-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_15802925-16017854

-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 CodingQuarry_transcript_18279-T1
Valid prediction for GlimmerHMM_glimmerT_37562-T1
Couldn't classify 98175, 98195
Sorry, prediction pasa_asmbl_15839.p1 fails validation.
(TTC)	 TC	98175-98195	GT	AGG
(GCG)	 AG	98873-99802	CC	AGC
-recovered pasa_asmbl_15839.p1, terminal, 98873, 99802
Valid prediction for snap_scaffold_15-snap.3135-T1
Valid prediction for HiQ_model.g25059.t1
Valid prediction for CodingQuarry_transcript_18274-T1
Valid prediction for snap_scaffold_15-snap.3126-T1
Valid prediction for Augustus_model.g25046.t1
Valid prediction for snap_scaffold_15-snap.3150-T1
Valid prediction for GlimmerHMM_glimmerT_37558-T1
Valid prediction for GlimmerHMM_glimmerT_37569-T1
Valid prediction for GlimmerHMM_glimmerT_37560-T1
Valid prediction for Augustus_model.g25052.t1
Valid prediction for snap_scaffold_15-snap.3148-T1
Valid prediction for GlimmerHMM_glimmerT_37554-T1
Valid prediction for Augustus_model.g25055.t1
Valid prediction for HiQ_model.g25054.t1
Valid prediction for snap_scaffold_15-snap.3128-T1
Valid prediction for CodingQuarry_transcript_18273-T1
Valid prediction for Augustus_model.g25063.t1
Valid prediction for snap_scaffold_15-snap.3153-T1
Valid prediction for GlimmerHMM_glimmerT_37578-T1
Valid prediction for pasa_asmbl_15848.p1
Valid prediction for GlimmerHMM_glimmerT_37565-T1
Valid prediction for snap_scaffold_15-snap.3130-T1
Valid prediction for HiQ_model.g25057.t1
Valid prediction for pasa_asmbl_15834.p1
Valid prediction for GlimmerHMM_glimmerT_37559-T1
Valid prediction for snap_scaffold_15-snap.3152-T1
Valid prediction for GlimmerHMM_glimmerT_37567-T1
Valid prediction for snap_scaffold_15-snap.3127-T1
Valid prediction for CodingQuarry_transcript_18270-T1
Valid prediction for GlimmerHMM_glimmerT_37574-T1
Valid prediction for pasa_asmbl_15822.p1
Valid prediction for snap_scaffold_15-snap.3158-T1
Valid prediction for pasa_asmbl_15846.p1
Valid prediction for snap_scaffold_15-snap.3154-T1
Valid prediction for CodingQuarry_transcript_18275-T1
Couldn't classify 122552, 122553
Sorry, prediction CodingQuarry_transcript_18281-T1 fails validation.
(ATG)	 GA	122552-122553	GT	ATG
(GGT)	 AG	123088-123205	GT	AGG
(ACC)	 AG	123294-123373	GT	AGG
(CAC)	 AG	123455-123522	GT	TGG
(GTG)	 AG	123711-123755	GT	CAG
(GTT)	 AG	123880-123983	GT	AGG
(ACA)	 AG	124108-124174	GT	TGG
(TGA)	 AG	124284-124362	GT	AGG
(GCT)	 AG	124554-124698	CG	AAC
add_exon() Sorry, CodingQuarry_transcript_18281-T1 123294-123373-terminal-2 is invalid.
-recovered CodingQuarry_transcript_18281-T1, terminal, 123294, 123373
-recovered CodingQuarry_transcript_18281-T1, terminal, 124554, 124698
-recovered CodingQuarry_transcript_18281-T1, internal, 123088, 123205
-recovered CodingQuarry_transcript_18281-T1, internal, 123294, 123373
-recovered CodingQuarry_transcript_18281-T1, internal, 123455, 123522
-recovered CodingQuarry_transcript_18281-T1, internal, 123711, 123755
-recovered CodingQuarry_transcript_18281-T1, internal, 123880, 123983
-recovered CodingQuarry_transcript_18281-T1, internal, 124108, 124174
-recovered CodingQuarry_transcript_18281-T1, internal, 124284, 124362
Valid prediction for snap_scaffold_15-snap.3139-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for pasa_asmbl_15837.p1
Valid prediction for GlimmerHMM_glimmerT_37563-T1
Valid prediction for snap_scaffold_15-snap.3132-T1
Valid prediction for snap_scaffold_15-snap.3141-T1
Valid prediction for snap_scaffold_15-snap.3136-T1
Valid prediction for CodingQuarry_transcript_18276-T1
Valid prediction for Augustus_model.g25051.t1
Valid prediction for HiQ_model.g25049.t1
Valid prediction for GlimmerHMM_glimmerT_37556-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 173938, 173992
Couldn't classify 174596, 174643
Sorry, prediction pasa_asmbl_14805.p1 fails validation.
(AAA)	 TG	173938-173992	GT	AGG
(AGA)	 AG	174094-174257	GT	AGG
(ATG)	 AG	174387-174500	GT	TGG
(GTT)	 AG	174596-174643	GA	AGG
-recovered pasa_asmbl_14805.p1, initial, 174387, 174500
-recovered pasa_asmbl_14805.p1, internal, 174094, 174257
-recovered pasa_asmbl_14805.p1, internal, 174387, 174500
Valid prediction for snap_scaffold_15-snap.3131-T1
Valid prediction for pasa_asmbl_14806.p1
Valid prediction for snap_scaffold_15-snap.3122-T1
Valid prediction for snap_scaffold_15-snap.3143-T1
Valid prediction for snap_scaffold_15-snap.3121-T1
Valid prediction for snap_scaffold_15-snap.3149-T1
Valid prediction for snap_scaffold_15-snap.3133-T1
Valid prediction for snap_scaffold_15-snap.3123-T1
Valid prediction for GlimmerHMM_glimmerT_37571-T1
Valid prediction for snap_scaffold_15-snap.3157-T1
Valid prediction for HiQ_model.g25048.t1
Valid prediction for GlimmerHMM_glimmerT_37568-T1
Valid prediction for snap_scaffold_15-snap.3137-T1
Valid prediction for Augustus_model.g25047.t1
Valid prediction for snap_scaffold_15-snap.3151-T1
Valid prediction for GlimmerHMM_glimmerT_37576-T1
Valid prediction for GlimmerHMM_glimmerT_37557-T1
Couldn't classify 189836, 190603
Sorry, prediction pasa_asmbl_14801.p1 fails validation.
(ATG)	 CC	189836-190603	GG	AAG
Valid prediction for GlimmerHMM_glimmerT_37566-T1
Valid prediction for snap_scaffold_15-snap.3134-T1
Valid prediction for pasa_asmbl_14816.p1
Valid prediction for GlimmerHMM_glimmerT_37577-T1
Valid prediction for snap_scaffold_15-snap.3124-T1
Valid prediction for GlimmerHMM_glimmerT_37573-T1
Valid prediction for GlimmerHMM_glimmerT_37570-T1
Valid prediction for snap_scaffold_15-snap.3144-T1
Valid prediction for snap_scaffold_15-snap.3156-T1
Valid prediction for snap_scaffold_15-snap.3142-T1
Valid prediction for snap_scaffold_15-snap.3155-T1
Valid prediction for pasa_asmbl_14807.p1
Valid prediction for Augustus_model.g25053.t1
Valid prediction for GlimmerHMM_glimmerT_37553-T1
Valid prediction for Augustus_model.g25062.t1
Valid prediction for GlimmerHMM_glimmerT_37564-T1
Valid prediction for HiQ_model.g25056.t1
Valid prediction for Augustus_model.g25061.t1
Valid prediction for snap_scaffold_15-snap.3140-T1
Valid prediction for snap_scaffold_15-snap.3129-T1
Valid prediction for snap_scaffold_15-snap.3145-T1
Couldn't classify 195043, 195355
Sorry, prediction pasa_asmbl_14798.p1 fails validation.
(CTG)	 AC	195043-195355	GT	CGG
(AGG)	 AG	195762-196027	GC	AGG
-recovered pasa_asmbl_14798.p1, terminal, 195762, 196027
-recovered pasa_asmbl_14798.p1, internal, 195762, 196027
Valid prediction for GlimmerHMM_glimmerT_37579-T1
Valid prediction for Augustus_model.g25060.t1
Valid prediction for GlimmerHMM_glimmerT_37575-T1
Valid prediction for HiQ_model.g25050.t1
Valid prediction for snap_scaffold_15-snap.3147-T1
Valid prediction for HiQ_model.g25058.t1
Valid prediction for snap_scaffold_15-snap.3146-T1
Valid prediction for CodingQuarry_transcript_18271-T1
Valid prediction for GlimmerHMM_glimmerT_37572-T1
Valid prediction for CodingQuarry_transcript_18278-T1
Valid prediction for GlimmerHMM_glimmerT_37555-T1
Valid prediction for snap_scaffold_15-snap.3138-T1
Couldn't classify 174740, 174794
Sorry, prediction pasa_asmbl_14803.p1 fails validation.
(GGT)	 AA	174740-174794	GT	AGG
(ATG)	 AG	175455-175576	GT	ATG
(ATG)	 AG	175661-175819	GT	AGG
(ATA)	 AG	175930-175996	GT	AGG
(AAA)	 AG	176125-176248	GT	AGG
(AGA)	 AG	176996-177141	GT	ATG
(CTG)	 AG	177328-177530	TA	AAT
add_exon() Sorry, pasa_asmbl_14803.p1 175455-175576-initial-1 is invalid.
-recovered pasa_asmbl_14803.p1, initial, 175455, 175576
-recovered pasa_asmbl_14803.p1, initial, 175661, 175819
-recovered pasa_asmbl_14803.p1, terminal, 177328, 177530
-recovered pasa_asmbl_14803.p1, internal, 175455, 175576
-recovered pasa_asmbl_14803.p1, internal, 175661, 175819
-recovered pasa_asmbl_14803.p1, internal, 175930, 175996
-recovered pasa_asmbl_14803.p1, internal, 176125, 176248
-recovered pasa_asmbl_14803.p1, internal, 176996, 177141
Valid prediction for snap_scaffold_15-snap.3125-T1
Valid prediction for GlimmerHMM_glimmerT_37561-T1
Couldn't classify 155255, 155363
Couldn't classify 155751, 155877
Sorry, prediction CodingQuarry_transcript_18272-T1 fails validation.
(ATG)	 AG	154509-154529	GT	AGG
(TGC)	 AG	154929-154983	GT	TAG
(TTA)	 AG	155075-155138	GT	AGG
(GAA)	 AG	155255-155363	TT	GGT
(CCA)	 TT	155751-155877	GT	AGG
(ATT)	 AG	156008-156130	GT	AGG
(GAG)	 AG	156233-156350	GT	CTG
(GTA)	 AG	156460-156556	AC	AAA
-recovered CodingQuarry_transcript_18272-T1, initial, 154509, 154529
-recovered CodingQuarry_transcript_18272-T1, terminal, 156460, 156556
-recovered CodingQuarry_transcript_18272-T1, internal, 154509, 154529
-recovered CodingQuarry_transcript_18272-T1, internal, 154929, 154983
-recovered CodingQuarry_transcript_18272-T1, internal, 155075, 155138
-recovered CodingQuarry_transcript_18272-T1, internal, 156008, 156130
-recovered CodingQuarry_transcript_18272-T1, internal, 156233, 156350
Valid prediction for CodingQuarry_transcript_18280-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 169136, rend_intergenic: 165172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187119, rend_intergenic: 169965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190846, rend_intergenic: 188173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 214930
-exon list size: 354


building trellis

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35.7    
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42.4    
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44.4    
44.7    
44.9    
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47.2    
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48.0    
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48.6    
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50.6    
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51.1    
51.4    
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52.5    
52.8    
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55.1    
55.3    
55.6    
55.9    
56.2    
56.5    
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58.4    
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60.4    
60.7    
61.0    
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64.0    
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64.6    
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83.4    
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86.5    
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87.6    
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89.6    
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91.3    
91.6    
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92.1    
92.4    
92.7    
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93.3    
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96.6    
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97.2    
97.5    
97.8    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 169136, rend_intergenic: 165172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187119, rend_intergenic: 169965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190846, rend_intergenic: 188173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support