-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_13419499-13692247

-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_11-snap.2867-T1
Valid prediction for CodingQuarry_transcript_8299-T1
Valid prediction for GlimmerHMM_glimmerT_28178-T1
Valid prediction for snap_scaffold_11-snap.2841-T1
Valid prediction for GlimmerHMM_glimmerT_28200-T1
Valid prediction for pasa_asmbl_6236.p1
Valid prediction for snap_scaffold_11-snap.2850-T1
Valid prediction for snap_scaffold_11-snap.2888-T1
Valid prediction for snap_scaffold_11-snap.2869-T1
Valid prediction for GlimmerHMM_glimmerT_28189-T1
Valid prediction for Augustus_model.g18672.t1
Valid prediction for CodingQuarry_transcript_8296-T1
Valid prediction for Augustus_model.g18656.t1
Valid prediction for snap_scaffold_11-snap.2851-T1
Valid prediction for GlimmerHMM_glimmerT_28186-T1
Couldn't classify 215990, 216253
Couldn't classify 220678, 220715
Sorry, prediction pasa_asmbl_6067.p1 fails validation.
(CAG)	 CG	215990-216253	GT	CGG
(ACG)	 AG	216443-216587	GT	CGG
(GTG)	 AG	216867-217005	GT	CGG
(GGA)	 AG	217109-217200	GT	CAG
(CGG)	 AG	217392-217551	GT	CAG
(ATT)	 AG	217783-217846	GT	AGG
(TCG)	 AG	218514-218602	GT	AGG
(AAC)	 AG	218977-219025	GT	AGG
(GTT)	 AG	220230-220365	GC	AGG
(TAA)	 AG	220678-220715	AG	GAA
-recovered pasa_asmbl_6067.p1, internal, 216443, 216587
-recovered pasa_asmbl_6067.p1, internal, 216867, 217005
-recovered pasa_asmbl_6067.p1, internal, 217109, 217200
-recovered pasa_asmbl_6067.p1, internal, 217392, 217551
-recovered pasa_asmbl_6067.p1, internal, 217783, 217846
-recovered pasa_asmbl_6067.p1, internal, 218514, 218602
-recovered pasa_asmbl_6067.p1, internal, 218977, 219025
-recovered pasa_asmbl_6067.p1, internal, 220230, 220365
Couldn't classify 60937, 61027
Couldn't classify 62664, 62708
Sorry, prediction pasa_asmbl_6057.p1 fails validation.
(CTT)	 CA	60937-61027	GT	AGG
(ATC)	 AG	61321-61490	GT	AGG
(GTG)	 AG	62664-62708	CA	CCC
-recovered pasa_asmbl_6057.p1, internal, 61321, 61490
Valid prediction for snap_scaffold_11-snap.2847-T1
Valid prediction for snap_scaffold_11-snap.2852-T1
Valid prediction for snap_scaffold_11-snap.2846-T1
Valid prediction for Augustus_model.g18664.t1
Valid prediction for snap_scaffold_11-snap.2866-T1
Valid prediction for snap_scaffold_11-snap.2878-T1
Valid prediction for Augustus_model.g18661.t1
Valid prediction for Augustus_model.g18684.t1
Valid prediction for GlimmerHMM_glimmerT_28182-T1
Valid prediction for CodingQuarry_transcript_8297-T1
Valid prediction for Augustus_model.g18659.t1
Valid prediction for snap_scaffold_11-snap.2886-T1
Couldn't classify 221130, 221232
Sorry, prediction pasa_asmbl_6068.p1 fails validation.
(GGC)	 AC	221130-221232	GT	GGG
(GGC)	 AG	221405-221511	GT	AGG
(GAA)	 AG	221671-221830	GT	AGG
(AGG)	 AG	222065-222225	GT	AGG
(GTG)	 AG	222405-222589	GT	AAG
(GGA)	 AG	222709-222778	GT	CAG
(ACG)	 AG	222865-222968	GT	AGG
(GGA)	 AG	223059-223245	GT	CGG
(CTG)	 AG	223586-223679	GT	AGG
(AGT)	 AG	223844-223938	GT	AGG
(GCT)	 AG	224206-224397	GT	CGG
(CAA)	 AG	224761-224929	GT	AGG
(AAA)	 AG	225068-225138	GT	AGG
(TAC)	 AG	225245-225333	GT	GAG
(CAA)	 AG	225562-225640	GT	AGG
(ATC)	 AG	225764-226031	GT	AGG
(TGA)	 AG	226158-226371	GT	AGG
(TTA)	 AG	227499-227502	AC	AAA
-recovered pasa_asmbl_6068.p1, terminal, 227499, 227502
-recovered pasa_asmbl_6068.p1, internal, 221405, 221511
-recovered pasa_asmbl_6068.p1, internal, 221671, 221830
-recovered pasa_asmbl_6068.p1, internal, 222065, 222225
-recovered pasa_asmbl_6068.p1, internal, 222405, 222589
-recovered pasa_asmbl_6068.p1, internal, 222709, 222778
-recovered pasa_asmbl_6068.p1, internal, 222865, 222968
-recovered pasa_asmbl_6068.p1, internal, 223059, 223245
-recovered pasa_asmbl_6068.p1, internal, 223586, 223679
-recovered pasa_asmbl_6068.p1, internal, 223844, 223938
-recovered pasa_asmbl_6068.p1, internal, 224206, 224397
-recovered pasa_asmbl_6068.p1, internal, 224761, 224929
-recovered pasa_asmbl_6068.p1, internal, 225068, 225138
-recovered pasa_asmbl_6068.p1, internal, 225245, 225333
-recovered pasa_asmbl_6068.p1, internal, 225562, 225640
-recovered pasa_asmbl_6068.p1, internal, 225764, 226031
-recovered pasa_asmbl_6068.p1, internal, 226158, 226371
Valid prediction for snap_scaffold_11-snap.2875-T1
Valid prediction for snap_scaffold_11-snap.2887-T1
Valid prediction for snap_scaffold_11-snap.2859-T1
Valid prediction for GlimmerHMM_glimmerT_28181-T1
Valid prediction for GlimmerHMM_glimmerT_28198-T1
Valid prediction for Augustus_model.g18680.t1
Valid prediction for GlimmerHMM_glimmerT_28195-T1
Valid prediction for snap_scaffold_11-snap.2855-T1
Couldn't classify 121676, 121772
Sorry, prediction pasa_asmbl_6060.p2 fails validation.
(GAC)	 TT	121676-121772	GT	TGG
(GCT)	 AG	121881-122057	GT	GGG
(GGG)	 AG	122156-122328	AA	AGA
-recovered pasa_asmbl_6060.p2, terminal, 122156, 122328
-recovered pasa_asmbl_6060.p2, internal, 121881, 122057
Valid prediction for snap_scaffold_11-snap.2860-T1
Valid prediction for GlimmerHMM_glimmerT_28184-T1
Valid prediction for Augustus_model.g18678.t1
Valid prediction for GlimmerHMM_glimmerT_28174-T1
Couldn't classify 260719, 260836
Sorry, prediction pasa_asmbl_6071.p1 fails validation.
(CCA)	 GA	260719-260836	GT	GGG
(GTC)	 AG	262194-262273	GT	AGG
(GTG)	 AG	262372-262470	GT	AGG
(GCA)	 AG	262715-262807	GT	AGG
(ATT)	 AG	262958-263134	GT	AGG
(GCG)	 AG	263294-263598	GT	AAG
(GGC)	 AG	264018-264120	GT	AGG
(TCT)	 AG	264479-264634	GT	GAG
-recovered pasa_asmbl_6071.p1, terminal, 264479, 264634
-recovered pasa_asmbl_6071.p1, internal, 262194, 262273
-recovered pasa_asmbl_6071.p1, internal, 262372, 262470
-recovered pasa_asmbl_6071.p1, internal, 262715, 262807
-recovered pasa_asmbl_6071.p1, internal, 262958, 263134
-recovered pasa_asmbl_6071.p1, internal, 263294, 263598
-recovered pasa_asmbl_6071.p1, internal, 264018, 264120
-recovered pasa_asmbl_6071.p1, internal, 264479, 264634
Valid prediction for snap_scaffold_11-snap.2856-T1
Couldn't classify 257976, 258042
Sorry, prediction pasa_asmbl_6070.p1 fails validation.
(ATG)	 AA	255824-255889	GT	AGG
(TGG)	 AG	256262-256307	GT	TGG
(ACA)	 AG	256420-256518	GT	TGG
(GTA)	 AG	256718-256795	GT	TGG
(TCA)	 AG	257340-257377	GT	AGG
(CTG)	 AG	257577-257713	GT	AGG
(TTC)	 AG	257976-258042	TG	TGT
-recovered pasa_asmbl_6070.p1, initial, 255824, 255889
-recovered pasa_asmbl_6070.p1, internal, 256262, 256307
-recovered pasa_asmbl_6070.p1, internal, 256420, 256518
-recovered pasa_asmbl_6070.p1, internal, 256718, 256795
-recovered pasa_asmbl_6070.p1, internal, 257340, 257377
-recovered pasa_asmbl_6070.p1, internal, 257577, 257713
Valid prediction for Augustus_model.g18663.t1
Valid prediction for GlimmerHMM_glimmerT_28176-T1
Valid prediction for snap_scaffold_11-snap.2844-T1
Couldn't classify 196774, 197979
Sorry, prediction pasa_asmbl_6064.p1 fails validation.
(CCC)	 CC	196774-197979	GG	GAG
Valid prediction for CodingQuarry_transcript_8300-T1
Valid prediction for Augustus_model.g18669.t1
Valid prediction for HiQ_model.g18673.t1
Valid prediction for snap_scaffold_11-snap.2879-T1
Valid prediction for HiQ_model.g18657.t1
Valid prediction for snap_scaffold_11-snap.2881-T1
Valid prediction for Augustus_model.g18679.t1
Valid prediction for snap_scaffold_11-snap.2858-T1
Valid prediction for snap_scaffold_11-snap.2870-T1
Valid prediction for snap_scaffold_11-snap.2876-T1
Valid prediction for snap_scaffold_11-snap.2854-T1
Valid prediction for snap_scaffold_11-snap.2849-T1
Valid prediction for Augustus_model.g18660.t1
Valid prediction for GlimmerHMM_glimmerT_28179-T1
Valid prediction for pasa_asmbl_6056.p1
Valid prediction for Augustus_model.g18668.t1
Valid prediction for GlimmerHMM_glimmerT_28183-T1
Valid prediction for Augustus_model.g18665.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_11-snap.2874-T1
Valid prediction for GlimmerHMM_glimmerT_28191-T1
Valid prediction for GlimmerHMM_glimmerT_28187-T1
Valid prediction for snap_scaffold_11-snap.2882-T1
Valid prediction for Augustus_model.g18682.t1
Valid prediction for GlimmerHMM_glimmerT_28185-T1
Valid prediction for snap_scaffold_11-snap.2864-T1
Valid prediction for Augustus_model.g18670.t1
Valid prediction for pasa_asmbl_7129.p1
Valid prediction for HiQ_model.g18681.t1
Valid prediction for snap_scaffold_11-snap.2865-T1
Valid prediction for pasa_asmbl_7136.p2
Valid prediction for snap_scaffold_11-snap.2880-T1
Valid prediction for snap_scaffold_11-snap.2848-T1
Valid prediction for HiQ_model.g18671.t1
Valid prediction for snap_scaffold_11-snap.2884-T1
Valid prediction for snap_scaffold_11-snap.2873-T1
Couldn't classify 111108, 111185
Sorry, prediction pasa_asmbl_7142.p1 fails validation.
(CAG)	 GA	111108-111185	GT	AGG
(GAA)	 AG	112124-112297	GT	AGG
(CTG)	 AG	112417-112548	GT	AGG
(GCA)	 AG	113071-113106	GT	AGG
(CTG)	 AG	115807-115962	AC	GAA
-recovered pasa_asmbl_7142.p1, terminal, 115807, 115962
-recovered pasa_asmbl_7142.p1, internal, 112124, 112297
-recovered pasa_asmbl_7142.p1, internal, 112417, 112548
-recovered pasa_asmbl_7142.p1, internal, 113071, 113106
Valid prediction for snap_scaffold_11-snap.2883-T1
Valid prediction for snap_scaffold_11-snap.2885-T1
Valid prediction for Augustus_model.g18675.t1
Valid prediction for GlimmerHMM_glimmerT_28194-T1
Valid prediction for snap_scaffold_11-snap.2871-T1
Valid prediction for Augustus_model.g18667.t1
Valid prediction for CodingQuarry_transcript_8302-T1
Valid prediction for Augustus_model.g18674.t1
Valid prediction for snap_scaffold_11-snap.2877-T1
Valid prediction for snap_scaffold_11-snap.2857-T1
Valid prediction for snap_scaffold_11-snap.2843-T1
Valid prediction for Augustus_model.g18676.t1
Valid prediction for GlimmerHMM_glimmerT_28188-T1
Valid prediction for snap_scaffold_11-snap.2889-T1
Valid prediction for GlimmerHMM_glimmerT_28180-T1
Valid prediction for snap_scaffold_11-snap.2845-T1
Valid prediction for Augustus_model.g18662.t1
Valid prediction for Augustus_model.g18683.t1
Valid prediction for HiQ_model.g18658.t1
Valid prediction for GlimmerHMM_glimmerT_28175-T1
Valid prediction for snap_scaffold_11-snap.2842-T1
Valid prediction for pasa_asmbl_7137.p1
Valid prediction for GlimmerHMM_glimmerT_28190-T1
Valid prediction for snap_scaffold_11-snap.2863-T1
Valid prediction for GlimmerHMM_glimmerT_28177-T1
Valid prediction for Augustus_model.g18666.t1
Valid prediction for GlimmerHMM_glimmerT_28196-T1
Valid prediction for Augustus_model.g18677.t1
Valid prediction for CodingQuarry_transcript_8301-T1
Valid prediction for snap_scaffold_11-snap.2862-T1
Valid prediction for snap_scaffold_11-snap.2872-T1
Couldn't classify 175163, 175263
Sorry, prediction pasa_asmbl_7133.p1 fails validation.
(ATG)	 TT	173949-173997	GT	AGG
(GGC)	 AG	174413-174523	GT	CAG
(TGG)	 AG	174912-175025	GT	TAG
(ATA)	 AG	175163-175263	AC	GCA
-recovered pasa_asmbl_7133.p1, initial, 173949, 173997
-recovered pasa_asmbl_7133.p1, internal, 174413, 174523
-recovered pasa_asmbl_7133.p1, internal, 174912, 175025
Valid prediction for GlimmerHMM_glimmerT_28197-T1
Valid prediction for GlimmerHMM_glimmerT_28193-T1
Valid prediction for pasa_asmbl_7151.p1
Valid prediction for GlimmerHMM_glimmerT_28199-T1
Valid prediction for snap_scaffold_11-snap.2861-T1
Couldn't classify 124642, 125040
Sorry, prediction pasa_asmbl_7140.p1 fails validation.
(TGC)	 TG	124642-125040	AG	AGA
Valid prediction for snap_scaffold_11-snap.2868-T1
Valid prediction for CodingQuarry_transcript_8298-T1
Valid prediction for GlimmerHMM_glimmerT_28192-T1
Valid prediction for CodingQuarry_transcript_8303-T1
Valid prediction for snap_scaffold_11-snap.2853-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14349, rend_intergenic: 6689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19943, rend_intergenic: 14659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32952, rend_intergenic: 20312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96549, rend_intergenic: 94932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106697, rend_intergenic: 96721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219067, rend_intergenic: 218936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222149, rend_intergenic: 220665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 272749
-exon list size: 455


building trellis

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94.1    
94.3    
94.5    
94.7    
95.0    
95.2    
95.4    
95.6    
95.8    
96.1    
96.3    
96.5    
96.7    
96.9    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 14349, rend_intergenic: 6689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19943, rend_intergenic: 14659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32952, rend_intergenic: 20312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96549, rend_intergenic: 94932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106697, rend_intergenic: 96721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219067, rend_intergenic: 218936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222149, rend_intergenic: 220665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support