-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_13964254-14103978

-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 Augustus_model.g25577.t1
Valid prediction for GlimmerHMM_glimmerT_38140-T1
Valid prediction for snap_scaffold_15-snap.2815-T1
Valid prediction for CodingQuarry_transcript_18173-T1
Valid prediction for pasa_asmbl_14613.p1
Valid prediction for GeneMark_model.65528_t
Valid prediction for snap_scaffold_15-snap.2809-T1
Valid prediction for snap_scaffold_15-snap.2787-T1
Valid prediction for GlimmerHMM_glimmerT_38136-T1
Valid prediction for snap_scaffold_15-snap.2795-T1
Valid prediction for GeneMark_model.65526_t
Valid prediction for pasa_asmbl_14605.p1
Valid prediction for HiQ_model.g25568.t1
Valid prediction for GlimmerHMM_glimmerT_38135-T1
Valid prediction for GlimmerHMM_glimmerT_38121-T1
Valid prediction for GeneMark_model.65514_t
Valid prediction for GlimmerHMM_glimmerT_38120-T1
Valid prediction for Augustus_model.g25582.t1
Valid prediction for GlimmerHMM_glimmerT_38142-T1
Valid prediction for Augustus_model.g25579.t1
Valid prediction for snap_scaffold_15-snap.2798-T1
Valid prediction for snap_scaffold_15-snap.2814-T1
Valid prediction for CodingQuarry_transcript_18169-T1
Valid prediction for GeneMark_model.65542_t
Valid prediction for Augustus_model.g25578.t1
Valid prediction for GeneMark_model.65529_t
Valid prediction for GeneMark_model.65520_t
Valid prediction for GeneMark_model.65523_t
Valid prediction for GlimmerHMM_glimmerT_38126-T1
Valid prediction for GeneMark_model.65535_t
Valid prediction for CodingQuarry_transcript_18175-T1
Valid prediction for pasa_asmbl_14606.p1
Valid prediction for GlimmerHMM_glimmerT_38125-T1
Valid prediction for snap_scaffold_15-snap.2790-T1
Valid prediction for HiQ_model.g25569.t1
Valid prediction for pasa_asmbl_14614.p1
Valid prediction for GlimmerHMM_glimmerT_38124-T1
Valid prediction for GeneMark_model.65524_t
Valid prediction for GeneMark_model.65522_t
Valid prediction for GeneMark_model.65516_t
Valid prediction for GeneMark_model.65537_t
Valid prediction for GlimmerHMM_glimmerT_38130-T1
Valid prediction for GeneMark_model.65509_t
Valid prediction for Augustus_model.g25573.t1
Valid prediction for GlimmerHMM_glimmerT_38129-T1
Valid prediction for GlimmerHMM_glimmerT_38137-T1
Valid prediction for HiQ_model.g25581.t1
Valid prediction for GlimmerHMM_glimmerT_38132-T1
Valid prediction for Augustus_model.g25586.t1
Valid prediction for snap_scaffold_15-snap.2802-T1
Valid prediction for GeneMark_model.65507_t
Valid prediction for GeneMark_model.65540_t
Valid prediction for snap_scaffold_15-snap.2797-T1
Valid prediction for snap_scaffold_15-snap.2810-T1
Valid prediction for snap_scaffold_15-snap.2805-T1
Valid prediction for snap_scaffold_15-snap.2791-T1
Valid prediction for GlimmerHMM_glimmerT_38133-T1
Valid prediction for GeneMark_model.65533_t
Valid prediction for GeneMark_model.65512_t
Valid prediction for GeneMark_model.65519_t
Valid prediction for HiQ_model.g25576.t1
Valid prediction for snap_scaffold_15-snap.2808-T1
Valid prediction for snap_scaffold_15-snap.2792-T1
Valid prediction for snap_scaffold_15-snap.2786-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 HiQ_model.g25570.t1
Valid prediction for Augustus_model.g25567.t1
Valid prediction for HiQ_model.g25580.t1
Valid prediction for snap_scaffold_15-snap.2796-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_18170-T1
Valid prediction for Augustus_model.g25572.t1
Valid prediction for snap_scaffold_15-snap.2813-T1
Valid prediction for pasa_asmbl_15709.p2
Valid prediction for snap_scaffold_15-snap.2807-T1
Valid prediction for GeneMark_model.65511_t
Couldn't classify 101584, 101703
Sorry, prediction pasa_asmbl_15717.p1 fails validation.
(ATG)	 TA	100627-100946	GT	CTG
(ATG)	 AG	101078-101177	GT	AGG
(ACA)	 AG	101584-101703	AA	CGA
-recovered pasa_asmbl_15717.p1, initial, 100627, 100946
-recovered pasa_asmbl_15717.p1, initial, 101078, 101177
-recovered pasa_asmbl_15717.p1, internal, 101078, 101177
Valid prediction for GeneMark_model.65527_t
Valid prediction for GeneMark_model.65539_t
Valid prediction for GlimmerHMM_glimmerT_38139-T1
Valid prediction for snap_scaffold_15-snap.2816-T1
Valid prediction for GlimmerHMM_glimmerT_38131-T1
Valid prediction for snap_scaffold_15-snap.2788-T1
Valid prediction for pasa_asmbl_15718.p1
Valid prediction for GlimmerHMM_glimmerT_38143-T1
Valid prediction for GlimmerHMM_glimmerT_38141-T1
Valid prediction for CodingQuarry_transcript_18174-T1
Valid prediction for HiQ_model.g25574.t1
Valid prediction for snap_scaffold_15-snap.2799-T1
Valid prediction for snap_scaffold_15-snap.2806-T1
Valid prediction for snap_scaffold_15-snap.2804-T1
Couldn't classify 121008, 121093
Sorry, prediction pasa_asmbl_15710.p1 fails validation.
(AGG)	 CT	121008-121093	GT	GGG
(GGC)	 AG	121202-121286	GT	AGG
(TTC)	 AG	121606-121712	GT	AGG
(AGT)	 AG	122570-122705	GT	GGG
(GAT)	 AG	123059-123138	GT	AGG
(CGT)	 AG	123346-123424	GT	AGG
(CTG)	 AG	123657-123736	GT	AGG
(TTT)	 AG	123902-124016	CA	AAC
-recovered pasa_asmbl_15710.p1, terminal, 123902, 124016
-recovered pasa_asmbl_15710.p1, internal, 121202, 121286
-recovered pasa_asmbl_15710.p1, internal, 121606, 121712
-recovered pasa_asmbl_15710.p1, internal, 122570, 122705
-recovered pasa_asmbl_15710.p1, internal, 123059, 123138
-recovered pasa_asmbl_15710.p1, internal, 123346, 123424
-recovered pasa_asmbl_15710.p1, internal, 123657, 123736
Valid prediction for snap_scaffold_15-snap.2801-T1
Valid prediction for snap_scaffold_15-snap.2785-T1
Valid prediction for GeneMark_model.65541_t
Valid prediction for GlimmerHMM_glimmerT_38128-T1
Valid prediction for GeneMark_model.65534_t
Valid prediction for Augustus_model.g25575.t1
Valid prediction for snap_scaffold_15-snap.2789-T1
Valid prediction for GeneMark_model.65532_t
Valid prediction for pasa_asmbl_15716.p1
Valid prediction for GlimmerHMM_glimmerT_38138-T1
Valid prediction for GeneMark_model.65515_t
Valid prediction for snap_scaffold_15-snap.2803-T1
Valid prediction for Augustus_model.g25587.t1
Valid prediction for Augustus_model.g25584.t1
Valid prediction for GeneMark_model.65525_t
Valid prediction for GlimmerHMM_glimmerT_38134-T1
Valid prediction for GeneMark_model.65518_t
Valid prediction for GeneMark_model.65538_t
Valid prediction for Augustus_model.g25585.t1
Valid prediction for GeneMark_model.65510_t
Couldn't classify 105942, 106361
Sorry, prediction pasa_asmbl_15714.p1 fails validation.
(TCC)	 AG	105942-106361	GT	TGG
(GTG)	 AG	106919-107200	GA	GAG
-recovered pasa_asmbl_15714.p1, terminal, 106919, 107200
-recovered pasa_asmbl_15714.p1, internal, 105942, 106361
Valid prediction for snap_scaffold_15-snap.2811-T1
Valid prediction for CodingQuarry_transcript_18171-T1
Valid prediction for GeneMark_model.65531_t
Valid prediction for GeneMark_model.65508_t
Valid prediction for GeneMark_model.65543_t
Valid prediction for GeneMark_model.65530_t
Valid prediction for GlimmerHMM_glimmerT_38127-T1
Valid prediction for GeneMark_model.65536_t
Valid prediction for Augustus_model.g25583.t1
Valid prediction for snap_scaffold_15-snap.2800-T1
Valid prediction for GlimmerHMM_glimmerT_38122-T1
Valid prediction for snap_scaffold_15-snap.2812-T1
Valid prediction for GlimmerHMM_glimmerT_38123-T1
Valid prediction for GeneMark_model.65517_t
Valid prediction for snap_scaffold_15-snap.2794-T1
Valid prediction for GeneMark_model.65521_t
Valid prediction for HiQ_model.g25571.t1
Valid prediction for snap_scaffold_15-snap.2784-T1
Valid prediction for GeneMark_model.65513_t
Valid prediction for snap_scaffold_15-snap.2793-T1
Couldn't classify 117975, 118013
Couldn't classify 119546, 119661
Sorry, prediction pasa_asmbl_15713.p2 fails validation.
(CAC)	 AC	117975-118013	GT	AGG
(CGG)	 AG	118921-119095	GT	AGG
(AGT)	 AG	119546-119661	GA	TAG
-recovered pasa_asmbl_15713.p2, internal, 118921, 119095

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24472, rend_intergenic: 16157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55379, rend_intergenic: 44461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57773, rend_intergenic: 55729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91045, rend_intergenic: 87067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116550, rend_intergenic: 106786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122424, rend_intergenic: 117341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131517, rend_intergenic: 128277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 139725
-exon list size: 533


building trellis

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98.9    
99.1    
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99.4    
99.6    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 24472, rend_intergenic: 16157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55379, rend_intergenic: 44461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57773, rend_intergenic: 55729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91045, rend_intergenic: 87067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116550, rend_intergenic: 106786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122424, rend_intergenic: 117341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131517, rend_intergenic: 128277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support