-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_9822592-10006382

-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 Augustus_model.g24487.t1
Valid prediction for snap_scaffold_15-snap.2056-T1
Valid prediction for snap_scaffold_15-snap.2029-T1
Valid prediction for snap_scaffold_15-snap.2038-T1
Valid prediction for GlimmerHMM_glimmerT_36782-T1
Valid prediction for snap_scaffold_15-snap.2047-T1
Valid prediction for Augustus_model.g24493.t1
Valid prediction for GlimmerHMM_glimmerT_36767-T1
Valid prediction for Augustus_model.g24499.t1
Valid prediction for snap_scaffold_15-snap.2036-T1
Valid prediction for Augustus_model.g24496.t1
Valid prediction for snap_scaffold_15-snap.2039-T1
Valid prediction for snap_scaffold_15-snap.2052-T1
Valid prediction for snap_scaffold_15-snap.2048-T1
Valid prediction for HiQ_model.g24490.t1
Valid prediction for GlimmerHMM_glimmerT_36781-T1
Valid prediction for GlimmerHMM_glimmerT_36786-T1
Valid prediction for CodingQuarry_transcript_18116-T1
Valid prediction for snap_scaffold_15-snap.2050-T1
Valid prediction for Augustus_model.g24498.t1
Valid prediction for GlimmerHMM_glimmerT_36784-T1
Valid prediction for GlimmerHMM_glimmerT_36774-T1
Valid prediction for snap_scaffold_15-snap.2032-T1
Valid prediction for GlimmerHMM_glimmerT_36772-T1
Valid prediction for snap_scaffold_15-snap.2024-T1
Valid prediction for GlimmerHMM_glimmerT_36770-T1
Valid prediction for CodingQuarry_transcript_18115-T1
Valid prediction for pasa_asmbl_15425.p1
Valid prediction for GlimmerHMM_glimmerT_36768-T1
Valid prediction for Augustus_model.g24497.t1
Valid prediction for snap_scaffold_15-snap.2020-T1
Valid prediction for CodingQuarry_transcript_18114-T1
Valid prediction for snap_scaffold_15-snap.2022-T1
Valid prediction for snap_scaffold_15-snap.2023-T1
Valid prediction for pasa_asmbl_15428.p1
Valid prediction for GlimmerHMM_glimmerT_36771-T1
Couldn't classify 106582, 106624
Sorry, prediction pasa_asmbl_15435.p1 fails validation.
(ATG)	 AC	104452-104544	GT	AGG
(CTG)	 AG	104990-105041	GT	AGG
(GGC)	 AG	105218-105254	GT	AGG
(CCC)	 AG	105944-106021	GT	AGG
(TAA)	 AG	106582-106624	AT	AGA
-recovered pasa_asmbl_15435.p1, initial, 104452, 104544
-recovered pasa_asmbl_15435.p1, internal, 104990, 105041
-recovered pasa_asmbl_15435.p1, internal, 105218, 105254
-recovered pasa_asmbl_15435.p1, internal, 105944, 106021
Valid prediction for snap_scaffold_15-snap.2027-T1
Valid prediction for snap_scaffold_15-snap.2035-T1
Valid prediction for GlimmerHMM_glimmerT_36776-T1
Couldn't classify 161895, 161981
Couldn't classify 165898, 166050
Sorry, prediction pasa_asmbl_15437.p1 fails validation.
(CAG)	 GC	161895-161981	GT	AGG
(GTG)	 AG	162215-162298	GT	AGG
(GGT)	 AG	164144-164257	GT	CGG
(AGG)	 AG	165898-166050	CT	CAC
-recovered pasa_asmbl_15437.p1, internal, 162215, 162298
-recovered pasa_asmbl_15437.p1, internal, 164144, 164257
Valid prediction for Augustus_model.g24491.t1
Valid prediction for GlimmerHMM_glimmerT_36769-T1
Valid prediction for snap_scaffold_15-snap.2043-T1
Valid prediction for pasa_asmbl_15432.p1

-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_15-snap.2033-T1
Valid prediction for HiQ_model.g24484.t1
Valid prediction for Augustus_model.g24488.t1
Valid prediction for snap_scaffold_15-snap.2034-T1
Valid prediction for snap_scaffold_15-snap.2046-T1
Valid prediction for GlimmerHMM_glimmerT_36777-T1
Valid prediction for GlimmerHMM_glimmerT_36783-T1
Valid prediction for CodingQuarry_transcript_18117-T1
Valid prediction for snap_scaffold_15-snap.2053-T1
Valid prediction for snap_scaffold_15-snap.2051-T1
Valid prediction for GlimmerHMM_glimmerT_36778-T1
Valid prediction for GlimmerHMM_glimmerT_36785-T1
Valid prediction for snap_scaffold_15-snap.2044-T1
Valid prediction for pasa_asmbl_14414.p1
Valid prediction for snap_scaffold_15-snap.2041-T1
Valid prediction for CodingQuarry_transcript_18118-T1
Valid prediction for GlimmerHMM_glimmerT_36763-T1
Valid prediction for pasa_asmbl_14420.p1
Valid prediction for snap_scaffold_15-snap.2040-T1
Valid prediction for snap_scaffold_15-snap.2055-T1
Valid prediction for snap_scaffold_15-snap.2030-T1
Valid prediction for HiQ_model.g24495.t1
Valid prediction for GlimmerHMM_glimmerT_36765-T1
Valid prediction for snap_scaffold_15-snap.2045-T1
Valid prediction for snap_scaffold_15-snap.2049-T1
Valid prediction for snap_scaffold_15-snap.2026-T1
Valid prediction for GlimmerHMM_glimmerT_36764-T1
Valid prediction for snap_scaffold_15-snap.2037-T1
Valid prediction for snap_scaffold_15-snap.2028-T1
Valid prediction for Augustus_model.g24485.t1
Couldn't classify 113905, 113959
Sorry, prediction pasa_asmbl_14923.p1 fails validation.
(CGC)	 GC	113905-113959	GT	CGG
(GTA)	 AG	114078-114251	GT	TGG
(ACT)	 AG	114410-114561	AG	AGA
-recovered pasa_asmbl_14923.p1, terminal, 114410, 114561
-recovered pasa_asmbl_14923.p1, internal, 114078, 114251
Valid prediction for pasa_asmbl_14413.p1
Valid prediction for snap_scaffold_15-snap.2021-T1
Valid prediction for snap_scaffold_15-snap.2042-T1
Valid prediction for GlimmerHMM_glimmerT_36775-T1
Valid prediction for snap_scaffold_15-snap.2025-T1
Valid prediction for GlimmerHMM_glimmerT_36780-T1
Valid prediction for Augustus_model.g24486.t1
Valid prediction for CodingQuarry_transcript_18113-T1
Valid prediction for Augustus_model.g24494.t1
Valid prediction for snap_scaffold_15-snap.2054-T1
Couldn't classify 108716, 108767
Couldn't classify 111550, 111641
Sorry, prediction pasa_asmbl_14872.p1 fails validation.
(GTG)	 AT	108716-108767	GT	AGG
(TGT)	 AG	108934-109125	GT	ATG
(GGT)	 AG	111550-111641	TA	CCT
-recovered pasa_asmbl_14872.p1, internal, 108934, 109125
Valid prediction for GlimmerHMM_glimmerT_36779-T1
Valid prediction for Augustus_model.g24489.t1
Valid prediction for Augustus_model.g24492.t1
Valid prediction for GlimmerHMM_glimmerT_36773-T1
Valid prediction for snap_scaffold_15-snap.2057-T1
Valid prediction for snap_scaffold_15-snap.2031-T1
Valid prediction for GlimmerHMM_glimmerT_36766-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26099, rend_intergenic: 13049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29992, rend_intergenic: 26737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37073, rend_intergenic: 36159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44946, rend_intergenic: 42443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53358, rend_intergenic: 46658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60511, rend_intergenic: 57329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79353, rend_intergenic: 69231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88155, rend_intergenic: 79882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96790, rend_intergenic: 88965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129692, rend_intergenic: 105923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138077, rend_intergenic: 130343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142134, rend_intergenic: 141199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155337, rend_intergenic: 142618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159748, rend_intergenic: 156141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172758, rend_intergenic: 159825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175176, rend_intergenic: 173385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181071, rend_intergenic: 175238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183791
-exon list size: 468


building trellis

0.2    
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0.6    
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1.1    
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2.6    
2.8    
3.0    
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8.9    
9.1    
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10.9    
11.1    
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11.9    
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19.6    
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20.9    
21.1    
21.3    
21.5    
21.7    
21.9    
22.1    
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22.6    
22.8    
23.0    
23.2    
23.4    
23.6    
23.8    
24.0    
24.3    
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24.7    
24.9    
25.1    
25.3    
25.5    
25.7    
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26.6    
26.8    
27.0    
27.2    
27.4    
27.7    
27.9    
28.1    
28.3    
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28.9    
29.1    
29.4    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.9    
31.1    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.4    
39.6    
39.8    
40.0    
40.2    
40.4    
40.6    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.1    
42.3    
42.6    
42.8    
43.0    
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44.0    
44.3    
44.5    
44.7    
44.9    
45.1    
45.3    
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46.4    
46.6    
46.8    
47.0    
47.2    
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48.1    
48.3    
48.5    
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51.3    
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52.6    
52.8    
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55.3    
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59.6    
59.8    
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60.2    
60.4    
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60.9    
61.1    
61.3    
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62.1    
62.3    
62.6    
62.8    
63.0    
63.2    
63.4    
63.6    
63.8    
64.0    
64.3    
64.5    
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64.9    
65.1    
65.3    
65.5    
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66.0    
66.2    
66.4    
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66.8    
67.0    
67.2    
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68.1    
68.3    
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68.9    
69.1    
69.4    
69.6    
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78.1    
78.3    
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78.7    
78.9    
79.1    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 26099, rend_intergenic: 13049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29992, rend_intergenic: 26737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37073, rend_intergenic: 36159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44946, rend_intergenic: 42443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53358, rend_intergenic: 46658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60511, rend_intergenic: 57329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79353, rend_intergenic: 69231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88155, rend_intergenic: 79882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96790, rend_intergenic: 88965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129692, rend_intergenic: 105923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138077, rend_intergenic: 130343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142134, rend_intergenic: 141199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155337, rend_intergenic: 142618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159748, rend_intergenic: 156141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172758, rend_intergenic: 159825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175176, rend_intergenic: 173385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181071, rend_intergenic: 175238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support