-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_1-150727

-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 pasa_asmbl_53753.p1
Valid prediction for GlimmerHMM_glimmerT_21439-T1
Valid prediction for snap_scaffold_9-snap.26-T1
Valid prediction for GlimmerHMM_glimmerT_21437-T1
Valid prediction for GlimmerHMM_glimmerT_21442-T1
Valid prediction for GlimmerHMM_glimmerT_21441-T1
Valid prediction for snap_scaffold_9-snap.38-T1
Valid prediction for GlimmerHMM_glimmerT_21436-T1
Valid prediction for snap_scaffold_9-snap.21-T1
Valid prediction for snap_scaffold_9-snap.6-T1
Valid prediction for snap_scaffold_9-snap.34-T1
Valid prediction for snap_scaffold_9-snap.8-T1
Valid prediction for GlimmerHMM_glimmerT_21427-T1
Valid prediction for CodingQuarry_transcript_62091-T1
Valid prediction for snap_scaffold_9-snap.23-T1
Valid prediction for GlimmerHMM_glimmerT_21425-T1
Valid prediction for Augustus_model.g14276.t1
Valid prediction for snap_scaffold_9-snap.28-T1
Valid prediction for snap_scaffold_9-snap.14-T1
Valid prediction for snap_scaffold_9-snap.2-T1
Valid prediction for GlimmerHMM_glimmerT_21419-T1
Valid prediction for snap_scaffold_9-snap.33-T1
Couldn't classify 119186, 119281
Couldn't classify 119331, 119369
Sorry, prediction CodingQuarry_transcript_62092-T1 fails validation.
(ATG)	 AG	118741-118793	GT	AGG
(GCT)	 AG	119186-119281	CC	GCC
(CCA)	 GT	119331-119369	GT	AGG
(CCT)	 AG	119546-120011	GA	AGG
-recovered CodingQuarry_transcript_62092-T1, initial, 118741, 118793
-recovered CodingQuarry_transcript_62092-T1, terminal, 119546, 120011
-recovered CodingQuarry_transcript_62092-T1, internal, 118741, 118793
Valid prediction for snap_scaffold_9-snap.22-T1
Valid prediction for snap_scaffold_9-snap.1-T1
Valid prediction for snap_scaffold_9-snap.16-T1
Valid prediction for Augustus_model.g14274.t1
Valid prediction for snap_scaffold_9-snap.5-T1
Valid prediction for GlimmerHMM_glimmerT_21440-T1
Valid prediction for Augustus_model.g14271.t1
Valid prediction for HiQ_model.g14279.t1
Valid prediction for snap_scaffold_9-snap.29-T1
Valid prediction for GlimmerHMM_glimmerT_21443-T1
Valid prediction for snap_scaffold_9-snap.12-T1
Valid prediction for GlimmerHMM_glimmerT_21433-T1
Valid prediction for GlimmerHMM_glimmerT_21421-T1
Valid prediction for Augustus_model.g14286.t1
Valid prediction for GlimmerHMM_glimmerT_21424-T1
Valid prediction for GlimmerHMM_glimmerT_21431-T1
Valid prediction for GlimmerHMM_glimmerT_21423-T1
Valid prediction for snap_scaffold_9-snap.37-T1
Valid prediction for GlimmerHMM_glimmerT_21418-T1
Valid prediction for HiQ_model.g14272.t1
Valid prediction for Augustus_model.g14283.t1
Valid prediction for pasa_asmbl_53751.p1
Valid prediction for CodingQuarry_transcript_62093-T1
Valid prediction for Augustus_model.g14282.t1
Valid prediction for Augustus_model.g14287.t1
Valid prediction for GlimmerHMM_glimmerT_21429-T1
Valid prediction for HiQ_model.g14284.t1
Valid prediction for pasa_asmbl_53748.p1
Valid prediction for CodingQuarry_transcript_62090-T1
Valid prediction for snap_scaffold_9-snap.31-T1
Valid prediction for snap_scaffold_9-snap.9-T1
Valid prediction for HiQ_model.g14278.t1
Valid prediction for snap_scaffold_9-snap.35-T1
Valid prediction for pasa_asmbl_53745.p1

-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 Augustus_model.g14281.t1
Valid prediction for snap_scaffold_9-snap.36-T1
Valid prediction for Augustus_model.g14285.t1
Valid prediction for snap_scaffold_9-snap.25-T1
Couldn't classify 82500, 82583
Sorry, prediction pasa_asmbl_54798.p1 fails validation.
(ATG)	 AA	74761-74835	GT	AGG
(ATG)	 AG	74987-75139	GT	AGG
(GTT)	 AG	75263-75395	GT	AGG
(GTC)	 AG	75658-75862	GT	AGG
(GAC)	 AG	76108-76224	GT	GGG
(GCA)	 AG	76424-76574	GT	AGG
(GCT)	 AG	76735-76889	GT	GAG
(GGA)	 AG	77321-77405	GT	AGG
(GCG)	 AG	78092-78229	GT	AGG
(GAC)	 AG	78582-78683	GT	TGG
(GAG)	 AG	80401-80457	GT	AGG
(AAT)	 AG	81867-82004	GT	AGG
(AGG)	 AG	82500-82583	TA	AGT
-recovered pasa_asmbl_54798.p1, initial, 74761, 74835
-recovered pasa_asmbl_54798.p1, initial, 74987, 75139
-recovered pasa_asmbl_54798.p1, internal, 74987, 75139
-recovered pasa_asmbl_54798.p1, internal, 75263, 75395
-recovered pasa_asmbl_54798.p1, internal, 75658, 75862
-recovered pasa_asmbl_54798.p1, internal, 76108, 76224
-recovered pasa_asmbl_54798.p1, internal, 76424, 76574
-recovered pasa_asmbl_54798.p1, internal, 76735, 76889
-recovered pasa_asmbl_54798.p1, internal, 77321, 77405
-recovered pasa_asmbl_54798.p1, internal, 78092, 78229
-recovered pasa_asmbl_54798.p1, internal, 78582, 78683
-recovered pasa_asmbl_54798.p1, internal, 80401, 80457
-recovered pasa_asmbl_54798.p1, internal, 81867, 82004
Couldn't classify 143519, 143602
Sorry, prediction pasa_asmbl_54791.p1 fails validation.
(GGT)	 AG	143519-143602	GT	GGG
(GAA)	 AG	144265-144321	GT	TGG
(GGT)	 AG	144618-144698	GT	TGG
(GTC)	 AG	144890-144954	GT	AAG
(GTA)	 AG	146195-146255	TG	GAT
-recovered pasa_asmbl_54791.p1, terminal, 146195, 146255
-recovered pasa_asmbl_54791.p1, internal, 143519, 143602
-recovered pasa_asmbl_54791.p1, internal, 144265, 144321
-recovered pasa_asmbl_54791.p1, internal, 144618, 144698
-recovered pasa_asmbl_54791.p1, internal, 144890, 144954
Valid prediction for snap_scaffold_9-snap.3-T1
Valid prediction for HiQ_model.g14277.t1
Valid prediction for Augustus_model.g14275.t1
Valid prediction for snap_scaffold_9-snap.13-T1
Valid prediction for GlimmerHMM_glimmerT_21430-T1
Valid prediction for Augustus_model.g14268.t1
Couldn't classify 87250, 87411
Sorry, prediction pasa_asmbl_54797.p2 fails validation.
(TTT)	 GG	87250-87411	GT	GGG
(GGG)	 AG	87926-88070	GT	GGG
(CCA)	 AG	88185-88345	GT	ATG
(GTG)	 AG	88448-88501	GT	AGG
(GGT)	 AG	88626-88757	GC	GAG
-recovered pasa_asmbl_54797.p2, terminal, 88626, 88757
-recovered pasa_asmbl_54797.p2, internal, 87926, 88070
-recovered pasa_asmbl_54797.p2, internal, 88185, 88345
-recovered pasa_asmbl_54797.p2, internal, 88448, 88501
-recovered pasa_asmbl_54797.p2, internal, 88626, 88757
Valid prediction for GlimmerHMM_glimmerT_21435-T1
Valid prediction for snap_scaffold_9-snap.20-T1
Valid prediction for GlimmerHMM_glimmerT_21438-T1
Valid prediction for snap_scaffold_9-snap.15-T1
Valid prediction for snap_scaffold_9-snap.7-T1
Valid prediction for CodingQuarry_transcript_62089-T1
Valid prediction for GlimmerHMM_glimmerT_21428-T1
Valid prediction for snap_scaffold_9-snap.4-T1
Valid prediction for Augustus_model.g14280.t1
Valid prediction for snap_scaffold_9-snap.19-T1
Valid prediction for snap_scaffold_9-snap.27-T1
Valid prediction for GlimmerHMM_glimmerT_21426-T1
Valid prediction for snap_scaffold_9-snap.32-T1
Valid prediction for Augustus_model.g14269.t1
Valid prediction for snap_scaffold_9-snap.18-T1
Valid prediction for GlimmerHMM_glimmerT_21420-T1
Valid prediction for snap_scaffold_9-snap.10-T1
Valid prediction for Augustus_model.g14270.t1
Valid prediction for snap_scaffold_9-snap.30-T1
Valid prediction for HiQ_model.g14273.t1
Couldn't classify 139025, 139245
Couldn't classify 139566, 139740
Sorry, prediction pasa_asmbl_54792.p1 fails validation.
(GAG)	 CG	139025-139245	GT	AGG
(GTC)	 AG	139566-139740	TA	GTT
Valid prediction for snap_scaffold_9-snap.24-T1
Valid prediction for GlimmerHMM_glimmerT_21434-T1
Valid prediction for snap_scaffold_9-snap.17-T1
Couldn't classify 116027, 116140
Couldn't classify 125266, 125358
Sorry, prediction pasa_asmbl_54794.p1 fails validation.
(CAG)	 TG	116027-116140	GT	AGG
(GAT)	 AG	117637-117684	GT	AGG
(ATT)	 AG	118424-118502	GT	AGG
(ACC)	 AG	118687-118824	GT	GGG
(AGG)	 AG	119298-119421	GT	AGG
(AAA)	 AG	119647-119723	GT	AGG
(CAC)	 AG	120196-120262	GT	AAG
(GGC)	 AG	120670-120718	GT	AGG
(AGA)	 AG	120894-120998	GT	CGG
(ACA)	 AG	121315-121494	GT	GGG
(GAG)	 AG	123449-123507	GT	AAG
(TAT)	 AG	123752-123797	GT	AGG
(GAC)	 AG	125266-125358	GG	ACG
add_exon() Sorry, pasa_asmbl_54794.p1 120196-120262-terminal-3 is invalid.
-recovered pasa_asmbl_54794.p1, terminal, 120196, 120262
-recovered pasa_asmbl_54794.p1, internal, 117637, 117684
-recovered pasa_asmbl_54794.p1, internal, 118424, 118502
-recovered pasa_asmbl_54794.p1, internal, 118687, 118824
-recovered pasa_asmbl_54794.p1, internal, 119298, 119421
-recovered pasa_asmbl_54794.p1, internal, 119647, 119723
-recovered pasa_asmbl_54794.p1, internal, 120196, 120262
-recovered pasa_asmbl_54794.p1, internal, 120670, 120718
-recovered pasa_asmbl_54794.p1, internal, 120894, 120998
-recovered pasa_asmbl_54794.p1, internal, 121315, 121494
-recovered pasa_asmbl_54794.p1, internal, 123449, 123507
-recovered pasa_asmbl_54794.p1, internal, 123752, 123797
Couldn't classify 97543, 98070
Sorry, prediction pasa_asmbl_54796.p1 fails validation.
(ATG)	 CG	96710-97192	GT	AGG
(GTG)	 AG	97543-98070	GG	GGG
-recovered pasa_asmbl_54796.p1, initial, 96710, 97192
Valid prediction for GlimmerHMM_glimmerT_21422-T1
Valid prediction for snap_scaffold_9-snap.11-T1
Valid prediction for GlimmerHMM_glimmerT_21432-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7630, rend_intergenic: 5997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19214, rend_intergenic: 11841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28089, rend_intergenic: 25253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38596, rend_intergenic: 28738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54046, rend_intergenic: 52400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62517, rend_intergenic: 58357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63519, rend_intergenic: 62738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74334, rend_intergenic: 64264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81387, rend_intergenic: 79589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102247, rend_intergenic: 100378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113971, rend_intergenic: 110012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129957, rend_intergenic: 125740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133966, rend_intergenic: 131922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140145, rend_intergenic: 137172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 150727
-exon list size: 337


building trellis

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31.6    
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35.4    
35.7    
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36.6    
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38.1    
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48.7    
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49.6    
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97.1    
97.3    
97.6    
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98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 7630, rend_intergenic: 5997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19214, rend_intergenic: 11841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28089, rend_intergenic: 25253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38596, rend_intergenic: 28738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54046, rend_intergenic: 52400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62517, rend_intergenic: 58357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63519, rend_intergenic: 62738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74334, rend_intergenic: 64264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81387, rend_intergenic: 79589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102247, rend_intergenic: 100378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113971, rend_intergenic: 110012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129957, rend_intergenic: 125740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133966, rend_intergenic: 131922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140145, rend_intergenic: 137172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support