-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_15005393-15229073

-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.22601_t
Valid prediction for snap_scaffold_5-snap.2792-T1
Couldn't classify 9113, 9231
Sorry, prediction pasa_asmbl_44638.p1 fails validation.
(GGG)	 CG	9113-9231	GT	AGG
(ATA)	 AG	9408-9459	GT	AGG
(CCA)	 AG	9707-9796	GT	AGG
(GTG)	 AG	9898-10071	CA	AAC
-recovered pasa_asmbl_44638.p1, terminal, 9898, 10071
-recovered pasa_asmbl_44638.p1, internal, 9408, 9459
-recovered pasa_asmbl_44638.p1, internal, 9707, 9796
Valid prediction for GlimmerHMM_glimmerT_13461-T1
Valid prediction for GeneMark_model.22615_t
Valid prediction for Augustus_model.g9001.t1
Valid prediction for HiQ_model.g9004.t1
Valid prediction for GeneMark_model.22618_t
Valid prediction for GeneMark_model.22623_t
Valid prediction for snap_scaffold_5-snap.2783-T1
Valid prediction for snap_scaffold_5-snap.2796-T1
Valid prediction for GlimmerHMM_glimmerT_13469-T1
Valid prediction for GeneMark_model.22598_t
Valid prediction for GeneMark_model.22604_t
Valid prediction for GeneMark_model.22594_t
Valid prediction for GlimmerHMM_glimmerT_13452-T1
Couldn't classify 217077, 217150
Sorry, prediction pasa_asmbl_44645.p1 fails validation.
(ATG)	 CC	212020-212151	GT	AGG
(GTG)	 AG	212285-212387	GT	CGG
(CCT)	 AG	213333-213535	GT	AGG
(TCT)	 AG	213912-214124	GT	AGG
(GAG)	 AG	214537-214685	GT	AGG
(GAT)	 AG	214865-214934	GT	AGG
(GCC)	 AG	215144-215299	GT	AGG
(GCG)	 AG	215534-215788	GT	AGG
(AAG)	 AG	216158-216283	GT	GGG
(GTT)	 AG	216441-216536	GT	AGG
(GAG)	 AG	216685-216772	GT	TAG
(GTC)	 AG	217077-217150	TC	CCT
-recovered pasa_asmbl_44645.p1, initial, 212020, 212151
-recovered pasa_asmbl_44645.p1, internal, 212285, 212387
-recovered pasa_asmbl_44645.p1, internal, 213333, 213535
-recovered pasa_asmbl_44645.p1, internal, 213912, 214124
-recovered pasa_asmbl_44645.p1, internal, 214537, 214685
-recovered pasa_asmbl_44645.p1, internal, 214865, 214934
-recovered pasa_asmbl_44645.p1, internal, 215144, 215299
-recovered pasa_asmbl_44645.p1, internal, 215534, 215788
-recovered pasa_asmbl_44645.p1, internal, 216158, 216283
-recovered pasa_asmbl_44645.p1, internal, 216441, 216536
-recovered pasa_asmbl_44645.p1, internal, 216685, 216772
Valid prediction for GeneMark_model.22591_t
Valid prediction for GlimmerHMM_glimmerT_13465-T1
Valid prediction for snap_scaffold_5-snap.2810-T1
Couldn't classify 12597, 12731
Sorry, prediction pasa_asmbl_44640.p2 fails validation.
(ATG)	 CG	11768-11812	GT	GGG
(GCT)	 AG	12024-12275	GT	GGG
(CTA)	 AG	12597-12731	GT	AGG
-recovered pasa_asmbl_44640.p2, initial, 11768, 11812
-recovered pasa_asmbl_44640.p2, internal, 12024, 12275
-recovered pasa_asmbl_44640.p2, internal, 12597, 12731
Valid prediction for GeneMark_model.22621_t
Valid prediction for GeneMark_model.22592_t
Valid prediction for GeneMark_model.22596_t
Valid prediction for snap_scaffold_5-snap.2784-T1
Valid prediction for CodingQuarry_transcript_52240-T1
Valid prediction for GlimmerHMM_glimmerT_13453-T1
Valid prediction for snap_scaffold_5-snap.2797-T1
Valid prediction for GlimmerHMM_glimmerT_13455-T1
Valid prediction for GeneMark_model.22590_t
Valid prediction for GlimmerHMM_glimmerT_13467-T1
Valid prediction for GeneMark_model.22608_t
Valid prediction for GlimmerHMM_glimmerT_13464-T1
Valid prediction for GlimmerHMM_glimmerT_13462-T1
Valid prediction for snap_scaffold_5-snap.2781-T1
Valid prediction for pasa_asmbl_44643.p1
Valid prediction for HiQ_model.g9016.t1
Valid prediction for snap_scaffold_5-snap.2795-T1
Valid prediction for snap_scaffold_5-snap.2793-T1
Valid prediction for Augustus_model.g8997.t1
Valid prediction for snap_scaffold_5-snap.2789-T1
Valid prediction for GeneMark_model.22606_t
Valid prediction for snap_scaffold_5-snap.2808-T1
Couldn't classify 35067, 35456
Sorry, prediction pasa_asmbl_44642.p1 fails validation.
(TTA)	 CC	35067-35456	AG	AGA
Valid prediction for Augustus_model.g8999.t1
Valid prediction for GeneMark_model.22599_t
Valid prediction for snap_scaffold_5-snap.2786-T1
Valid prediction for snap_scaffold_5-snap.2782-T1
Valid prediction for snap_scaffold_5-snap.2791-T1
Valid prediction for GeneMark_model.22603_t
Valid prediction for GlimmerHMM_glimmerT_13479-T1
Valid prediction for Augustus_model.g8998.t1
Valid prediction for GeneMark_model.22620_t
Valid prediction for GlimmerHMM_glimmerT_13476-T1
Valid prediction for GlimmerHMM_glimmerT_13478-T1
Valid prediction for GlimmerHMM_glimmerT_13457-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.22619_t
Valid prediction for snap_scaffold_5-snap.2801-T1
Valid prediction for GlimmerHMM_glimmerT_13472-T1
Valid prediction for GeneMark_model.22607_t
Valid prediction for snap_scaffold_5-snap.2804-T1
Valid prediction for CodingQuarry_transcript_52245-T1
Valid prediction for GeneMark_model.22602_t
Valid prediction for pasa_asmbl_46026.p1
Valid prediction for Augustus_model.g9002.t1
Valid prediction for CodingQuarry_transcript_52239-T1
Valid prediction for HiQ_model.g9013.t1
Valid prediction for GeneMark_model.22617_t
Valid prediction for snap_scaffold_5-snap.2800-T1
Valid prediction for snap_scaffold_5-snap.2785-T1
Valid prediction for snap_scaffold_5-snap.2794-T1
Valid prediction for snap_scaffold_5-snap.2787-T1
Valid prediction for snap_scaffold_5-snap.2798-T1
Valid prediction for CodingQuarry_transcript_52243-T1
Valid prediction for HiQ_model.g9000.t1
Valid prediction for GlimmerHMM_glimmerT_13460-T1
Valid prediction for GlimmerHMM_glimmerT_13473-T1
Valid prediction for GlimmerHMM_glimmerT_13474-T1
Valid prediction for GlimmerHMM_glimmerT_13459-T1
Valid prediction for GeneMark_model.22616_t
Valid prediction for GlimmerHMM_glimmerT_13471-T1
Valid prediction for CodingQuarry_transcript_52237-T1
Valid prediction for pasa_asmbl_46037.p1
Valid prediction for snap_scaffold_5-snap.2788-T1
Valid prediction for snap_scaffold_5-snap.2806-T1
Valid prediction for GeneMark_model.22622_t
Valid prediction for GlimmerHMM_glimmerT_13458-T1
Valid prediction for Augustus_model.g9005.t1
Valid prediction for HiQ_model.g9007.t1
Valid prediction for HiQ_model.g9011.t1
Valid prediction for Augustus_model.g9006.t1
Valid prediction for GeneMark_model.22611_t
Valid prediction for Augustus_model.g9003.t1
Valid prediction for HiQ_model.g9010.t1
Valid prediction for GlimmerHMM_glimmerT_13468-T1
Valid prediction for GlimmerHMM_glimmerT_13475-T1
Valid prediction for GeneMark_model.22595_t
Valid prediction for CodingQuarry_transcript_52241-T1
Valid prediction for GlimmerHMM_glimmerT_13470-T1
Valid prediction for GlimmerHMM_glimmerT_13466-T1
Valid prediction for CodingQuarry_transcript_52246-T1
Valid prediction for GeneMark_model.22593_t
Valid prediction for CodingQuarry_transcript_52244-T1
Valid prediction for GlimmerHMM_glimmerT_13477-T1
Valid prediction for GlimmerHMM_glimmerT_13456-T1
Valid prediction for GeneMark_model.22609_t
Valid prediction for snap_scaffold_5-snap.2799-T1
Valid prediction for GlimmerHMM_glimmerT_13454-T1
Valid prediction for GeneMark_model.22597_t
Valid prediction for snap_scaffold_5-snap.2790-T1
Valid prediction for pasa_asmbl_46015.p1
Valid prediction for GeneMark_model.22624_t
Valid prediction for snap_scaffold_5-snap.2802-T1
Valid prediction for HiQ_model.g9014.t1
Valid prediction for pasa_asmbl_46035.p1
Valid prediction for snap_scaffold_5-snap.2803-T1
Valid prediction for Augustus_model.g9015.t1
Valid prediction for HiQ_model.g9008.t1
Valid prediction for GeneMark_model.22600_t
Couldn't classify 108072, 108327
Sorry, prediction pasa_asmbl_46030.p1 fails validation.
(GGA)	 CA	108072-108327	GT	CGG
(AAT)	 AG	109117-109195	GT	CGG
(TCA)	 AG	110167-110290	GT	GAG
-recovered pasa_asmbl_46030.p1, terminal, 110167, 110290
-recovered pasa_asmbl_46030.p1, internal, 109117, 109195
-recovered pasa_asmbl_46030.p1, internal, 110167, 110290
Valid prediction for CodingQuarry_transcript_52242-T1
Valid prediction for snap_scaffold_5-snap.2809-T1
Valid prediction for snap_scaffold_5-snap.2807-T1
Valid prediction for GlimmerHMM_glimmerT_13451-T1
Valid prediction for HiQ_model.g9009.t1
Valid prediction for GeneMark_model.22610_t
Valid prediction for GeneMark_model.22605_t
Valid prediction for GeneMark_model.22612_t
Valid prediction for Augustus_model.g9012.t1
Valid prediction for pasa_asmbl_46012.p1
Valid prediction for snap_scaffold_5-snap.2805-T1
Valid prediction for GlimmerHMM_glimmerT_13463-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 59446, rend_intergenic: 51050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66762, rend_intergenic: 66333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73038, rend_intergenic: 68117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218611, rend_intergenic: 212800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 223681
-exon list size: 423


building trellis

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96.9    
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97.6    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 59446, rend_intergenic: 51050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66762, rend_intergenic: 66333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73038, rend_intergenic: 68117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218611, rend_intergenic: 212800  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