-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_1-156370

-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: +)Couldn't classify 33463, 33552
Sorry, prediction pasa_asmbl_24067.p1 fails validation.
(ATG)	 TG	32953-33064	GT	AGG
(AGG)	 AG	33154-33281	GT	AGG
(GCA)	 AG	33463-33552	GG	CAG
-recovered pasa_asmbl_24067.p1, initial, 32953, 33064
-recovered pasa_asmbl_24067.p1, internal, 33154, 33281
Valid prediction for GlimmerHMM_glimmerT_2999-T1
Valid prediction for snap_scaffold_2-snap.8-T1
Couldn't classify 150903, 151140
Couldn't classify 153938, 153977
Sorry, prediction pasa_asmbl_24077.p1 fails validation.
(GAG)	 CA	150903-151140	GT	CAG
(TCA)	 AG	151536-151646	GT	TGG
(ATG)	 AG	152463-152699	GT	AGG
(GTA)	 AG	152967-153091	GT	AGG
(ATG)	 AG	153399-153496	GT	AGG
(GCC)	 AG	153938-153977	TG	CCT
add_exon() Sorry, pasa_asmbl_24077.p1 152463-152699-initial-1 is invalid.
-recovered pasa_asmbl_24077.p1, initial, 152463, 152699
-recovered pasa_asmbl_24077.p1, initial, 153399, 153496
-recovered pasa_asmbl_24077.p1, internal, 151536, 151646
-recovered pasa_asmbl_24077.p1, internal, 152463, 152699
-recovered pasa_asmbl_24077.p1, internal, 152967, 153091
-recovered pasa_asmbl_24077.p1, internal, 153399, 153496
Valid prediction for snap_scaffold_2-snap.13-T1
Valid prediction for snap_scaffold_2-snap.34-T1
Valid prediction for snap_scaffold_2-snap.10-T1
Couldn't classify 103544, 103672
Couldn't classify 103709, 103942
Sorry, prediction CodingQuarry_transcript_28412-T1 fails validation.
(ATG)	 AG	103421-103453	GT	AGG
(AAC)	 AG	103544-103672	CT	CAC
(CTC)	 CC	103709-103942	AC	GAA
-recovered CodingQuarry_transcript_28412-T1, initial, 103421, 103453
-recovered CodingQuarry_transcript_28412-T1, internal, 103421, 103453
Valid prediction for GlimmerHMM_glimmerT_3001-T1
Valid prediction for GlimmerHMM_glimmerT_3000-T1
Valid prediction for Augustus_model.g2055.t1
Valid prediction for snap_scaffold_2-snap.5-T1
Valid prediction for Augustus_model.g2057.t1
Valid prediction for CodingQuarry_transcript_28408-T1
Valid prediction for GlimmerHMM_glimmerT_3013-T1
Couldn't classify 142810, 142994
Couldn't classify 149124, 149236
Sorry, prediction pasa_asmbl_25398.p1 fails validation.
(GTC)	 AT	142810-142994	GT	GGG
(GTT)	 AG	143998-144182	GT	AGG
(GTC)	 AG	144261-144584	GT	CTG
(CTC)	 AG	145305-145501	GT	AGG
(TCC)	 AG	145868-146085	GT	GGG
(GTA)	 AG	147585-147775	GT	CGG
(GAG)	 AG	149124-149236	GA	TGG
-recovered pasa_asmbl_25398.p1, internal, 143998, 144182
-recovered pasa_asmbl_25398.p1, internal, 144261, 144584
-recovered pasa_asmbl_25398.p1, internal, 145305, 145501
-recovered pasa_asmbl_25398.p1, internal, 145868, 146085
-recovered pasa_asmbl_25398.p1, internal, 147585, 147775
Valid prediction for HiQ_model.g2053.t1
Valid prediction for snap_scaffold_2-snap.32-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.17-T1
Couldn't classify 101303, 101621
Sorry, prediction pasa_asmbl_24073.p1 fails validation.
(TTA)	 CC	101303-101621	GT	ATG
(GCA)	 AG	103328-103453	GT	AGG
(AAC)	 AG	103544-104511	TG	GAT
-recovered pasa_asmbl_24073.p1, terminal, 103544, 104511
-recovered pasa_asmbl_24073.p1, internal, 103328, 103453
Couldn't classify 103544, 103672
Couldn't classify 103697, 103942
Sorry, prediction CodingQuarry_transcript_28414-T1 fails validation.
(ATG)	 AG	103421-103453	GT	AGG
(AAC)	 AG	103544-103672	CT	CAC
(CTC)	 CC	103697-103942	AC	GAA
-recovered CodingQuarry_transcript_28414-T1, initial, 103421, 103453
-recovered CodingQuarry_transcript_28414-T1, internal, 103421, 103453
Valid prediction for GlimmerHMM_glimmerT_2997-T1
Valid prediction for Augustus_model.g2059.t1
Valid prediction for Augustus_model.g2050.t1
Valid prediction for snap_scaffold_2-snap.31-T1
Valid prediction for GlimmerHMM_glimmerT_3015-T1
Valid prediction for snap_scaffold_2-snap.28-T1
Valid prediction for Augustus_model.g2056.t1
Valid prediction for snap_scaffold_2-snap.20-T1
Valid prediction for CodingQuarry_transcript_28415-T1
Valid prediction for Augustus_model.g2054.t1
Valid prediction for Augustus_model.g2048.t1
Valid prediction for GlimmerHMM_glimmerT_3009-T1
Valid prediction for GlimmerHMM_glimmerT_2993-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_3011-T1
Valid prediction for GlimmerHMM_glimmerT_3004-T1
Valid prediction for snap_scaffold_2-snap.26-T1
Couldn't classify 1624, 1696
Couldn't classify 4261, 4439
Sorry, prediction pasa_asmbl_24059.p2 fails validation.
(TCC)	 GG	1624-1696	GT	AGG
(ATA)	 AG	2891-3145	GC	AGG
(ATG)	 AG	4261-4439	CA	TCC
-recovered pasa_asmbl_24059.p2, internal, 2891, 3145
Couldn't classify 1623, 1696
Sorry, prediction snap_scaffold_2-snap.3-T1 fails validation.
(GTC)	 AG	1623-1696	GT	AGG
(ATA)	 AG	2891-3243	CA	GAC
-recovered snap_scaffold_2-snap.3-T1, terminal, 2891, 3243
-recovered snap_scaffold_2-snap.3-T1, internal, 1623, 1696
Valid prediction for GlimmerHMM_glimmerT_2996-T1
Valid prediction for GlimmerHMM_glimmerT_3008-T1
Valid prediction for Augustus_model.g2047.t1
Valid prediction for snap_scaffold_2-snap.22-T1
Valid prediction for GlimmerHMM_glimmerT_3002-T1
Valid prediction for CodingQuarry_transcript_28407-T1
Valid prediction for CodingQuarry_transcript_28409-T1
Valid prediction for GlimmerHMM_glimmerT_2992-T1
Valid prediction for snap_scaffold_2-snap.6-T1
Valid prediction for Augustus_model.g2058.t1
Couldn't classify 33463, 33552
Sorry, prediction pasa_asmbl_24063.p1 fails validation.
(ATG)	 CG	29794-29877	GT	AAG
(AAT)	 AG	30004-30116	GT	AGG
(GTG)	 AG	30653-30794	GT	AGG
(GGT)	 AG	30939-31080	GT	GGG
(ATC)	 AG	31533-31692	GT	AGG
(GAA)	 AG	32150-32349	GT	AGG
(AGT)	 AG	32936-33064	GT	AGG
(AGG)	 AG	33154-33281	GT	AGG
(GCA)	 AG	33463-33552	GG	CAG
-recovered pasa_asmbl_24063.p1, initial, 29794, 29877
add_exon() Sorry, pasa_asmbl_24063.p1 32150-32349-terminal-2 is invalid.
-recovered pasa_asmbl_24063.p1, terminal, 32150, 32349
-recovered pasa_asmbl_24063.p1, internal, 30004, 30116
-recovered pasa_asmbl_24063.p1, internal, 30653, 30794
-recovered pasa_asmbl_24063.p1, internal, 30939, 31080
-recovered pasa_asmbl_24063.p1, internal, 31533, 31692
-recovered pasa_asmbl_24063.p1, internal, 32150, 32349
-recovered pasa_asmbl_24063.p1, internal, 32936, 33064
-recovered pasa_asmbl_24063.p1, internal, 33154, 33281
Valid prediction for GlimmerHMM_glimmerT_3010-T1
Valid prediction for snap_scaffold_2-snap.19-T1
Couldn't classify 115633, 115672
Couldn't classify 117427, 117616
Sorry, prediction pasa_asmbl_24076.p1 fails validation.
(GAA)	 AG	115633-115672	GT	AGG
(GAA)	 AG	116268-116475	GT	CGG
(CTT)	 AG	117427-117616	TC	GAT
-recovered pasa_asmbl_24076.p1, internal, 115633, 115672
-recovered pasa_asmbl_24076.p1, internal, 116268, 116475
Valid prediction for GlimmerHMM_glimmerT_3012-T1
Valid prediction for GlimmerHMM_glimmerT_3006-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 Augustus_model.g2052.t1
Valid prediction for snap_scaffold_2-snap.2-T1
Valid prediction for snap_scaffold_2-snap.33-T1
Valid prediction for CodingQuarry_transcript_28405-T1
Valid prediction for snap_scaffold_2-snap.21-T1
Valid prediction for GlimmerHMM_glimmerT_3005-T1
Valid prediction for snap_scaffold_2-snap.25-T1
Valid prediction for GlimmerHMM_glimmerT_3007-T1
Valid prediction for GlimmerHMM_glimmerT_3003-T1
Valid prediction for pasa_asmbl_22783.p1
Valid prediction for CodingQuarry_transcript_28404-T1
Valid prediction for snap_scaffold_2-snap.1-T1
Valid prediction for snap_scaffold_2-snap.27-T1
Valid prediction for CodingQuarry_transcript_28403-T1
Valid prediction for snap_scaffold_2-snap.35-T1
Valid prediction for snap_scaffold_2-snap.23-T1
Valid prediction for HiQ_model.g2051.t1
Valid prediction for snap_scaffold_2-snap.9-T1
Valid prediction for snap_scaffold_2-snap.30-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_2998-T1
Valid prediction for snap_scaffold_2-snap.14-T1
Valid prediction for snap_scaffold_2-snap.16-T1
Valid prediction for GlimmerHMM_glimmerT_2995-T1
Valid prediction for GlimmerHMM_glimmerT_2994-T1
Valid prediction for snap_scaffold_2-snap.7-T1
Couldn't classify 147997, 148295
Couldn't classify 149620, 149707
Sorry, prediction pasa_asmbl_24058.p2 fails validation.
(CCA)	 CT	147997-148295	GT	AGG
(GTC)	 AG	149620-149707	AC	ACA
Valid prediction for GlimmerHMM_glimmerT_2991-T1
Valid prediction for snap_scaffold_2-snap.11-T1
Valid prediction for snap_scaffold_2-snap.18-T1
Valid prediction for snap_scaffold_2-snap.29-T1
Valid prediction for snap_scaffold_2-snap.4-T1
Valid prediction for HiQ_model.g2049.t1
Valid prediction for snap_scaffold_2-snap.12-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.15-T1
Valid prediction for GlimmerHMM_glimmerT_3014-T1
Valid prediction for snap_scaffold_2-snap.24-T1
Valid prediction for pasa_asmbl_22781.p1
Valid prediction for CodingQuarry_transcript_28406-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 3318, rend_intergenic: 1623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11775, rend_intergenic: 4184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20287, rend_intergenic: 18834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23724, rend_intergenic: 20332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39466, rend_intergenic: 32237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59464, rend_intergenic: 44971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92968, rend_intergenic: 79200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96610, rend_intergenic: 95609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104511, rend_intergenic: 100966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119577, rend_intergenic: 118234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124686, rend_intergenic: 119723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138375, rend_intergenic: 128444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144066, rend_intergenic: 138460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149362, rend_intergenic: 145786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154196, rend_intergenic: 150120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 156370
-exon list size: 298


building trellis

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40.7    
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42.3    
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45.0    
45.3    
45.7    
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97.0    
97.3    
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98.0    
98.3    
98.7    
99.0    
99.3    
99.7    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 3318, rend_intergenic: 1623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11775, rend_intergenic: 4184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20287, rend_intergenic: 18834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23724, rend_intergenic: 20332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39466, rend_intergenic: 32237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59464, rend_intergenic: 44971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92968, rend_intergenic: 79200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96610, rend_intergenic: 95609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104511, rend_intergenic: 100966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119577, rend_intergenic: 118234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124686, rend_intergenic: 119723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138375, rend_intergenic: 128444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144066, rend_intergenic: 138460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149362, rend_intergenic: 145786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154196, rend_intergenic: 150120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support