-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_8/scaffold_8_5781343-6001730

-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_20259-T1
Couldn't classify 191087, 191145
Couldn't classify 191706, 191874
Sorry, prediction pasa_asmbl_52596.p1 fails validation.
(ATT)	 CG	191087-191145	GT	TGG
(GGT)	 AG	191248-191400	GT	AGG
(GGT)	 AG	191541-191594	GT	AAG
(ACA)	 AG	191706-191874	TC	AGT
-recovered pasa_asmbl_52596.p1, internal, 191248, 191400
-recovered pasa_asmbl_52596.p1, internal, 191541, 191594
Valid prediction for Augustus_model.g13551.t1
Couldn't classify 141481, 142065
Sorry, prediction pasa_asmbl_51902.p1 fails validation.
(CTG)	 GT	141481-142065	GT	AGG
(GGC)	 AG	143043-143234	GT	AGG
(GTG)	 AG	143347-143518	GT	AGG
(ATA)	 AG	143661-143842	GT	AAG
-recovered pasa_asmbl_51902.p1, terminal, 143661, 143842
-recovered pasa_asmbl_51902.p1, internal, 143043, 143234
-recovered pasa_asmbl_51902.p1, internal, 143347, 143518
-recovered pasa_asmbl_51902.p1, internal, 143661, 143842
Valid prediction for GeneMark_model.34682_t
Valid prediction for snap_scaffold_8-snap.1190-T1
Couldn't classify 185540, 185540
Sorry, prediction CodingQuarry_transcript_59519-T1 fails validation.
(AGT)	 CA	185540-185540	GT	AAG
(TGG)	 AG	185639-185709	GT	AGG
(AAT)	 AG	185820-185924	GT	AAG
(GGT)	 AG	186047-186133	GT	TGG
(TCG)	 AG	186711-186766	GT	GGG
(TGG)	 AG	186875-186956	GT	ATG
(GAC)	 AG	187049-187117	GT	GTG
(TAT)	 AG	187225-187331	GT	AGG
(TAC)	 AG	187459-187584	GT	GGG
(CTA)	 AG	187767-187842	TC	GAT
-recovered CodingQuarry_transcript_59519-T1, terminal, 187767, 187842
-recovered CodingQuarry_transcript_59519-T1, internal, 185639, 185709
-recovered CodingQuarry_transcript_59519-T1, internal, 185820, 185924
-recovered CodingQuarry_transcript_59519-T1, internal, 186047, 186133
-recovered CodingQuarry_transcript_59519-T1, internal, 186711, 186766
-recovered CodingQuarry_transcript_59519-T1, internal, 186875, 186956
-recovered CodingQuarry_transcript_59519-T1, internal, 187049, 187117
-recovered CodingQuarry_transcript_59519-T1, internal, 187225, 187331
-recovered CodingQuarry_transcript_59519-T1, internal, 187459, 187584
Valid prediction for snap_scaffold_8-snap.1200-T1
Valid prediction for GlimmerHMM_glimmerT_20258-T1
Valid prediction for pasa_asmbl_51903.p1
Valid prediction for snap_scaffold_8-snap.1180-T1
Valid prediction for GeneMark_model.34690_t
Valid prediction for snap_scaffold_8-snap.1196-T1
Valid prediction for GlimmerHMM_glimmerT_20273-T1
Valid prediction for GlimmerHMM_glimmerT_20268-T1
Valid prediction for GlimmerHMM_glimmerT_20269-T1
Valid prediction for GlimmerHMM_glimmerT_20266-T1
Valid prediction for CodingQuarry_transcript_59516-T1
Valid prediction for GeneMark_model.34672_t
Valid prediction for Augustus_model.g13548.t1
Valid prediction for snap_scaffold_8-snap.1191-T1
Valid prediction for Augustus_model.g13541.t1
Valid prediction for snap_scaffold_8-snap.1204-T1
Valid prediction for GeneMark_model.34696_t
Valid prediction for GeneMark_model.34669_t
Valid prediction for snap_scaffold_8-snap.1192-T1
Valid prediction for GeneMark_model.34692_t
Valid prediction for GeneMark_model.34678_t
Valid prediction for GeneMark_model.34674_t
Valid prediction for Augustus_model.g13544.t1
Valid prediction for GeneMark_model.34688_t
Valid prediction for GeneMark_model.34680_t
Valid prediction for snap_scaffold_8-snap.1198-T1
Valid prediction for GeneMark_model.34686_t
Valid prediction for GlimmerHMM_glimmerT_20270-T1
Valid prediction for GeneMark_model.34693_t
Valid prediction for GlimmerHMM_glimmerT_20263-T1
Valid prediction for GeneMark_model.34667_t
Valid prediction for GlimmerHMM_glimmerT_20250-T1
Valid prediction for Augustus_model.g13553.t1
Valid prediction for Augustus_model.g13555.t1
Valid prediction for GlimmerHMM_glimmerT_20271-T1
Valid prediction for GeneMark_model.34683_t
Valid prediction for GlimmerHMM_glimmerT_20254-T1
Valid prediction for Augustus_model.g13547.t1
Couldn't classify 140989, 141357
Sorry, prediction pasa_asmbl_51901.p2 fails validation.
(AGA)	 CC	140989-141357	GG	AGG
Valid prediction for HiQ_model.g13554.t1
Valid prediction for snap_scaffold_8-snap.1181-T1
Valid prediction for snap_scaffold_8-snap.1173-T1
Valid prediction for snap_scaffold_8-snap.1203-T1
Valid prediction for snap_scaffold_8-snap.1195-T1
Valid prediction for snap_scaffold_8-snap.1199-T1
Valid prediction for snap_scaffold_8-snap.1176-T1
Valid prediction for GeneMark_model.34695_t
Valid prediction for snap_scaffold_8-snap.1175-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 GeneMark_model.34691_t
Valid prediction for GeneMark_model.34685_t
Couldn't classify 72225, 72326
Sorry, prediction pasa_asmbl_52844.p1 fails validation.
(ATG)	 CC	69975-70092	GT	CTG
(ATG)	 AG	70785-70876	GT	AGG
(CTC)	 AG	70968-71133	GT	GGG
(AGT)	 AG	71211-71371	GT	AGG
(TAC)	 AG	71982-72125	GT	AGG
(TCC)	 AG	72225-72326	AG	GAA
-recovered pasa_asmbl_52844.p1, initial, 69975, 70092
add_exon() Sorry, pasa_asmbl_52844.p1 70785-70876-initial-1 is invalid.
-recovered pasa_asmbl_52844.p1, initial, 70785, 70876
-recovered pasa_asmbl_52844.p1, internal, 70785, 70876
-recovered pasa_asmbl_52844.p1, internal, 70968, 71133
-recovered pasa_asmbl_52844.p1, internal, 71211, 71371
-recovered pasa_asmbl_52844.p1, internal, 71982, 72125
Valid prediction for GeneMark_model.34666_t
Valid prediction for Augustus_model.g13543.t1
Valid prediction for GlimmerHMM_glimmerT_20256-T1
Valid prediction for GeneMark_model.34677_t
Valid prediction for GeneMark_model.34689_t
Valid prediction for GlimmerHMM_glimmerT_20260-T1
Valid prediction for GeneMark_model.34697_t
Valid prediction for GeneMark_model.34687_t
Valid prediction for GeneMark_model.34694_t
Valid prediction for GlimmerHMM_glimmerT_20252-T1
Valid prediction for GeneMark_model.34681_t
Valid prediction for snap_scaffold_8-snap.1184-T1
Valid prediction for GlimmerHMM_glimmerT_20257-T1
Valid prediction for GlimmerHMM_glimmerT_20265-T1
Valid prediction for Augustus_model.g13542.t1
Valid prediction for snap_scaffold_8-snap.1187-T1
Valid prediction for snap_scaffold_8-snap.1178-T1
Valid prediction for snap_scaffold_8-snap.1183-T1
Valid prediction for snap_scaffold_8-snap.1188-T1
Valid prediction for GlimmerHMM_glimmerT_20264-T1
Valid prediction for snap_scaffold_8-snap.1185-T1
Valid prediction for GlimmerHMM_glimmerT_20261-T1
Valid prediction for GlimmerHMM_glimmerT_20267-T1
Valid prediction for snap_scaffold_8-snap.1182-T1
Couldn't classify 23992, 24427
Sorry, prediction pasa_asmbl_52846.p1 fails validation.
(ACC)	 CG	23992-24427	GT	AGG
(GCC)	 AG	24973-25565	GA	GAG
-recovered pasa_asmbl_52846.p1, terminal, 24973, 25565
Valid prediction for Augustus_model.g13552.t1
Valid prediction for GlimmerHMM_glimmerT_20249-T1
Valid prediction for snap_scaffold_8-snap.1179-T1
Valid prediction for CodingQuarry_transcript_59517-T1
Valid prediction for GlimmerHMM_glimmerT_20251-T1
Valid prediction for GeneMark_model.34679_t
Valid prediction for snap_scaffold_8-snap.1172-T1
Valid prediction for snap_scaffold_8-snap.1193-T1
Valid prediction for Augustus_model.g13540.t1
Valid prediction for GlimmerHMM_glimmerT_20274-T1
Valid prediction for HiQ_model.g13549.t1
Valid prediction for Augustus_model.g13558.t1
Valid prediction for GeneMark_model.34684_t
Valid prediction for snap_scaffold_8-snap.1177-T1
Valid prediction for GeneMark_model.34673_t
Couldn't classify 133344, 133739
Sorry, prediction pasa_asmbl_52841.p1 fails validation.
(ATT)	 TG	133344-133739	GC	GAG
Valid prediction for CodingQuarry_transcript_59518-T1
Valid prediction for snap_scaffold_8-snap.1202-T1
Valid prediction for snap_scaffold_8-snap.1186-T1
Valid prediction for GeneMark_model.34675_t
Valid prediction for snap_scaffold_8-snap.1197-T1
Couldn't classify 167144, 167256
Sorry, prediction pasa_asmbl_52838.p1 fails validation.
(AAC)	 TG	167144-167256	GT	AGG
(GAA)	 AG	167926-168046	GT	GGG
(AAA)	 AG	168174-168633	GT	TGG
(AAC)	 AG	169295-169349	GT	CTG
(GGC)	 AG	169533-169704	GT	AGG
(GTT)	 AG	169801-169845	GT	AGG
(AAG)	 AG	169953-170063	TG	AGT
-recovered pasa_asmbl_52838.p1, terminal, 169953, 170063
-recovered pasa_asmbl_52838.p1, internal, 167926, 168046
-recovered pasa_asmbl_52838.p1, internal, 168174, 168633
-recovered pasa_asmbl_52838.p1, internal, 169295, 169349
-recovered pasa_asmbl_52838.p1, internal, 169533, 169704
-recovered pasa_asmbl_52838.p1, internal, 169801, 169845
Valid prediction for pasa_asmbl_52845.p1
Valid prediction for Augustus_model.g13539.t1
Valid prediction for snap_scaffold_8-snap.1201-T1
Valid prediction for Augustus_model.g13546.t1
Valid prediction for GlimmerHMM_glimmerT_20262-T1
Valid prediction for snap_scaffold_8-snap.1189-T1
Valid prediction for Augustus_model.g13545.t1
Valid prediction for snap_scaffold_8-snap.1174-T1
Valid prediction for HiQ_model.g13556.t1
Valid prediction for GeneMark_model.34676_t
Valid prediction for GlimmerHMM_glimmerT_20253-T1
Valid prediction for Augustus_model.g13557.t1
Valid prediction for snap_scaffold_8-snap.1194-T1
Valid prediction for GlimmerHMM_glimmerT_20255-T1
Valid prediction for GlimmerHMM_glimmerT_20248-T1
Couldn't classify 72472, 72598
Sorry, prediction pasa_asmbl_52843.p1 fails validation.
(CTG)	 AC	72472-72598	GT	GGG
(GAT)	 AG	72856-72968	GT	GGG
(GGA)	 AG	73051-73148	GT	AAG
(ATT)	 AG	73254-73346	GT	AAG
(CTG)	 AG	73670-73754	AT	AAA
-recovered pasa_asmbl_52843.p1, terminal, 73670, 73754
-recovered pasa_asmbl_52843.p1, internal, 72856, 72968
-recovered pasa_asmbl_52843.p1, internal, 73051, 73148
-recovered pasa_asmbl_52843.p1, internal, 73254, 73346
Valid prediction for GlimmerHMM_glimmerT_20272-T1
Valid prediction for GeneMark_model.34670_t
Valid prediction for CodingQuarry_transcript_59515-T1
Valid prediction for GeneMark_model.34671_t
Valid prediction for GeneMark_model.34668_t
Valid prediction for HiQ_model.g13550.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 57778, rend_intergenic: 55736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183344, rend_intergenic: 178578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208601, rend_intergenic: 204367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 220388
-exon list size: 454


building trellis

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14.9    
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27.9    
28.1    
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28.9    
29.2    
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29.8    
30.0    
30.3    
30.5    
30.7    
30.9    
31.1    
31.4    
31.6    
31.8    
32.0    
32.2    
32.5    
32.7    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.9    
35.1    
35.3    
35.5    
35.7    
36.0    
36.2    
36.4    
36.6    
36.8    
37.1    
37.3    
37.5    
37.7    
37.9    
38.2    
38.4    
38.6    
38.8    
39.0    
39.3    
39.5    
39.7    
39.9    
40.1    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
41.7    
41.9    
42.1    
42.3    
42.5    
42.8    
43.0    
43.2    
43.4    
43.6    
43.9    
44.1    
44.3    
44.5    
44.7    
45.0    
45.2    
45.4    
45.6    
45.8    
46.1    
46.3    
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46.7    
46.9    
47.1    
47.4    
47.6    
47.8    
48.0    
48.2    
48.5    
48.7    
48.9    
49.1    
49.3    
49.6    
49.8    
50.0    
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50.7    
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51.8    
52.0    
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52.9    
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53.9    
54.2    
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54.6    
54.8    
55.0    
55.3    
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55.7    
55.9    
56.1    
56.4    
56.6    
56.8    
57.0    
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58.6    
58.8    
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59.2    
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61.8    
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62.9    
63.2    
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63.6    
63.8    
64.0    
64.3    
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64.7    
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65.1    
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65.6    
65.8    
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74.8    
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75.7    
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77.0    
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81.8    
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82.9    
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83.6    
83.8    
84.0    
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84.4    
84.6    
84.9    
85.1    
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85.5    
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86.0    
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86.8    
87.1    
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87.9    
88.2    
88.4    
88.6    
88.8    
89.0    
89.3    
89.5    
89.7    
89.9    
90.1    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.7    
91.9    
92.1    
92.3    
92.5    
92.8    
93.0    
93.2    
93.4    
93.6    
93.9    
94.1    
94.3    
94.5    
94.7    
95.0    
95.2    
95.4    
95.6    
95.8    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.0    
98.2    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 57778, rend_intergenic: 55736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183344, rend_intergenic: 178578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208601, rend_intergenic: 204367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 205518 - 220388
-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