-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_8522247-8712993

-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 snap_scaffold_3-snap.1746-T1
Valid prediction for snap_scaffold_3-snap.1758-T1
Valid prediction for snap_scaffold_3-snap.1745-T1
Valid prediction for snap_scaffold_3-snap.1735-T1
Valid prediction for GlimmerHMM_glimmerT_6977-T1
Valid prediction for GlimmerHMM_glimmerT_6986-T1
Valid prediction for Augustus_model.g4562.t1
Valid prediction for snap_scaffold_3-snap.1757-T1
Valid prediction for snap_scaffold_3-snap.1737-T1
Valid prediction for snap_scaffold_3-snap.1732-T1
Valid prediction for GlimmerHMM_glimmerT_6969-T1
Valid prediction for snap_scaffold_3-snap.1761-T1
Valid prediction for snap_scaffold_3-snap.1731-T1
Valid prediction for Augustus_model.g4561.t1
Valid prediction for snap_scaffold_3-snap.1752-T1
Valid prediction for Augustus_model.g4567.t1
Valid prediction for GlimmerHMM_glimmerT_6978-T1
Valid prediction for snap_scaffold_3-snap.1741-T1
Valid prediction for snap_scaffold_3-snap.1762-T1
Valid prediction for Augustus_model.g4564.t1
Valid prediction for GlimmerHMM_glimmerT_6979-T1
Valid prediction for snap_scaffold_3-snap.1733-T1
Valid prediction for GlimmerHMM_glimmerT_6981-T1
Valid prediction for GlimmerHMM_glimmerT_6973-T1
Valid prediction for HiQ_model.g4558.t1
Valid prediction for GlimmerHMM_glimmerT_6971-T1
Valid prediction for GlimmerHMM_glimmerT_6967-T1
Valid prediction for snap_scaffold_3-snap.1749-T1
Valid prediction for GlimmerHMM_glimmerT_6975-T1
Valid prediction for GlimmerHMM_glimmerT_6968-T1
Valid prediction for snap_scaffold_3-snap.1744-T1
Couldn't classify 65147, 65285
Couldn't classify 68122, 68157
Sorry, prediction pasa_asmbl_40219.p1 fails validation.
(ACC)	 AC	65147-65285	GT	CTG
(GCC)	 AG	66177-66233	GT	TGG
(TTC)	 AG	66927-67117	GT	ACG
(CAC)	 AG	67216-67344	GT	AGG
(GTG)	 AG	67494-67700	GT	AGG
(GGC)	 AG	68122-68157	AG	CCA
-recovered pasa_asmbl_40219.p1, internal, 66177, 66233
-recovered pasa_asmbl_40219.p1, internal, 66927, 67117
-recovered pasa_asmbl_40219.p1, internal, 67216, 67344
-recovered pasa_asmbl_40219.p1, internal, 67494, 67700
Valid prediction for snap_scaffold_3-snap.1759-T1
Valid prediction for pasa_asmbl_40217.p1
Valid prediction for GlimmerHMM_glimmerT_6976-T1
Valid prediction for snap_scaffold_3-snap.1755-T1
Valid prediction for Augustus_model.g4559.t1
Valid prediction for snap_scaffold_3-snap.1736-T1
Valid prediction for snap_scaffold_3-snap.1763-T1
Valid prediction for snap_scaffold_3-snap.1751-T1
Valid prediction for CodingQuarry_transcript_46231-T1
Valid prediction for GlimmerHMM_glimmerT_6983-T1
Valid prediction for snap_scaffold_3-snap.1760-T1
Valid prediction for Augustus_model.g4565.t1
Valid prediction for GlimmerHMM_glimmerT_6991-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 pasa_asmbl_39043.p1
Valid prediction for snap_scaffold_3-snap.1748-T1
Valid prediction for GlimmerHMM_glimmerT_6984-T1
Valid prediction for GlimmerHMM_glimmerT_6966-T1
Valid prediction for Augustus_model.g4570.t1
Valid prediction for snap_scaffold_3-snap.1756-T1
Valid prediction for snap_scaffold_3-snap.1743-T1
Valid prediction for GlimmerHMM_glimmerT_6987-T1
Valid prediction for snap_scaffold_3-snap.1742-T1
Valid prediction for snap_scaffold_3-snap.1740-T1
Valid prediction for GlimmerHMM_glimmerT_6982-T1
Valid prediction for GlimmerHMM_glimmerT_6965-T1
Valid prediction for snap_scaffold_3-snap.1738-T1
Valid prediction for Augustus_model.g4568.t1
Valid prediction for GlimmerHMM_glimmerT_6992-T1
Valid prediction for Augustus_model.g4569.t1
Valid prediction for GlimmerHMM_glimmerT_6988-T1
Valid prediction for snap_scaffold_3-snap.1730-T1
Valid prediction for GlimmerHMM_glimmerT_6974-T1
Valid prediction for GlimmerHMM_glimmerT_6989-T1
Valid prediction for GlimmerHMM_glimmerT_6970-T1
Valid prediction for GlimmerHMM_glimmerT_6990-T1
Valid prediction for snap_scaffold_3-snap.1747-T1
Valid prediction for snap_scaffold_3-snap.1754-T1
Valid prediction for snap_scaffold_3-snap.1734-T1
Valid prediction for Augustus_model.g4560.t1
Valid prediction for Augustus_model.g4571.t1
Valid prediction for Augustus_model.g4557.t1
Valid prediction for GlimmerHMM_glimmerT_6980-T1
Valid prediction for Augustus_model.g4566.t1
Valid prediction for snap_scaffold_3-snap.1729-T1
Valid prediction for snap_scaffold_3-snap.1750-T1
Valid prediction for Augustus_model.g4563.t1
Valid prediction for snap_scaffold_3-snap.1753-T1
Valid prediction for GlimmerHMM_glimmerT_6972-T1
Valid prediction for CodingQuarry_transcript_46230-T1
Valid prediction for GlimmerHMM_glimmerT_6985-T1
Valid prediction for snap_scaffold_3-snap.1739-T1
Valid prediction for HiQ_model.g4556.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18353, rend_intergenic: 16259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20369, rend_intergenic: 18802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34501, rend_intergenic: 23682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69027, rend_intergenic: 46351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113709, rend_intergenic: 108276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190747
-exon list size: 359


building trellis

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44.0    
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45.4    
45.7    
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85.6    
85.9    
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89.5    
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90.0    
90.3    
90.6    
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91.1    
91.4    
91.7    
92.0    
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92.8    
93.1    
93.4    
93.6    
93.9    
94.2    
94.5    
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95.3    
95.6    
95.8    
96.1    
96.4    
96.7    
97.0    
97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 18353, rend_intergenic: 16259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20369, rend_intergenic: 18802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34501, rend_intergenic: 23682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69027, rend_intergenic: 46351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113709, rend_intergenic: 108276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 180577 - 190747
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

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