-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_14/scaffold_14_14532109-14700367

-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 Augustus_model.g23508.t1
Valid prediction for snap_scaffold_14-snap.3014-T1
Valid prediction for Augustus_model.g23512.t1
Valid prediction for GlimmerHMM_glimmerT_35164-T1
Valid prediction for snap_scaffold_14-snap.2987-T1
Couldn't classify 31552, 31588
Sorry, prediction pasa_asmbl_12764.p1 fails validation.
(GTA)	 CA	31552-31588	GT	GTG
(GTG)	 AG	31868-32328	CC	AAC
-recovered pasa_asmbl_12764.p1, terminal, 31868, 32328
Valid prediction for snap_scaffold_14-snap.2988-T1
Valid prediction for Augustus_model.g23507.t1
Valid prediction for Augustus_model.g23513.t1
Valid prediction for GlimmerHMM_glimmerT_35151-T1
Valid prediction for snap_scaffold_14-snap.3002-T1
Valid prediction for HiQ_model.g23511.t1
Valid prediction for snap_scaffold_14-snap.3016-T1
Valid prediction for GlimmerHMM_glimmerT_35157-T1
Valid prediction for snap_scaffold_14-snap.3007-T1
Valid prediction for GlimmerHMM_glimmerT_35168-T1
Valid prediction for snap_scaffold_14-snap.2999-T1
Valid prediction for snap_scaffold_14-snap.2990-T1
Valid prediction for snap_scaffold_14-snap.2993-T1
Valid prediction for Augustus_model.g23503.t1
Valid prediction for Augustus_model.g23506.t1
Valid prediction for GlimmerHMM_glimmerT_35154-T1
Valid prediction for snap_scaffold_14-snap.2985-T1
Valid prediction for Augustus_model.g23499.t1
Valid prediction for GlimmerHMM_glimmerT_35169-T1
Valid prediction for Augustus_model.g23514.t1
Valid prediction for CodingQuarry_transcript_15939-T1
Valid prediction for snap_scaffold_14-snap.3022-T1
Valid prediction for snap_scaffold_14-snap.3017-T1
Valid prediction for GlimmerHMM_glimmerT_35165-T1
Valid prediction for snap_scaffold_14-snap.3019-T1
Valid prediction for snap_scaffold_14-snap.2997-T1
Valid prediction for GlimmerHMM_glimmerT_35162-T1
Valid prediction for snap_scaffold_14-snap.3023-T1
Valid prediction for snap_scaffold_14-snap.3025-T1
Valid prediction for GlimmerHMM_glimmerT_35146-T1
Valid prediction for snap_scaffold_14-snap.3004-T1
Valid prediction for snap_scaffold_14-snap.3011-T1
Valid prediction for GlimmerHMM_glimmerT_35155-T1
Valid prediction for GlimmerHMM_glimmerT_35153-T1
Valid prediction for GlimmerHMM_glimmerT_35161-T1
Couldn't classify 119654, 119861
Couldn't classify 121002, 121201
Sorry, prediction pasa_asmbl_12555.p1 fails validation.
(GCC)	 GA	119654-119861	GT	GGG
(ACC)	 AG	121002-121201	GT	AGG
-recovered pasa_asmbl_12555.p1, internal, 121002, 121201
Valid prediction for GlimmerHMM_glimmerT_35163-T1
Valid prediction for snap_scaffold_14-snap.3005-T1
Couldn't classify 105719, 105794
Sorry, prediction pasa_asmbl_12552.p1 fails validation.
(TCC)	 CC	105719-105794	GT	AGG
(AGA)	 AG	107785-108041	GT	AGG
(TAG)	 AG	108503-108505	AT	AGA
-recovered pasa_asmbl_12552.p1, terminal, 108503, 108505
-recovered pasa_asmbl_12552.p1, internal, 107785, 108041
Valid prediction for snap_scaffold_14-snap.2996-T1
Valid prediction for GlimmerHMM_glimmerT_35156-T1
Valid prediction for GlimmerHMM_glimmerT_35167-T1
Valid prediction for GlimmerHMM_glimmerT_35150-T1
Couldn't classify 114072, 114146
Sorry, prediction pasa_asmbl_12554.p1 fails validation.
(ATG)	 AG	110329-110528	GT	AGG
(GAC)	 AG	111230-111358	GT	TGG
(GTA)	 AG	111527-111591	GT	AGG
(TGG)	 AG	111941-112239	GT	AGG
(TGG)	 AG	112540-112741	GT	AGG
(TGA)	 AG	113011-113141	GT	AGG
(GGT)	 AG	113386-113490	GT	AGG
(GTG)	 AG	114072-114146	GT	AGG
-recovered pasa_asmbl_12554.p1, initial, 110329, 110528
-recovered pasa_asmbl_12554.p1, internal, 110329, 110528
-recovered pasa_asmbl_12554.p1, internal, 111230, 111358
-recovered pasa_asmbl_12554.p1, internal, 111527, 111591
-recovered pasa_asmbl_12554.p1, internal, 111941, 112239
-recovered pasa_asmbl_12554.p1, internal, 112540, 112741
-recovered pasa_asmbl_12554.p1, internal, 113011, 113141
-recovered pasa_asmbl_12554.p1, internal, 113386, 113490
-recovered pasa_asmbl_12554.p1, internal, 114072, 114146
Valid prediction for Augustus_model.g23516.t1
Valid prediction for snap_scaffold_14-snap.3013-T1
Valid prediction for GlimmerHMM_glimmerT_35158-T1
Valid prediction for snap_scaffold_14-snap.2986-T1
Valid prediction for snap_scaffold_14-snap.3026-T1
Valid prediction for Augustus_model.g23509.t1
Valid prediction for Augustus_model.g23515.t1
Valid prediction for snap_scaffold_14-snap.2994-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_35147-T1
Valid prediction for snap_scaffold_14-snap.3010-T1
Valid prediction for HiQ_model.g23510.t1
Valid prediction for snap_scaffold_14-snap.3015-T1
Valid prediction for snap_scaffold_14-snap.2998-T1
Valid prediction for snap_scaffold_14-snap.2983-T1
Couldn't classify 117584, 117636
Sorry, prediction pasa_asmbl_13695.p1 fails validation.
(GAC)	 GT	117584-117636	GT	AGG
(CAT)	 AG	118034-118249	GT	GAG
(CGA)	 AG	118415-118921	GT	ATG
(ATT)	 AG	119222-119355	GT	AGG
(AAG)	 AG	119624-119775	CC	AGC
add_exon() Sorry, pasa_asmbl_13695.p1 119222-119355-terminal-2 is invalid.
-recovered pasa_asmbl_13695.p1, terminal, 119222, 119355
-recovered pasa_asmbl_13695.p1, terminal, 119624, 119775
-recovered pasa_asmbl_13695.p1, internal, 118034, 118249
-recovered pasa_asmbl_13695.p1, internal, 118415, 118921
-recovered pasa_asmbl_13695.p1, internal, 119222, 119355
Valid prediction for snap_scaffold_14-snap.2991-T1
Couldn't classify 162348, 162419
Sorry, prediction pasa_asmbl_13690.p1 fails validation.
(ATG)	 AA	158414-158482	GT	TGG
(CAA)	 AG	158830-158939	GT	GAG
(GAA)	 AG	159053-159140	GT	TGG
(GTC)	 AG	159245-159331	GT	AGG
(GTC)	 AG	159466-159531	GT	AGG
(CAA)	 AG	159901-159981	GT	AGG
(GGT)	 AG	162348-162419	GG	CAG
-recovered pasa_asmbl_13690.p1, initial, 158414, 158482
-recovered pasa_asmbl_13690.p1, internal, 158830, 158939
-recovered pasa_asmbl_13690.p1, internal, 159053, 159140
-recovered pasa_asmbl_13690.p1, internal, 159245, 159331
-recovered pasa_asmbl_13690.p1, internal, 159466, 159531
-recovered pasa_asmbl_13690.p1, internal, 159901, 159981
Valid prediction for snap_scaffold_14-snap.3021-T1
Valid prediction for HiQ_model.g23502.t1
Valid prediction for Augustus_model.g23498.t1
Couldn't classify 145598, 145609
Couldn't classify 148258, 148317
Sorry, prediction pasa_asmbl_13694.p1 fails validation.
(GGA)	 CT	145598-145609	GC	AGG
(GGC)	 AG	146037-146174	GT	ACG
(CAA)	 AG	146387-146500	GT	AGG
(ATC)	 AG	146912-147082	GT	TGG
(GTG)	 AG	147478-147591	GT	TGG
(GCG)	 AG	147866-148003	GT	AGG
(GCC)	 AG	148258-148317	GT	CAG
-recovered pasa_asmbl_13694.p1, internal, 146037, 146174
-recovered pasa_asmbl_13694.p1, internal, 146387, 146500
-recovered pasa_asmbl_13694.p1, internal, 146912, 147082
-recovered pasa_asmbl_13694.p1, internal, 147478, 147591
-recovered pasa_asmbl_13694.p1, internal, 147866, 148003
-recovered pasa_asmbl_13694.p1, internal, 148258, 148317
Valid prediction for snap_scaffold_14-snap.3000-T1
Valid prediction for GlimmerHMM_glimmerT_35159-T1
Valid prediction for snap_scaffold_14-snap.3001-T1
Valid prediction for GlimmerHMM_glimmerT_35145-T1
Valid prediction for snap_scaffold_14-snap.3020-T1
Valid prediction for Augustus_model.g23500.t1
Valid prediction for snap_scaffold_14-snap.3003-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_14-snap.3018-T1
Valid prediction for snap_scaffold_14-snap.2995-T1
Valid prediction for GlimmerHMM_glimmerT_35149-T1
Valid prediction for Augustus_model.g23505.t1
Valid prediction for GlimmerHMM_glimmerT_35166-T1
Valid prediction for GlimmerHMM_glimmerT_35144-T1
Couldn't classify 151558, 151611
Sorry, prediction pasa_asmbl_13693.p1 fails validation.
(ATG)	 AG	149685-149735	GT	AGG
(AAG)	 AG	149994-150111	GT	AGG
(GTG)	 AG	150332-150423	GT	AGG
(GTC)	 AG	150700-150875	GT	CGG
(GGT)	 AG	151052-151127	GT	AGG
(CTG)	 AG	151558-151611	CC	AGC
-recovered pasa_asmbl_13693.p1, initial, 149685, 149735
-recovered pasa_asmbl_13693.p1, internal, 149685, 149735
-recovered pasa_asmbl_13693.p1, internal, 149994, 150111
-recovered pasa_asmbl_13693.p1, internal, 150332, 150423
-recovered pasa_asmbl_13693.p1, internal, 150700, 150875
-recovered pasa_asmbl_13693.p1, internal, 151052, 151127
Couldn't classify 158830, 158940
Sorry, prediction CodingQuarry_transcript_15935-T1 fails validation.
(ATG)	 AA	158414-158482	GT	TGG
(CAA)	 AG	158830-158940	TA	AGT
(GAA)	 AG	159053-159073	AA	AAA
-recovered CodingQuarry_transcript_15935-T1, initial, 158414, 158482
-recovered CodingQuarry_transcript_15935-T1, terminal, 159053, 159073
Valid prediction for snap_scaffold_14-snap.3012-T1
Valid prediction for snap_scaffold_14-snap.3009-T1
Valid prediction for GlimmerHMM_glimmerT_35152-T1
Valid prediction for GlimmerHMM_glimmerT_35160-T1
Valid prediction for Augustus_model.g23501.t1
Valid prediction for GlimmerHMM_glimmerT_35143-T1
Valid prediction for CodingQuarry_transcript_15938-T1
Valid prediction for snap_scaffold_14-snap.3008-T1
Valid prediction for pasa_asmbl_13697.p1
Valid prediction for GlimmerHMM_glimmerT_35148-T1
Valid prediction for snap_scaffold_14-snap.2989-T1
Valid prediction for Augustus_model.g23504.t1
Valid prediction for GlimmerHMM_glimmerT_35142-T1
Valid prediction for snap_scaffold_14-snap.3024-T1
Valid prediction for Augustus_model.g23497.t1
Valid prediction for snap_scaffold_14-snap.2992-T1
Valid prediction for CodingQuarry_transcript_15937-T1
Valid prediction for snap_scaffold_14-snap.3006-T1
Couldn't classify 113974, 114008
Couldn't classify 117459, 117478
Sorry, prediction pasa_asmbl_13696.p1 fails validation.
(CAA)	 TT	113974-114008	GT	AGG
(CGG)	 AG	114427-114635	GT	AGG
(TGG)	 AG	114917-115087	GT	AGG
(CTG)	 AG	115368-115480	GT	AGG
(GGT)	 AG	117056-117194	GT	AGG
(GTG)	 AG	117459-117478	GC	AGG
-recovered pasa_asmbl_13696.p1, internal, 114427, 114635
-recovered pasa_asmbl_13696.p1, internal, 114917, 115087
-recovered pasa_asmbl_13696.p1, internal, 115368, 115480
-recovered pasa_asmbl_13696.p1, internal, 117056, 117194
-recovered pasa_asmbl_13696.p1, internal, 117459, 117478
Valid prediction for snap_scaffold_14-snap.2984-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24847, rend_intergenic: 13595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27830, rend_intergenic: 24924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46127, rend_intergenic: 41688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53823, rend_intergenic: 49675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58874, rend_intergenic: 57651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60836, rend_intergenic: 59113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73392, rend_intergenic: 66041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77999, rend_intergenic: 73464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78228, rend_intergenic: 78093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85744, rend_intergenic: 78228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90908, rend_intergenic: 88367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98257, rend_intergenic: 95300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117495, rend_intergenic: 111234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117573, rend_intergenic: 117570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129339, rend_intergenic: 117601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138224, rend_intergenic: 130520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140348, rend_intergenic: 139004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143486, rend_intergenic: 140368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154434, rend_intergenic: 143532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163963, rend_intergenic: 157922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 168259
-exon list size: 442


building trellis

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98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 24847, rend_intergenic: 13595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27830, rend_intergenic: 24924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46127, rend_intergenic: 41688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53823, rend_intergenic: 49675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58874, rend_intergenic: 57651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60836, rend_intergenic: 59113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73392, rend_intergenic: 66041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77999, rend_intergenic: 73464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78228, rend_intergenic: 78093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85744, rend_intergenic: 78228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90908, rend_intergenic: 88367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98257, rend_intergenic: 95300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117495, rend_intergenic: 111234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117573, rend_intergenic: 117570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129339, rend_intergenic: 117601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138224, rend_intergenic: 130520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140348, rend_intergenic: 139004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143486, rend_intergenic: 140368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154434, rend_intergenic: 143532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163963, rend_intergenic: 157922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support