-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_926332-1033850

-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.103821_t
Couldn't classify 95038, 95206
Sorry, prediction pasa_asmbl_37994.p1 fails validation.
(CTC)	 GT	95038-95206	GT	AGG
(GAA)	 AG	95325-95508	GT	AGG
(GTA)	 AG	95774-95929	GT	AGG
(TGA)	 AG	97183-97419	GT	CAG
(TTT)	 AG	97634-97778	GG	GAG
-recovered pasa_asmbl_37994.p1, terminal, 97634, 97778
-recovered pasa_asmbl_37994.p1, internal, 95325, 95508
-recovered pasa_asmbl_37994.p1, internal, 95774, 95929
-recovered pasa_asmbl_37994.p1, internal, 97183, 97419
Valid prediction for HiQ_model.g39579.t1
Valid prediction for snap_scaffold_28-snap.226-T1
Valid prediction for GeneMark_model.103799_t
Valid prediction for snap_scaffold_28-snap.221-T1
Valid prediction for snap_scaffold_28-snap.211-T1
Valid prediction for GeneMark_model.103816_t
Valid prediction for GeneMark_model.103809_t
Valid prediction for GlimmerHMM_glimmerT_59459-T1
Couldn't classify 5174, 5477
Sorry, prediction pasa_asmbl_37989.p1 fails validation.
(ATG)	 CC	4101-4561	GT	CGG
(AGT)	 AG	5174-5477	CC	CCC
-recovered pasa_asmbl_37989.p1, initial, 4101, 4561
Valid prediction for GlimmerHMM_glimmerT_59471-T1
Valid prediction for GeneMark_model.103813_t
Valid prediction for snap_scaffold_28-snap.207-T1
Valid prediction for snap_scaffold_28-snap.214-T1
Valid prediction for GeneMark_model.103804_t
Valid prediction for GeneMark_model.103802_t
Valid prediction for GlimmerHMM_glimmerT_59456-T1
Valid prediction for GlimmerHMM_glimmerT_59470-T1
Valid prediction for GeneMark_model.103824_t
Valid prediction for pasa_asmbl_37992.p1
Valid prediction for GeneMark_model.103807_t
Valid prediction for snap_scaffold_28-snap.200-T1
Valid prediction for snap_scaffold_28-snap.205-T1
Valid prediction for Augustus_model.g39567.t1
Valid prediction for snap_scaffold_28-snap.204-T1
Valid prediction for snap_scaffold_28-snap.202-T1
Valid prediction for Augustus_model.g39569.t1
Valid prediction for GeneMark_model.103800_t
Valid prediction for GeneMark_model.103818_t
Valid prediction for snap_scaffold_28-snap.198-T1
Valid prediction for snap_scaffold_28-snap.209-T1
Valid prediction for GeneMark_model.103825_t
Valid prediction for snap_scaffold_28-snap.223-T1
Valid prediction for snap_scaffold_28-snap.220-T1
Valid prediction for GeneMark_model.103814_t
Valid prediction for CodingQuarry_transcript_43438-T1
Valid prediction for Augustus_model.g39566.t1
Valid prediction for snap_scaffold_28-snap.199-T1
Valid prediction for snap_scaffold_28-snap.225-T1
Valid prediction for snap_scaffold_28-snap.215-T1
Valid prediction for GlimmerHMM_glimmerT_59463-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 GeneMark_model.103823_t
Valid prediction for GlimmerHMM_glimmerT_59464-T1
Couldn't classify 48134, 48168
Sorry, prediction pasa_asmbl_37274.p1 fails validation.
(TGC)	 TC	48134-48168	GT	AGG
(GCG)	 AG	50225-50339	GT	AGG
(AGG)	 AG	50656-50815	GT	GGG
(AGG)	 AG	50989-51179	GA	AGG
-recovered pasa_asmbl_37274.p1, terminal, 50989, 51179
-recovered pasa_asmbl_37274.p1, internal, 50225, 50339
-recovered pasa_asmbl_37274.p1, internal, 50656, 50815
Valid prediction for Augustus_model.g39568.t1
Valid prediction for snap_scaffold_28-snap.212-T1
Valid prediction for Augustus_model.g39572.t1
Valid prediction for Augustus_model.g39573.t1
Valid prediction for Augustus_model.g39571.t1
Valid prediction for GlimmerHMM_glimmerT_59462-T1
Valid prediction for snap_scaffold_28-snap.206-T1
Valid prediction for snap_scaffold_28-snap.218-T1
Valid prediction for HiQ_model.g39576.t1
Valid prediction for Augustus_model.g39575.t1
Valid prediction for GlimmerHMM_glimmerT_59468-T1
Valid prediction for GlimmerHMM_glimmerT_59461-T1
Valid prediction for Augustus_model.g39574.t1
Valid prediction for snap_scaffold_28-snap.219-T1
Valid prediction for snap_scaffold_28-snap.222-T1
Valid prediction for GeneMark_model.103806_t
Valid prediction for GeneMark_model.103803_t
Valid prediction for snap_scaffold_28-snap.201-T1
Valid prediction for GeneMark_model.103808_t
Valid prediction for snap_scaffold_28-snap.213-T1
Couldn't classify 88787, 88876
Couldn't classify 90323, 90853
Sorry, prediction pasa_asmbl_37269.p1 fails validation.
(CTG)	 AC	88787-88876	GT	CAG
(GGT)	 AG	89040-89113	GT	AGG
(GTT)	 AG	89239-89360	GT	AGG
(CCA)	 AG	89888-90042	GT	AGG
(TGT)	 AG	90323-90853	CA	AAC
-recovered pasa_asmbl_37269.p1, internal, 89040, 89113
-recovered pasa_asmbl_37269.p1, internal, 89239, 89360
-recovered pasa_asmbl_37269.p1, internal, 89888, 90042
Valid prediction for snap_scaffold_28-snap.210-T1
Couldn't classify 84468, 84498
Couldn't classify 87861, 87919
Sorry, prediction pasa_asmbl_37270.p1 fails validation.
(AGC)	 TC	84468-84498	GT	CAG
(CGC)	 AG	86599-86801	GT	AGG
(GGA)	 AG	87188-87275	GT	ACG
(GCA)	 AG	87454-87567	GT	AGG
(TGT)	 AG	87861-87919	GT	TGG
-recovered pasa_asmbl_37270.p1, internal, 86599, 86801
-recovered pasa_asmbl_37270.p1, internal, 87188, 87275
-recovered pasa_asmbl_37270.p1, internal, 87454, 87567
-recovered pasa_asmbl_37270.p1, internal, 87861, 87919
Valid prediction for GlimmerHMM_glimmerT_59457-T1
Valid prediction for GlimmerHMM_glimmerT_59460-T1
Valid prediction for CodingQuarry_transcript_43436-T1
Valid prediction for snap_scaffold_28-snap.217-T1
Couldn't classify 24905, 25015
Sorry, prediction pasa_asmbl_37281.p1 fails validation.
(TGC)	 AC	24905-25015	GT	GAG
(AAT)	 AG	25756-25845	GT	AGG
(ATA)	 AG	26202-26438	AT	AAA
-recovered pasa_asmbl_37281.p1, terminal, 26202, 26438
-recovered pasa_asmbl_37281.p1, internal, 25756, 25845
Valid prediction for CodingQuarry_transcript_43437-T1
Valid prediction for snap_scaffold_28-snap.208-T1
Valid prediction for pasa_asmbl_37276.p1
Valid prediction for GeneMark_model.103810_t
Valid prediction for GlimmerHMM_glimmerT_59465-T1
Valid prediction for snap_scaffold_28-snap.216-T1
Valid prediction for snap_scaffold_28-snap.203-T1
Valid prediction for GlimmerHMM_glimmerT_59467-T1
Valid prediction for HiQ_model.g39578.t1
Valid prediction for GlimmerHMM_glimmerT_59469-T1
Couldn't classify 52043, 52348
Sorry, prediction pasa_asmbl_37273.p2 fails validation.
(CCG)	 GG	52043-52348	AC	AAA
Valid prediction for GeneMark_model.103817_t
Valid prediction for Augustus_model.g39570.t1
Valid prediction for GeneMark_model.103805_t
Valid prediction for Augustus_model.g39577.t1
Valid prediction for snap_scaffold_28-snap.224-T1
Valid prediction for GeneMark_model.103820_t
Valid prediction for GeneMark_model.103819_t
Valid prediction for GlimmerHMM_glimmerT_59458-T1
Valid prediction for GlimmerHMM_glimmerT_59466-T1
Valid prediction for GeneMark_model.103815_t
Valid prediction for GeneMark_model.103812_t
Valid prediction for GeneMark_model.103801_t
Valid prediction for GeneMark_model.103811_t
Valid prediction for GeneMark_model.103822_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15487, rend_intergenic: 12989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17669, rend_intergenic: 16227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23272, rend_intergenic: 18168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35541, rend_intergenic: 28297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44607, rend_intergenic: 43027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54330, rend_intergenic: 49196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59176, rend_intergenic: 56341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77139, rend_intergenic: 69740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94715, rend_intergenic: 88041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 107519
-exon list size: 402


building trellis

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98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 15487, rend_intergenic: 12989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17669, rend_intergenic: 16227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23272, rend_intergenic: 18168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35541, rend_intergenic: 28297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44607, rend_intergenic: 43027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54330, rend_intergenic: 49196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59176, rend_intergenic: 56341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77139, rend_intergenic: 69740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94715, rend_intergenic: 88041  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