-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_15074542-15326642

-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_25984-T1
Valid prediction for snap_scaffold_10-snap.3060-T1
Valid prediction for snap_scaffold_10-snap.3043-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_25998-T1
Valid prediction for snap_scaffold_10-snap.3070-T1
Valid prediction for Augustus_model.g17281.t1
Valid prediction for snap_scaffold_10-snap.3055-T1
Valid prediction for snap_scaffold_10-snap.3045-T1
Valid prediction for snap_scaffold_10-snap.3048-T1
Valid prediction for snap_scaffold_10-snap.3073-T1
Couldn't classify 234691, 235266
Sorry, prediction pasa_asmbl_3677.p1 fails validation.
(AAC)	 CC	234691-235266	AT	TGA
Valid prediction for snap_scaffold_10-snap.3049-T1
Valid prediction for GlimmerHMM_glimmerT_25983-T1
Valid prediction for snap_scaffold_10-snap.3056-T1
Valid prediction for GlimmerHMM_glimmerT_26002-T1
Valid prediction for GlimmerHMM_glimmerT_25989-T1
Valid prediction for Augustus_model.g17271.t1
Valid prediction for snap_scaffold_10-snap.3039-T1
Valid prediction for snap_scaffold_10-snap.3050-T1
Valid prediction for snap_scaffold_10-snap.3053-T1
Valid prediction for snap_scaffold_10-snap.3063-T1
Valid prediction for snap_scaffold_10-snap.3080-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_25996-T1
Valid prediction for snap_scaffold_10-snap.3042-T1
Valid prediction for GlimmerHMM_glimmerT_25976-T1
Valid prediction for snap_scaffold_10-snap.3066-T1
Valid prediction for snap_scaffold_10-snap.3047-T1
Valid prediction for snap_scaffold_10-snap.3065-T1
Valid prediction for GlimmerHMM_glimmerT_25977-T1
Valid prediction for GlimmerHMM_glimmerT_25988-T1
Valid prediction for snap_scaffold_10-snap.3054-T1
Valid prediction for Augustus_model.g17274.t1
Valid prediction for snap_scaffold_10-snap.3059-T1
Valid prediction for snap_scaffold_10-snap.3075-T1
Valid prediction for snap_scaffold_10-snap.3041-T1
Valid prediction for snap_scaffold_10-snap.3071-T1
Valid prediction for snap_scaffold_10-snap.3084-T1
Valid prediction for GlimmerHMM_glimmerT_25986-T1
Valid prediction for snap_scaffold_10-snap.3037-T1
Valid prediction for Augustus_model.g17283.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 snap_scaffold_10-snap.3077-T1
Valid prediction for snap_scaffold_10-snap.3067-T1
Valid prediction for Augustus_model.g17269.t1
Valid prediction for snap_scaffold_10-snap.3083-T1
Valid prediction for GlimmerHMM_glimmerT_26000-T1
Valid prediction for snap_scaffold_10-snap.3076-T1
Valid prediction for snap_scaffold_10-snap.3078-T1
Valid prediction for snap_scaffold_10-snap.3052-T1
Valid prediction for GlimmerHMM_glimmerT_25997-T1
Valid prediction for snap_scaffold_10-snap.3079-T1
Valid prediction for Augustus_model.g17276.t1
Valid prediction for GlimmerHMM_glimmerT_25992-T1
Valid prediction for snap_scaffold_10-snap.3085-T1
Valid prediction for snap_scaffold_10-snap.3068-T1
Valid prediction for snap_scaffold_10-snap.3082-T1
Valid prediction for GlimmerHMM_glimmerT_25995-T1
Valid prediction for Augustus_model.g17268.t1
Valid prediction for GlimmerHMM_glimmerT_25979-T1
Valid prediction for snap_scaffold_10-snap.3062-T1
Valid prediction for GlimmerHMM_glimmerT_25978-T1
Valid prediction for Augustus_model.g17263.t1
Valid prediction for CodingQuarry_transcript_5659-T1
Valid prediction for GlimmerHMM_glimmerT_25981-T1
Couldn't classify 101187, 101318
Couldn't classify 101730, 101885
Sorry, prediction pasa_asmbl_5111.p1 fails validation.
(GAG)	 GG	101187-101318	GT	AGG
(GGG)	 AG	101551-101628	GT	TGG
(AGT)	 AG	101730-101885	AC	AGA
-recovered pasa_asmbl_5111.p1, internal, 101551, 101628
Valid prediction for GlimmerHMM_glimmerT_25985-T1
Valid prediction for snap_scaffold_10-snap.3064-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.3061-T1
Valid prediction for Augustus_model.g17282.t1
Valid prediction for GlimmerHMM_glimmerT_25994-T1
Valid prediction for GlimmerHMM_glimmerT_26003-T1
Valid prediction for Augustus_model.g17262.t1
Valid prediction for CodingQuarry_transcript_5658-T1
Valid prediction for snap_scaffold_10-snap.3072-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_25987-T1
Couldn't classify 23969, 24043
Sorry, prediction pasa_asmbl_4977.p1 fails validation.
(ACT)	 TC	23969-24043	GT	GGG
(ATG)	 AG	24334-24468	GT	AAG
(GCA)	 AG	25289-25504	TT	AGT
-recovered pasa_asmbl_4977.p1, initial, 24334, 24468
-recovered pasa_asmbl_4977.p1, terminal, 25289, 25504
-recovered pasa_asmbl_4977.p1, internal, 24334, 24468
Valid prediction for GlimmerHMM_glimmerT_26001-T1
Valid prediction for Augustus_model.g17264.t1
Valid prediction for Augustus_model.g17265.t1
Valid prediction for snap_scaffold_10-snap.3038-T1
Valid prediction for GlimmerHMM_glimmerT_25999-T1
Valid prediction for Augustus_model.g17261.t1
Valid prediction for snap_scaffold_10-snap.3044-T1
Valid prediction for snap_scaffold_10-snap.3058-T1
Valid prediction for GlimmerHMM_glimmerT_25980-T1
Valid prediction for Augustus_model.g17277.t1
Valid prediction for snap_scaffold_10-snap.3046-T1
Valid prediction for GlimmerHMM_glimmerT_26004-T1
Valid prediction for snap_scaffold_10-snap.3069-T1
Valid prediction for snap_scaffold_10-snap.3040-T1
Valid prediction for Augustus_model.g17278.t1
Valid prediction for pasa_asmbl_5172.p1
Valid prediction for GlimmerHMM_glimmerT_25990-T1
Valid prediction for GlimmerHMM_glimmerT_25982-T1
Valid prediction for Augustus_model.g17267.t1
Valid prediction for Augustus_model.g17275.t1
Valid prediction for Augustus_model.g17273.t1
Valid prediction for GlimmerHMM_glimmerT_25993-T1
Couldn't classify 20133, 20250
Couldn't classify 22171, 22318
Sorry, prediction pasa_asmbl_4979.p1 fails validation.
(TAC)	 AG	20133-20250	GT	GGG
(GCG)	 AG	21116-21266	GT	AAG
(CAT)	 AG	22171-22318	AA	AGA
-recovered pasa_asmbl_4979.p1, internal, 20133, 20250
-recovered pasa_asmbl_4979.p1, internal, 21116, 21266
Valid prediction for snap_scaffold_10-snap.3081-T1
Valid prediction for Augustus_model.g17266.t1
Valid prediction for snap_scaffold_10-snap.3051-T1
Valid prediction for GlimmerHMM_glimmerT_25991-T1
Valid prediction for snap_scaffold_10-snap.3057-T1
Valid prediction for snap_scaffold_10-snap.3086-T1
Couldn't classify 23319, 23570
Sorry, prediction pasa_asmbl_4978.p2 fails validation.
(ATG)	 AC	22804-22911	GT	CGG
(TCT)	 AG	23319-23570	GA	CCG
-recovered pasa_asmbl_4978.p2, initial, 22804, 22911
Valid prediction for HiQ_model.g17279.t1
Valid prediction for Augustus_model.g17280.t1
Valid prediction for Augustus_model.g17272.t1
Valid prediction for pasa_asmbl_4976.p1
Valid prediction for snap_scaffold_10-snap.3074-T1
Valid prediction for Augustus_model.g17270.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8094, rend_intergenic: 6772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22906, rend_intergenic: 19929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33118, rend_intergenic: 22974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37801, rend_intergenic: 33235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42477, rend_intergenic: 38640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43828, rend_intergenic: 43612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69509, rend_intergenic: 46828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74395, rend_intergenic: 71487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94797, rend_intergenic: 75947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108701, rend_intergenic: 94933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128461, rend_intergenic: 110239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130767, rend_intergenic: 128464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140102, rend_intergenic: 137761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153693, rend_intergenic: 140935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174104, rend_intergenic: 170794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177657, rend_intergenic: 174990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182087, rend_intergenic: 178200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182385, rend_intergenic: 182233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187521, rend_intergenic: 183341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218412, rend_intergenic: 210990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 252101
-exon list size: 477


building trellis

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-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 8094, rend_intergenic: 6772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22906, rend_intergenic: 19929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33118, rend_intergenic: 22974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37801, rend_intergenic: 33235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42477, rend_intergenic: 38640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43828, rend_intergenic: 43612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69509, rend_intergenic: 46828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74395, rend_intergenic: 71487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94797, rend_intergenic: 75947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108701, rend_intergenic: 94933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128461, rend_intergenic: 110239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130767, rend_intergenic: 128464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140102, rend_intergenic: 137761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153693, rend_intergenic: 140935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174104, rend_intergenic: 170794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177657, rend_intergenic: 174990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182087, rend_intergenic: 178200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182385, rend_intergenic: 182233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187521, rend_intergenic: 183341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218412, rend_intergenic: 210990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 18506
-exon list size: 8


building trellis

10.0    
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-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10003
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
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85.7    
-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

-building DP trellis

-building trellis in range 238678 - 252101
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-found 3 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support