.39424_t
Valid prediction for GlimmerHMM_glimmerT_22999-T1
Valid prediction for GeneMark_model.39453_t
Valid prediction for snap_scaffold_9-snap.1636-T1
Valid prediction for pasa_asmbl_55077.p2
Valid prediction for GlimmerHMM_glimmerT_22993-T1
Valid prediction for GlimmerHMM_glimmerT_23023-T1
Valid prediction for pasa_asmbl_55075.p1
Valid prediction for snap_scaffold_9-snap.1626-T1
Valid prediction for Augustus_model.g15387.t1
Valid prediction for GeneMark_model.39443_t
Valid prediction for snap_scaffold_9-snap.1661-T1
Valid prediction for HiQ_model.g15382.t1
Valid prediction for HiQ_model.g15393.t1
Valid prediction for snap_scaffold_9-snap.1648-T1
Valid prediction for GeneMark_model.39456_t
Valid prediction for Augustus_model.g15381.t1
Valid prediction for GlimmerHMM_glimmerT_23017-T1
Valid prediction for snap_scaffold_9-snap.1627-T1
Valid prediction for GlimmerHMM_glimmerT_22992-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 102086, rend_intergenic: 101418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 254558, rend_intergenic: 235960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 288783, rend_intergenic: 284340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 294642
-exon list size: 736


building trellis

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81.4    
81.6    
81.7    
81.8    
82.0    
82.1    
82.2    
82.4    
82.5    
82.7    
82.8    
82.9    
83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.9    
84.0    
84.1    
84.3    
84.4    
84.6    
84.7    
84.8    
85.0    
85.1    
85.2    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.6    
86.7    
86.9    
87.0    
87.1    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 102086, rend_intergenic: 101418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 254558, rend_intergenic: 235960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 288783, rend_intergenic: 284340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 27087
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 1 - 15321
	-no exons in range 15468 - 27087