-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_13771162-14035113

-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 GlimmerHMM_glimmerT_35059-T1
Valid prediction for pasa_asmbl_12512.p2
Valid prediction for GlimmerHMM_glimmerT_35069-T1
Valid prediction for GlimmerHMM_glimmerT_35068-T1
Valid prediction for snap_scaffold_14-snap.2840-T1
Valid prediction for HiQ_model.g23442.t1
Valid prediction for snap_scaffold_14-snap.2876-T1
Valid prediction for snap_scaffold_14-snap.2850-T1
Valid prediction for GlimmerHMM_glimmerT_35050-T1
Valid prediction for HiQ_model.g23439.t1
Valid prediction for HiQ_model.g23443.t1
Valid prediction for GlimmerHMM_glimmerT_35066-T1
Valid prediction for GlimmerHMM_glimmerT_35055-T1
Valid prediction for HiQ_model.g23444.t1
Valid prediction for snap_scaffold_14-snap.2874-T1
Valid prediction for snap_scaffold_14-snap.2875-T1
Valid prediction for snap_scaffold_14-snap.2863-T1
Valid prediction for GlimmerHMM_glimmerT_35046-T1
Valid prediction for snap_scaffold_14-snap.2861-T1
Valid prediction for CodingQuarry_transcript_15925-T1
Valid prediction for GlimmerHMM_glimmerT_35045-T1
Valid prediction for Augustus_model.g23437.t1
Valid prediction for GlimmerHMM_glimmerT_35053-T1
Valid prediction for snap_scaffold_14-snap.2844-T1
Valid prediction for snap_scaffold_14-snap.2847-T1
Valid prediction for GlimmerHMM_glimmerT_35054-T1
Valid prediction for GlimmerHMM_glimmerT_35065-T1
Valid prediction for snap_scaffold_14-snap.2873-T1
Valid prediction for snap_scaffold_14-snap.2843-T1
Valid prediction for snap_scaffold_14-snap.2872-T1
Valid prediction for pasa_asmbl_12517.p1
Valid prediction for snap_scaffold_14-snap.2837-T1
Valid prediction for snap_scaffold_14-snap.2854-T1
Valid prediction for snap_scaffold_14-snap.2871-T1
Valid prediction for snap_scaffold_14-snap.2866-T1
Valid prediction for snap_scaffold_14-snap.2841-T1
Valid prediction for snap_scaffold_14-snap.2839-T1
Valid prediction for GlimmerHMM_glimmerT_35048-T1
Valid prediction for GlimmerHMM_glimmerT_35063-T1
Valid prediction for snap_scaffold_14-snap.2864-T1
Couldn't classify 89566, 90573
Sorry, prediction pasa_asmbl_12505.p1 fails validation.
(GGA)	 GT	89566-90573	AT	AGA
Valid prediction for snap_scaffold_14-snap.2852-T1
Valid prediction for snap_scaffold_14-snap.2845-T1
Valid prediction for GlimmerHMM_glimmerT_35062-T1
Valid prediction for pasa_asmbl_12507.p1
Valid prediction for CodingQuarry_transcript_15926-T1
Valid prediction for snap_scaffold_14-snap.2855-T1
Valid prediction for CodingQuarry_transcript_15922-T1
Valid prediction for GlimmerHMM_glimmerT_35049-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: -)Couldn't classify 111569, 111638
Couldn't classify 113489, 113564
Sorry, prediction pasa_asmbl_13669.p1 fails validation.
(CAG)	 CT	111569-111638	GT	TGG
(GCT)	 AG	112835-112965	GT	AGG
(AGA)	 AG	113233-113345	GT	AGG
(ATT)	 AG	113489-113564	AA	GGA
-recovered pasa_asmbl_13669.p1, internal, 112835, 112965
-recovered pasa_asmbl_13669.p1, internal, 113233, 113345
Valid prediction for HiQ_model.g23441.t1
Valid prediction for Augustus_model.g23438.t1
Valid prediction for snap_scaffold_14-snap.2858-T1
Valid prediction for Augustus_model.g23452.t1
Valid prediction for Augustus_model.g23446.t1
Valid prediction for HiQ_model.g23451.t1
Valid prediction for snap_scaffold_14-snap.2870-T1
Sorry, intron length (7) is less than minimum required (10)
Sorry, intron length (7) is less than minimum required (10)
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_14-snap.2838-T1
Valid prediction for GlimmerHMM_glimmerT_35057-T1
Valid prediction for snap_scaffold_14-snap.2877-T1
Valid prediction for GlimmerHMM_glimmerT_35058-T1
Valid prediction for snap_scaffold_14-snap.2856-T1
Valid prediction for Augustus_model.g23450.t1
Valid prediction for snap_scaffold_14-snap.2859-T1
Valid prediction for Augustus_model.g23447.t1
Valid prediction for snap_scaffold_14-snap.2849-T1
Couldn't classify 118408, 118637
Couldn't classify 121770, 122509
Sorry, prediction pasa_asmbl_13860.p1 fails validation.
(TAC)	 GT	118408-118637	GT	AGG
(GTT)	 AG	119200-119359	GT	ACG
(GCG)	 AG	120002-120319	GT	AGG
(AGA)	 AG	121201-121468	GT	AGG
(GAG)	 AG	121770-122509	TC	CTT
-recovered pasa_asmbl_13860.p1, internal, 119200, 119359
-recovered pasa_asmbl_13860.p1, internal, 120002, 120319
-recovered pasa_asmbl_13860.p1, internal, 121201, 121468
Valid prediction for pasa_asmbl_13657.p1
Valid prediction for snap_scaffold_14-snap.2860-T1
Valid prediction for snap_scaffold_14-snap.2868-T1
Valid prediction for GlimmerHMM_glimmerT_35060-T1
Valid prediction for snap_scaffold_14-snap.2842-T1
Couldn't classify 123170, 124237
Sorry, prediction pasa_asmbl_13667.p1 fails validation.
(ATC)	 AG	123170-124237	CA	TGC
Valid prediction for CodingQuarry_transcript_15924-T1
Valid prediction for snap_scaffold_14-snap.2851-T1
Valid prediction for snap_scaffold_14-snap.2867-T1
Valid prediction for HiQ_model.g23440.t1
Valid prediction for snap_scaffold_14-snap.2862-T1
Valid prediction for GlimmerHMM_glimmerT_35047-T1
Valid prediction for snap_scaffold_14-snap.2857-T1
Valid prediction for Augustus_model.g23448.t1
Valid prediction for snap_scaffold_14-snap.2865-T1
Valid prediction for CodingQuarry_transcript_15923-T1
Valid prediction for GlimmerHMM_glimmerT_35052-T1
Valid prediction for snap_scaffold_14-snap.2869-T1
Valid prediction for snap_scaffold_14-snap.2853-T1
Valid prediction for GlimmerHMM_glimmerT_35056-T1
Valid prediction for GlimmerHMM_glimmerT_35061-T1
Valid prediction for GlimmerHMM_glimmerT_35064-T1
Valid prediction for snap_scaffold_14-snap.2848-T1
Valid prediction for Augustus_model.g23449.t1
Valid prediction for Augustus_model.g23445.t1
Valid prediction for GlimmerHMM_glimmerT_35051-T1
Valid prediction for snap_scaffold_14-snap.2846-T1
Valid prediction for GlimmerHMM_glimmerT_35067-T1
Valid prediction for pasa_asmbl_13658.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10811, rend_intergenic: 10191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14118, rend_intergenic: 11159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42271, rend_intergenic: 40909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155418, rend_intergenic: 143552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184057, rend_intergenic: 174619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194779, rend_intergenic: 187498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199111, rend_intergenic: 195704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202345, rend_intergenic: 201027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205334, rend_intergenic: 203341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 247468, rend_intergenic: 225595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 263952
-exon list size: 281


building trellis

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45.6    
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48.1    
48.4    
48.8    
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49.5    
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50.2    
50.5    
50.9    
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51.6    
51.9    
52.3    
52.7    
53.0    
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55.1    
55.5    
55.8    
56.2    
56.5    
56.9    
57.2    
57.6    
58.0    
58.3    
58.7    
59.0    
59.4    
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60.1    
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63.3    
63.6    
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64.3    
64.7    
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65.4    
65.7    
66.1    
66.4    
66.8    
67.1    
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68.6    
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69.3    
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70.0    
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70.7    
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80.2    
80.6    
80.9    
81.3    
81.6    
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82.7    
83.0    
83.4    
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84.8    
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86.2    
86.6    
86.9    
87.3    
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88.0    
88.3    
88.7    
89.0    
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91.2    
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97.2    
97.5    
97.9    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 10811, rend_intergenic: 10191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14118, rend_intergenic: 11159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42271, rend_intergenic: 40909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155418, rend_intergenic: 143552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184057, rend_intergenic: 174619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194779, rend_intergenic: 187498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199111, rend_intergenic: 195704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202345, rend_intergenic: 201027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205334, rend_intergenic: 203341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 247468, rend_intergenic: 225595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11307
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

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