-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_16704030-16944392

-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_13429-T1
Valid prediction for GlimmerHMM_glimmerT_13425-T1
Valid prediction for GlimmerHMM_glimmerT_13418-T1
Valid prediction for GlimmerHMM_glimmerT_13431-T1
Valid prediction for snap_scaffold_5-snap.3090-T1
Valid prediction for snap_scaffold_5-snap.3109-T1
Valid prediction for snap_scaffold_5-snap.3123-T1
Valid prediction for GlimmerHMM_glimmerT_13416-T1
Valid prediction for Augustus_model.g8920.t1
Valid prediction for GlimmerHMM_glimmerT_13423-T1
Valid prediction for Augustus_model.g8933.t1
Valid prediction for snap_scaffold_5-snap.3124-T1
Valid prediction for GlimmerHMM_glimmerT_13406-T1
Valid prediction for snap_scaffold_5-snap.3126-T1
Valid prediction for GlimmerHMM_glimmerT_13421-T1
Valid prediction for snap_scaffold_5-snap.3116-T1
Valid prediction for GlimmerHMM_glimmerT_13434-T1
Valid prediction for Augustus_model.g8935.t1
Valid prediction for snap_scaffold_5-snap.3129-T1
Valid prediction for Augustus_model.g8927.t1
Valid prediction for snap_scaffold_5-snap.3131-T1
Valid prediction for snap_scaffold_5-snap.3113-T1
Valid prediction for GlimmerHMM_glimmerT_13428-T1
Valid prediction for snap_scaffold_5-snap.3089-T1
Valid prediction for GlimmerHMM_glimmerT_13403-T1
Valid prediction for snap_scaffold_5-snap.3093-T1
Valid prediction for snap_scaffold_5-snap.3088-T1
Valid prediction for Augustus_model.g8932.t1
Valid prediction for Augustus_model.g8917.t1
Valid prediction for GlimmerHMM_glimmerT_13407-T1
Valid prediction for snap_scaffold_5-snap.3121-T1
Valid prediction for GlimmerHMM_glimmerT_13430-T1
Valid prediction for GlimmerHMM_glimmerT_13411-T1
Valid prediction for GlimmerHMM_glimmerT_13417-T1
Valid prediction for GlimmerHMM_glimmerT_13437-T1
Valid prediction for GlimmerHMM_glimmerT_13427-T1
Valid prediction for snap_scaffold_5-snap.3112-T1
Valid prediction for snap_scaffold_5-snap.3092-T1
Valid prediction for GlimmerHMM_glimmerT_13409-T1
Valid prediction for snap_scaffold_5-snap.3118-T1
Valid prediction for snap_scaffold_5-snap.3103-T1
Valid prediction for snap_scaffold_5-snap.3107-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: -)Couldn't classify 185932, 185948
Sorry, prediction pasa_asmbl_44776.p1 fails validation.
(ATG)	 CC	184948-184981	GT	CTG
(TGC)	 AG	185248-185277	GT	AGG
(TGA)	 AG	185363-185407	GT	TGG
(GGA)	 AG	185532-185667	GT	AAG
(GTG)	 AG	185751-185860	GT	AAG
(TTT)	 AG	185932-185948	AT	ACA
-recovered pasa_asmbl_44776.p1, initial, 184948, 184981
-recovered pasa_asmbl_44776.p1, internal, 185248, 185277
-recovered pasa_asmbl_44776.p1, internal, 185363, 185407
-recovered pasa_asmbl_44776.p1, internal, 185532, 185667
-recovered pasa_asmbl_44776.p1, internal, 185751, 185860
Valid prediction for GlimmerHMM_glimmerT_13424-T1
Valid prediction for snap_scaffold_5-snap.3105-T1
Valid prediction for snap_scaffold_5-snap.3111-T1
Valid prediction for snap_scaffold_5-snap.3128-T1
Valid prediction for snap_scaffold_5-snap.3097-T1
Valid prediction for CodingQuarry_transcript_52420-T1
Valid prediction for Augustus_model.g8923.t1
Valid prediction for pasa_asmbl_44773.p1
Valid prediction for snap_scaffold_5-snap.3091-T1
Valid prediction for GlimmerHMM_glimmerT_13414-T1
Valid prediction for HiQ_model.g8925.t1
Valid prediction for snap_scaffold_5-snap.3130-T1
Valid prediction for snap_scaffold_5-snap.3114-T1
Valid prediction for Augustus_model.g8930.t1
Valid prediction for GlimmerHMM_glimmerT_13426-T1
Valid prediction for Augustus_model.g8921.t1
Valid prediction for snap_scaffold_5-snap.3120-T1
Valid prediction for snap_scaffold_5-snap.3119-T1
Valid prediction for Augustus_model.g8922.t1
Valid prediction for snap_scaffold_5-snap.3096-T1
Valid prediction for snap_scaffold_5-snap.3100-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_13404-T1
Valid prediction for Augustus_model.g8924.t1
Valid prediction for pasa_asmbl_44785.p1
Valid prediction for GlimmerHMM_glimmerT_13419-T1
Valid prediction for Augustus_model.g8915.t1
Valid prediction for snap_scaffold_5-snap.3117-T1
Valid prediction for Augustus_model.g8919.t1
Valid prediction for Augustus_model.g8929.t1
Valid prediction for GlimmerHMM_glimmerT_13435-T1
Valid prediction for GlimmerHMM_glimmerT_13433-T1
Valid prediction for snap_scaffold_5-snap.3099-T1
Valid prediction for snap_scaffold_5-snap.3132-T1
Valid prediction for snap_scaffold_5-snap.3122-T1
Valid prediction for GlimmerHMM_glimmerT_13422-T1
Valid prediction for snap_scaffold_5-snap.3108-T1
Valid prediction for GlimmerHMM_glimmerT_13438-T1
Valid prediction for snap_scaffold_5-snap.3127-T1
Valid prediction for GlimmerHMM_glimmerT_13410-T1
Valid prediction for Augustus_model.g8928.t1
Valid prediction for pasa_asmbl_44779.p1
Valid prediction for GlimmerHMM_glimmerT_13408-T1
Valid prediction for snap_scaffold_5-snap.3133-T1
Valid prediction for HiQ_model.g8918.t1
Valid prediction for snap_scaffold_5-snap.3106-T1
Valid prediction for snap_scaffold_5-snap.3095-T1
Valid prediction for GlimmerHMM_glimmerT_13432-T1
Valid prediction for snap_scaffold_5-snap.3115-T1
Couldn't classify 202558, 202603
Couldn't classify 204047, 204048
Sorry, prediction pasa_asmbl_44775.p1 fails validation.
(GGA)	 TT	202558-202603	GT	AAG
(TCA)	 AG	202717-202761	GT	CGG
(GGA)	 AG	202865-203000	GT	ATG
(GTG)	 AG	203869-203969	GT	CTG
(AGT)	 AG	204047-204048	TA	AGT
-recovered pasa_asmbl_44775.p1, internal, 202717, 202761
-recovered pasa_asmbl_44775.p1, internal, 202865, 203000
-recovered pasa_asmbl_44775.p1, internal, 203869, 203969
Valid prediction for snap_scaffold_5-snap.3094-T1
Valid prediction for Augustus_model.g8931.t1
Valid prediction for snap_scaffold_5-snap.3102-T1
Valid prediction for snap_scaffold_5-snap.3087-T1
Valid prediction for GlimmerHMM_glimmerT_13415-T1
Valid prediction for snap_scaffold_5-snap.3104-T1
Valid prediction for GlimmerHMM_glimmerT_13405-T1
Valid prediction for GlimmerHMM_glimmerT_13412-T1
Valid prediction for CodingQuarry_transcript_52424-T1
Valid prediction for snap_scaffold_5-snap.3098-T1
Valid prediction for snap_scaffold_5-snap.3101-T1
Couldn't classify 158130, 158172
Sorry, prediction pasa_asmbl_44777.p1 fails validation.
(ACG)	 TG	158130-158172	GT	TGG
(AGA)	 AG	158273-158408	GT	ATG
(GTG)	 AG	158472-158581	GT	AGG
(TGA)	 AG	158649-158665	GA	AGG
add_exon() Sorry, pasa_asmbl_44777.p1 158472-158581-terminal-2 is invalid.
-recovered pasa_asmbl_44777.p1, terminal, 158472, 158581
-recovered pasa_asmbl_44777.p1, terminal, 158649, 158665
-recovered pasa_asmbl_44777.p1, internal, 158273, 158408
-recovered pasa_asmbl_44777.p1, internal, 158472, 158581
Valid prediction for GlimmerHMM_glimmerT_13436-T1
Valid prediction for CodingQuarry_transcript_52422-T1
Valid prediction for snap_scaffold_5-snap.3125-T1
Valid prediction for Augustus_model.g8926.t1
Valid prediction for GlimmerHMM_glimmerT_13420-T1
Valid prediction for HiQ_model.g8936.t1
Valid prediction for Augustus_model.g8916.t1
Valid prediction for Augustus_model.g8934.t1
Valid prediction for snap_scaffold_5-snap.3110-T1
Valid prediction for CodingQuarry_transcript_52421-T1
Valid prediction for GlimmerHMM_glimmerT_13413-T1
Couldn't classify 186230, 186291
Couldn't classify 189183, 189264
Sorry, prediction pasa_asmbl_44939.p1 fails validation.
(GCA)	 CA	186230-186291	GT	AAG
(ATG)	 AG	186374-186483	GT	AAG
(TGA)	 AG	188783-188827	GT	TGG
(GGA)	 AG	188932-189067	GT	ATG
(GTG)	 AG	189183-189264	GA	TGG
add_exon() Sorry, pasa_asmbl_44939.p1 186374-186483-initial-1 is invalid.
-recovered pasa_asmbl_44939.p1, initial, 186374, 186483
-recovered pasa_asmbl_44939.p1, internal, 186374, 186483
-recovered pasa_asmbl_44939.p1, internal, 188783, 188827
-recovered pasa_asmbl_44939.p1, internal, 188932, 189067

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 76895, rend_intergenic: 63026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94747, rend_intergenic: 94505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102237, rend_intergenic: 95418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122628, rend_intergenic: 120336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142273, rend_intergenic: 133830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148911, rend_intergenic: 148416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170279, rend_intergenic: 158242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198426, rend_intergenic: 191220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221042, rend_intergenic: 220760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224051, rend_intergenic: 221769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229029, rend_intergenic: 224432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 11385, rend_intergenic: 11382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 240363
-exon list size: 426


building trellis

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34.6    
34.8    
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36.9    
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37.6    
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44.6    
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96.7    
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97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 76895, rend_intergenic: 63026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94747, rend_intergenic: 94505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102237, rend_intergenic: 95418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122628, rend_intergenic: 120336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142273, rend_intergenic: 133830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148911, rend_intergenic: 148416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170279, rend_intergenic: 158242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198426, rend_intergenic: 191220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221042, rend_intergenic: 220760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224051, rend_intergenic: 221769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229029, rend_intergenic: 224432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 11385, rend_intergenic: 11382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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