-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_8/scaffold_8_15655576-15840849

-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 38044, 38374
Sorry, prediction pasa_asmbl_53414.p1 fails validation.
(GAG)	 CA	38044-38374	GT	GGG
(GGA)	 AG	38948-39129	AC	GAA
-recovered pasa_asmbl_53414.p1, terminal, 38948, 39129
Valid prediction for snap_scaffold_8-snap.2861-T1
Valid prediction for snap_scaffold_8-snap.2865-T1
Valid prediction for snap_scaffold_8-snap.2854-T1
Valid prediction for snap_scaffold_8-snap.2880-T1
Valid prediction for pasa_asmbl_53415.p1
Valid prediction for GlimmerHMM_glimmerT_21001-T1
Valid prediction for GlimmerHMM_glimmerT_21019-T1
Valid prediction for HiQ_model.g13972.t1
Valid prediction for Augustus_model.g13970.t1
Valid prediction for CodingQuarry_transcript_59911-T1
Valid prediction for snap_scaffold_8-snap.2857-T1
Valid prediction for Augustus_model.g13966.t1
Valid prediction for CodingQuarry_transcript_59910-T1
Valid prediction for snap_scaffold_8-snap.2851-T1
Valid prediction for GlimmerHMM_glimmerT_21010-T1
Valid prediction for GlimmerHMM_glimmerT_21012-T1
Valid prediction for Augustus_model.g13973.t1
Valid prediction for Augustus_model.g13964.t1
Valid prediction for HiQ_model.g13971.t1
Valid prediction for Augustus_model.g13976.t1
Valid prediction for pasa_asmbl_53419.p1
Valid prediction for GlimmerHMM_glimmerT_21000-T1
Valid prediction for snap_scaffold_8-snap.2866-T1
Couldn't classify 107300, 107390
Sorry, prediction pasa_asmbl_53421.p1 fails validation.
(CAG)	 TG	107300-107390	GT	CAG
(TTC)	 AG	107824-107926	GT	AGG
(CTT)	 AG	109511-109619	GT	AGG
(GTG)	 AG	110689-110807	GT	AGG
(GAA)	 AG	111034-111121	GT	GAG
-recovered pasa_asmbl_53421.p1, terminal, 111034, 111121
-recovered pasa_asmbl_53421.p1, internal, 107824, 107926
-recovered pasa_asmbl_53421.p1, internal, 109511, 109619
-recovered pasa_asmbl_53421.p1, internal, 110689, 110807
-recovered pasa_asmbl_53421.p1, internal, 111034, 111121
Valid prediction for GlimmerHMM_glimmerT_20996-T1
Valid prediction for snap_scaffold_8-snap.2871-T1
Valid prediction for GlimmerHMM_glimmerT_21003-T1
Valid prediction for GlimmerHMM_glimmerT_20994-T1
Valid prediction for snap_scaffold_8-snap.2868-T1
Valid prediction for GlimmerHMM_glimmerT_20989-T1
Valid prediction for snap_scaffold_8-snap.2853-T1
Valid prediction for snap_scaffold_8-snap.2869-T1
Valid prediction for snap_scaffold_8-snap.2856-T1
Valid prediction for snap_scaffold_8-snap.2860-T1
Valid prediction for GlimmerHMM_glimmerT_20990-T1
Couldn't classify 83835, 83885
Sorry, prediction pasa_asmbl_53418.p1 fails validation.
(ATG)	 CA	80131-80221	GT	AGG
(AAA)	 AG	80460-80689	GT	AGG
(GAC)	 AG	81067-81236	GT	AGG
(GAA)	 AG	81565-81679	GT	AGG
(GAC)	 AG	81790-81882	GT	AGG
(GTG)	 AG	82081-82218	GT	AGG
(GCT)	 AG	82611-82730	GT	AGG
(GAC)	 AG	82830-82937	GT	AGG
(CTG)	 AG	83124-83270	GT	TGG
(CTG)	 AG	83367-83512	GT	AAG
(GAT)	 AG	83632-83728	GT	AGG
(ATC)	 AG	83835-83885	AG	GGA
-recovered pasa_asmbl_53418.p1, initial, 80131, 80221
-recovered pasa_asmbl_53418.p1, internal, 80460, 80689
-recovered pasa_asmbl_53418.p1, internal, 81067, 81236
-recovered pasa_asmbl_53418.p1, internal, 81565, 81679
-recovered pasa_asmbl_53418.p1, internal, 81790, 81882
-recovered pasa_asmbl_53418.p1, internal, 82081, 82218
-recovered pasa_asmbl_53418.p1, internal, 82611, 82730
-recovered pasa_asmbl_53418.p1, internal, 82830, 82937
-recovered pasa_asmbl_53418.p1, internal, 83124, 83270
-recovered pasa_asmbl_53418.p1, internal, 83367, 83512
-recovered pasa_asmbl_53418.p1, internal, 83632, 83728
Valid prediction for GlimmerHMM_glimmerT_21016-T1
Valid prediction for GlimmerHMM_glimmerT_20986-T1
Valid prediction for Augustus_model.g13975.t1
Valid prediction for GlimmerHMM_glimmerT_21004-T1
Valid prediction for snap_scaffold_8-snap.2858-T1
Valid prediction for GlimmerHMM_glimmerT_21014-T1
Valid prediction for Augustus_model.g13978.t1
Valid prediction for snap_scaffold_8-snap.2872-T1
Valid prediction for GlimmerHMM_glimmerT_20987-T1
Valid prediction for snap_scaffold_8-snap.2875-T1
Couldn't classify 37105, 37634
Sorry, prediction pasa_asmbl_53412.p1 fails validation.
(ATG)	 CC	36047-36283	GT	CGG
(ATC)	 AG	36810-36951	GT	CGG
(GCC)	 AG	37105-37634	CT	ACC
-recovered pasa_asmbl_53412.p1, initial, 36047, 36283
-recovered pasa_asmbl_53412.p1, internal, 36810, 36951
Valid prediction for GlimmerHMM_glimmerT_21005-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 GlimmerHMM_glimmerT_21007-T1
Valid prediction for GlimmerHMM_glimmerT_21015-T1
Valid prediction for GlimmerHMM_glimmerT_21008-T1
Valid prediction for GlimmerHMM_glimmerT_20995-T1
Couldn't classify 133040, 133093
Couldn't classify 135362, 135401
Sorry, prediction pasa_asmbl_52343.p1 fails validation.
(CAG)	 TT	133040-133093	GT	AGG
(GGT)	 AG	134132-134380	GT	AGG
(GGG)	 AG	134638-134780	GT	AGG
(TCC)	 AG	135362-135401	AC	TGA
add_exon() Sorry, pasa_asmbl_52343.p1 134638-134780-terminal-2 is invalid.
-recovered pasa_asmbl_52343.p1, terminal, 134638, 134780
-recovered pasa_asmbl_52343.p1, internal, 134132, 134380
-recovered pasa_asmbl_52343.p1, internal, 134638, 134780
Valid prediction for snap_scaffold_8-snap.2870-T1
Valid prediction for Augustus_model.g13974.t1
Valid prediction for GlimmerHMM_glimmerT_20999-T1
Valid prediction for GlimmerHMM_glimmerT_20998-T1
Valid prediction for snap_scaffold_8-snap.2863-T1
Valid prediction for snap_scaffold_8-snap.2849-T1
Valid prediction for snap_scaffold_8-snap.2864-T1
Valid prediction for Augustus_model.g13969.t1
Valid prediction for GlimmerHMM_glimmerT_21018-T1
Valid prediction for CodingQuarry_transcript_59908-T1
Valid prediction for snap_scaffold_8-snap.2879-T1
Couldn't classify 135605, 135834
Sorry, prediction pasa_asmbl_52341.p1 fails validation.
(GGC)	 TA	135605-135834	GT	AGG
(CTG)	 AG	135989-136080	GT	AGG
(GTG)	 AG	136327-136487	GT	AGG
(GGT)	 AG	136832-136966	GT	ATG
(GTG)	 AG	137871-137982	GT	CTG
(ACC)	 AG	138206-138319	GT	AGG
(ATT)	 AG	139071-139270	GT	AGG
(GCG)	 AG	139915-140118	GT	AGG
(GTG)	 AG	140278-140439	GT	AGG
(GGA)	 AG	140542-140791	GT	AAG
(AAA)	 AG	140989-141200	CA	AGC
-recovered pasa_asmbl_52341.p1, terminal, 140989, 141200
-recovered pasa_asmbl_52341.p1, internal, 135989, 136080
-recovered pasa_asmbl_52341.p1, internal, 136327, 136487
-recovered pasa_asmbl_52341.p1, internal, 136832, 136966
-recovered pasa_asmbl_52341.p1, internal, 137871, 137982
-recovered pasa_asmbl_52341.p1, internal, 138206, 138319
-recovered pasa_asmbl_52341.p1, internal, 139071, 139270
-recovered pasa_asmbl_52341.p1, internal, 139915, 140118
-recovered pasa_asmbl_52341.p1, internal, 140278, 140439
-recovered pasa_asmbl_52341.p1, internal, 140542, 140791
Valid prediction for snap_scaffold_8-snap.2877-T1
Valid prediction for GlimmerHMM_glimmerT_21002-T1
Valid prediction for GlimmerHMM_glimmerT_21017-T1
Valid prediction for GlimmerHMM_glimmerT_20991-T1
Valid prediction for Augustus_model.g13977.t1
Valid prediction for Augustus_model.g13968.t1
Valid prediction for snap_scaffold_8-snap.2852-T1
Valid prediction for snap_scaffold_8-snap.2876-T1
Valid prediction for GlimmerHMM_glimmerT_21011-T1
Valid prediction for Augustus_model.g13965.t1
Valid prediction for GlimmerHMM_glimmerT_21006-T1
Valid prediction for GlimmerHMM_glimmerT_20993-T1
Valid prediction for snap_scaffold_8-snap.2850-T1
Valid prediction for Augustus_model.g13967.t1
Valid prediction for snap_scaffold_8-snap.2878-T1
Valid prediction for snap_scaffold_8-snap.2874-T1
Valid prediction for Augustus_model.g13979.t1
Valid prediction for GlimmerHMM_glimmerT_21009-T1
Valid prediction for GlimmerHMM_glimmerT_20988-T1
Valid prediction for GlimmerHMM_glimmerT_21013-T1
Valid prediction for snap_scaffold_8-snap.2867-T1
Couldn't classify 152898, 152963
Sorry, prediction pasa_asmbl_52339.p1 fails validation.
(CAA)	 CA	152898-152963	GT	TGG
(GGC)	 AG	153695-153786	GT	AGG
(AAC)	 AG	154599-154764	CT	AAC
-recovered pasa_asmbl_52339.p1, terminal, 154599, 154764
-recovered pasa_asmbl_52339.p1, internal, 153695, 153786
Valid prediction for GlimmerHMM_glimmerT_20992-T1
Couldn't classify 110529, 111413
Sorry, prediction pasa_asmbl_52344.p1 fails validation.
(ATG)	 AC	110529-111413	GA	GGG
Valid prediction for snap_scaffold_8-snap.2855-T1
Valid prediction for snap_scaffold_8-snap.2862-T1
Valid prediction for snap_scaffold_8-snap.2859-T1
Valid prediction for GlimmerHMM_glimmerT_20997-T1
Valid prediction for snap_scaffold_8-snap.2873-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 45468, rend_intergenic: 44075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57313, rend_intergenic: 46320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87048, rend_intergenic: 81009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102246, rend_intergenic: 100165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111121, rend_intergenic: 103608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134581, rend_intergenic: 128650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141594, rend_intergenic: 134797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156684, rend_intergenic: 147794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 185274
-exon list size: 334


building trellis

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-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 45468, rend_intergenic: 44075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57313, rend_intergenic: 46320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87048, rend_intergenic: 81009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102246, rend_intergenic: 100165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111121, rend_intergenic: 103608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134581, rend_intergenic: 128650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141594, rend_intergenic: 134797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156684, rend_intergenic: 147794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 168176 - 185274
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
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-found 1 predictions from path traversal
GOT 5prime partial gene.

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