-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_5195228-5487399

-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_13-snap.1012-T1
Valid prediction for GlimmerHMM_glimmerT_32369-T1
Valid prediction for GlimmerHMM_glimmerT_32354-T1
Valid prediction for snap_scaffold_13-snap.1009-T1
Valid prediction for snap_scaffold_13-snap.1004-T1
Valid prediction for HiQ_model.g21679.t1
Valid prediction for snap_scaffold_13-snap.1003-T1
Valid prediction for GlimmerHMM_glimmerT_32382-T1
Couldn't classify 130732, 130836
Couldn't classify 130862, 130888
Sorry, prediction CodingQuarry_transcript_12985-T1 fails validation.
(ATG)	 CC	130732-130836	CC	AGC
(CCC)	 CC	130862-130888	CT	AGC
Valid prediction for GeneMark_model.55358_t
Valid prediction for GlimmerHMM_glimmerT_32362-T1
Valid prediction for pasa_asmbl_10823.p1
Couldn't classify 266828, 266993
Sorry, prediction pasa_asmbl_10835.p1 fails validation.
(CGG)	 CG	266828-266993	GT	AGG
(GCA)	 AG	267762-267822	GT	TGG
(GGA)	 AG	268002-268062	GT	TGG
(GGT)	 AG	268281-268358	GT	AGG
(CAT)	 AG	268466-268555	GT	AGG
(CTG)	 AG	268682-268747	GT	ATG
(TCT)	 AG	268840-268890	GT	TGG
(GAG)	 AG	269083-269168	GT	CTG
(GAT)	 AG	269274-269562	GC	AGG
-recovered pasa_asmbl_10835.p1, terminal, 269274, 269562
-recovered pasa_asmbl_10835.p1, internal, 267762, 267822
-recovered pasa_asmbl_10835.p1, internal, 268002, 268062
-recovered pasa_asmbl_10835.p1, internal, 268281, 268358
-recovered pasa_asmbl_10835.p1, internal, 268466, 268555
-recovered pasa_asmbl_10835.p1, internal, 268682, 268747
-recovered pasa_asmbl_10835.p1, internal, 268840, 268890
-recovered pasa_asmbl_10835.p1, internal, 269083, 269168
-recovered pasa_asmbl_10835.p1, internal, 269274, 269562
Valid prediction for snap_scaffold_13-snap.1001-T1
Valid prediction for GlimmerHMM_glimmerT_32374-T1
Valid prediction for CodingQuarry_transcript_12991-T1
Valid prediction for CodingQuarry_transcript_12984-T1
Valid prediction for GlimmerHMM_glimmerT_32381-T1
Valid prediction for GlimmerHMM_glimmerT_32364-T1
Valid prediction for GeneMark_model.55356_t
Valid prediction for CodingQuarry_transcript_12992-T1
Valid prediction for GeneMark_model.55361_t
Valid prediction for GeneMark_model.55369_t
Valid prediction for CodingQuarry_transcript_12987-T1
Valid prediction for snap_scaffold_13-snap.1024-T1
Valid prediction for snap_scaffold_13-snap.1000-T1
Valid prediction for HiQ_model.g21662.t1
Valid prediction for GlimmerHMM_glimmerT_32379-T1
Valid prediction for snap_scaffold_13-snap.1025-T1
Valid prediction for GeneMark_model.55350_t
Valid prediction for GeneMark_model.55366_t
Valid prediction for snap_scaffold_13-snap.998-T1
Valid prediction for Augustus_model.g21678.t1
Valid prediction for Augustus_model.g21673.t1
Valid prediction for GlimmerHMM_glimmerT_32363-T1
Valid prediction for GeneMark_model.55349_t
Valid prediction for GlimmerHMM_glimmerT_32352-T1
Valid prediction for HiQ_model.g21668.t1
Valid prediction for Augustus_model.g21672.t1
Valid prediction for GlimmerHMM_glimmerT_32368-T1
Valid prediction for CodingQuarry_transcript_12993-T1
Couldn't classify 185967, 186017
Couldn't classify 187793, 187888
Sorry, prediction pasa_asmbl_10825.p1 fails validation.
(AAT)	 GA	185967-186017	GT	TTG
(AAA)	 AG	186104-186190	GT	GGG
(CCT)	 AG	186276-186401	GT	GGG
(ATT)	 AG	186487-186546	GT	TGG
(GCC)	 AG	186681-186935	GT	AGG
(CCC)	 AG	187793-187888	AC	GCA
-recovered pasa_asmbl_10825.p1, internal, 186104, 186190
-recovered pasa_asmbl_10825.p1, internal, 186276, 186401
-recovered pasa_asmbl_10825.p1, internal, 186487, 186546
-recovered pasa_asmbl_10825.p1, internal, 186681, 186935
Valid prediction for snap_scaffold_13-snap.991-T1
Valid prediction for GlimmerHMM_glimmerT_32378-T1
Valid prediction for GeneMark_model.55357_t
Valid prediction for snap_scaffold_13-snap.1011-T1
Valid prediction for GeneMark_model.55373_t
Valid prediction for GlimmerHMM_glimmerT_32372-T1
Valid prediction for CodingQuarry_transcript_12986-T1
Valid prediction for GeneMark_model.55362_t
Valid prediction for snap_scaffold_13-snap.999-T1
Valid prediction for HiQ_model.g21666.t1
Valid prediction for GlimmerHMM_glimmerT_32370-T1
Valid prediction for snap_scaffold_13-snap.1028-T1
Valid prediction for snap_scaffold_13-snap.1013-T1
Valid prediction for snap_scaffold_13-snap.997-T1
Valid prediction for pasa_asmbl_10831.p1
Valid prediction for pasa_asmbl_10818.p1
Valid prediction for CodingQuarry_transcript_12988-T1
Valid prediction for snap_scaffold_13-snap.1023-T1
Valid prediction for CodingQuarry_transcript_12982-T1
Valid prediction for pasa_asmbl_10811.p1
Valid prediction for GeneMark_model.55370_t
Valid prediction for CodingQuarry_transcript_12981-T1
Valid prediction for snap_scaffold_13-snap.1010-T1
Valid prediction for Augustus_model.g21681.t1
Valid prediction for pasa_asmbl_10817.p1
Couldn't classify 188362, 188421
Sorry, prediction pasa_asmbl_10829.p1 fails validation.
(ACC)	 AG	188362-188421	GT	CCG
(GAC)	 AG	189139-189224	GT	AGG
(GGA)	 AG	189388-189460	GT	AGG
(GAG)	 AG	189631-189792	GT	GGG
(ATC)	 AG	189885-190082	GT	AGG
(GCT)	 AG	190318-190482	GT	TGG
(GAG)	 AG	190838-190943	GT	AGG
(ATC)	 AG	191212-191342	GT	AGG
(CCT)	 AG	191442-191508	GT	AGG
(ACG)	 AG	192680-192762	GT	AGG
(AAA)	 AG	192932-192995	GT	TGG
(GTA)	 AG	194552-194733	GT	CTG
(GAT)	 AG	195597-195613	GT	AGG
(TTT)	 AG	196116-196140	AG	AGA
-recovered pasa_asmbl_10829.p1, terminal, 196116, 196140
-recovered pasa_asmbl_10829.p1, internal, 188362, 188421
-recovered pasa_asmbl_10829.p1, internal, 189139, 189224
-recovered pasa_asmbl_10829.p1, internal, 189388, 189460
-recovered pasa_asmbl_10829.p1, internal, 189631, 189792
-recovered pasa_asmbl_10829.p1, internal, 189885, 190082
-recovered pasa_asmbl_10829.p1, internal, 190318, 190482
-recovered pasa_asmbl_10829.p1, internal, 190838, 190943
-recovered pasa_asmbl_10829.p1, internal, 191212, 191342
-recovered pasa_asmbl_10829.p1, internal, 191442, 191508
-recovered pasa_asmbl_10829.p1, internal, 192680, 192762
-recovered pasa_asmbl_10829.p1, internal, 192932, 192995
-recovered pasa_asmbl_10829.p1, internal, 194552, 194733
-recovered pasa_asmbl_10829.p1, internal, 195597, 195613
Valid prediction for Augustus_model.g21671.t1
Valid prediction for snap_scaffold_13-snap.1026-T1
Valid prediction for HiQ_model.g21667.t1
Valid prediction for GeneMark_model.55351_t
Valid prediction for GlimmerHMM_glimmerT_32356-T1
Valid prediction for snap_scaffold_13-snap.1022-T1
Sorry, intron length (8) is less than minimum required (10)

-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_13-snap.988-T1
Valid prediction for CodingQuarry_transcript_12983-T1
Valid prediction for GlimmerHMM_glimmerT_32376-T1
Valid prediction for Augustus_model.g21670.t1
Valid prediction for snap_scaffold_13-snap.1002-T1
Valid prediction for snap_scaffold_13-snap.1021-T1
Valid prediction for GeneMark_model.55352_t
Valid prediction for GlimmerHMM_glimmerT_32366-T1
Valid prediction for GlimmerHMM_glimmerT_32360-T1
Valid prediction for GeneMark_model.55364_t
Valid prediction for GeneMark_model.55348_t
Valid prediction for Augustus_model.g21675.t1
Valid prediction for snap_scaffold_13-snap.1019-T1
Couldn't classify 178153, 178275
Couldn't classify 182089, 182170
Sorry, prediction pasa_asmbl_9647.p1 fails validation.
(ATT)	 AG	178153-178275	GT	AGG
(TAC)	 AG	178609-178694	GT	AAG
(CTT)	 AG	178851-178926	GT	ATG
(ATA)	 AG	179134-179220	GT	AGG
(GAC)	 AG	180675-180775	GT	GGG
(GCT)	 AG	180907-180976	GT	CGG
(TCC)	 AG	181342-181429	GT	CCG
(ATA)	 AG	181829-181877	GT	ATG
(CTG)	 AG	182089-182170	AC	ACA
-recovered pasa_asmbl_9647.p1, internal, 178153, 178275
-recovered pasa_asmbl_9647.p1, internal, 178609, 178694
-recovered pasa_asmbl_9647.p1, internal, 178851, 178926
-recovered pasa_asmbl_9647.p1, internal, 179134, 179220
-recovered pasa_asmbl_9647.p1, internal, 180675, 180775
-recovered pasa_asmbl_9647.p1, internal, 180907, 180976
-recovered pasa_asmbl_9647.p1, internal, 181342, 181429
-recovered pasa_asmbl_9647.p1, internal, 181829, 181877
Valid prediction for GeneMark_model.55374_t
Valid prediction for GeneMark_model.55372_t
Valid prediction for GeneMark_model.55363_t
Valid prediction for pasa_asmbl_9649.p1
Valid prediction for snap_scaffold_13-snap.1007-T1
Valid prediction for Augustus_model.g21669.t1
Valid prediction for GlimmerHMM_glimmerT_32375-T1
Valid prediction for snap_scaffold_13-snap.1008-T1
Valid prediction for HiQ_model.g21676.t1
Valid prediction for snap_scaffold_13-snap.994-T1
Valid prediction for snap_scaffold_13-snap.992-T1
Valid prediction for snap_scaffold_13-snap.1020-T1
Valid prediction for GlimmerHMM_glimmerT_32373-T1
Valid prediction for GeneMark_model.55354_t
Valid prediction for GlimmerHMM_glimmerT_32384-T1
Valid prediction for GlimmerHMM_glimmerT_32359-T1
Valid prediction for GeneMark_model.55367_t
Valid prediction for snap_scaffold_13-snap.1017-T1
Valid prediction for GlimmerHMM_glimmerT_32380-T1
Valid prediction for CodingQuarry_transcript_12989-T1
Valid prediction for snap_scaffold_13-snap.1029-T1
Valid prediction for HiQ_model.g21674.t1
Valid prediction for GlimmerHMM_glimmerT_32351-T1
Valid prediction for snap_scaffold_13-snap.993-T1
Valid prediction for GlimmerHMM_glimmerT_32365-T1
Valid prediction for snap_scaffold_13-snap.1015-T1
Valid prediction for Augustus_model.g21664.t1
Couldn't classify 188032, 188059
Sorry, prediction pasa_asmbl_9645.p1 fails validation.
(AGG)	 CA	188032-188059	GT	AGG
(TGG)	 AG	188232-188746	GT	CAG
(GGC)	 AG	188868-188990	GT	GGG
(ATC)	 AG	189565-189639	CA	GAC
-recovered pasa_asmbl_9645.p1, terminal, 189565, 189639
-recovered pasa_asmbl_9645.p1, internal, 188232, 188746
-recovered pasa_asmbl_9645.p1, internal, 188868, 188990
Valid prediction for HiQ_model.g21677.t1
Valid prediction for Augustus_model.g21665.t1
Couldn't classify 184185, 184295
Couldn't classify 185410, 185502
Sorry, prediction pasa_asmbl_9646.p1 fails validation.
(AGC)	 CC	184185-184295	GT	AGG
(GAG)	 AG	184438-184523	GT	AGG
(TGG)	 AG	184642-184757	GT	AGG
(CCA)	 AG	184927-184994	GT	CAG
(TTG)	 AG	185114-185221	GT	AGG
(CCC)	 AG	185410-185502	GG	GGG
-recovered pasa_asmbl_9646.p1, terminal, 184642, 184757
-recovered pasa_asmbl_9646.p1, internal, 184438, 184523
-recovered pasa_asmbl_9646.p1, internal, 184642, 184757
-recovered pasa_asmbl_9646.p1, internal, 184927, 184994
-recovered pasa_asmbl_9646.p1, internal, 185114, 185221
Valid prediction for Augustus_model.g21683.t1
Valid prediction for GeneMark_model.55360_t
Valid prediction for GlimmerHMM_glimmerT_32353-T1
Valid prediction for Augustus_model.g21661.t1
Valid prediction for GeneMark_model.55365_t
Valid prediction for pasa_asmbl_9652.p1
Valid prediction for snap_scaffold_13-snap.1018-T1
Valid prediction for GeneMark_model.55355_t
Valid prediction for snap_scaffold_13-snap.995-T1
Valid prediction for snap_scaffold_13-snap.989-T1
Valid prediction for GlimmerHMM_glimmerT_32371-T1
Valid prediction for snap_scaffold_13-snap.1027-T1
Valid prediction for GeneMark_model.55353_t
Valid prediction for GeneMark_model.55371_t
Couldn't classify 51482, 51610
Sorry, prediction pasa_asmbl_9651.p1 fails validation.
(ATG)	 GA	48467-48508	GT	AGG
(GTC)	 AG	49007-49163	GT	CCG
(TTG)	 AG	49275-49342	GT	AGG
(GTG)	 AG	49507-49637	GT	GAG
(ATA)	 AG	49854-50001	GT	TGG
(GTC)	 AG	50234-50360	GT	AAG
(GAG)	 AG	50610-50752	GT	ACG
(GTG)	 AG	50979-51050	GT	AGG
(GCC)	 AG	51212-51370	GT	CCG
(GGA)	 AG	51482-51610	CG	TGC
-recovered pasa_asmbl_9651.p1, initial, 48467, 48508
-recovered pasa_asmbl_9651.p1, internal, 49007, 49163
-recovered pasa_asmbl_9651.p1, internal, 49275, 49342
-recovered pasa_asmbl_9651.p1, internal, 49507, 49637
-recovered pasa_asmbl_9651.p1, internal, 49854, 50001
-recovered pasa_asmbl_9651.p1, internal, 50234, 50360
-recovered pasa_asmbl_9651.p1, internal, 50610, 50752
-recovered pasa_asmbl_9651.p1, internal, 50979, 51050
-recovered pasa_asmbl_9651.p1, internal, 51212, 51370
Valid prediction for CodingQuarry_transcript_12990-T1
Valid prediction for Augustus_model.g21682.t1
Valid prediction for Augustus_model.g21680.t1
Couldn't classify 207128, 207191
Sorry, prediction pasa_asmbl_9642.p1 fails validation.
(ATG)	 AG	205446-205523	GT	CTG
(GCA)	 AG	206491-206607	GT	ATG
(AAC)	 AG	206795-206874	GT	CCG
(GGA)	 AG	207128-207191	GT	GGG
-recovered pasa_asmbl_9642.p1, initial, 205446, 205523
-recovered pasa_asmbl_9642.p1, internal, 205446, 205523
-recovered pasa_asmbl_9642.p1, internal, 206491, 206607
-recovered pasa_asmbl_9642.p1, internal, 206795, 206874
-recovered pasa_asmbl_9642.p1, internal, 207128, 207191
Valid prediction for Augustus_model.g21663.t1
Valid prediction for snap_scaffold_13-snap.996-T1
Valid prediction for GeneMark_model.55368_t
Valid prediction for GlimmerHMM_glimmerT_32358-T1
Valid prediction for GlimmerHMM_glimmerT_32383-T1
Valid prediction for snap_scaffold_13-snap.990-T1
Valid prediction for snap_scaffold_13-snap.987-T1
Valid prediction for snap_scaffold_13-snap.1005-T1
Valid prediction for GlimmerHMM_glimmerT_32355-T1
Valid prediction for GlimmerHMM_glimmerT_32361-T1
Valid prediction for snap_scaffold_13-snap.1006-T1
Valid prediction for GeneMark_model.55359_t
Valid prediction for GlimmerHMM_glimmerT_32377-T1
Valid prediction for snap_scaffold_13-snap.1014-T1
Valid prediction for snap_scaffold_13-snap.1016-T1
Valid prediction for GlimmerHMM_glimmerT_32367-T1
Valid prediction for GlimmerHMM_glimmerT_32357-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 161731, rend_intergenic: 156880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163399, rend_intergenic: 161821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196262, rend_intergenic: 194748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 292172
-exon list size: 545


building trellis

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66.0    
66.2    
66.4    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
69.8    
70.0    
70.2    
70.4    
70.6    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.2    
76.4    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.5    
81.7    
81.9    
82.1    
82.3    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 161731, rend_intergenic: 156880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163399, rend_intergenic: 161821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196262, rend_intergenic: 194748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support