-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_1908059-2082536

-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 GlimmerHMM_glimmerT_31164-T1
Valid prediction for snap_scaffold_13-snap.389-T1
Valid prediction for snap_scaffold_13-snap.360-T1
Valid prediction for GlimmerHMM_glimmerT_31155-T1
Valid prediction for GlimmerHMM_glimmerT_31157-T1
Valid prediction for GlimmerHMM_glimmerT_31169-T1
Valid prediction for GlimmerHMM_glimmerT_31159-T1
Valid prediction for snap_scaffold_13-snap.358-T1
Valid prediction for snap_scaffold_13-snap.351-T1
Valid prediction for snap_scaffold_13-snap.371-T1
Valid prediction for GlimmerHMM_glimmerT_31160-T1
Couldn't classify 73451, 73702
Sorry, prediction pasa_asmbl_10575.p1 fails validation.
(CTT)	 AG	73451-73702	GT	CGG
(TTG)	 AG	73828-73929	GT	GGG
(GAA)	 AG	74045-74152	GT	AAG
(CAA)	 AG	74274-74468	AA	AGA
-recovered pasa_asmbl_10575.p1, terminal, 74274, 74468
-recovered pasa_asmbl_10575.p1, internal, 73451, 73702
-recovered pasa_asmbl_10575.p1, internal, 73828, 73929
-recovered pasa_asmbl_10575.p1, internal, 74045, 74152
Valid prediction for GlimmerHMM_glimmerT_31170-T1
Valid prediction for CodingQuarry_transcript_12876-T1
Valid prediction for snap_scaffold_13-snap.363-T1
Valid prediction for snap_scaffold_13-snap.381-T1
Valid prediction for snap_scaffold_13-snap.365-T1
Valid prediction for GlimmerHMM_glimmerT_31171-T1
Valid prediction for Augustus_model.g20689.t1
Valid prediction for snap_scaffold_13-snap.388-T1
Valid prediction for snap_scaffold_13-snap.356-T1
Valid prediction for GlimmerHMM_glimmerT_31152-T1
Valid prediction for snap_scaffold_13-snap.368-T1
Valid prediction for GlimmerHMM_glimmerT_31172-T1
Valid prediction for snap_scaffold_13-snap.373-T1
Valid prediction for HiQ_model.g20691.t1
Valid prediction for Augustus_model.g20703.t1
Valid prediction for Augustus_model.g20698.t1
Valid prediction for GlimmerHMM_glimmerT_31153-T1
Valid prediction for snap_scaffold_13-snap.366-T1
Valid prediction for Augustus_model.g20704.t1
Valid prediction for HiQ_model.g20702.t1
Valid prediction for GlimmerHMM_glimmerT_31145-T1
Valid prediction for snap_scaffold_13-snap.350-T1
Valid prediction for snap_scaffold_13-snap.382-T1
Valid prediction for GlimmerHMM_glimmerT_31149-T1
Valid prediction for GlimmerHMM_glimmerT_31147-T1
Valid prediction for GlimmerHMM_glimmerT_31154-T1
Valid prediction for snap_scaffold_13-snap.362-T1
Valid prediction for GlimmerHMM_glimmerT_31158-T1
Valid prediction for snap_scaffold_13-snap.370-T1
Valid prediction for snap_scaffold_13-snap.390-T1
Valid prediction for Augustus_model.g20692.t1
Valid prediction for pasa_asmbl_10578.p1
Valid prediction for snap_scaffold_13-snap.359-T1
Valid prediction for GlimmerHMM_glimmerT_31156-T1
Valid prediction for snap_scaffold_13-snap.364-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.372-T1
Valid prediction for GlimmerHMM_glimmerT_31151-T1
Valid prediction for Augustus_model.g20694.t1
Valid prediction for snap_scaffold_13-snap.380-T1
Valid prediction for Augustus_model.g20695.t1
Valid prediction for Augustus_model.g20690.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.g20701.t1
Valid prediction for Augustus_model.g20696.t1
Valid prediction for Augustus_model.g20699.t1
Valid prediction for GlimmerHMM_glimmerT_31161-T1
Valid prediction for snap_scaffold_13-snap.361-T1
Valid prediction for GlimmerHMM_glimmerT_31162-T1
Valid prediction for snap_scaffold_13-snap.384-T1
Valid prediction for Augustus_model.g20700.t1
Couldn't classify 145488, 145823
Sorry, prediction pasa_asmbl_9432.p1 fails validation.
(ATG)	 CA	144819-144918	GT	AGG
(ATA)	 AG	145015-145148	GT	AGG
(GAT)	 AG	145488-145823	TC	TGT
-recovered pasa_asmbl_9432.p1, initial, 144819, 144918
-recovered pasa_asmbl_9432.p1, internal, 145015, 145148
Valid prediction for snap_scaffold_13-snap.383-T1
Valid prediction for snap_scaffold_13-snap.386-T1
Valid prediction for GlimmerHMM_glimmerT_31148-T1
Valid prediction for snap_scaffold_13-snap.369-T1
Valid prediction for snap_scaffold_13-snap.349-T1
Valid prediction for CodingQuarry_transcript_12874-T1
Valid prediction for snap_scaffold_13-snap.379-T1
Valid prediction for snap_scaffold_13-snap.387-T1
Valid prediction for GlimmerHMM_glimmerT_31150-T1
Valid prediction for snap_scaffold_13-snap.374-T1
Valid prediction for GlimmerHMM_glimmerT_31168-T1
Valid prediction for GlimmerHMM_glimmerT_31166-T1
Valid prediction for snap_scaffold_13-snap.385-T1
Valid prediction for snap_scaffold_13-snap.375-T1
Valid prediction for snap_scaffold_13-snap.355-T1
Valid prediction for snap_scaffold_13-snap.353-T1
Valid prediction for snap_scaffold_13-snap.376-T1
Valid prediction for Augustus_model.g20697.t1
Valid prediction for Augustus_model.g20693.t1
Valid prediction for Augustus_model.g20688.t1
Valid prediction for snap_scaffold_13-snap.377-T1
Valid prediction for snap_scaffold_13-snap.367-T1
Valid prediction for GlimmerHMM_glimmerT_31146-T1
Valid prediction for snap_scaffold_13-snap.391-T1
Valid prediction for snap_scaffold_13-snap.378-T1
Valid prediction for GlimmerHMM_glimmerT_31167-T1
Valid prediction for GlimmerHMM_glimmerT_31163-T1
Valid prediction for CodingQuarry_transcript_12875-T1
Valid prediction for snap_scaffold_13-snap.354-T1
Valid prediction for snap_scaffold_13-snap.352-T1
Valid prediction for GlimmerHMM_glimmerT_31165-T1
Valid prediction for snap_scaffold_13-snap.357-T1
Couldn't classify 146218, 146300
Sorry, prediction pasa_asmbl_10332.p1 fails validation.
(TGT)	 TG	146218-146300	GT	AGG
(GTG)	 AG	146500-146623	GT	TGG
(GTG)	 AG	146741-146856	GT	ACG
(GTT)	 AG	146996-147068	GG	GAG
-recovered pasa_asmbl_10332.p1, terminal, 146996, 147068
-recovered pasa_asmbl_10332.p1, internal, 146500, 146623
-recovered pasa_asmbl_10332.p1, internal, 146741, 146856
Valid prediction for Augustus_model.g20687.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 39827, rend_intergenic: 36675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83585, rend_intergenic: 79110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95856, rend_intergenic: 86740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113330, rend_intergenic: 98789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 174478
-exon list size: 331


building trellis

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99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 39827, rend_intergenic: 36675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83585, rend_intergenic: 79110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95856, rend_intergenic: 86740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113330, rend_intergenic: 98789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10912
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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