-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_14671254-14878787

-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_16-snap.2818-T1
Valid prediction for GlimmerHMM_glimmerT_39482-T1
Valid prediction for snap_scaffold_16-snap.2847-T1
Valid prediction for Augustus_model.g26333.t1
Valid prediction for Augustus_model.g26340.t1
Valid prediction for snap_scaffold_16-snap.2832-T1
Valid prediction for GlimmerHMM_glimmerT_39484-T1
Valid prediction for snap_scaffold_16-snap.2830-T1
Valid prediction for Augustus_model.g26334.t1
Valid prediction for GlimmerHMM_glimmerT_39477-T1
Valid prediction for snap_scaffold_16-snap.2851-T1
Valid prediction for Augustus_model.g26331.t1
Valid prediction for snap_scaffold_16-snap.2806-T1
Valid prediction for HiQ_model.g26325.t1
Valid prediction for GlimmerHMM_glimmerT_39490-T1
Valid prediction for pasa_asmbl_16706.p1
Couldn't classify 31661, 31724
Sorry, prediction pasa_asmbl_16707.p1 fails validation.
(AGG)	 CC	31661-31724	GT	CGG
(GCA)	 AG	34709-34753	GT	ATG
(CCA)	 AG	35545-35703	GT	TGG
(GGT)	 AG	36833-36942	GT	AGG
(AGG)	 AG	37511-37609	TA	AGT
-recovered pasa_asmbl_16707.p1, terminal, 37511, 37609
-recovered pasa_asmbl_16707.p1, internal, 34709, 34753
-recovered pasa_asmbl_16707.p1, internal, 35545, 35703
-recovered pasa_asmbl_16707.p1, internal, 36833, 36942
Valid prediction for CodingQuarry_transcript_20137-T1
Valid prediction for snap_scaffold_16-snap.2808-T1
Valid prediction for GlimmerHMM_glimmerT_39499-T1
Valid prediction for snap_scaffold_16-snap.2821-T1
Valid prediction for Augustus_model.g26339.t1
Valid prediction for snap_scaffold_16-snap.2838-T1
Valid prediction for GlimmerHMM_glimmerT_39495-T1
Valid prediction for snap_scaffold_16-snap.2837-T1
Valid prediction for GlimmerHMM_glimmerT_39487-T1
Valid prediction for snap_scaffold_16-snap.2840-T1
Valid prediction for GlimmerHMM_glimmerT_39473-T1
Valid prediction for CodingQuarry_transcript_20136-T1
Couldn't classify 112805, 112930
Sorry, prediction pasa_asmbl_16814.p1 fails validation.
(ATG)	 AT	107658-107681	GT	AGG
(GTG)	 AG	108872-108991	GT	GGG
(ATC)	 AG	110862-111024	GT	AGG
(GGT)	 AG	111321-111478	GT	AGG
(GTG)	 AG	112189-112317	GT	AGG
(GCT)	 AG	112805-112930	TC	CCT
-recovered pasa_asmbl_16814.p1, initial, 107658, 107681
-recovered pasa_asmbl_16814.p1, internal, 108872, 108991
-recovered pasa_asmbl_16814.p1, internal, 110862, 111024
-recovered pasa_asmbl_16814.p1, internal, 111321, 111478
-recovered pasa_asmbl_16814.p1, internal, 112189, 112317
Couldn't classify 43169, 43312
Sorry, prediction pasa_asmbl_16710.p2 fails validation.
(ATG)	 CG	38825-38966	GT	GGG
(TCT)	 AG	39570-39740	GT	TGG
(GAG)	 AG	41345-41442	GT	TGG
(GGC)	 AG	43169-43312	GG	TTG
-recovered pasa_asmbl_16710.p2, initial, 38825, 38966
-recovered pasa_asmbl_16710.p2, internal, 39570, 39740
-recovered pasa_asmbl_16710.p2, internal, 41345, 41442
Valid prediction for snap_scaffold_16-snap.2825-T1
Valid prediction for GlimmerHMM_glimmerT_39492-T1
Valid prediction for snap_scaffold_16-snap.2827-T1
Couldn't classify 144430, 144837
Sorry, prediction pasa_asmbl_17498.p1 fails validation.
(CTC)	 CC	144430-144837	TG	AGT
Valid prediction for snap_scaffold_16-snap.2849-T1
Valid prediction for snap_scaffold_16-snap.2834-T1
Valid prediction for GlimmerHMM_glimmerT_39478-T1
Couldn't classify 113635, 113767
Couldn't classify 116381, 116507
Sorry, prediction pasa_asmbl_16713.p1 fails validation.
(CTG)	 AG	113635-113767	GT	AGG
(TGG)	 AG	113962-114071	GT	AGG
(GCG)	 AG	114509-114634	GT	TGG
(GTG)	 AG	115161-115210	GT	AGG
(GTG)	 AG	115359-115452	GT	AGG
(GCC)	 AG	115635-115741	GT	CAG
(GCT)	 AG	115945-116079	GT	AAG
(GTT)	 AG	116381-116507	GT	AGG
-recovered pasa_asmbl_16713.p1, internal, 113635, 113767
-recovered pasa_asmbl_16713.p1, internal, 113962, 114071
-recovered pasa_asmbl_16713.p1, internal, 114509, 114634
-recovered pasa_asmbl_16713.p1, internal, 115161, 115210
-recovered pasa_asmbl_16713.p1, internal, 115359, 115452
-recovered pasa_asmbl_16713.p1, internal, 115635, 115741
-recovered pasa_asmbl_16713.p1, internal, 115945, 116079
-recovered pasa_asmbl_16713.p1, internal, 116381, 116507
Valid prediction for GlimmerHMM_glimmerT_39497-T1
Valid prediction for snap_scaffold_16-snap.2802-T1
Valid prediction for snap_scaffold_16-snap.2844-T1
Valid prediction for snap_scaffold_16-snap.2845-T1
Valid prediction for snap_scaffold_16-snap.2811-T1
Valid prediction for snap_scaffold_16-snap.2809-T1
Valid prediction for Augustus_model.g26342.t1
Valid prediction for snap_scaffold_16-snap.2813-T1
Valid prediction for snap_scaffold_16-snap.2820-T1
Valid prediction for snap_scaffold_16-snap.2846-T1
Valid prediction for GlimmerHMM_glimmerT_39491-T1
Valid prediction for Augustus_model.g26329.t1
Valid prediction for Augustus_model.g26328.t1
Valid prediction for snap_scaffold_16-snap.2835-T1
Valid prediction for GlimmerHMM_glimmerT_39489-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 snap_scaffold_16-snap.2826-T1
Valid prediction for snap_scaffold_16-snap.2810-T1
Valid prediction for GlimmerHMM_glimmerT_39474-T1
Valid prediction for CodingQuarry_transcript_20138-T1
Valid prediction for GlimmerHMM_glimmerT_39488-T1
Valid prediction for Augustus_model.g26336.t1
Valid prediction for snap_scaffold_16-snap.2823-T1
Valid prediction for snap_scaffold_16-snap.2836-T1
Valid prediction for snap_scaffold_16-snap.2807-T1
Valid prediction for pasa_asmbl_17500.p1
Valid prediction for snap_scaffold_16-snap.2842-T1
Valid prediction for snap_scaffold_16-snap.2828-T1
Valid prediction for GlimmerHMM_glimmerT_39493-T1
Valid prediction for snap_scaffold_16-snap.2831-T1
Valid prediction for snap_scaffold_16-snap.2812-T1
Valid prediction for GlimmerHMM_glimmerT_39486-T1
Valid prediction for GlimmerHMM_glimmerT_39476-T1
Valid prediction for Augustus_model.g26337.t1
Valid prediction for HiQ_model.g26335.t1
Valid prediction for snap_scaffold_16-snap.2822-T1
Couldn't classify 112805, 113004
Sorry, prediction pasa_asmbl_17495.p1 fails validation.
(AAA)	 GC	112805-113004	GT	TGG
(GTG)	 AG	114021-114173	GT	ACG
(ACT)	 AG	114439-114544	GT	AGG
(GAG)	 AG	114999-115095	GT	AGG
(GAT)	 AG	115746-115861	GT	AGG
(GTG)	 AG	116786-116872	GT	AGG
(ACA)	 AG	117104-117256	GT	AGG
(ACA)	 AG	117708-117790	GT	TGG
(GTG)	 AG	117895-118024	GT	CGG
(GTC)	 AG	119453-119575	CA	AGC
-recovered pasa_asmbl_17495.p1, terminal, 119453, 119575
-recovered pasa_asmbl_17495.p1, internal, 114021, 114173
-recovered pasa_asmbl_17495.p1, internal, 114439, 114544
-recovered pasa_asmbl_17495.p1, internal, 114999, 115095
-recovered pasa_asmbl_17495.p1, internal, 115746, 115861
-recovered pasa_asmbl_17495.p1, internal, 116786, 116872
-recovered pasa_asmbl_17495.p1, internal, 117104, 117256
-recovered pasa_asmbl_17495.p1, internal, 117708, 117790
-recovered pasa_asmbl_17495.p1, internal, 117895, 118024
Couldn't classify 62026, 62142
Sorry, prediction pasa_asmbl_17499.p1 fails validation.
(ATG)	 AA	57304-57387	GT	AGG
(CTC)	 AG	58133-58330	GT	AGG
(GAC)	 AG	61292-61387	GT	TCG
(GTG)	 AG	62026-62142	AG	ACA
-recovered pasa_asmbl_17499.p1, initial, 57304, 57387
-recovered pasa_asmbl_17499.p1, internal, 58133, 58330
-recovered pasa_asmbl_17499.p1, internal, 61292, 61387
Valid prediction for CodingQuarry_transcript_20139-T1
Valid prediction for Augustus_model.g26341.t1
Valid prediction for snap_scaffold_16-snap.2817-T1
Valid prediction for snap_scaffold_16-snap.2816-T1
Valid prediction for GlimmerHMM_glimmerT_39498-T1
Valid prediction for GlimmerHMM_glimmerT_39494-T1
Valid prediction for Augustus_model.g26332.t1
Valid prediction for GlimmerHMM_glimmerT_39496-T1
Valid prediction for snap_scaffold_16-snap.2829-T1
Valid prediction for GlimmerHMM_glimmerT_39475-T1
Valid prediction for snap_scaffold_16-snap.2824-T1
Valid prediction for snap_scaffold_16-snap.2803-T1
Valid prediction for HiQ_model.g26343.t1
Valid prediction for HiQ_model.g26326.t1
Valid prediction for Augustus_model.g26344.t1
Valid prediction for snap_scaffold_16-snap.2833-T1
Valid prediction for Augustus_model.g26327.t1
Valid prediction for GlimmerHMM_glimmerT_39481-T1
Valid prediction for snap_scaffold_16-snap.2805-T1
Valid prediction for GlimmerHMM_glimmerT_39483-T1
Valid prediction for GlimmerHMM_glimmerT_39479-T1
Valid prediction for snap_scaffold_16-snap.2814-T1
Valid prediction for snap_scaffold_16-snap.2843-T1
Valid prediction for snap_scaffold_16-snap.2819-T1
Valid prediction for snap_scaffold_16-snap.2850-T1
Valid prediction for Augustus_model.g26330.t1
Valid prediction for snap_scaffold_16-snap.2815-T1
Valid prediction for GlimmerHMM_glimmerT_39485-T1
Valid prediction for snap_scaffold_16-snap.2841-T1
Valid prediction for GlimmerHMM_glimmerT_39480-T1
Valid prediction for HiQ_model.g26345.t1
Valid prediction for pasa_asmbl_17497.p1
Valid prediction for snap_scaffold_16-snap.2804-T1
Valid prediction for snap_scaffold_16-snap.2848-T1
Couldn't classify 191392, 191441
Sorry, prediction pasa_asmbl_17494.p1 fails validation.
(CAG)	 AC	191392-191441	GT	GAG
(GTC)	 AG	191914-192143	GT	AGG
(AGG)	 AG	193060-193148	TG	GAT
-recovered pasa_asmbl_17494.p1, terminal, 193060, 193148
-recovered pasa_asmbl_17494.p1, internal, 191914, 192143
Valid prediction for HiQ_model.g26338.t1
Valid prediction for snap_scaffold_16-snap.2839-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 187439, rend_intergenic: 187436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13259, rend_intergenic: 3884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19327, rend_intergenic: 15070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20961, rend_intergenic: 20433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26691, rend_intergenic: 20977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37609, rend_intergenic: 32555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46812, rend_intergenic: 39478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52883, rend_intergenic: 48775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61406, rend_intergenic: 58101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66352, rend_intergenic: 61659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68415, rend_intergenic: 67218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85505, rend_intergenic: 73953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93618, rend_intergenic: 89499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104969, rend_intergenic: 99555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122957, rend_intergenic: 108842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134931, rend_intergenic: 133413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135728, rend_intergenic: 135110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149300, rend_intergenic: 145366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174588, rend_intergenic: 152102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187077, rend_intergenic: 176061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193004, rend_intergenic: 187330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198409, rend_intergenic: 198150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 207534
-exon list size: 465


building trellis

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27.8    
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29.1    
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29.6    
29.8    
30.0    
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30.6    
30.8    
31.0    
31.3    
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31.9    
32.1    
32.3    
32.5    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.3    
34.5    
34.7    
34.9    
35.1    
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35.5    
35.8    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
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37.7    
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38.1    
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65.3    
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90.4    
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91.0    
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91.6    
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98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 38 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 187439, rend_intergenic: 187436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13259, rend_intergenic: 3884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19327, rend_intergenic: 15070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20961, rend_intergenic: 20433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26691, rend_intergenic: 20977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37609, rend_intergenic: 32555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46812, rend_intergenic: 39478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52883, rend_intergenic: 48775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61406, rend_intergenic: 58101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66352, rend_intergenic: 61659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68415, rend_intergenic: 67218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85505, rend_intergenic: 73953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93618, rend_intergenic: 89499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104969, rend_intergenic: 99555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122957, rend_intergenic: 108842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134931, rend_intergenic: 133413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135728, rend_intergenic: 135110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149300, rend_intergenic: 145366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174588, rend_intergenic: 152102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187077, rend_intergenic: 176061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193004, rend_intergenic: 187330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198409, rend_intergenic: 198150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support