-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_10421572-10659444

-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_7-snap.2018-T1
Valid prediction for GlimmerHMM_glimmerT_18431-T1
Valid prediction for snap_scaffold_7-snap.2019-T1
Valid prediction for snap_scaffold_7-snap.2035-T1
Valid prediction for snap_scaffold_7-snap.2039-T1
Valid prediction for snap_scaffold_7-snap.2026-T1
Valid prediction for GeneMark_model.30911_t
Valid prediction for GeneMark_model.30930_t
Valid prediction for GlimmerHMM_glimmerT_18444-T1
Valid prediction for snap_scaffold_7-snap.2016-T1
Valid prediction for GeneMark_model.30938_t
Valid prediction for GeneMark_model.30925_t
Valid prediction for pasa_asmbl_51010.p1
Valid prediction for snap_scaffold_7-snap.2015-T1
Valid prediction for GeneMark_model.30898_t
Valid prediction for GeneMark_model.30894_t
Valid prediction for GlimmerHMM_glimmerT_18427-T1
Valid prediction for GeneMark_model.30934_t
Valid prediction for GeneMark_model.30928_t
Valid prediction for snap_scaffold_7-snap.2011-T1
Valid prediction for GlimmerHMM_glimmerT_18434-T1
Valid prediction for Augustus_model.g12437.t1
Valid prediction for Augustus_model.g12432.t1
Valid prediction for GeneMark_model.30920_t
Valid prediction for Augustus_model.g12428.t1
Valid prediction for Augustus_model.g12444.t1
Valid prediction for snap_scaffold_7-snap.2031-T1
Valid prediction for GeneMark_model.30906_t
Valid prediction for GeneMark_model.30900_t
Valid prediction for snap_scaffold_7-snap.2027-T1
Valid prediction for Augustus_model.g12429.t1
Valid prediction for GeneMark_model.30891_t
Valid prediction for GlimmerHMM_glimmerT_18443-T1
Valid prediction for GlimmerHMM_glimmerT_18430-T1
Valid prediction for Augustus_model.g12431.t1
Valid prediction for snap_scaffold_7-snap.2025-T1
Valid prediction for Augustus_model.g12430.t1
Valid prediction for GeneMark_model.30936_t
Valid prediction for GeneMark_model.30909_t
Valid prediction for pasa_asmbl_51008.p1
Valid prediction for GeneMark_model.30902_t
Valid prediction for GeneMark_model.30904_t
Valid prediction for GeneMark_model.30932_t
Valid prediction for Augustus_model.g12441.t1
Valid prediction for snap_scaffold_7-snap.2037-T1
Valid prediction for GeneMark_model.30907_t
Valid prediction for GeneMark_model.30916_t
Valid prediction for GlimmerHMM_glimmerT_18424-T1
Valid prediction for snap_scaffold_7-snap.2049-T1
Couldn't classify 131663, 132631
Sorry, prediction pasa_asmbl_51013.p1 fails validation.
(ATG)	 AG	131663-132631	GA	CCG
Valid prediction for GlimmerHMM_glimmerT_18441-T1
Valid prediction for GlimmerHMM_glimmerT_18448-T1
Valid prediction for GeneMark_model.30923_t
Valid prediction for Augustus_model.g12438.t1
Valid prediction for GlimmerHMM_glimmerT_18436-T1
Valid prediction for GeneMark_model.30889_t
Valid prediction for HiQ_model.g12435.t1
Valid prediction for snap_scaffold_7-snap.2009-T1
Valid prediction for GlimmerHMM_glimmerT_18446-T1
Valid prediction for Augustus_model.g12443.t1
Valid prediction for snap_scaffold_7-snap.2014-T1
Valid prediction for snap_scaffold_7-snap.2044-T1
Valid prediction for GeneMark_model.30918_t
Valid prediction for snap_scaffold_7-snap.2034-T1
Valid prediction for snap_scaffold_7-snap.2029-T1
Valid prediction for CodingQuarry_transcript_57468-T1
Valid prediction for snap_scaffold_7-snap.2020-T1
Valid prediction for snap_scaffold_7-snap.2040-T1
Valid prediction for snap_scaffold_7-snap.2013-T1
Valid prediction for snap_scaffold_7-snap.2033-T1
Valid prediction for GeneMark_model.30913_t
Valid prediction for snap_scaffold_7-snap.2045-T1
Valid prediction for snap_scaffold_7-snap.2024-T1
Valid prediction for GlimmerHMM_glimmerT_18440-T1
Valid prediction for snap_scaffold_7-snap.2017-T1
Valid prediction for Augustus_model.g12425.t1
Valid prediction for GeneMark_model.30896_t
Valid prediction for snap_scaffold_7-snap.2042-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 HiQ_model.g12434.t1
Valid prediction for HiQ_model.g12436.t1
Valid prediction for GeneMark_model.30893_t
Valid prediction for GlimmerHMM_glimmerT_18447-T1
Valid prediction for snap_scaffold_7-snap.2032-T1
Valid prediction for GeneMark_model.30892_t
Valid prediction for GeneMark_model.30927_t
Valid prediction for GlimmerHMM_glimmerT_18423-T1
Valid prediction for GeneMark_model.30899_t
Valid prediction for snap_scaffold_7-snap.2021-T1
Valid prediction for snap_scaffold_7-snap.2043-T1
Couldn't classify 87761, 88028
Sorry, prediction pasa_asmbl_49948.p1 fails validation.
(GCC)	 CT	87761-88028	GT	AGG
(GTG)	 AG	90692-90771	TT	AGT
-recovered pasa_asmbl_49948.p1, terminal, 90692, 90771
Valid prediction for snap_scaffold_7-snap.2048-T1
Valid prediction for GeneMark_model.30897_t
Valid prediction for snap_scaffold_7-snap.2022-T1
Valid prediction for Augustus_model.g12427.t1
Valid prediction for GlimmerHMM_glimmerT_18439-T1
Valid prediction for snap_scaffold_7-snap.2023-T1
Valid prediction for pasa_asmbl_49942.p1
Valid prediction for GeneMark_model.30912_t
Valid prediction for GeneMark_model.30929_t
Valid prediction for Augustus_model.g12423.t1
Valid prediction for Augustus_model.g12426.t1
Valid prediction for Augustus_model.g12433.t1
Valid prediction for snap_scaffold_7-snap.2047-T1
Valid prediction for Augustus_model.g12439.t1
Valid prediction for snap_scaffold_7-snap.2041-T1
Valid prediction for snap_scaffold_7-snap.2008-T1
Valid prediction for GeneMark_model.30931_t
Valid prediction for CodingQuarry_transcript_57469-T1
Valid prediction for snap_scaffold_7-snap.2012-T1
Valid prediction for GeneMark_model.30901_t
Valid prediction for GeneMark_model.30926_t
Valid prediction for GeneMark_model.30915_t
Valid prediction for GeneMark_model.30914_t
Valid prediction for GeneMark_model.30895_t
Valid prediction for snap_scaffold_7-snap.2007-T1
Valid prediction for GlimmerHMM_glimmerT_18449-T1
Valid prediction for GeneMark_model.30924_t
Valid prediction for GlimmerHMM_glimmerT_18437-T1
Valid prediction for CodingQuarry_transcript_57467-T1
Valid prediction for snap_scaffold_7-snap.2036-T1
Valid prediction for GeneMark_model.30905_t
Valid prediction for GlimmerHMM_glimmerT_18432-T1
Valid prediction for GlimmerHMM_glimmerT_18442-T1
Valid prediction for GeneMark_model.30887_t
Valid prediction for Augustus_model.g12440.t1
Valid prediction for snap_scaffold_7-snap.2028-T1
Valid prediction for GeneMark_model.30922_t
Valid prediction for GlimmerHMM_glimmerT_18426-T1
Valid prediction for GeneMark_model.30921_t
Valid prediction for GeneMark_model.30919_t
Valid prediction for GeneMark_model.30917_t
Valid prediction for Augustus_model.g12442.t1
Valid prediction for GlimmerHMM_glimmerT_18438-T1
Valid prediction for snap_scaffold_7-snap.2046-T1
Valid prediction for snap_scaffold_7-snap.2030-T1
Valid prediction for Augustus_model.g12424.t1
Valid prediction for GlimmerHMM_glimmerT_18433-T1
Valid prediction for GeneMark_model.30935_t
Valid prediction for GlimmerHMM_glimmerT_18429-T1
Valid prediction for GeneMark_model.30888_t
Valid prediction for Augustus_model.g12446.t1
Valid prediction for GeneMark_model.30890_t
Valid prediction for GeneMark_model.30933_t
Valid prediction for GlimmerHMM_glimmerT_18435-T1
Valid prediction for pasa_asmbl_49939.p1
Valid prediction for GlimmerHMM_glimmerT_18425-T1
Valid prediction for GlimmerHMM_glimmerT_18428-T1
Valid prediction for GeneMark_model.30937_t
Valid prediction for GeneMark_model.30903_t
Valid prediction for Augustus_model.g12445.t1
Valid prediction for HiQ_model.g12447.t1
Valid prediction for GeneMark_model.30908_t
Valid prediction for GlimmerHMM_glimmerT_18445-T1
Valid prediction for snap_scaffold_7-snap.2010-T1
Valid prediction for GeneMark_model.30910_t
Valid prediction for snap_scaffold_7-snap.2038-T1
Couldn't classify 12216, 12297
Sorry, prediction pasa_asmbl_49950.p1 fails validation.
(AGA)	 TC	12216-12297	GT	GGG
(AGA)	 AG	12529-12944	GT	ATG
(GTT)	 AG	13086-13314	GT	CAG
(ATG)	 AG	14072-14187	GA	GAG
-recovered pasa_asmbl_49950.p1, terminal, 14072, 14187
-recovered pasa_asmbl_49950.p1, internal, 12529, 12944
-recovered pasa_asmbl_49950.p1, internal, 13086, 13314

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 152659, rend_intergenic: 147417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157742, rend_intergenic: 152935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160977, rend_intergenic: 158361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172777, rend_intergenic: 161521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181044, rend_intergenic: 179291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182525, rend_intergenic: 181201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184492, rend_intergenic: 183004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189272, rend_intergenic: 185124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195162, rend_intergenic: 190194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215982, rend_intergenic: 214231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 237873
-exon list size: 544


building trellis

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41.2    
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41.6    
41.8    
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42.1    
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42.9    
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43.4    
43.6    
43.8    
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44.1    
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44.5    
44.7    
44.9    
45.1    
45.2    
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45.8    
46.0    
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47.1    
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54.8    
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58.8    
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60.1    
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60.6    
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75.8    
76.0    
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77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
78.9    
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83.2    
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90.7    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
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93.0    
93.2    
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93.8    
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94.1    
94.3    
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94.9    
95.1    
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95.6    
95.8    
96.0    
96.2    
96.3    
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96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 152659, rend_intergenic: 147417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157742, rend_intergenic: 152935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160977, rend_intergenic: 158361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172777, rend_intergenic: 161521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181044, rend_intergenic: 179291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182525, rend_intergenic: 181201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184492, rend_intergenic: 183004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189272, rend_intergenic: 185124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195162, rend_intergenic: 190194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215982, rend_intergenic: 214231  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 225716 - 237873
-exon list size: 18


building trellis

5.0    
10.0    
15.0    
20.0    
25.0    
30.0    
35.0    
40.0    
45.0    
50.0    
55.0    
60.0    
65.0    
70.0    
75.0    
80.0    
85.0    
90.0    
95.0    
-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 226870 - 237873
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-found 1 predictions from path traversal

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