-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_8/scaffold_8_12271780-12519758

-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_8-snap.2255-T1
Valid prediction for snap_scaffold_8-snap.2272-T1
Valid prediction for snap_scaffold_8-snap.2268-T1
Valid prediction for snap_scaffold_8-snap.2256-T1
Valid prediction for GeneMark_model.35875_t
Valid prediction for GeneMark_model.35868_t
Valid prediction for snap_scaffold_8-snap.2267-T1
Valid prediction for Augustus_model.g14100.t1
Valid prediction for GlimmerHMM_glimmerT_21019-T1
Valid prediction for GeneMark_model.35860_t
Valid prediction for GeneMark_model.35837_t
Valid prediction for GlimmerHMM_glimmerT_21005-T1
Valid prediction for pasa_asmbl_52301.p1
Valid prediction for GlimmerHMM_glimmerT_21018-T1
Valid prediction for pasa_asmbl_52299.p1
Valid prediction for snap_scaffold_8-snap.2259-T1
Valid prediction for GeneMark_model.35851_t
Valid prediction for snap_scaffold_8-snap.2275-T1
Valid prediction for snap_scaffold_8-snap.2253-T1
Valid prediction for Augustus_model.g14094.t1
Valid prediction for GeneMark_model.35850_t
Valid prediction for GeneMark_model.35836_t
Valid prediction for GeneMark_model.35874_t
Valid prediction for GlimmerHMM_glimmerT_21026-T1
Valid prediction for GlimmerHMM_glimmerT_21004-T1
Valid prediction for GeneMark_model.35839_t
Valid prediction for GeneMark_model.35834_t
Valid prediction for snap_scaffold_8-snap.2252-T1
Valid prediction for GeneMark_model.35872_t
Valid prediction for GlimmerHMM_glimmerT_21023-T1
Valid prediction for HiQ_model.g14103.t1
Valid prediction for snap_scaffold_8-snap.2257-T1
Valid prediction for GeneMark_model.35857_t
Valid prediction for snap_scaffold_8-snap.2262-T1
Valid prediction for Augustus_model.g14101.t1
Valid prediction for snap_scaffold_8-snap.2241-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.35870_t
Valid prediction for GlimmerHMM_glimmerT_21014-T1
Valid prediction for CodingQuarry_transcript_59699-T1
Valid prediction for Augustus_model.g14108.t1
Valid prediction for snap_scaffold_8-snap.2271-T1
Valid prediction for snap_scaffold_8-snap.2277-T1
Valid prediction for HiQ_model.g14104.t1
Valid prediction for GlimmerHMM_glimmerT_21016-T1
Valid prediction for GlimmerHMM_glimmerT_21024-T1
Valid prediction for GeneMark_model.35856_t
Valid prediction for GlimmerHMM_glimmerT_21015-T1
Valid prediction for GeneMark_model.35842_t
Valid prediction for snap_scaffold_8-snap.2251-T1
Valid prediction for snap_scaffold_8-snap.2273-T1
Valid prediction for GeneMark_model.35854_t
Valid prediction for snap_scaffold_8-snap.2243-T1
Valid prediction for GlimmerHMM_glimmerT_21017-T1
Valid prediction for GeneMark_model.35862_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_21028-T1
Valid prediction for GlimmerHMM_glimmerT_21027-T1
Valid prediction for Augustus_model.g14110.t1
Valid prediction for Augustus_model.g14095.t1
Valid prediction for snap_scaffold_8-snap.2261-T1
Valid prediction for snap_scaffold_8-snap.2247-T1
Valid prediction for Augustus_model.g14096.t1
Valid prediction for GlimmerHMM_glimmerT_21011-T1
Valid prediction for Augustus_model.g14097.t1
Valid prediction for GeneMark_model.35869_t
Valid prediction for Augustus_model.g14105.t1
Valid prediction for snap_scaffold_8-snap.2246-T1
Valid prediction for GeneMark_model.35841_t
Valid prediction for GeneMark_model.35838_t
Valid prediction for GeneMark_model.35849_t
Valid prediction for GeneMark_model.35844_t
Valid prediction for GeneMark_model.35864_t
Valid prediction for GlimmerHMM_glimmerT_21022-T1
Valid prediction for GlimmerHMM_glimmerT_21006-T1
Valid prediction for snap_scaffold_8-snap.2254-T1
Valid prediction for snap_scaffold_8-snap.2274-T1
Valid prediction for GeneMark_model.35873_t
Valid prediction for snap_scaffold_8-snap.2242-T1
Valid prediction for snap_scaffold_8-snap.2270-T1
Valid prediction for GeneMark_model.35855_t
Couldn't classify 165690, 165747
Couldn't classify 167177, 167207
Sorry, prediction pasa_asmbl_53654.p1 fails validation.
(AAC)	 AG	165690-165747	GT	CAG
(TAT)	 AG	166144-166271	GT	AGG
(TAC)	 AG	166938-167044	GT	TGG
(GTG)	 AG	167177-167207	GT	AGG
-recovered pasa_asmbl_53654.p1, internal, 165690, 165747
-recovered pasa_asmbl_53654.p1, internal, 166144, 166271
-recovered pasa_asmbl_53654.p1, internal, 166938, 167044
-recovered pasa_asmbl_53654.p1, internal, 167177, 167207
Valid prediction for CodingQuarry_transcript_59700-T1
Valid prediction for GeneMark_model.35863_t
Valid prediction for snap_scaffold_8-snap.2250-T1
Couldn't classify 171186, 171239
Couldn't classify 174859, 174966
Sorry, prediction pasa_asmbl_53200.p1 fails validation.
(AAC)	 TC	171186-171239	GT	AGG
(GTG)	 AG	171393-171468	GT	AGG
(ATT)	 AG	171884-171987	GT	CGG
(GTT)	 AG	172301-172454	GT	AGG
(ATG)	 AG	172780-172859	GT	AGG
(GCG)	 AG	173056-173115	GT	AGG
(GTG)	 AG	173860-174010	GT	AGG
(TGT)	 AG	174189-174305	GT	GGG
(GTA)	 AG	174601-174704	GC	AAG
(GCG)	 AG	174859-174966	AC	TCA
add_exon() Sorry, pasa_asmbl_53200.p1 172780-172859-initial-1 is invalid.
-recovered pasa_asmbl_53200.p1, initial, 172780, 172859
-recovered pasa_asmbl_53200.p1, internal, 171393, 171468
-recovered pasa_asmbl_53200.p1, internal, 171884, 171987
-recovered pasa_asmbl_53200.p1, internal, 172301, 172454
-recovered pasa_asmbl_53200.p1, internal, 172780, 172859
-recovered pasa_asmbl_53200.p1, internal, 173056, 173115
-recovered pasa_asmbl_53200.p1, internal, 173860, 174010
-recovered pasa_asmbl_53200.p1, internal, 174189, 174305
-recovered pasa_asmbl_53200.p1, internal, 174601, 174704
Valid prediction for snap_scaffold_8-snap.2258-T1
Valid prediction for Augustus_model.g14099.t1
Couldn't classify 49048, 49135
Couldn't classify 58611, 58742
Sorry, prediction pasa_asmbl_53205.p1 fails validation.
(CCC)	 CC	49048-49135	GT	TGG
(AGA)	 AG	49397-49524	GT	AGG
(AGA)	 AG	52306-52426	GT	GGG
(GTT)	 AG	55243-55323	GT	GGG
(CTC)	 AG	58215-58372	GT	TGG
(GTG)	 AG	58611-58742	AA	GGA
-recovered pasa_asmbl_53205.p1, internal, 49397, 49524
-recovered pasa_asmbl_53205.p1, internal, 52306, 52426
-recovered pasa_asmbl_53205.p1, internal, 55243, 55323
-recovered pasa_asmbl_53205.p1, internal, 58215, 58372
Valid prediction for GlimmerHMM_glimmerT_21021-T1
Valid prediction for GeneMark_model.35876_t
Valid prediction for GeneMark_model.35853_t
Valid prediction for snap_scaffold_8-snap.2249-T1
Valid prediction for GeneMark_model.35835_t
Valid prediction for snap_scaffold_8-snap.2245-T1
Valid prediction for snap_scaffold_8-snap.2248-T1
Valid prediction for snap_scaffold_8-snap.2269-T1
Valid prediction for Augustus_model.g14106.t1
Couldn't classify 167777, 167834
Couldn't classify 168346, 168489
Sorry, prediction pasa_asmbl_53201.p1 fails validation.
(TTA)	 AC	167777-167834	GT	CAG
(GCA)	 AG	168055-168155	GT	AGG
(TAT)	 AG	168346-168489	TA	AGT
-recovered pasa_asmbl_53201.p1, internal, 168055, 168155
Couldn't classify 2856, 3176
Sorry, prediction pasa_asmbl_53207.p1 fails validation.
(GAT)	 TG	2856-3176	AT	ACA
Valid prediction for Augustus_model.g14098.t1
Couldn't classify 64681, 64837
Sorry, prediction pasa_asmbl_53603.p1 fails validation.
(GGT)	 AG	64681-64837	GT	AGG
(CTG)	 AG	64977-65128	TT	AAT
add_exon() Sorry, pasa_asmbl_53603.p1 64681-64837-terminal-3 is invalid.
-recovered pasa_asmbl_53603.p1, terminal, 64681, 64837
-recovered pasa_asmbl_53603.p1, terminal, 64977, 65128
-recovered pasa_asmbl_53603.p1, internal, 64681, 64837
Valid prediction for GlimmerHMM_glimmerT_21025-T1
Valid prediction for GlimmerHMM_glimmerT_21007-T1
Valid prediction for GeneMark_model.35865_t
Valid prediction for GlimmerHMM_glimmerT_21008-T1
Valid prediction for GeneMark_model.35871_t
Valid prediction for snap_scaffold_8-snap.2265-T1
Valid prediction for GeneMark_model.35866_t
Valid prediction for snap_scaffold_8-snap.2263-T1
Valid prediction for Augustus_model.g14113.t1
Valid prediction for GlimmerHMM_glimmerT_21013-T1
Valid prediction for Augustus_model.g14107.t1
Valid prediction for pasa_asmbl_53187.p1
Valid prediction for snap_scaffold_8-snap.2244-T1
Valid prediction for snap_scaffold_8-snap.2266-T1
Valid prediction for GlimmerHMM_glimmerT_21012-T1
Valid prediction for GeneMark_model.35858_t
Valid prediction for CodingQuarry_transcript_59698-T1
Valid prediction for pasa_asmbl_53199.p1
Valid prediction for GeneMark_model.35848_t
Valid prediction for snap_scaffold_8-snap.2278-T1
Valid prediction for Augustus_model.g14109.t1
Valid prediction for Augustus_model.g14115.t1
Valid prediction for GeneMark_model.35840_t
Valid prediction for GlimmerHMM_glimmerT_21009-T1
Couldn't classify 187195, 187480
Sorry, prediction pasa_asmbl_53197.p1 fails validation.
(ATG)	 AG	181893-181934	GT	AGG
(GTT)	 AG	182041-182197	GT	AGG
(ATG)	 AG	182338-182459	GT	AGG
(AAA)	 AG	182998-183167	GT	CGG
(GAT)	 AG	183375-183637	GT	TGG
(CCA)	 AG	183843-184066	GT	CGG
(GTT)	 AG	184182-184274	GT	AGG
(ATC)	 AG	184372-184737	GT	AGG
(GTG)	 AG	184908-184997	GT	AGG
(ATG)	 AG	185337-185492	GT	AGG
(GCG)	 AG	186023-186284	GT	CGG
(TGC)	 AG	186640-186800	GT	AGG
(ATC)	 AG	186922-187043	GT	AGG
(GTG)	 AG	187195-187480	TA	GCT
-recovered pasa_asmbl_53197.p1, initial, 181893, 181934
add_exon() Sorry, pasa_asmbl_53197.p1 182338-182459-initial-1 is invalid.
-recovered pasa_asmbl_53197.p1, initial, 182338, 182459
-recovered pasa_asmbl_53197.p1, initial, 185337, 185492
-recovered pasa_asmbl_53197.p1, internal, 181893, 181934
-recovered pasa_asmbl_53197.p1, internal, 182041, 182197
-recovered pasa_asmbl_53197.p1, internal, 182338, 182459
-recovered pasa_asmbl_53197.p1, internal, 182998, 183167
-recovered pasa_asmbl_53197.p1, internal, 183375, 183637
-recovered pasa_asmbl_53197.p1, internal, 183843, 184066
-recovered pasa_asmbl_53197.p1, internal, 184182, 184274
-recovered pasa_asmbl_53197.p1, internal, 184372, 184737
-recovered pasa_asmbl_53197.p1, internal, 184908, 184997
-recovered pasa_asmbl_53197.p1, internal, 185337, 185492
-recovered pasa_asmbl_53197.p1, internal, 186023, 186284
-recovered pasa_asmbl_53197.p1, internal, 186640, 186800
-recovered pasa_asmbl_53197.p1, internal, 186922, 187043
Valid prediction for CodingQuarry_transcript_59697-T1
Valid prediction for Augustus_model.g14114.t1
Valid prediction for snap_scaffold_8-snap.2276-T1
Valid prediction for GeneMark_model.35845_t
Couldn't classify 159876, 159901
Sorry, prediction pasa_asmbl_53202.p1 fails validation.
(ATG)	 CA	152079-152178	GT	AGG
(GAA)	 AG	153626-153669	GT	TGG
(AGT)	 AG	154241-154283	GT	TGG
(GAA)	 AG	156329-156424	GT	AAG
(CAA)	 AG	158084-158185	GT	AGG
(AGA)	 AG	159876-159901	AC	ACA
-recovered pasa_asmbl_53202.p1, initial, 152079, 152178
-recovered pasa_asmbl_53202.p1, internal, 153626, 153669
-recovered pasa_asmbl_53202.p1, internal, 154241, 154283
-recovered pasa_asmbl_53202.p1, internal, 156329, 156424
-recovered pasa_asmbl_53202.p1, internal, 158084, 158185
Valid prediction for GeneMark_model.35861_t
Valid prediction for GeneMark_model.35867_t
Valid prediction for Augustus_model.g14111.t1
Valid prediction for GeneMark_model.35859_t
Valid prediction for snap_scaffold_8-snap.2279-T1
Valid prediction for Augustus_model.g14112.t1
Valid prediction for snap_scaffold_8-snap.2264-T1
Valid prediction for GeneMark_model.35833_t
Couldn't classify 27958, 27987
Couldn't classify 33034, 33076
Sorry, prediction pasa_asmbl_53645.p1 fails validation.
(CAG)	 CC	27958-27987	GT	TGG
(GTC)	 AG	29400-29483	GT	CTG
(GAG)	 AG	30131-30288	GT	AGG
(GAC)	 AG	33034-33076	GG	TGG
-recovered pasa_asmbl_53645.p1, internal, 29400, 29483
-recovered pasa_asmbl_53645.p1, internal, 30131, 30288
Valid prediction for Augustus_model.g14102.t1
Valid prediction for GlimmerHMM_glimmerT_21020-T1
Valid prediction for GeneMark_model.35843_t
Valid prediction for snap_scaffold_8-snap.2260-T1
Valid prediction for GeneMark_model.35846_t
Valid prediction for snap_scaffold_8-snap.2240-T1
Valid prediction for GlimmerHMM_glimmerT_21010-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23658, rend_intergenic: 18174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141760, rend_intergenic: 141530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145997, rend_intergenic: 143297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150761, rend_intergenic: 146196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158213, rend_intergenic: 151512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186798, rend_intergenic: 174005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188820, rend_intergenic: 187108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220350, rend_intergenic: 196881  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231161, rend_intergenic: 222819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240345, rend_intergenic: 237071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 247979
-exon list size: 663


building trellis

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62.6    
62.7    
62.9    
63.0    
63.2    
63.3    
63.5    
63.6    
63.8    
63.9    
64.1    
64.2    
64.4    
64.5    
64.7    
64.8    
65.0    
65.1    
65.3    
65.4    
65.6    
65.7    
65.9    
66.0    
66.2    
66.3    
66.5    
66.6    
66.8    
66.9    
67.1    
67.2    
67.4    
67.5    
67.7    
67.8    
68.0    
68.1    
68.3    
68.4    
68.6    
68.7    
68.9    
69.0    
69.2    
69.3    
69.5    
69.6    
69.8    
69.9    
70.1    
70.2    
70.4    
70.5    
70.7    
70.8    
71.0    
71.1    
71.3    
71.4    
71.6    
71.7    
71.9    
72.0    
72.2    
72.3    
72.5    
72.6    
72.8    
72.9    
73.1    
73.2    
73.4    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.2    
75.3    
75.5    
75.6    
75.8    
75.9    
76.1    
76.2    
76.4    
76.5    
76.7    
76.8    
77.0    
77.1    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.2    
78.3    
78.5    
78.6    
78.8    
78.9    
79.1    
79.2    
79.4    
79.5    
79.7    
79.8    
80.0    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.9    
83.0    
83.2    
83.3    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 23658, rend_intergenic: 18174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141760, rend_intergenic: 141530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145997, rend_intergenic: 143297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150761, rend_intergenic: 146196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158213, rend_intergenic: 151512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186798, rend_intergenic: 174005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188820, rend_intergenic: 187108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220350, rend_intergenic: 196881  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231161, rend_intergenic: 222819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240345, rend_intergenic: 237071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 15354
-exon list size: 22


building trellis

4.2    
8.3    
12.5    
16.7    
20.8    
25.0    
29.2    
33.3    
37.5    
41.7    
45.8    
50.0    
54.2    
58.3    
62.5    
66.7    
70.8    
75.0    
79.2    
83.3    
87.5    
91.7    
95.8    
-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