-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_16016289-16247131

-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_5170-T1
Valid prediction for Augustus_model.g3503.t1
Valid prediction for Augustus_model.g3505.t1
Valid prediction for snap_scaffold_2-snap.3073-T1
Valid prediction for GlimmerHMM_glimmerT_5178-T1
Valid prediction for snap_scaffold_2-snap.3080-T1
Valid prediction for CodingQuarry_transcript_28783-T1
Valid prediction for Augustus_model.g3494.t1
Valid prediction for GlimmerHMM_glimmerT_5174-T1
Valid prediction for pasa_asmbl_25095.p1
Valid prediction for snap_scaffold_2-snap.3084-T1
Valid prediction for snap_scaffold_2-snap.3079-T1
Valid prediction for snap_scaffold_2-snap.3099-T1
Valid prediction for GlimmerHMM_glimmerT_5182-T1
Valid prediction for snap_scaffold_2-snap.3096-T1
Valid prediction for Augustus_model.g3492.t1
Valid prediction for GlimmerHMM_glimmerT_5173-T1
Valid prediction for CodingQuarry_transcript_28785-T1
Valid prediction for snap_scaffold_2-snap.3093-T1
Valid prediction for HiQ_model.g3493.t1
Valid prediction for GlimmerHMM_glimmerT_5183-T1
Valid prediction for GlimmerHMM_glimmerT_5176-T1
Valid prediction for GlimmerHMM_glimmerT_5184-T1
Valid prediction for snap_scaffold_2-snap.3092-T1
Valid prediction for snap_scaffold_2-snap.3106-T1
Valid prediction for Augustus_model.g3496.t1
Valid prediction for pasa_asmbl_25100.p1
Valid prediction for snap_scaffold_2-snap.3089-T1
Valid prediction for snap_scaffold_2-snap.3074-T1
Valid prediction for Augustus_model.g3507.t1
Valid prediction for GlimmerHMM_glimmerT_5195-T1
Valid prediction for snap_scaffold_2-snap.3087-T1
Valid prediction for Augustus_model.g3500.t1
Valid prediction for Augustus_model.g3514.t1
Valid prediction for snap_scaffold_2-snap.3082-T1
Valid prediction for Augustus_model.g3504.t1
Valid prediction for Augustus_model.g3488.t1
Valid prediction for snap_scaffold_2-snap.3102-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_5188-T1
Valid prediction for pasa_asmbl_25098.p1
Valid prediction for snap_scaffold_2-snap.3108-T1
Valid prediction for GlimmerHMM_glimmerT_5187-T1
Valid prediction for HiQ_model.g3490.t1
Valid prediction for GlimmerHMM_glimmerT_5185-T1
Valid prediction for snap_scaffold_2-snap.3091-T1
Valid prediction for GlimmerHMM_glimmerT_5189-T1
Valid prediction for CodingQuarry_transcript_28784-T1
Valid prediction for snap_scaffold_2-snap.3071-T1
Valid prediction for Augustus_model.g3487.t1
Valid prediction for snap_scaffold_2-snap.3078-T1
Valid prediction for GlimmerHMM_glimmerT_5193-T1
Valid prediction for GlimmerHMM_glimmerT_5172-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_5175-T1
Valid prediction for HiQ_model.g3495.t1
Valid prediction for snap_scaffold_2-snap.3104-T1
Valid prediction for snap_scaffold_2-snap.3090-T1
Valid prediction for GlimmerHMM_glimmerT_5171-T1
Valid prediction for GlimmerHMM_glimmerT_5180-T1
Valid prediction for snap_scaffold_2-snap.3081-T1
Valid prediction for HiQ_model.g3491.t1
Couldn't classify 143990, 144052
Sorry, prediction pasa_asmbl_23676.p2 fails validation.
(CCT)	 AA	143990-144052	GT	TGG
(GAG)	 AG	144557-144666	GT	GTG
(ATA)	 AG	144997-145123	GG	GAG
-recovered pasa_asmbl_23676.p2, terminal, 144997, 145123
-recovered pasa_asmbl_23676.p2, internal, 144557, 144666
Valid prediction for GlimmerHMM_glimmerT_5165-T1
Valid prediction for pasa_asmbl_24043.p1
Couldn't classify 194695, 194859
Sorry, prediction pasa_asmbl_24011.p1 fails validation.
(ATG)	 TG	193885-193909	GT	TGG
(CCA)	 AG	194343-194509	GT	AGG
(ATC)	 AG	194695-194859	AA	AGA
-recovered pasa_asmbl_24011.p1, initial, 193885, 193909
-recovered pasa_asmbl_24011.p1, internal, 194343, 194509
Valid prediction for Augustus_model.g3509.t1
Valid prediction for snap_scaffold_2-snap.3075-T1
Valid prediction for snap_scaffold_2-snap.3094-T1
Valid prediction for Augustus_model.g3502.t1
Valid prediction for Augustus_model.g3497.t1
Valid prediction for GlimmerHMM_glimmerT_5190-T1
Valid prediction for GlimmerHMM_glimmerT_5164-T1
Valid prediction for snap_scaffold_2-snap.3098-T1
Valid prediction for snap_scaffold_2-snap.3107-T1
Valid prediction for Augustus_model.g3508.t1
Valid prediction for HiQ_model.g3501.t1
Valid prediction for snap_scaffold_2-snap.3077-T1
Valid prediction for GlimmerHMM_glimmerT_5186-T1
Valid prediction for Augustus_model.g3498.t1
Couldn't classify 186131, 186460
Sorry, prediction pasa_asmbl_23982.p1 fails validation.
(ATG)	 TC	185583-185685	GC	AGG
(AGG)	 AG	185875-185954	GT	AGG
(CTT)	 AG	186131-186460	TT	CCT
-recovered pasa_asmbl_23982.p1, initial, 185583, 185685
-recovered pasa_asmbl_23982.p1, internal, 185875, 185954
Valid prediction for GlimmerHMM_glimmerT_5167-T1
Valid prediction for Augustus_model.g3506.t1
Valid prediction for CodingQuarry_transcript_28787-T1
Valid prediction for GlimmerHMM_glimmerT_5181-T1
Valid prediction for GlimmerHMM_glimmerT_5169-T1
Valid prediction for GlimmerHMM_glimmerT_5192-T1
Valid prediction for snap_scaffold_2-snap.3103-T1
Valid prediction for snap_scaffold_2-snap.3095-T1
Valid prediction for pasa_asmbl_23673.p1
Valid prediction for snap_scaffold_2-snap.3086-T1
Valid prediction for snap_scaffold_2-snap.3101-T1
Valid prediction for Augustus_model.g3510.t1
Valid prediction for snap_scaffold_2-snap.3100-T1
Valid prediction for snap_scaffold_2-snap.3097-T1
Valid prediction for GlimmerHMM_glimmerT_5191-T1
Valid prediction for Augustus_model.g3513.t1
Valid prediction for CodingQuarry_transcript_28788-T1
Valid prediction for pasa_asmbl_23665.p1
Valid prediction for CodingQuarry_transcript_28786-T1
Valid prediction for snap_scaffold_2-snap.3083-T1
Valid prediction for snap_scaffold_2-snap.3085-T1
Valid prediction for Augustus_model.g3486.t1
Valid prediction for snap_scaffold_2-snap.3088-T1
Valid prediction for snap_scaffold_2-snap.3072-T1
Valid prediction for GlimmerHMM_glimmerT_5168-T1
Valid prediction for Augustus_model.g3512.t1
Couldn't classify 168150, 168325
Sorry, prediction pasa_asmbl_23947.p1 fails validation.
(GAC)	 AT	168150-168325	GT	AAG
(AGC)	 AG	168424-168518	GT	CAG
(GTG)	 AG	168675-168838	GT	AGG
(GTC)	 AG	169035-169235	GT	TTG
(ACG)	 AG	169359-169506	GT	AGG
(GTG)	 AG	169612-169786	GT	ACG
(AGC)	 AG	169888-170070	GT	AAG
(GGA)	 AG	170306-170424	GT	GGG
(GTG)	 AG	170581-170675	GT	AGG
(GTC)	 AG	170770-170893	GT	AGG
(GCG)	 AG	170982-171824	GT	AGG
(GGA)	 AG	171934-172133	GT	AGG
(GTT)	 AG	172234-172428	CA	GAC
-recovered pasa_asmbl_23947.p1, terminal, 172234, 172428
-recovered pasa_asmbl_23947.p1, internal, 168424, 168518
-recovered pasa_asmbl_23947.p1, internal, 168675, 168838
-recovered pasa_asmbl_23947.p1, internal, 169035, 169235
-recovered pasa_asmbl_23947.p1, internal, 169359, 169506
-recovered pasa_asmbl_23947.p1, internal, 169612, 169786
-recovered pasa_asmbl_23947.p1, internal, 169888, 170070
-recovered pasa_asmbl_23947.p1, internal, 170306, 170424
-recovered pasa_asmbl_23947.p1, internal, 170581, 170675
-recovered pasa_asmbl_23947.p1, internal, 170770, 170893
-recovered pasa_asmbl_23947.p1, internal, 170982, 171824
-recovered pasa_asmbl_23947.p1, internal, 171934, 172133
Valid prediction for Augustus_model.g3511.t1
Valid prediction for snap_scaffold_2-snap.3105-T1
Valid prediction for HiQ_model.g3499.t1
Valid prediction for Augustus_model.g3489.t1
Valid prediction for GlimmerHMM_glimmerT_5166-T1
Valid prediction for GlimmerHMM_glimmerT_5179-T1
Valid prediction for snap_scaffold_2-snap.3076-T1
Valid prediction for GlimmerHMM_glimmerT_5177-T1
Valid prediction for GlimmerHMM_glimmerT_5194-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17063, rend_intergenic: 10223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100458, rend_intergenic: 94923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172348, rend_intergenic: 159763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182440, rend_intergenic: 179581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202988, rend_intergenic: 196507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 230843
-exon list size: 464


building trellis

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32.6    
32.8    
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35.8    
36.1    
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36.5    
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37.3    
37.6    
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38.6    
38.8    
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96.8    
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97.4    
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97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 17063, rend_intergenic: 10223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100458, rend_intergenic: 94923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172348, rend_intergenic: 159763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182440, rend_intergenic: 179581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202988, rend_intergenic: 196507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 216004 - 230843
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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

-building DP trellis

-building trellis in range 218671 - 230843
-exon list size: 1


building trellis

33.3    
66.7    
-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
	-no exons in range 218874 - 230843