-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_876539-1025577

-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_1-snap.171-T1
Valid prediction for CodingQuarry_transcript_2509-T1
Valid prediction for snap_scaffold_1-snap.176-T1
Valid prediction for Augustus_model.g97.t1
Valid prediction for GlimmerHMM_glimmerT_128-T1
Valid prediction for GeneMark_model.153_t
Valid prediction for GlimmerHMM_glimmerT_118-T1
Valid prediction for GeneMark_model.134_t
Valid prediction for GeneMark_model.160_t
Valid prediction for GeneMark_model.141_t
Valid prediction for pasa_asmbl_1442.p1
Valid prediction for snap_scaffold_1-snap.161-T1
Valid prediction for Augustus_model.g108.t1
Valid prediction for snap_scaffold_1-snap.184-T1
Valid prediction for snap_scaffold_1-snap.169-T1
Valid prediction for snap_scaffold_1-snap.178-T1
Valid prediction for GlimmerHMM_glimmerT_121-T1
Couldn't classify 43704, 43796
Sorry, prediction pasa_asmbl_1436.p1 fails validation.
(GGG)	 AA	43704-43796	GT	AGG
(TGG)	 AG	44040-44111	GT	TGG
(GAA)	 AG	44277-44394	GT	AGG
(GCG)	 AG	44507-44576	GT	AGG
(CGA)	 AG	44740-44987	GT	CGG
(AGG)	 AG	45227-45433	GT	TGG
(GGA)	 AG	46439-46491	TG	GAT
-recovered pasa_asmbl_1436.p1, terminal, 46439, 46491
-recovered pasa_asmbl_1436.p1, internal, 44040, 44111
-recovered pasa_asmbl_1436.p1, internal, 44277, 44394
-recovered pasa_asmbl_1436.p1, internal, 44507, 44576
-recovered pasa_asmbl_1436.p1, internal, 44740, 44987
-recovered pasa_asmbl_1436.p1, internal, 45227, 45433
Valid prediction for snap_scaffold_1-snap.160-T1
Valid prediction for CodingQuarry_transcript_2508-T1
Couldn't classify 40601, 40754
Sorry, prediction pasa_asmbl_1434.p1 fails validation.
(ATG)	 AT	37717-37735	GT	CGG
(AGT)	 AG	38176-38201	GT	AGG
(GAA)	 AG	38348-38520	GT	TGG
(TTG)	 AG	38834-38974	GT	CTG
(AGA)	 AG	39312-39474	GT	AGG
(ATC)	 AG	40103-40212	GT	AGG
(CTG)	 AG	40378-40497	GT	AGG
(AAC)	 AG	40601-40754	GT	CGG
-recovered pasa_asmbl_1434.p1, initial, 37717, 37735
-recovered pasa_asmbl_1434.p1, internal, 38176, 38201
-recovered pasa_asmbl_1434.p1, internal, 38348, 38520
-recovered pasa_asmbl_1434.p1, internal, 38834, 38974
-recovered pasa_asmbl_1434.p1, internal, 39312, 39474
-recovered pasa_asmbl_1434.p1, internal, 40103, 40212
-recovered pasa_asmbl_1434.p1, internal, 40378, 40497
-recovered pasa_asmbl_1434.p1, internal, 40601, 40754
Valid prediction for GlimmerHMM_glimmerT_120-T1
Valid prediction for CodingQuarry_transcript_2506-T1
Valid prediction for GeneMark_model.127_t
Valid prediction for HiQ_model.g102.t1
Valid prediction for snap_scaffold_1-snap.167-T1
Valid prediction for GeneMark_model.149_t
Valid prediction for GeneMark_model.158_t
Valid prediction for GeneMark_model.132_t
Valid prediction for pasa_asmbl_1433.p2
Valid prediction for snap_scaffold_1-snap.163-T1
Valid prediction for Augustus_model.g94.t1
Valid prediction for snap_scaffold_1-snap.181-T1
Valid prediction for GlimmerHMM_glimmerT_126-T1
Valid prediction for GeneMark_model.138_t
Valid prediction for GeneMark_model.156_t
Valid prediction for GlimmerHMM_glimmerT_123-T1
Valid prediction for snap_scaffold_1-snap.182-T1
Couldn't classify 12205, 12275
Couldn't classify 14730, 14756
Sorry, prediction pasa_asmbl_1431.p3 fails validation.
(TTC)	 AG	12205-12275	GT	CAG
(GAG)	 AG	13649-13793	GT	AGG
(GGA)	 AG	14418-14558	GT	AGG
(TCC)	 AG	14730-14756	TC	GCT
-recovered pasa_asmbl_1431.p3, internal, 12205, 12275
-recovered pasa_asmbl_1431.p3, internal, 13649, 13793
-recovered pasa_asmbl_1431.p3, internal, 14418, 14558
Couldn't classify 111804, 111920
Sorry, prediction pasa_asmbl_1444.p1 fails validation.
(CTC)	 CT	111804-111920	GT	AGG
(CTG)	 AG	112290-112363	GT	GTG
(CTA)	 AG	112508-112601	GT	CTG
(GTG)	 AG	114106-114173	GT	ATG
(GAA)	 AG	114486-114556	GT	TGG
(ACA)	 AG	114708-114757	TT	GAT
-recovered pasa_asmbl_1444.p1, terminal, 114708, 114757
-recovered pasa_asmbl_1444.p1, internal, 112290, 112363
-recovered pasa_asmbl_1444.p1, internal, 112508, 112601
-recovered pasa_asmbl_1444.p1, internal, 114106, 114173
-recovered pasa_asmbl_1444.p1, internal, 114486, 114556
Valid prediction for GeneMark_model.136_t
Valid prediction for GeneMark_model.144_t
Valid prediction for snap_scaffold_1-snap.168-T1
Valid prediction for GeneMark_model.128_t
Valid prediction for snap_scaffold_1-snap.172-T1
Valid prediction for GeneMark_model.146_t
Valid prediction for GlimmerHMM_glimmerT_117-T1
Valid prediction for snap_scaffold_1-snap.188-T1
Valid prediction for HiQ_model.g95.t1
Valid prediction for GeneMark_model.142_t
Valid prediction for GlimmerHMM_glimmerT_132-T1
Valid prediction for CodingQuarry_transcript_2514-T1
Valid prediction for snap_scaffold_1-snap.165-T1
Couldn't classify 15039, 15179
Sorry, prediction pasa_asmbl_1432.p1 fails validation.
(GGC)	 AG	15039-15179	GT	AGG
(GTG)	 AG	15358-15509	GT	AGG
(GAA)	 AG	15632-15729	GT	AGG
(GTA)	 AG	16030-16140	GT	AGG
(ACG)	 AG	16798-16958	TC	GAT
add_exon() Sorry, pasa_asmbl_1432.p1 15632-15729-terminal-2 is invalid.
-recovered pasa_asmbl_1432.p1, terminal, 15632, 15729
-recovered pasa_asmbl_1432.p1, terminal, 16798, 16958
-recovered pasa_asmbl_1432.p1, internal, 15039, 15179
-recovered pasa_asmbl_1432.p1, internal, 15358, 15509
-recovered pasa_asmbl_1432.p1, internal, 15632, 15729
-recovered pasa_asmbl_1432.p1, internal, 16030, 16140
Valid prediction for snap_scaffold_1-snap.175-T1
Valid prediction for Augustus_model.g99.t1
Valid prediction for snap_scaffold_1-snap.162-T1
Valid prediction for snap_scaffold_1-snap.173-T1
Valid prediction for Augustus_model.g98.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_1-snap.166-T1
Valid prediction for Augustus_model.g101.t1
Valid prediction for GeneMark_model.155_t
Valid prediction for GlimmerHMM_glimmerT_127-T1
Valid prediction for CodingQuarry_transcript_2510-T1
Valid prediction for GlimmerHMM_glimmerT_133-T1
Valid prediction for snap_scaffold_1-snap.186-T1
Valid prediction for snap_scaffold_1-snap.183-T1
Valid prediction for snap_scaffold_1-snap.170-T1
Valid prediction for GlimmerHMM_glimmerT_129-T1
Valid prediction for GeneMark_model.150_t
Valid prediction for CodingQuarry_transcript_2512-T1
Valid prediction for snap_scaffold_1-snap.187-T1
Valid prediction for Augustus_model.g106.t1
Valid prediction for GlimmerHMM_glimmerT_125-T1
Valid prediction for GlimmerHMM_glimmerT_134-T1
Valid prediction for HiQ_model.g105.t1
Valid prediction for GeneMark_model.147_t
Valid prediction for snap_scaffold_1-snap.179-T1
Valid prediction for Augustus_model.g100.t1
Valid prediction for GeneMark_model.148_t
Valid prediction for GeneMark_model.129_t
Valid prediction for GeneMark_model.143_t
Valid prediction for pasa_asmbl_44.p1
Valid prediction for Augustus_model.g104.t1
Valid prediction for GlimmerHMM_glimmerT_131-T1
Valid prediction for GeneMark_model.152_t
Valid prediction for GlimmerHMM_glimmerT_135-T1
Valid prediction for GeneMark_model.137_t
Valid prediction for GeneMark_model.157_t
Valid prediction for GeneMark_model.154_t
Couldn't classify 117880, 117990
Sorry, prediction pasa_asmbl_33.p1 fails validation.
(AGG)	 CC	117880-117990	GT	AGG
(GAG)	 AG	118310-118452	GT	AAG
(GGT)	 AG	118771-118955	GT	AGG
(GGT)	 AG	119277-119374	GT	CTG
(GCT)	 AG	119525-119665	GT	AGG
(GTA)	 AG	119844-120125	GT	AGG
(GTG)	 AG	120255-120406	GT	AGG
(ACG)	 AG	120731-120933	GT	CAG
(GCC)	 AG	121058-121171	GT	CGG
(CTC)	 AG	121429-121500	GT	GGG
(GCT)	 AG	121717-121806	GT	TGG
(GAC)	 AG	122081-122196	GT	AGG
(AAA)	 AG	122359-122403	GT	AAG
add_exon() Sorry, pasa_asmbl_33.p1 118771-118955-terminal-2 is invalid.
-recovered pasa_asmbl_33.p1, terminal, 118771, 118955
-recovered pasa_asmbl_33.p1, terminal, 122359, 122403
-recovered pasa_asmbl_33.p1, internal, 118310, 118452
-recovered pasa_asmbl_33.p1, internal, 118771, 118955
-recovered pasa_asmbl_33.p1, internal, 119277, 119374
-recovered pasa_asmbl_33.p1, internal, 119525, 119665
-recovered pasa_asmbl_33.p1, internal, 119844, 120125
-recovered pasa_asmbl_33.p1, internal, 120255, 120406
-recovered pasa_asmbl_33.p1, internal, 120731, 120933
-recovered pasa_asmbl_33.p1, internal, 121058, 121171
-recovered pasa_asmbl_33.p1, internal, 121429, 121500
-recovered pasa_asmbl_33.p1, internal, 121717, 121806
-recovered pasa_asmbl_33.p1, internal, 122081, 122196
-recovered pasa_asmbl_33.p1, internal, 122359, 122403
Valid prediction for Augustus_model.g103.t1
Valid prediction for GlimmerHMM_glimmerT_130-T1
Couldn't classify 46020, 46138
Sorry, prediction pasa_asmbl_42.p1 fails validation.
(CAG)	 AG	46020-46138	GT	TGG
(GAG)	 AG	46519-46654	GT	GGG
(GGA)	 AG	46995-47118	GT	GGG
(TGT)	 AG	47605-47687	GG	GAG
-recovered pasa_asmbl_42.p1, terminal, 47605, 47687
-recovered pasa_asmbl_42.p1, internal, 46020, 46138
-recovered pasa_asmbl_42.p1, internal, 46519, 46654
-recovered pasa_asmbl_42.p1, internal, 46995, 47118
Valid prediction for CodingQuarry_transcript_2511-T1
Valid prediction for GeneMark_model.140_t
Valid prediction for snap_scaffold_1-snap.174-T1
Valid prediction for HiQ_model.g107.t1
Valid prediction for HiQ_model.g96.t1
Valid prediction for GlimmerHMM_glimmerT_119-T1
Valid prediction for GlimmerHMM_glimmerT_122-T1
Valid prediction for GeneMark_model.133_t
Valid prediction for snap_scaffold_1-snap.180-T1
Valid prediction for GeneMark_model.159_t
Valid prediction for Augustus_model.g109.t1
Valid prediction for GeneMark_model.139_t
Valid prediction for GeneMark_model.151_t
Valid prediction for GlimmerHMM_glimmerT_124-T1
Valid prediction for CodingQuarry_transcript_2513-T1
Valid prediction for pasa_asmbl_37.p1
Valid prediction for GeneMark_model.145_t
Valid prediction for GeneMark_model.131_t
Valid prediction for snap_scaffold_1-snap.177-T1
Valid prediction for snap_scaffold_1-snap.164-T1
Valid prediction for snap_scaffold_1-snap.185-T1
Valid prediction for CodingQuarry_transcript_2507-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 32906, rend_intergenic: 26878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60060, rend_intergenic: 53834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68341, rend_intergenic: 60395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85866, rend_intergenic: 79816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89884, rend_intergenic: 86552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97348, rend_intergenic: 92391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105805, rend_intergenic: 101353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 149039
-exon list size: 434


building trellis

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30.7    
31.0    
31.2    
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31.9    
32.1    
32.3    
32.6    
32.8    
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34.9    
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40.6    
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92.4    
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98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 32906, rend_intergenic: 26878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60060, rend_intergenic: 53834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68341, rend_intergenic: 60395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85866, rend_intergenic: 79816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89884, rend_intergenic: 86552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97348, rend_intergenic: 92391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105805, rend_intergenic: 101353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11111
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 1 - 10514