-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_5109851-5484771

-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_17393-T1
Valid prediction for GlimmerHMM_glimmerT_17400-T1
Valid prediction for GlimmerHMM_glimmerT_17380-T1
Valid prediction for GlimmerHMM_glimmerT_17387-T1
Valid prediction for snap_scaffold_7-snap.1141-T1
Valid prediction for Augustus_model.g11652.t1
Valid prediction for CodingQuarry_transcript_57509-T1
Valid prediction for Augustus_model.g11651.t1
Valid prediction for snap_scaffold_7-snap.1110-T1
Valid prediction for Augustus_model.g11648.t1
Valid prediction for snap_scaffold_7-snap.1098-T1
Valid prediction for snap_scaffold_7-snap.1137-T1
Valid prediction for snap_scaffold_7-snap.1140-T1
Valid prediction for Augustus_model.g11650.t1
Valid prediction for GlimmerHMM_glimmerT_17386-T1
Valid prediction for snap_scaffold_7-snap.1104-T1
Valid prediction for Augustus_model.g11633.t1
Valid prediction for snap_scaffold_7-snap.1095-T1
Valid prediction for pasa_asmbl_49791.p1
Valid prediction for GlimmerHMM_glimmerT_17388-T1
Valid prediction for snap_scaffold_7-snap.1120-T1
Valid prediction for GlimmerHMM_glimmerT_17397-T1
Valid prediction for HiQ_model.g11630.t1
Valid prediction for snap_scaffold_7-snap.1108-T1
Valid prediction for GlimmerHMM_glimmerT_17405-T1
Valid prediction for snap_scaffold_7-snap.1127-T1
Couldn't classify 123088, 123179
Sorry, prediction pasa_asmbl_49798.p1 fails validation.
(GAC)	 GA	123088-123179	GT	GGG
(CTG)	 AG	123406-123631	GT	AGG
(GTG)	 AG	123984-124097	GT	AGG
(TTC)	 AG	124479-124645	GT	TGG
(GTA)	 AG	125458-125668	GC	AGG
(GAG)	 AG	126876-126959	GT	AGG
(GTG)	 AG	127095-127283	GT	AGG
(GAG)	 AG	127471-127662	GT	AGG
(GTG)	 AG	127912-128124	GT	AGG
(GAG)	 AG	128495-128630	GT	TGG
(ATA)	 AG	128855-128943	GT	AGG
(GAG)	 AG	129062-129208	GT	AGG
(GTA)	 AG	129311-129431	GT	AGG
(GGA)	 AG	129508-129693	GT	GGG
(ACG)	 AG	129966-130171	GT	AGG
(AAG)	 AG	130567-130623	AT	GAA
add_exon() Sorry, pasa_asmbl_49798.p1 129311-129431-terminal-3 is invalid.
-recovered pasa_asmbl_49798.p1, terminal, 129311, 129431
-recovered pasa_asmbl_49798.p1, terminal, 130567, 130623
-recovered pasa_asmbl_49798.p1, internal, 123406, 123631
-recovered pasa_asmbl_49798.p1, internal, 123984, 124097
-recovered pasa_asmbl_49798.p1, internal, 124479, 124645
-recovered pasa_asmbl_49798.p1, internal, 125458, 125668
-recovered pasa_asmbl_49798.p1, internal, 126876, 126959
-recovered pasa_asmbl_49798.p1, internal, 127095, 127283
-recovered pasa_asmbl_49798.p1, internal, 127471, 127662
-recovered pasa_asmbl_49798.p1, internal, 127912, 128124
-recovered pasa_asmbl_49798.p1, internal, 128495, 128630
-recovered pasa_asmbl_49798.p1, internal, 128855, 128943
-recovered pasa_asmbl_49798.p1, internal, 129062, 129208
-recovered pasa_asmbl_49798.p1, internal, 129311, 129431
-recovered pasa_asmbl_49798.p1, internal, 129508, 129693
-recovered pasa_asmbl_49798.p1, internal, 129966, 130171
Valid prediction for CodingQuarry_transcript_57506-T1
Valid prediction for GlimmerHMM_glimmerT_17404-T1
Valid prediction for GlimmerHMM_glimmerT_17409-T1
Valid prediction for snap_scaffold_7-snap.1123-T1
Valid prediction for GlimmerHMM_glimmerT_17408-T1
Valid prediction for snap_scaffold_7-snap.1132-T1
Valid prediction for snap_scaffold_7-snap.1114-T1
Valid prediction for snap_scaffold_7-snap.1099-T1
Couldn't classify 361411, 361691
Sorry, prediction pasa_asmbl_49811.p2 fails validation.
(ATG)	 CA	360809-360889	GT	CAG
(TGC)	 AG	361101-361146	GT	GGG
(ATA)	 AG	361411-361691	GG	GAG
-recovered pasa_asmbl_49811.p2, initial, 360809, 360889
-recovered pasa_asmbl_49811.p2, internal, 361101, 361146
Valid prediction for snap_scaffold_7-snap.1096-T1
Valid prediction for Augustus_model.g11636.t1
Valid prediction for GlimmerHMM_glimmerT_17377-T1
Valid prediction for CodingQuarry_transcript_57508-T1
Valid prediction for snap_scaffold_7-snap.1097-T1
Valid prediction for Augustus_model.g11628.t1
Valid prediction for pasa_asmbl_49803.p1
Valid prediction for snap_scaffold_7-snap.1103-T1
Couldn't classify 182836, 183016
Sorry, prediction pasa_asmbl_49808.p1 fails validation.
(CAG)	 TG	182836-183016	GT	CAG
(GTG)	 AG	183536-183780	TC	AGT
-recovered pasa_asmbl_49808.p1, terminal, 183536, 183780
Valid prediction for snap_scaffold_7-snap.1139-T1
Valid prediction for CodingQuarry_transcript_57504-T1
Couldn't classify 151931, 152241
Sorry, prediction pasa_asmbl_49804.p1 fails validation.
(TCA)	 GC	151931-152241	GT	CGG
(GAC)	 AG	152828-152981	GG	GAG
-recovered pasa_asmbl_49804.p1, terminal, 152828, 152981
Valid prediction for HiQ_model.g11638.t1
Valid prediction for snap_scaffold_7-snap.1119-T1
Valid prediction for CodingQuarry_transcript_57512-T1
Valid prediction for snap_scaffold_7-snap.1105-T1
Couldn't classify 114124, 114191
Sorry, prediction pasa_asmbl_49794.p1 fails validation.
(ACG)	 CT	114124-114191	GT	AGG
(GTG)	 AG	114832-114938	GT	AGG
(TTC)	 AG	115041-115176	GT	AAG
(GGA)	 AG	115438-115504	GT	AGG
(GCA)	 AG	115601-115712	GT	TAG
(GTC)	 AG	115834-115897	GT	AGG
(ACC)	 AG	116042-116216	GT	AGG
(GTG)	 AG	116322-116393	AG	AAA
add_exon() Sorry, pasa_asmbl_49794.p1 114832-114938-terminal-2 is invalid.
-recovered pasa_asmbl_49794.p1, terminal, 114832, 114938
-recovered pasa_asmbl_49794.p1, terminal, 116322, 116393
-recovered pasa_asmbl_49794.p1, internal, 114832, 114938
-recovered pasa_asmbl_49794.p1, internal, 115041, 115176
-recovered pasa_asmbl_49794.p1, internal, 115438, 115504
-recovered pasa_asmbl_49794.p1, internal, 115601, 115712
-recovered pasa_asmbl_49794.p1, internal, 115834, 115897
-recovered pasa_asmbl_49794.p1, internal, 116042, 116216
Valid prediction for GlimmerHMM_glimmerT_17403-T1
Couldn't classify 119593, 119637
Couldn't classify 122724, 122803
Sorry, prediction pasa_asmbl_49796.p1 fails validation.
(CTA)	 CC	119593-119637	GT	GGG
(CTC)	 AG	119767-119799	GT	AGG
(AAC)	 AG	120061-120087	GT	CGG
(CCC)	 AG	120526-120722	GT	AGG
(CGC)	 AG	120881-121007	GT	CGG
(CAC)	 AG	121250-121369	GT	ATG
(AAC)	 AG	122390-122579	GT	AGG
(ATG)	 AG	122724-122803	CC	CCC
-recovered pasa_asmbl_49796.p1, internal, 119767, 119799
-recovered pasa_asmbl_49796.p1, internal, 120061, 120087
-recovered pasa_asmbl_49796.p1, internal, 120526, 120722
-recovered pasa_asmbl_49796.p1, internal, 120881, 121007
-recovered pasa_asmbl_49796.p1, internal, 121250, 121369
-recovered pasa_asmbl_49796.p1, internal, 122390, 122579
Valid prediction for GlimmerHMM_glimmerT_17395-T1
Valid prediction for Augustus_model.g11625.t1
Valid prediction for Augustus_model.g11649.t1
Valid prediction for Augustus_model.g11632.t1
Valid prediction for snap_scaffold_7-snap.1112-T1
Valid prediction for snap_scaffold_7-snap.1116-T1
Valid prediction for GlimmerHMM_glimmerT_17392-T1
Valid prediction for GlimmerHMM_glimmerT_17406-T1
Valid prediction for GlimmerHMM_glimmerT_17384-T1
Valid prediction for Augustus_model.g11624.t1
Valid prediction for Augustus_model.g11643.t1
Valid prediction for CodingQuarry_transcript_57505-T1
Valid prediction for Augustus_model.g11634.t1
Valid prediction for GlimmerHMM_glimmerT_17390-T1
Valid prediction for snap_scaffold_7-snap.1115-T1
Valid prediction for pasa_asmbl_49809.p1
Valid prediction for snap_scaffold_7-snap.1107-T1
Valid prediction for snap_scaffold_7-snap.1109-T1
Valid prediction for snap_scaffold_7-snap.1124-T1
Valid prediction for GlimmerHMM_glimmerT_17385-T1
Valid prediction for snap_scaffold_7-snap.1135-T1
Valid prediction for Augustus_model.g11640.t1
Valid prediction for Augustus_model.g11629.t1
Valid prediction for GlimmerHMM_glimmerT_17381-T1
Valid prediction for Augustus_model.g11637.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 GlimmerHMM_glimmerT_17382-T1
Valid prediction for Augustus_model.g11627.t1
Valid prediction for snap_scaffold_7-snap.1100-T1
Valid prediction for Augustus_model.g11635.t1
Valid prediction for Augustus_model.g11626.t1
Valid prediction for GlimmerHMM_glimmerT_17378-T1
Valid prediction for Augustus_model.g11644.t1
Valid prediction for GlimmerHMM_glimmerT_17394-T1
Couldn't classify 316276, 316395
Sorry, prediction pasa_asmbl_50872.p1 fails validation.
(CCT)	 CC	316276-316395	GT	AGG
(GTA)	 AG	316527-316706	AA	GAA
-recovered pasa_asmbl_50872.p1, terminal, 316527, 316706
Valid prediction for snap_scaffold_7-snap.1142-T1
Couldn't classify 137599, 137982
Sorry, prediction pasa_asmbl_50884.p1 fails validation.
(CCT)	 TG	137599-137982	GT	AGG
(GTG)	 AG	138069-138191	GT	AGG
(GTC)	 AG	138376-138522	GT	AGG
(GTG)	 AG	138755-139276	GT	AGG
(GTG)	 AG	139388-139492	GT	AGG
(GTG)	 AG	139652-139834	AC	AAA
-recovered pasa_asmbl_50884.p1, terminal, 139652, 139834
-recovered pasa_asmbl_50884.p1, internal, 138069, 138191
-recovered pasa_asmbl_50884.p1, internal, 138376, 138522
-recovered pasa_asmbl_50884.p1, internal, 138755, 139276
-recovered pasa_asmbl_50884.p1, internal, 139388, 139492
Valid prediction for snap_scaffold_7-snap.1113-T1
Valid prediction for snap_scaffold_7-snap.1125-T1
Valid prediction for Augustus_model.g11642.t1
Valid prediction for Augustus_model.g11646.t1
Valid prediction for snap_scaffold_7-snap.1138-T1
Valid prediction for GlimmerHMM_glimmerT_17383-T1
Valid prediction for GlimmerHMM_glimmerT_17402-T1
Valid prediction for Augustus_model.g11631.t1
Valid prediction for GlimmerHMM_glimmerT_17391-T1
Valid prediction for GlimmerHMM_glimmerT_17407-T1
Valid prediction for GlimmerHMM_glimmerT_17376-T1
Valid prediction for snap_scaffold_7-snap.1129-T1
Valid prediction for GlimmerHMM_glimmerT_17379-T1
Valid prediction for snap_scaffold_7-snap.1117-T1
Valid prediction for Augustus_model.g11647.t1
Valid prediction for snap_scaffold_7-snap.1134-T1
Valid prediction for snap_scaffold_7-snap.1130-T1
Valid prediction for pasa_asmbl_50886.p1
Valid prediction for GlimmerHMM_glimmerT_17401-T1
Valid prediction for GlimmerHMM_glimmerT_17389-T1
Couldn't classify 161312, 161492
Sorry, prediction pasa_asmbl_50881.p2 fails validation.
(ATG)	 GG	159931-160094	GT	AGG
(GGC)	 AG	160493-160663	GT	AGG
(GAC)	 AG	161312-161492	AC	GCA
-recovered pasa_asmbl_50881.p2, initial, 159931, 160094
-recovered pasa_asmbl_50881.p2, internal, 160493, 160663
Valid prediction for snap_scaffold_7-snap.1122-T1
Valid prediction for snap_scaffold_7-snap.1121-T1
Valid prediction for snap_scaffold_7-snap.1136-T1
Valid prediction for snap_scaffold_7-snap.1106-T1
Valid prediction for Augustus_model.g11623.t1
Valid prediction for snap_scaffold_7-snap.1111-T1
Valid prediction for snap_scaffold_7-snap.1131-T1
Valid prediction for Augustus_model.g11639.t1
Valid prediction for snap_scaffold_7-snap.1128-T1
Couldn't classify 162326, 162388
Sorry, prediction pasa_asmbl_50880.p2 fails validation.
(GCA)	 CA	162326-162388	GT	AGG
(CGT)	 AG	162684-162769	GT	AGG
(GGA)	 AG	162857-162984	GT	GGG
(CCA)	 AG	163147-163196	GT	AGG
(CGG)	 AG	163360-163409	GT	TGG
(CTT)	 AG	163528-163575	GT	AGG
(TTC)	 AG	163678-163774	GA	AGG
-recovered pasa_asmbl_50880.p2, terminal, 163678, 163774
-recovered pasa_asmbl_50880.p2, internal, 162684, 162769
-recovered pasa_asmbl_50880.p2, internal, 162857, 162984
-recovered pasa_asmbl_50880.p2, internal, 163147, 163196
-recovered pasa_asmbl_50880.p2, internal, 163360, 163409
-recovered pasa_asmbl_50880.p2, internal, 163528, 163575
Couldn't classify 302553, 302616
Sorry, prediction pasa_asmbl_50873.p1 fails validation.
(TGG)	 AG	302553-302616	GT	AGG
(GGA)	 AG	303483-303604	GT	AGG
(GAA)	 AG	303699-303765	GT	AGG
(GCT)	 AG	303872-304034	GT	TCG
(TTA)	 AG	304109-304177	GT	CGG
(CAC)	 AG	304493-304649	CC	AGC
-recovered pasa_asmbl_50873.p1, terminal, 304493, 304649
-recovered pasa_asmbl_50873.p1, internal, 302553, 302616
-recovered pasa_asmbl_50873.p1, internal, 303483, 303604
-recovered pasa_asmbl_50873.p1, internal, 303699, 303765
-recovered pasa_asmbl_50873.p1, internal, 303872, 304034
-recovered pasa_asmbl_50873.p1, internal, 304109, 304177
Valid prediction for GlimmerHMM_glimmerT_17398-T1
Valid prediction for snap_scaffold_7-snap.1102-T1
Valid prediction for snap_scaffold_7-snap.1133-T1
Valid prediction for GlimmerHMM_glimmerT_17399-T1
Valid prediction for Augustus_model.g11645.t1
Valid prediction for snap_scaffold_7-snap.1126-T1
Valid prediction for snap_scaffold_7-snap.1101-T1
Valid prediction for CodingQuarry_transcript_57510-T1
Valid prediction for Augustus_model.g11641.t1
Valid prediction for snap_scaffold_7-snap.1118-T1
Valid prediction for CodingQuarry_transcript_57511-T1
Valid prediction for GlimmerHMM_glimmerT_17396-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 231399, rend_intergenic: 224446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253461, rend_intergenic: 246195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 288585, rend_intergenic: 283152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 314972, rend_intergenic: 311112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 318726, rend_intergenic: 315331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 374895, rend_intergenic: 368116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 374921
-exon list size: 528


building trellis

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70.8    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.6    
72.8    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.3    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.7    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.3    
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    
87.4    
87.5    
87.7    
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    
90.6    
90.8    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 231399, rend_intergenic: 224446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253461, rend_intergenic: 246195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 288585, rend_intergenic: 283152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 314972, rend_intergenic: 311112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 318726, rend_intergenic: 315331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 374895, rend_intergenic: 368116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 28650
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 2 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 20726
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 14308
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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

-building DP trellis

-building trellis in range 2282 - 14308
-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