-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_15445883-15626800

-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 46812, 46999
Sorry, prediction pasa_asmbl_14750.p1 fails validation.
(CCA)	 AC	46812-46999	GT	AAG
(GAT)	 AG	47161-47311	GT	AGG
(GCC)	 AG	47409-47556	GT	TGG
(GAA)	 AG	48015-48181	GT	TGG
(GTC)	 AG	48384-48521	GT	CTG
(CCC)	 AG	48673-48794	GT	GGG
(GGG)	 AG	48974-49047	GT	AGG
(GTC)	 AG	49265-49338	GT	AGG
(GTA)	 AG	49461-49535	AG	AAA
-recovered pasa_asmbl_14750.p1, terminal, 49461, 49535
-recovered pasa_asmbl_14750.p1, internal, 47161, 47311
-recovered pasa_asmbl_14750.p1, internal, 47409, 47556
-recovered pasa_asmbl_14750.p1, internal, 48015, 48181
-recovered pasa_asmbl_14750.p1, internal, 48384, 48521
-recovered pasa_asmbl_14750.p1, internal, 48673, 48794
-recovered pasa_asmbl_14750.p1, internal, 48974, 49047
-recovered pasa_asmbl_14750.p1, internal, 49265, 49338
Valid prediction for GlimmerHMM_glimmerT_38338-T1
Valid prediction for GlimmerHMM_glimmerT_38345-T1
Valid prediction for GeneMark_model.65783_t
Valid prediction for GlimmerHMM_glimmerT_38326-T1
Valid prediction for GeneMark_model.65776_t
Valid prediction for snap_scaffold_15-snap.3090-T1
Valid prediction for snap_scaffold_15-snap.3104-T1
Valid prediction for snap_scaffold_15-snap.3098-T1
Valid prediction for CodingQuarry_transcript_18225-T1
Valid prediction for GlimmerHMM_glimmerT_38323-T1
Valid prediction for snap_scaffold_15-snap.3105-T1
Valid prediction for GeneMark_model.65786_t
Valid prediction for GlimmerHMM_glimmerT_38341-T1
Valid prediction for GlimmerHMM_glimmerT_38347-T1
Valid prediction for Augustus_model.g25737.t1
Valid prediction for snap_scaffold_15-snap.3103-T1
Valid prediction for CodingQuarry_transcript_18224-T1
Valid prediction for Augustus_model.g25744.t1
Valid prediction for Augustus_model.g25723.t1
Couldn't classify 164468, 164601
Sorry, prediction pasa_asmbl_14763.p1 fails validation.
(CAG)	 TG	164468-164601	GT	CGG
(GTT)	 AG	166844-166903	GT	AGG
(CAT)	 AG	167277-167385	GT	AGG
(CTG)	 AG	167622-167675	GT	CGG
(GTG)	 AG	167882-167932	GT	AGG
(GTA)	 AG	168068-168187	GT	AGG
(GTA)	 AG	168338-168465	GT	CCG
(GAC)	 AG	169211-169312	GT	CGG
(GGA)	 AG	169491-169734	CA	GAC
-recovered pasa_asmbl_14763.p1, terminal, 169491, 169734
-recovered pasa_asmbl_14763.p1, internal, 166844, 166903
-recovered pasa_asmbl_14763.p1, internal, 167277, 167385
-recovered pasa_asmbl_14763.p1, internal, 167622, 167675
-recovered pasa_asmbl_14763.p1, internal, 167882, 167932
-recovered pasa_asmbl_14763.p1, internal, 168068, 168187
-recovered pasa_asmbl_14763.p1, internal, 168338, 168465
-recovered pasa_asmbl_14763.p1, internal, 169211, 169312
Valid prediction for snap_scaffold_15-snap.3094-T1
Valid prediction for Augustus_model.g25746.t1
Valid prediction for GeneMark_model.65782_t
Valid prediction for snap_scaffold_15-snap.3083-T1
Valid prediction for pasa_asmbl_14751.p1
Valid prediction for GeneMark_model.65791_t
Valid prediction for Augustus_model.g25727.t1
Valid prediction for GlimmerHMM_glimmerT_38334-T1
Valid prediction for GeneMark_model.65793_t
Valid prediction for Augustus_model.g25742.t1
Valid prediction for Augustus_model.g25740.t1
Valid prediction for GeneMark_model.65772_t
Valid prediction for snap_scaffold_15-snap.3084-T1
Valid prediction for GeneMark_model.65770_t
Valid prediction for GeneMark_model.65777_t
Valid prediction for GeneMark_model.65788_t
Valid prediction for snap_scaffold_15-snap.3099-T1
Valid prediction for snap_scaffold_15-snap.3097-T1
Valid prediction for Augustus_model.g25738.t1
Valid prediction for Augustus_model.g25743.t1
Valid prediction for CodingQuarry_transcript_18228-T1
Valid prediction for GlimmerHMM_glimmerT_38325-T1
Couldn't classify 123225, 123647
Sorry, prediction pasa_asmbl_14758.p1 fails validation.
(CCT)	 CT	123225-123647	GT	TGG
(TCA)	 AG	123907-123969	CA	GAC
-recovered pasa_asmbl_14758.p1, terminal, 123907, 123969
Valid prediction for CodingQuarry_transcript_18227-T1
Valid prediction for snap_scaffold_15-snap.3100-T1
Valid prediction for GlimmerHMM_glimmerT_38333-T1
Valid prediction for snap_scaffold_15-snap.3101-T1
Valid prediction for Augustus_model.g25726.t1
Valid prediction for HiQ_model.g25728.t1
Valid prediction for GeneMark_model.65792_t
Valid prediction for snap_scaffold_15-snap.3107-T1
Valid prediction for snap_scaffold_15-snap.3076-T1
Valid prediction for snap_scaffold_15-snap.3106-T1
Valid prediction for GlimmerHMM_glimmerT_38330-T1
Valid prediction for snap_scaffold_15-snap.3109-T1
Valid prediction for GlimmerHMM_glimmerT_38344-T1
Valid prediction for Augustus_model.g25734.t1
Valid prediction for snap_scaffold_15-snap.3080-T1
Valid prediction for GlimmerHMM_glimmerT_38320-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_38335-T1
Valid prediction for GlimmerHMM_glimmerT_38328-T1
Valid prediction for Augustus_model.g25735.t1
Valid prediction for GlimmerHMM_glimmerT_38336-T1
Valid prediction for Augustus_model.g25739.t1
Valid prediction for GlimmerHMM_glimmerT_38340-T1
Valid prediction for Augustus_model.g25725.t1
Valid prediction for snap_scaffold_15-snap.3085-T1
Valid prediction for GeneMark_model.65778_t
Valid prediction for snap_scaffold_15-snap.3088-T1
Valid prediction for Augustus_model.g25736.t1
Valid prediction for GlimmerHMM_glimmerT_38343-T1
Valid prediction for GlimmerHMM_glimmerT_38329-T1
Valid prediction for snap_scaffold_15-snap.3081-T1
Valid prediction for GeneMark_model.65785_t
Valid prediction for GlimmerHMM_glimmerT_38322-T1
Valid prediction for HiQ_model.g25730.t1
Valid prediction for Augustus_model.g25732.t1
Valid prediction for GeneMark_model.65790_t
Valid prediction for snap_scaffold_15-snap.3092-T1
Valid prediction for GlimmerHMM_glimmerT_38331-T1
Valid prediction for snap_scaffold_15-snap.3089-T1
Valid prediction for snap_scaffold_15-snap.3096-T1
Valid prediction for GlimmerHMM_glimmerT_38327-T1
Valid prediction for snap_scaffold_15-snap.3086-T1
Valid prediction for snap_scaffold_15-snap.3077-T1
Valid prediction for Augustus_model.g25733.t1
Valid prediction for Augustus_model.g25729.t1
Valid prediction for GeneMark_model.65784_t
Valid prediction for snap_scaffold_15-snap.3102-T1
Valid prediction for GlimmerHMM_glimmerT_38339-T1
Couldn't classify 100430, 100525
Couldn't classify 101027, 101070
Sorry, prediction pasa_asmbl_15945.p1 fails validation.
(CTG)	 AA	100430-100525	GT	AGG
(GAC)	 AG	100708-100936	GT	ACG
(AGA)	 AG	101027-101070	AG	AGA
-recovered pasa_asmbl_15945.p1, internal, 100708, 100936
Valid prediction for GeneMark_model.65774_t
Valid prediction for GeneMark_model.65781_t
Valid prediction for GlimmerHMM_glimmerT_38324-T1
Valid prediction for Augustus_model.g25741.t1
Valid prediction for snap_scaffold_15-snap.3095-T1
Valid prediction for GlimmerHMM_glimmerT_38342-T1
Valid prediction for GlimmerHMM_glimmerT_38332-T1
Valid prediction for Augustus_model.g25722.t1
Valid prediction for snap_scaffold_15-snap.3082-T1
Couldn't classify 81469, 81653
Sorry, prediction pasa_asmbl_15808.p1 fails validation.
(ATG)	 TG	76653-76676	GT	CGG
(GTG)	 AG	78056-78151	GT	AGG
(GGT)	 AG	78629-78908	GT	AGG
(GTA)	 AG	81469-81653	TG	TGT
-recovered pasa_asmbl_15808.p1, initial, 76653, 76676
-recovered pasa_asmbl_15808.p1, internal, 78056, 78151
-recovered pasa_asmbl_15808.p1, internal, 78629, 78908
Valid prediction for snap_scaffold_15-snap.3078-T1
Valid prediction for GeneMark_model.65773_t
Valid prediction for GlimmerHMM_glimmerT_38321-T1
Couldn't classify 20087, 20530
Sorry, prediction pasa_asmbl_14762.p1 fails validation.
(CTC)	 AT	20087-20530	CA	CTC
Valid prediction for snap_scaffold_15-snap.3093-T1
Valid prediction for Augustus_model.g25721.t1
Valid prediction for GeneMark_model.65789_t
Couldn't classify 67158, 67195
Sorry, prediction pasa_asmbl_15810.p1 fails validation.
(GTG)	 AT	67158-67195	GT	AGG
(TTT)	 AG	68195-68327	GT	AGG
(CAT)	 AG	68447-68545	GT	AGG
(CTT)	 AG	68676-68861	GT	AGG
(ATT)	 AG	68999-69301	TT	AAT
-recovered pasa_asmbl_15810.p1, terminal, 68999, 69301
-recovered pasa_asmbl_15810.p1, internal, 68195, 68327
-recovered pasa_asmbl_15810.p1, internal, 68447, 68545
-recovered pasa_asmbl_15810.p1, internal, 68676, 68861
Valid prediction for snap_scaffold_15-snap.3110-T1
Valid prediction for GeneMark_model.65771_t
Valid prediction for Augustus_model.g25745.t1
Valid prediction for Augustus_model.g25731.t1
Valid prediction for Augustus_model.g25724.t1
Valid prediction for GlimmerHMM_glimmerT_38346-T1
Couldn't classify 105550, 105927
Sorry, prediction pasa_asmbl_15804.p1 fails validation.
(CAC)	 CC	105550-105927	GT	GAG
Valid prediction for snap_scaffold_15-snap.3079-T1
Valid prediction for GeneMark_model.65775_t
Valid prediction for GeneMark_model.65787_t
Valid prediction for snap_scaffold_15-snap.3091-T1
Valid prediction for snap_scaffold_15-snap.3108-T1
Valid prediction for snap_scaffold_15-snap.3087-T1
Valid prediction for GeneMark_model.65780_t
Valid prediction for GlimmerHMM_glimmerT_38337-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 105166, rend_intergenic: 99550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 180918
-exon list size: 389


building trellis

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-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 105166, rend_intergenic: 99550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support