-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_14776193-14921471

-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_1990-T1
Valid prediction for GlimmerHMM_glimmerT_1997-T1
Valid prediction for GeneMark_model.2765_t
Valid prediction for snap_scaffold_1-snap.2571-T1
Valid prediction for GlimmerHMM_glimmerT_1989-T1
Valid prediction for GeneMark_model.2748_t
Valid prediction for Augustus_model.g1481.t1
Valid prediction for GeneMark_model.2770_t
Valid prediction for Augustus_model.g1477.t1
Valid prediction for GlimmerHMM_glimmerT_1992-T1
Valid prediction for snap_scaffold_1-snap.2567-T1
Valid prediction for snap_scaffold_1-snap.2568-T1
Couldn't classify 54505, 54602
Couldn't classify 62802, 62944
Sorry, prediction pasa_asmbl_2390.p1 fails validation.
(GCA)	 AA	54505-54602	GT	GAG
(CCC)	 AG	55807-55897	GT	CGG
(GTG)	 AG	57190-57342	GT	AGG
(GAA)	 AG	58218-58307	GT	AGG
(GCA)	 AG	59390-59486	GT	AGG
(TGG)	 AG	61205-61366	GT	TGG
(TGA)	 AG	62802-62944	GT	AGG
-recovered pasa_asmbl_2390.p1, internal, 55807, 55897
-recovered pasa_asmbl_2390.p1, internal, 57190, 57342
-recovered pasa_asmbl_2390.p1, internal, 58218, 58307
-recovered pasa_asmbl_2390.p1, internal, 59390, 59486
-recovered pasa_asmbl_2390.p1, internal, 61205, 61366
-recovered pasa_asmbl_2390.p1, internal, 62802, 62944
Valid prediction for Augustus_model.g1482.t1
Valid prediction for GeneMark_model.2754_t
Valid prediction for Augustus_model.g1480.t1
Valid prediction for GeneMark_model.2757_t
Valid prediction for GlimmerHMM_glimmerT_1991-T1
Valid prediction for snap_scaffold_1-snap.2570-T1
Valid prediction for GeneMark_model.2760_t
Valid prediction for GeneMark_model.2773_t
Valid prediction for GlimmerHMM_glimmerT_1995-T1
Valid prediction for GeneMark_model.2774_t
Valid prediction for snap_scaffold_1-snap.2583-T1
Valid prediction for GlimmerHMM_glimmerT_1986-T1
Valid prediction for Augustus_model.g1476.t1
Valid prediction for snap_scaffold_1-snap.2585-T1
Valid prediction for snap_scaffold_1-snap.2578-T1
Valid prediction for GlimmerHMM_glimmerT_1996-T1
Valid prediction for snap_scaffold_1-snap.2573-T1
Valid prediction for GlimmerHMM_glimmerT_2007-T1
Valid prediction for snap_scaffold_1-snap.2572-T1
Valid prediction for GlimmerHMM_glimmerT_2001-T1
Valid prediction for snap_scaffold_1-snap.2594-T1
Valid prediction for GlimmerHMM_glimmerT_1998-T1
Valid prediction for GlimmerHMM_glimmerT_1983-T1
Valid prediction for GeneMark_model.2750_t
Valid prediction for GlimmerHMM_glimmerT_2003-T1
Valid prediction for GeneMark_model.2752_t
Valid prediction for snap_scaffold_1-snap.2586-T1
Valid prediction for GeneMark_model.2767_t
Valid prediction for GlimmerHMM_glimmerT_2006-T1
Valid prediction for GlimmerHMM_glimmerT_1987-T1
Valid prediction for snap_scaffold_1-snap.2580-T1
Valid prediction for GeneMark_model.2746_t
Valid prediction for snap_scaffold_1-snap.2574-T1
Valid prediction for snap_scaffold_1-snap.2563-T1
Valid prediction for Augustus_model.g1474.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_2005-T1
Valid prediction for GeneMark_model.2755_t
Valid prediction for GlimmerHMM_glimmerT_2004-T1
Valid prediction for snap_scaffold_1-snap.2564-T1
Valid prediction for Augustus_model.g1478.t1
Valid prediction for snap_scaffold_1-snap.2595-T1
Couldn't classify 17475, 17513
Couldn't classify 17676, 17948
Sorry, prediction pasa_asmbl_1258.p1 fails validation.
(GAA)	 AG	17475-17513	GT	AGG
(TTC)	 AG	17676-17948	GC	AGG
-recovered pasa_asmbl_1258.p1, internal, 17475, 17513
-recovered pasa_asmbl_1258.p1, internal, 17676, 17948
Valid prediction for snap_scaffold_1-snap.2565-T1
Valid prediction for snap_scaffold_1-snap.2582-T1
Valid prediction for GlimmerHMM_glimmerT_1993-T1
Valid prediction for GeneMark_model.2761_t
Valid prediction for Augustus_model.g1479.t1
Valid prediction for GlimmerHMM_glimmerT_1984-T1
Valid prediction for snap_scaffold_1-snap.2569-T1
Valid prediction for Augustus_model.g1475.t1
Valid prediction for snap_scaffold_1-snap.2576-T1
Valid prediction for GeneMark_model.2758_t
Valid prediction for snap_scaffold_1-snap.2584-T1
Valid prediction for snap_scaffold_1-snap.2579-T1
Valid prediction for snap_scaffold_1-snap.2581-T1
Valid prediction for GlimmerHMM_glimmerT_1994-T1
Valid prediction for GlimmerHMM_glimmerT_1985-T1
Valid prediction for snap_scaffold_1-snap.2575-T1
Valid prediction for snap_scaffold_1-snap.2590-T1
Valid prediction for GeneMark_model.2743_t
Valid prediction for GlimmerHMM_glimmerT_2002-T1
Valid prediction for GeneMark_model.2753_t
Valid prediction for GeneMark_model.2772_t
Valid prediction for GeneMark_model.2769_t
Valid prediction for snap_scaffold_1-snap.2593-T1
Valid prediction for GlimmerHMM_glimmerT_1999-T1
Valid prediction for GeneMark_model.2751_t
Valid prediction for GeneMark_model.2762_t
Valid prediction for Augustus_model.g1484.t1
Valid prediction for snap_scaffold_1-snap.2577-T1
Valid prediction for GeneMark_model.2747_t
Valid prediction for GeneMark_model.2766_t
Valid prediction for snap_scaffold_1-snap.2589-T1
Valid prediction for GeneMark_model.2764_t
Valid prediction for GeneMark_model.2759_t
Valid prediction for snap_scaffold_1-snap.2591-T1
Valid prediction for Augustus_model.g1485.t1
Valid prediction for GlimmerHMM_glimmerT_1988-T1
Valid prediction for GeneMark_model.2744_t
Valid prediction for GeneMark_model.2768_t
Valid prediction for GeneMark_model.2745_t
Valid prediction for snap_scaffold_1-snap.2587-T1
Valid prediction for Augustus_model.g1483.t1
Valid prediction for snap_scaffold_1-snap.2592-T1
Valid prediction for GeneMark_model.2771_t
Valid prediction for snap_scaffold_1-snap.2588-T1
Valid prediction for GeneMark_model.2756_t
Valid prediction for GeneMark_model.2749_t
Valid prediction for GlimmerHMM_glimmerT_2000-T1
Valid prediction for snap_scaffold_1-snap.2566-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26824, rend_intergenic: 23864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72259, rend_intergenic: 60674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73461, rend_intergenic: 72755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76259, rend_intergenic: 73639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88157, rend_intergenic: 81203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96012, rend_intergenic: 95457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101525, rend_intergenic: 96187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105756, rend_intergenic: 101540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135661, rend_intergenic: 133436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 145279
-exon list size: 430


building trellis

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88.0    
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91.9    
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92.6    
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98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 17 predictions from path traversal
Error with prediction: snap lend_intergenic: 26824, rend_intergenic: 23864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72259, rend_intergenic: 60674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73461, rend_intergenic: 72755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76259, rend_intergenic: 73639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88157, rend_intergenic: 81203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96012, rend_intergenic: 95457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101525, rend_intergenic: 96187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105756, rend_intergenic: 101540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135661, rend_intergenic: 133436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 8 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 129731 - 145279
-exon list size: 22


building trellis

4.2    
8.3    
12.5    
16.7    
20.8    
25.0    
29.2    
33.3    
37.5    
41.7    
45.8    
50.0    
54.2    
58.3    
62.5    
66.7    
70.8    
75.0    
79.2    
83.3    
87.5    
91.7    
95.8    
-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