-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_13991830-14149228

-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_13-snap.2685-T1
Valid prediction for GlimmerHMM_glimmerT_32711-T1
Valid prediction for snap_scaffold_13-snap.2665-T1
Valid prediction for snap_scaffold_13-snap.2680-T1
Valid prediction for GlimmerHMM_glimmerT_32718-T1
Valid prediction for snap_scaffold_13-snap.2674-T1
Valid prediction for snap_scaffold_13-snap.2687-T1
Valid prediction for CodingQuarry_transcript_13295-T1
Valid prediction for snap_scaffold_13-snap.2678-T1
Valid prediction for snap_scaffold_13-snap.2669-T1
Valid prediction for snap_scaffold_13-snap.2684-T1
Valid prediction for snap_scaffold_13-snap.2673-T1
Valid prediction for CodingQuarry_transcript_13294-T1
Valid prediction for snap_scaffold_13-snap.2696-T1
Valid prediction for CodingQuarry_transcript_13296-T1
Valid prediction for GlimmerHMM_glimmerT_32733-T1
Valid prediction for GlimmerHMM_glimmerT_32716-T1
Valid prediction for Augustus_model.g21832.t1
Valid prediction for snap_scaffold_13-snap.2700-T1
Valid prediction for snap_scaffold_13-snap.2675-T1
Valid prediction for snap_scaffold_13-snap.2671-T1
Valid prediction for GlimmerHMM_glimmerT_32722-T1
Valid prediction for GlimmerHMM_glimmerT_32726-T1
Valid prediction for snap_scaffold_13-snap.2690-T1
Valid prediction for Augustus_model.g21840.t1
Valid prediction for GlimmerHMM_glimmerT_32728-T1
Valid prediction for Augustus_model.g21837.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_13-snap.2695-T1
Valid prediction for Augustus_model.g21838.t1
Valid prediction for GlimmerHMM_glimmerT_32734-T1
Valid prediction for Augustus_model.g21834.t1
Valid prediction for Augustus_model.g21831.t1
Valid prediction for Augustus_model.g21829.t1
Valid prediction for snap_scaffold_13-snap.2683-T1
Valid prediction for CodingQuarry_transcript_13293-T1
Valid prediction for snap_scaffold_13-snap.2666-T1
Valid prediction for snap_scaffold_13-snap.2691-T1
Valid prediction for snap_scaffold_13-snap.2667-T1
Valid prediction for GlimmerHMM_glimmerT_32717-T1
Valid prediction for snap_scaffold_13-snap.2698-T1
Valid prediction for snap_scaffold_13-snap.2668-T1
Valid prediction for GlimmerHMM_glimmerT_32724-T1
Valid prediction for GlimmerHMM_glimmerT_32731-T1
Valid prediction for snap_scaffold_13-snap.2682-T1
Valid prediction for GlimmerHMM_glimmerT_32720-T1
Couldn't classify 24474, 24651
Couldn't classify 25588, 25674
Sorry, prediction pasa_asmbl_10169.p1 fails validation.
(CAG)	 AG	24474-24651	GT	CGG
(AGT)	 AG	24863-25011	GT	GCG
(GTG)	 AG	25202-25432	GT	CTG
(GGC)	 AG	25588-25674	AA	TGA
-recovered pasa_asmbl_10169.p1, internal, 24474, 24651
-recovered pasa_asmbl_10169.p1, internal, 24863, 25011
-recovered pasa_asmbl_10169.p1, internal, 25202, 25432
Valid prediction for snap_scaffold_13-snap.2672-T1
Valid prediction for snap_scaffold_13-snap.2688-T1
Valid prediction for snap_scaffold_13-snap.2686-T1
Valid prediction for GlimmerHMM_glimmerT_32729-T1
Valid prediction for GlimmerHMM_glimmerT_32730-T1
Valid prediction for snap_scaffold_13-snap.2676-T1
Valid prediction for snap_scaffold_13-snap.2670-T1
Valid prediction for GlimmerHMM_glimmerT_32725-T1
Valid prediction for snap_scaffold_13-snap.2689-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_32723-T1
Valid prediction for snap_scaffold_13-snap.2681-T1
Valid prediction for CodingQuarry_transcript_13298-T1
Valid prediction for GlimmerHMM_glimmerT_32735-T1
Couldn't classify 51322, 51371
Sorry, prediction pasa_asmbl_10389.p1 fails validation.
(GTC)	 AT	51322-51371	GT	GGG
(GAT)	 AG	51476-51544	GT	TGG
(GGG)	 AG	52325-52394	GT	AGG
(TTA)	 AG	52723-52816	GT	GGG
(GCT)	 AG	53102-53217	GT	AGG
(CAC)	 AG	53591-53764	AC	AGA
-recovered pasa_asmbl_10389.p1, terminal, 53591, 53764
-recovered pasa_asmbl_10389.p1, internal, 51476, 51544
-recovered pasa_asmbl_10389.p1, internal, 52325, 52394
-recovered pasa_asmbl_10389.p1, internal, 52723, 52816
-recovered pasa_asmbl_10389.p1, internal, 53102, 53217
Valid prediction for Augustus_model.g21835.t1
Valid prediction for snap_scaffold_13-snap.2664-T1
Valid prediction for Augustus_model.g21842.t1
Valid prediction for snap_scaffold_13-snap.2679-T1
Valid prediction for GlimmerHMM_glimmerT_32732-T1
Valid prediction for GlimmerHMM_glimmerT_32727-T1
Valid prediction for GlimmerHMM_glimmerT_32713-T1
Valid prediction for Augustus_model.g21833.t1
Valid prediction for snap_scaffold_13-snap.2692-T1
Valid prediction for Augustus_model.g21841.t1
Valid prediction for GlimmerHMM_glimmerT_32719-T1
Valid prediction for GlimmerHMM_glimmerT_32712-T1
Valid prediction for snap_scaffold_13-snap.2677-T1
Valid prediction for snap_scaffold_13-snap.2694-T1
Valid prediction for GlimmerHMM_glimmerT_32715-T1
Valid prediction for CodingQuarry_transcript_13292-T1
Valid prediction for snap_scaffold_13-snap.2693-T1
Valid prediction for Augustus_model.g21839.t1
Valid prediction for Augustus_model.g21836.t1
Valid prediction for snap_scaffold_13-snap.2697-T1
Valid prediction for pasa_asmbl_10167.p1
Valid prediction for GlimmerHMM_glimmerT_32714-T1
Valid prediction for GlimmerHMM_glimmerT_32721-T1
Valid prediction for HiQ_model.g21830.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15459, rend_intergenic: 6447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34084, rend_intergenic: 26600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35367, rend_intergenic: 34543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47844, rend_intergenic: 35897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83400, rend_intergenic: 81009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85518, rend_intergenic: 84371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101111, rend_intergenic: 98108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106318, rend_intergenic: 103636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115832, rend_intergenic: 110000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128189, rend_intergenic: 120836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136531, rend_intergenic: 133339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 124926, rend_intergenic: 124923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 157399
-exon list size: 263


building trellis

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16.2    
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20.0    
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38.1    
38.5    
38.9    
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39.6    
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44.2    
44.5    
44.9    
45.3    
45.7    
46.0    
46.4    
46.8    
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47.9    
48.3    
48.7    
49.1    
49.4    
49.8    
50.2    
50.6    
50.9    
51.3    
51.7    
52.1    
52.5    
52.8    
53.2    
53.6    
54.0    
54.3    
54.7    
55.1    
55.5    
55.8    
56.2    
56.6    
57.0    
57.4    
57.7    
58.1    
58.5    
58.9    
59.2    
59.6    
60.0    
60.4    
60.8    
61.1    
61.5    
61.9    
62.3    
62.6    
63.0    
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63.8    
64.2    
64.5    
64.9    
65.3    
65.7    
66.0    
66.4    
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67.2    
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67.9    
68.3    
68.7    
69.1    
69.4    
69.8    
70.2    
70.6    
70.9    
71.3    
71.7    
72.1    
72.5    
72.8    
73.2    
73.6    
74.0    
74.3    
74.7    
75.1    
75.5    
75.8    
76.2    
76.6    
77.0    
77.4    
77.7    
78.1    
78.5    
78.9    
79.2    
79.6    
80.0    
80.4    
80.8    
81.1    
81.5    
81.9    
82.3    
82.6    
83.0    
83.4    
83.8    
84.2    
84.5    
84.9    
85.3    
85.7    
86.0    
86.4    
86.8    
87.2    
87.5    
87.9    
88.3    
88.7    
89.1    
89.4    
89.8    
90.2    
90.6    
90.9    
91.3    
91.7    
92.1    
92.5    
92.8    
93.2    
93.6    
94.0    
94.3    
94.7    
95.1    
95.5    
95.8    
96.2    
96.6    
97.0    
97.4    
97.7    
98.1    
98.5    
98.9    
99.2    
99.6    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 15459, rend_intergenic: 6447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34084, rend_intergenic: 26600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35367, rend_intergenic: 34543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47844, rend_intergenic: 35897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83400, rend_intergenic: 81009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85518, rend_intergenic: 84371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101111, rend_intergenic: 98108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106318, rend_intergenic: 103636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115832, rend_intergenic: 110000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128189, rend_intergenic: 120836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136531, rend_intergenic: 133339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 124926, rend_intergenic: 124923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 144495 - 157399
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 1 predictions from path traversal

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