-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_3684053-3872237

-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 CodingQuarry_transcript_12932-T1
Valid prediction for GeneMark_model.55024_t
Valid prediction for GlimmerHMM_glimmerT_32138-T1
Valid prediction for GlimmerHMM_glimmerT_32136-T1
Valid prediction for snap_scaffold_13-snap.690-T1
Valid prediction for pasa_asmbl_10706.p1
Valid prediction for snap_scaffold_13-snap.678-T1
Valid prediction for GlimmerHMM_glimmerT_32132-T1
Valid prediction for GlimmerHMM_glimmerT_32146-T1
Valid prediction for snap_scaffold_13-snap.696-T1
Valid prediction for GlimmerHMM_glimmerT_32122-T1
Valid prediction for GeneMark_model.55042_t
Valid prediction for GeneMark_model.55028_t
Valid prediction for GlimmerHMM_glimmerT_32125-T1
Valid prediction for GeneMark_model.55016_t
Valid prediction for CodingQuarry_transcript_12936-T1
Valid prediction for HiQ_model.g21500.t1
Valid prediction for pasa_asmbl_10712.p1
Valid prediction for Augustus_model.g21497.t1
Valid prediction for GlimmerHMM_glimmerT_32126-T1
Couldn't classify 60489, 61253
Sorry, prediction pasa_asmbl_10720.p1 fails validation.
(TCT)	 CG	60489-61253	AA	GCA
Valid prediction for GlimmerHMM_glimmerT_32128-T1
Valid prediction for GeneMark_model.55040_t
Valid prediction for CodingQuarry_transcript_12927-T1
Valid prediction for CodingQuarry_transcript_12933-T1
Valid prediction for Augustus_model.g21482.t1
Valid prediction for GlimmerHMM_glimmerT_32134-T1
Valid prediction for snap_scaffold_13-snap.688-T1
Valid prediction for GlimmerHMM_glimmerT_32151-T1
Valid prediction for GeneMark_model.55013_t
Valid prediction for Augustus_model.g21510.t1
Valid prediction for GeneMark_model.55015_t
Valid prediction for snap_scaffold_13-snap.686-T1
Valid prediction for HiQ_model.g21491.t1
Valid prediction for snap_scaffold_13-snap.707-T1
Valid prediction for snap_scaffold_13-snap.692-T1
Valid prediction for GlimmerHMM_glimmerT_32152-T1
Valid prediction for GeneMark_model.55027_t
Valid prediction for GlimmerHMM_glimmerT_32139-T1
Valid prediction for Augustus_model.g21493.t1
Couldn't classify 90056, 90086
Sorry, prediction pasa_asmbl_10725.p1 fails validation.
(AGT)	 CC	90056-90086	GT	AGG
(GTG)	 AG	90227-90846	TA	AAT
-recovered pasa_asmbl_10725.p1, terminal, 90227, 90846
Valid prediction for GlimmerHMM_glimmerT_32140-T1
Valid prediction for Augustus_model.g21495.t1
Valid prediction for HiQ_model.g21489.t1
Valid prediction for Augustus_model.g21503.t1
Valid prediction for Augustus_model.g21485.t1
Valid prediction for GlimmerHMM_glimmerT_32135-T1
Valid prediction for GeneMark_model.55039_t
Valid prediction for GeneMark_model.55026_t
Valid prediction for snap_scaffold_13-snap.676-T1
Valid prediction for GlimmerHMM_glimmerT_32124-T1
Valid prediction for pasa_asmbl_10723.p1
Couldn't classify 60132, 60434
Sorry, prediction pasa_asmbl_10719.p1 fails validation.
(ATG)	 CA	60132-60434	CT	CCC
Valid prediction for GeneMark_model.55019_t
Valid prediction for GlimmerHMM_glimmerT_32130-T1
Valid prediction for snap_scaffold_13-snap.699-T1
Valid prediction for CodingQuarry_transcript_12935-T1
Valid prediction for snap_scaffold_13-snap.682-T1
Valid prediction for snap_scaffold_13-snap.706-T1
Valid prediction for GlimmerHMM_glimmerT_32144-T1
Valid prediction for HiQ_model.g21486.t1
Valid prediction for Augustus_model.g21484.t1
Valid prediction for CodingQuarry_transcript_12926-T1
Valid prediction for pasa_asmbl_10704.p1
Valid prediction for GlimmerHMM_glimmerT_32154-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_32123-T1
Valid prediction for snap_scaffold_13-snap.697-T1
Valid prediction for snap_scaffold_13-snap.677-T1
Valid prediction for pasa_asmbl_9551.p1
Valid prediction for GeneMark_model.55031_t
Valid prediction for pasa_asmbl_9530.p1
Valid prediction for GeneMark_model.55035_t
Valid prediction for Augustus_model.g21494.t1
Valid prediction for GeneMark_model.55037_t
Valid prediction for CodingQuarry_transcript_12934-T1
Valid prediction for GlimmerHMM_glimmerT_32131-T1
Valid prediction for GeneMark_model.55033_t
Valid prediction for HiQ_model.g21487.t1
Valid prediction for GlimmerHMM_glimmerT_32129-T1
Couldn't classify 153927, 155720
Sorry, prediction pasa_asmbl_9529.p1 fails validation.
(ATG)	 AA	153927-155720	TA	GGT
Valid prediction for Augustus_model.g21498.t1
Valid prediction for GlimmerHMM_glimmerT_32155-T1
Valid prediction for GlimmerHMM_glimmerT_32133-T1
Valid prediction for GlimmerHMM_glimmerT_32142-T1
Valid prediction for GeneMark_model.55030_t
Valid prediction for CodingQuarry_transcript_12928-T1
Couldn't classify 167760, 167919
Couldn't classify 167950, 168080
Sorry, prediction CodingQuarry_transcript_12929-T1 fails validation.
(ATG)	 TC	164925-165016	GT	AGG
(TGC)	 AG	166862-166913	GT	TGG
(GAC)	 AG	167202-167723	GC	AGG
(CAA)	 AG	167760-167919	AA	GCA
(CCC)	 GC	167950-168080	AG	GAA
-recovered CodingQuarry_transcript_12929-T1, initial, 164925, 165016
-recovered CodingQuarry_transcript_12929-T1, internal, 166862, 166913
-recovered CodingQuarry_transcript_12929-T1, internal, 167202, 167723
Valid prediction for Augustus_model.g21488.t1
Valid prediction for GlimmerHMM_glimmerT_32148-T1
Valid prediction for snap_scaffold_13-snap.679-T1
Valid prediction for snap_scaffold_13-snap.701-T1
Valid prediction for snap_scaffold_13-snap.680-T1
Valid prediction for snap_scaffold_13-snap.694-T1
Valid prediction for pasa_asmbl_9545.p1
Valid prediction for Augustus_model.g21496.t1
Valid prediction for snap_scaffold_13-snap.691-T1
Valid prediction for GeneMark_model.55036_t
Valid prediction for GlimmerHMM_glimmerT_32143-T1
Valid prediction for snap_scaffold_13-snap.681-T1
Valid prediction for GeneMark_model.55021_t
Valid prediction for GeneMark_model.55038_t
Couldn't classify 92631, 92733
Couldn't classify 95802, 95986
Sorry, prediction pasa_asmbl_9537.p1 fails validation.
(TTT)	 AA	92631-92733	GT	TGG
(GTC)	 AG	92983-93177	GT	AGG
(ATA)	 AG	94124-94291	GT	AAG
(AGA)	 AG	94618-94797	GT	TTG
(TCC)	 AG	94870-94905	GT	AAG
(AAC)	 AG	95153-95191	GT	AGG
(AGG)	 AG	95370-95408	GT	ATG
(TGA)	 AG	95529-95690	GT	AGG
(AAC)	 AG	95802-95986	TG	AGT
add_exon() Sorry, pasa_asmbl_9537.p1 92983-93177-terminal-1 is invalid.
-recovered pasa_asmbl_9537.p1, terminal, 92983, 93177
-recovered pasa_asmbl_9537.p1, terminal, 94870, 94905
add_exon() Sorry, pasa_asmbl_9537.p1 95529-95690-terminal-1 is invalid.
-recovered pasa_asmbl_9537.p1, terminal, 95529, 95690
-recovered pasa_asmbl_9537.p1, internal, 92983, 93177
-recovered pasa_asmbl_9537.p1, internal, 94124, 94291
-recovered pasa_asmbl_9537.p1, internal, 94618, 94797
-recovered pasa_asmbl_9537.p1, internal, 94870, 94905
-recovered pasa_asmbl_9537.p1, internal, 95153, 95191
-recovered pasa_asmbl_9537.p1, internal, 95370, 95408
-recovered pasa_asmbl_9537.p1, internal, 95529, 95690
Valid prediction for Augustus_model.g21490.t1
Valid prediction for GlimmerHMM_glimmerT_32141-T1
Valid prediction for GlimmerHMM_glimmerT_32127-T1
Valid prediction for CodingQuarry_transcript_12938-T1
Valid prediction for snap_scaffold_13-snap.708-T1
Valid prediction for GlimmerHMM_glimmerT_32145-T1
Valid prediction for Augustus_model.g21507.t1
Valid prediction for CodingQuarry_transcript_12931-T1
Valid prediction for snap_scaffold_13-snap.689-T1
Valid prediction for GeneMark_model.55023_t
Couldn't classify 178431, 178582
Sorry, prediction pasa_asmbl_10289.p1 fails validation.
(ATG)	 TC	177826-177836	GT	CGG
(TTT)	 AG	177976-178322	GT	AGG
(ATA)	 AG	178431-178582	GT	AGG
-recovered pasa_asmbl_10289.p1, initial, 177826, 177836
-recovered pasa_asmbl_10289.p1, internal, 177976, 178322
-recovered pasa_asmbl_10289.p1, internal, 178431, 178582
Valid prediction for HiQ_model.g21492.t1
Valid prediction for GlimmerHMM_glimmerT_32153-T1
Valid prediction for Augustus_model.g21502.t1
Valid prediction for HiQ_model.g21504.t1
Valid prediction for Augustus_model.g21505.t1
Couldn't classify 130858, 131206
Couldn't classify 133181, 133359
Sorry, prediction pasa_asmbl_9533.p1 fails validation.
(GTT)	 AT	130858-131206	GT	AGG
(AAT)	 AG	131970-132520	GT	CTG
(GCC)	 AG	132688-132853	GT	GTG
(GCA)	 AG	133181-133359	CT	GCC
-recovered pasa_asmbl_9533.p1, internal, 131970, 132520
-recovered pasa_asmbl_9533.p1, internal, 132688, 132853
Valid prediction for snap_scaffold_13-snap.702-T1
Couldn't classify 86080, 86137
Sorry, prediction pasa_asmbl_9540.p1 fails validation.
(GAG)	 AG	86080-86137	GT	AGG
(TGT)	 AG	86841-86876	GT	AGG
(GCT)	 AG	87081-87168	GT	AAG
(GTT)	 AG	88474-88635	GT	TGG
(GGA)	 AG	89028-89128	GT	AAG
(TCC)	 AG	89271-89412	GT	AGG
(ATA)	 AG	89495-89531	GA	GAG
-recovered pasa_asmbl_9540.p1, terminal, 89495, 89531
-recovered pasa_asmbl_9540.p1, internal, 86080, 86137
-recovered pasa_asmbl_9540.p1, internal, 86841, 86876
-recovered pasa_asmbl_9540.p1, internal, 87081, 87168
-recovered pasa_asmbl_9540.p1, internal, 88474, 88635
-recovered pasa_asmbl_9540.p1, internal, 89028, 89128
-recovered pasa_asmbl_9540.p1, internal, 89271, 89412
Valid prediction for Augustus_model.g21506.t1
Valid prediction for snap_scaffold_13-snap.684-T1
Couldn't classify 75845, 75987
Couldn't classify 79603, 79667
Sorry, prediction pasa_asmbl_9542.p1 fails validation.
(AGA)	 GA	75845-75987	GT	GGG
(AAC)	 AG	76825-76930	GT	CAG
(ACG)	 AG	77061-77130	GT	CTG
(CTA)	 AG	77231-77293	GT	AGG
(TTA)	 AG	77416-77468	GT	AGG
(GAT)	 AG	77708-77796	GT	AGG
(GTC)	 AG	78272-78485	GT	AGG
(AAC)	 AG	78881-78979	GT	TGG
(GAC)	 AG	79360-79438	GT	GGG
(AAA)	 AG	79603-79667	GT	CGG
-recovered pasa_asmbl_9542.p1, internal, 76825, 76930
-recovered pasa_asmbl_9542.p1, internal, 77061, 77130
-recovered pasa_asmbl_9542.p1, internal, 77231, 77293
-recovered pasa_asmbl_9542.p1, internal, 77416, 77468
-recovered pasa_asmbl_9542.p1, internal, 77708, 77796
-recovered pasa_asmbl_9542.p1, internal, 78272, 78485
-recovered pasa_asmbl_9542.p1, internal, 78881, 78979
-recovered pasa_asmbl_9542.p1, internal, 79360, 79438
-recovered pasa_asmbl_9542.p1, internal, 79603, 79667
Valid prediction for snap_scaffold_13-snap.703-T1
Valid prediction for snap_scaffold_13-snap.704-T1
Couldn't classify 133438, 134099
Couldn't classify 134574, 134610
Sorry, prediction pasa_asmbl_9532.p1 fails validation.
(GGT)	 AT	133438-134099	GT	AAG
(TGA)	 AG	134189-134230	GT	CTG
(GAT)	 AG	134331-134453	GT	TGG
(GTG)	 AG	134574-134610	TG	CCT
-recovered pasa_asmbl_9532.p1, internal, 134189, 134230
-recovered pasa_asmbl_9532.p1, internal, 134331, 134453
Valid prediction for snap_scaffold_13-snap.695-T1
Valid prediction for GeneMark_model.55022_t
Valid prediction for GeneMark_model.55014_t
Valid prediction for snap_scaffold_13-snap.705-T1
Valid prediction for GlimmerHMM_glimmerT_32147-T1
Valid prediction for Augustus_model.g21499.t1
Valid prediction for Augustus_model.g21508.t1
Couldn't classify 130232, 130560
Sorry, prediction pasa_asmbl_9534.p1 fails validation.
(ATG)	 CT	129070-129091	GT	TGG
(ACA)	 AG	130232-130560	GA	AGG
-recovered pasa_asmbl_9534.p1, initial, 129070, 129091
Valid prediction for snap_scaffold_13-snap.683-T1
Valid prediction for HiQ_model.g21501.t1
Valid prediction for snap_scaffold_13-snap.698-T1
Valid prediction for snap_scaffold_13-snap.685-T1
Couldn't classify 179951, 180112
Sorry, prediction pasa_asmbl_9522.p1 fails validation.
(CAG)	 TT	179951-180112	GT	AGG
(CCA)	 AG	180200-180398	GT	TGG
(GCC)	 AG	180728-180880	GT	AGG
(GTG)	 AG	180990-181111	GT	AGG
(TAT)	 AG	181262-181421	GT	CGG
(GGT)	 AG	181647-181795	GG	GAG
-recovered pasa_asmbl_9522.p1, terminal, 181647, 181795
-recovered pasa_asmbl_9522.p1, internal, 180200, 180398
-recovered pasa_asmbl_9522.p1, internal, 180728, 180880
-recovered pasa_asmbl_9522.p1, internal, 180990, 181111
-recovered pasa_asmbl_9522.p1, internal, 181262, 181421
Valid prediction for Augustus_model.g21483.t1
Valid prediction for snap_scaffold_13-snap.687-T1
Valid prediction for pasa_asmbl_9525.p1
Valid prediction for CodingQuarry_transcript_12937-T1
Valid prediction for HiQ_model.g21509.t1
Valid prediction for GeneMark_model.55018_t
Valid prediction for GlimmerHMM_glimmerT_32150-T1
Valid prediction for GlimmerHMM_glimmerT_32137-T1
Valid prediction for GlimmerHMM_glimmerT_32149-T1
Valid prediction for snap_scaffold_13-snap.700-T1
Valid prediction for snap_scaffold_13-snap.693-T1
Valid prediction for GeneMark_model.55041_t
Valid prediction for CodingQuarry_transcript_12930-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 175139, rend_intergenic: 172621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 188185
-exon list size: 466


building trellis

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96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 175139, rend_intergenic: 172621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 175140 - 188185
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 1 predictions from path traversal

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