-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_1221172-1459682

-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 GeneMark_model.194_t
Valid prediction for CodingQuarry_transcript_2520-T1
Valid prediction for GlimmerHMM_glimmerT_173-T1
Valid prediction for CodingQuarry_transcript_2526-T1
Valid prediction for GeneMark_model.202_t
Valid prediction for GlimmerHMM_glimmerT_184-T1
Valid prediction for GlimmerHMM_glimmerT_176-T1
Valid prediction for snap_scaffold_1-snap.254-T1
Couldn't classify 124544, 124818
Couldn't classify 126373, 126553
Sorry, prediction pasa_asmbl_1472.p1 fails validation.
(CAA)	 AA	124544-124818	GT	GTG
(CCG)	 AG	124904-124986	GT	TGG
(AAT)	 AG	125191-125334	GT	AGG
(GTA)	 AG	125448-125609	GT	TGG
(GTC)	 AG	125842-125986	GT	AGG
(TTC)	 AG	126144-126260	GT	ATG
(CTA)	 AG	126373-126553	CC	AGC
-recovered pasa_asmbl_1472.p1, internal, 124904, 124986
-recovered pasa_asmbl_1472.p1, internal, 125191, 125334
-recovered pasa_asmbl_1472.p1, internal, 125448, 125609
-recovered pasa_asmbl_1472.p1, internal, 125842, 125986
-recovered pasa_asmbl_1472.p1, internal, 126144, 126260
Valid prediction for snap_scaffold_1-snap.253-T1
Valid prediction for GeneMark_model.216_t
Valid prediction for GlimmerHMM_glimmerT_188-T1
Valid prediction for snap_scaffold_1-snap.235-T1
Valid prediction for Augustus_model.g142.t1
Valid prediction for snap_scaffold_1-snap.245-T1
Valid prediction for Augustus_model.g148.t1
Valid prediction for snap_scaffold_1-snap.259-T1
Valid prediction for GlimmerHMM_glimmerT_180-T1
Valid prediction for GeneMark_model.206_t
Valid prediction for GeneMark_model.200_t
Valid prediction for snap_scaffold_1-snap.228-T1
Valid prediction for Augustus_model.g156.t1
Valid prediction for snap_scaffold_1-snap.238-T1
Valid prediction for Augustus_model.g139.t1
Valid prediction for snap_scaffold_1-snap.229-T1
Valid prediction for snap_scaffold_1-snap.231-T1
Valid prediction for pasa_asmbl_1477.p1
Couldn't classify 14711, 14725
Sorry, prediction pasa_asmbl_1461.p1 fails validation.
(CCC)	 AC	14711-14725	GT	CGG
(CGT)	 AG	15036-15157	GT	AAG
(GAA)	 AG	15299-16211	GT	AGG
(CCA)	 AG	16575-16592	GT	AAG
-recovered pasa_asmbl_1461.p1, terminal, 16575, 16592
-recovered pasa_asmbl_1461.p1, internal, 15036, 15157
-recovered pasa_asmbl_1461.p1, internal, 15299, 16211
-recovered pasa_asmbl_1461.p1, internal, 16575, 16592
Valid prediction for CodingQuarry_transcript_2524-T1
Valid prediction for GlimmerHMM_glimmerT_193-T1
Valid prediction for snap_scaffold_1-snap.263-T1
Valid prediction for Augustus_model.g138.t1
Valid prediction for Augustus_model.g144.t1
Valid prediction for GlimmerHMM_glimmerT_183-T1
Valid prediction for snap_scaffold_1-snap.257-T1
Valid prediction for HiQ_model.g134.t1
Valid prediction for GeneMark_model.198_t
Valid prediction for CodingQuarry_transcript_2523-T1
Valid prediction for snap_scaffold_1-snap.244-T1
Valid prediction for snap_scaffold_1-snap.248-T1
Valid prediction for GeneMark_model.195_t
Valid prediction for pasa_asmbl_1471.p1
Valid prediction for GlimmerHMM_glimmerT_187-T1
Valid prediction for snap_scaffold_1-snap.230-T1
Valid prediction for Augustus_model.g136.t1
Valid prediction for GlimmerHMM_glimmerT_192-T1
Valid prediction for Augustus_model.g141.t1
Valid prediction for HiQ_model.g149.t1
Valid prediction for snap_scaffold_1-snap.242-T1
Valid prediction for GlimmerHMM_glimmerT_172-T1
Valid prediction for snap_scaffold_1-snap.243-T1
Valid prediction for snap_scaffold_1-snap.239-T1
Valid prediction for GlimmerHMM_glimmerT_195-T1
Valid prediction for pasa_asmbl_1464.p1
Valid prediction for snap_scaffold_1-snap.265-T1
Valid prediction for Augustus_model.g133.t1
Valid prediction for snap_scaffold_1-snap.249-T1
Valid prediction for GlimmerHMM_glimmerT_186-T1
Valid prediction for GeneMark_model.219_t
Valid prediction for snap_scaffold_1-snap.255-T1
Valid prediction for pasa_asmbl_1478.p1
Valid prediction for GeneMark_model.212_t
Couldn't classify 5316, 5437
Sorry, prediction pasa_asmbl_1460.p1 fails validation.
(GTG)	 AG	5316-5437	GT	AGG
(ACT)	 AG	5882-6080	GT	TAG
(GAC)	 AG	6783-6956	GT	TGG
(ATT)	 AG	7309-7434	TT	AAT
-recovered pasa_asmbl_1460.p1, terminal, 7309, 7434
-recovered pasa_asmbl_1460.p1, internal, 5316, 5437
-recovered pasa_asmbl_1460.p1, internal, 5882, 6080
-recovered pasa_asmbl_1460.p1, internal, 6783, 6956
Valid prediction for GlimmerHMM_glimmerT_189-T1
Couldn't classify 235380, 235793
Sorry, prediction pasa_asmbl_1267.p1 fails validation.
(GGT)	 TG	235380-235793	TT	GTT
Valid prediction for GlimmerHMM_glimmerT_200-T1
Valid prediction for snap_scaffold_1-snap.261-T1
Valid prediction for GlimmerHMM_glimmerT_179-T1
Valid prediction for Augustus_model.g143.t1
Couldn't classify 104817, 104886
Sorry, prediction pasa_asmbl_1468.p1 fails validation.
(ATG)	 AG	103264-103267	GT	GTG
(CCT)	 AG	103709-103846	GT	AGG
(GAA)	 AG	103928-104074	GC	CGG
(AGT)	 AG	104282-104426	GT	AGG
(GAA)	 AG	104583-104714	GT	GAG
(CTA)	 AG	104817-104886	AC	GCA
-recovered pasa_asmbl_1468.p1, initial, 103264, 103267
-recovered pasa_asmbl_1468.p1, internal, 103264, 103267
-recovered pasa_asmbl_1468.p1, internal, 103709, 103846
-recovered pasa_asmbl_1468.p1, internal, 103928, 104074
-recovered pasa_asmbl_1468.p1, internal, 104282, 104426
-recovered pasa_asmbl_1468.p1, internal, 104583, 104714
Valid prediction for GlimmerHMM_glimmerT_182-T1
Valid prediction for snap_scaffold_1-snap.246-T1
Valid prediction for GlimmerHMM_glimmerT_205-T1
Valid prediction for GlimmerHMM_glimmerT_198-T1
Valid prediction for GlimmerHMM_glimmerT_203-T1
Valid prediction for snap_scaffold_1-snap.247-T1
Valid prediction for CodingQuarry_transcript_2527-T1
Valid prediction for snap_scaffold_1-snap.251-T1
Valid prediction for Augustus_model.g132.t1
Valid prediction for GlimmerHMM_glimmerT_196-T1
Valid prediction for Augustus_model.g146.t1
Valid prediction for GeneMark_model.210_t
Valid prediction for GlimmerHMM_glimmerT_174-T1
Valid prediction for GlimmerHMM_glimmerT_185-T1
Valid prediction for HiQ_model.g151.t1
Valid prediction for GeneMark_model.203_t

-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 GlimmerHMM_glimmerT_178-T1
Valid prediction for snap_scaffold_1-snap.232-T1
Valid prediction for GeneMark_model.201_t
Valid prediction for snap_scaffold_1-snap.262-T1
Valid prediction for Augustus_model.g140.t1
Valid prediction for pasa_asmbl_56.p1
Valid prediction for HiQ_model.g155.t1
Couldn't classify 34405, 34580
Sorry, prediction pasa_asmbl_65.p1 fails validation.
(CTT)	 CC	34405-34580	GT	GGG
(AAA)	 AG	34716-34827	GT	AGG
(CCC)	 AG	34980-35081	GT	TGG
(TCC)	 AG	35190-35240	GT	AGG
(CAA)	 AG	35565-35624	GT	AGG
(GCC)	 AG	36809-36892	GT	AGG
(CTG)	 AG	37130-37240	GT	AGG
(ATG)	 AG	37900-38001	GC	AGG
(TTG)	 AG	38131-38231	GT	AGG
(GCA)	 AG	38568-38716	GT	CTG
(ACC)	 AG	38896-38985	GT	AGG
(GCA)	 AG	39371-39489	TG	AAT
-recovered pasa_asmbl_65.p1, initial, 37900, 38001
-recovered pasa_asmbl_65.p1, terminal, 39371, 39489
-recovered pasa_asmbl_65.p1, internal, 34716, 34827
-recovered pasa_asmbl_65.p1, internal, 34980, 35081
-recovered pasa_asmbl_65.p1, internal, 35190, 35240
-recovered pasa_asmbl_65.p1, internal, 35565, 35624
-recovered pasa_asmbl_65.p1, internal, 36809, 36892
-recovered pasa_asmbl_65.p1, internal, 37130, 37240
-recovered pasa_asmbl_65.p1, internal, 37900, 38001
-recovered pasa_asmbl_65.p1, internal, 38131, 38231
-recovered pasa_asmbl_65.p1, internal, 38568, 38716
-recovered pasa_asmbl_65.p1, internal, 38896, 38985
Valid prediction for GlimmerHMM_glimmerT_194-T1
Valid prediction for snap_scaffold_1-snap.233-T1
Valid prediction for snap_scaffold_1-snap.252-T1
Valid prediction for GlimmerHMM_glimmerT_202-T1
Valid prediction for HiQ_model.g153.t1
Valid prediction for Augustus_model.g135.t1
Valid prediction for GeneMark_model.205_t
Valid prediction for GeneMark_model.217_t
Valid prediction for GlimmerHMM_glimmerT_199-T1
Valid prediction for CodingQuarry_transcript_2521-T1
Valid prediction for GeneMark_model.196_t
Valid prediction for pasa_asmbl_63.p1
Valid prediction for snap_scaffold_1-snap.260-T1
Valid prediction for Augustus_model.g145.t1
Valid prediction for GeneMark_model.211_t
Valid prediction for snap_scaffold_1-snap.234-T1
Valid prediction for CodingQuarry_transcript_2529-T1
Valid prediction for CodingQuarry_transcript_2525-T1
Valid prediction for snap_scaffold_1-snap.240-T1
Valid prediction for GeneMark_model.208_t
Valid prediction for GlimmerHMM_glimmerT_204-T1
Valid prediction for snap_scaffold_1-snap.258-T1
Couldn't classify 215982, 216194
Sorry, prediction pasa_asmbl_53.p2 fails validation.
(AGC)	 CC	215982-216194	GT	CGG
(ACG)	 AG	216620-216814	CC	GAC
-recovered pasa_asmbl_53.p2, terminal, 216620, 216814
Valid prediction for HiQ_model.g150.t1
Valid prediction for GeneMark_model.214_t
Valid prediction for HiQ_model.g152.t1
Valid prediction for GlimmerHMM_glimmerT_201-T1
Valid prediction for snap_scaffold_1-snap.237-T1
Couldn't classify 212017, 212235
Couldn't classify 213039, 213190
Sorry, prediction pasa_asmbl_54.p2 fails validation.
(TCA)	 AG	212017-212235	GT	AAG
(GTA)	 AG	212399-212591	GT	AGG
(GCT)	 AG	213039-213190	AG	CGA
-recovered pasa_asmbl_54.p2, internal, 212017, 212235
-recovered pasa_asmbl_54.p2, internal, 212399, 212591
Valid prediction for Augustus_model.g154.t1
Valid prediction for CodingQuarry_transcript_2528-T1
Valid prediction for snap_scaffold_1-snap.241-T1
Valid prediction for GlimmerHMM_glimmerT_190-T1
Valid prediction for GlimmerHMM_glimmerT_175-T1
Valid prediction for GlimmerHMM_glimmerT_191-T1
Valid prediction for GlimmerHMM_glimmerT_177-T1
Valid prediction for Augustus_model.g137.t1
Valid prediction for snap_scaffold_1-snap.250-T1
Valid prediction for pasa_asmbl_71.p1
Valid prediction for GeneMark_model.197_t
Valid prediction for GeneMark_model.213_t
Valid prediction for Augustus_model.g147.t1
Couldn't classify 187490, 187565
Sorry, prediction pasa_asmbl_60.p1 fails validation.
(GAC)	 GT	187490-187565	GT	AAG
(AAA)	 AG	187716-188071	AG	AAA
-recovered pasa_asmbl_60.p1, terminal, 187716, 188071
Valid prediction for snap_scaffold_1-snap.236-T1
Valid prediction for GeneMark_model.218_t
Valid prediction for GlimmerHMM_glimmerT_181-T1
Valid prediction for snap_scaffold_1-snap.264-T1
Valid prediction for GeneMark_model.215_t
Valid prediction for GlimmerHMM_glimmerT_197-T1
Valid prediction for snap_scaffold_1-snap.256-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 220151, rend_intergenic: 215995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 238511
-exon list size: 462


building trellis

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99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 220151, rend_intergenic: 215995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support