-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_6534460-6734562

-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_51173-T1
Valid prediction for Augustus_model.g34240.t1
Valid prediction for Augustus_model.g34238.t1
Valid prediction for CodingQuarry_transcript_35695-T1
Valid prediction for HiQ_model.g34243.t1
Valid prediction for snap_scaffold_23-snap.1211-T1
Valid prediction for GlimmerHMM_glimmerT_51188-T1
Valid prediction for CodingQuarry_transcript_35692-T1
Valid prediction for Augustus_model.g34235.t1
Valid prediction for pasa_asmbl_31631.p1
Valid prediction for snap_scaffold_23-snap.1203-T1
Valid prediction for GlimmerHMM_glimmerT_51180-T1
Valid prediction for snap_scaffold_23-snap.1179-T1
Valid prediction for CodingQuarry_transcript_35694-T1
Valid prediction for snap_scaffold_23-snap.1195-T1
Valid prediction for Augustus_model.g34249.t1
Valid prediction for snap_scaffold_23-snap.1191-T1
Valid prediction for snap_scaffold_23-snap.1193-T1
Valid prediction for GlimmerHMM_glimmerT_51175-T1
Valid prediction for snap_scaffold_23-snap.1198-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 123312, 123327
Couldn't classify 130738, 130830
Sorry, prediction pasa_asmbl_31641.p1 fails validation.
(GAC)	 TG	123312-123327	GT	CAG
(GCA)	 AG	125855-125933	GT	AAG
(GCT)	 AG	126257-126346	GT	AGG
(GTT)	 AG	127145-127201	GT	AAG
(AAG)	 AG	129415-129478	GT	TGG
(CCT)	 AG	129690-129764	GT	GGG
(ATG)	 AG	130738-130830	CA	TGC
-recovered pasa_asmbl_31641.p1, internal, 125855, 125933
-recovered pasa_asmbl_31641.p1, internal, 126257, 126346
-recovered pasa_asmbl_31641.p1, internal, 127145, 127201
-recovered pasa_asmbl_31641.p1, internal, 129415, 129478
-recovered pasa_asmbl_31641.p1, internal, 129690, 129764
Valid prediction for snap_scaffold_23-snap.1207-T1
Valid prediction for snap_scaffold_23-snap.1214-T1
Valid prediction for Augustus_model.g34248.t1
Valid prediction for snap_scaffold_23-snap.1175-T1
Couldn't classify 70556, 70707
Sorry, prediction pasa_asmbl_31625.p1 fails validation.
(ATG)	 TC	69654-69840	GT	GGG
(CGG)	 AG	70556-70707	CT	ACC
-recovered pasa_asmbl_31625.p1, initial, 69654, 69840
Valid prediction for GlimmerHMM_glimmerT_51174-T1
Valid prediction for snap_scaffold_23-snap.1192-T1
Valid prediction for Augustus_model.g34233.t1
Valid prediction for GlimmerHMM_glimmerT_51187-T1
Valid prediction for GlimmerHMM_glimmerT_51186-T1
Valid prediction for GlimmerHMM_glimmerT_51192-T1
Valid prediction for GlimmerHMM_glimmerT_51178-T1
Valid prediction for pasa_asmbl_31628.p1
Couldn't classify 143987, 144232
Sorry, prediction pasa_asmbl_31644.p1 fails validation.
(ATC)	 GC	143987-144232	GT	AGG
(GAT)	 AG	146624-146680	GT	AAG
(GTG)	 AG	148694-148879	GT	AGG
(ATG)	 AG	149532-149624	GT	ACG
(GGG)	 AG	149745-149819	GT	AGG
(GCG)	 AG	149947-150054	AG	AGA
-recovered pasa_asmbl_31644.p1, initial, 149532, 149624
-recovered pasa_asmbl_31644.p1, terminal, 149947, 150054
-recovered pasa_asmbl_31644.p1, internal, 146624, 146680
-recovered pasa_asmbl_31644.p1, internal, 148694, 148879
-recovered pasa_asmbl_31644.p1, internal, 149532, 149624
-recovered pasa_asmbl_31644.p1, internal, 149745, 149819
Valid prediction for snap_scaffold_23-snap.1201-T1
Valid prediction for pasa_asmbl_31634.p1
Valid prediction for GlimmerHMM_glimmerT_51182-T1
Valid prediction for snap_scaffold_23-snap.1190-T1
Valid prediction for CodingQuarry_transcript_35690-T1
Valid prediction for Augustus_model.g34239.t1
Valid prediction for snap_scaffold_23-snap.1187-T1
Valid prediction for Augustus_model.g34234.t1
Valid prediction for GlimmerHMM_glimmerT_51179-T1
Valid prediction for snap_scaffold_23-snap.1209-T1
Valid prediction for Augustus_model.g34231.t1
Valid prediction for snap_scaffold_23-snap.1188-T1
Valid prediction for GlimmerHMM_glimmerT_51191-T1
Valid prediction for snap_scaffold_23-snap.1196-T1
Valid prediction for snap_scaffold_23-snap.1182-T1
Valid prediction for snap_scaffold_23-snap.1176-T1
Valid prediction for GlimmerHMM_glimmerT_51170-T1
Valid prediction for Augustus_model.g34244.t1
Valid prediction for CodingQuarry_transcript_35691-T1
Valid prediction for GlimmerHMM_glimmerT_51172-T1
Valid prediction for HiQ_model.g34241.t1
Valid prediction for Augustus_model.g34237.t1
Valid prediction for snap_scaffold_23-snap.1216-T1
Valid prediction for Augustus_model.g34245.t1
Valid prediction for snap_scaffold_23-snap.1213-T1
Couldn't classify 156725, 156907
Sorry, prediction CodingQuarry_transcript_35696-T1 fails validation.
(ATG)	 GT	155855-155885	GT	AGG
(GGA)	 AG	156306-156460	GT	GCG
(TCG)	 TG	156725-156907	GT	AGG
(ACC)	 AG	157086-157264	GT	AAG
(GAT)	 AG	157364-157494	GT	AGG
(AGG)	 AG	157593-157701	GT	AGG
(GAG)	 AG	157835-157948	GT	AGG
(GGG)	 AG	158838-158909	GT	AGG
(AGG)	 AG	159021-159138	GT	AGG
(GTG)	 AG	159522-159653	AC	GAA
-recovered CodingQuarry_transcript_35696-T1, initial, 155855, 155885
-recovered CodingQuarry_transcript_35696-T1, terminal, 159522, 159653
-recovered CodingQuarry_transcript_35696-T1, internal, 156306, 156460
-recovered CodingQuarry_transcript_35696-T1, internal, 157086, 157264
-recovered CodingQuarry_transcript_35696-T1, internal, 157364, 157494
-recovered CodingQuarry_transcript_35696-T1, internal, 157593, 157701
-recovered CodingQuarry_transcript_35696-T1, internal, 157835, 157948
-recovered CodingQuarry_transcript_35696-T1, internal, 158838, 158909
-recovered CodingQuarry_transcript_35696-T1, internal, 159021, 159138
Valid prediction for Augustus_model.g34229.t1
Valid prediction for snap_scaffold_23-snap.1189-T1
Valid prediction for pasa_asmbl_31932.p1
Valid prediction for GlimmerHMM_glimmerT_51176-T1
Valid prediction for GlimmerHMM_glimmerT_51185-T1
Valid prediction for snap_scaffold_23-snap.1184-T1
Valid prediction for HiQ_model.g34246.t1
Couldn't classify 137365, 137436
Couldn't classify 142753, 143116
Sorry, prediction pasa_asmbl_31642.p1 fails validation.
(AGG)	 CC	137365-137436	GT	AGG
(TCC)	 AG	138927-139026	GT	GTG
(ACA)	 AG	139966-140087	GT	GGG
(GAG)	 AG	141154-141327	GT	AGG
(GTG)	 AG	141576-141758	GT	AGG
(GAC)	 AG	142013-142115	GT	AAG
(ACG)	 AG	142323-142506	GT	AGG
(ACA)	 AG	142753-143116	GC	GGG
add_exon() Sorry, pasa_asmbl_31642.p1 142013-142115-terminal-3 is invalid.
-recovered pasa_asmbl_31642.p1, terminal, 142013, 142115
-recovered pasa_asmbl_31642.p1, internal, 138927, 139026
-recovered pasa_asmbl_31642.p1, internal, 139966, 140087
-recovered pasa_asmbl_31642.p1, internal, 141154, 141327
-recovered pasa_asmbl_31642.p1, internal, 141576, 141758
-recovered pasa_asmbl_31642.p1, internal, 142013, 142115
-recovered pasa_asmbl_31642.p1, internal, 142323, 142506
-recovered pasa_asmbl_31642.p1, internal, 142753, 143116

-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_23-snap.1177-T1
Valid prediction for GlimmerHMM_glimmerT_51189-T1
Valid prediction for CodingQuarry_transcript_35693-T1
Valid prediction for snap_scaffold_23-snap.1204-T1
Valid prediction for snap_scaffold_23-snap.1183-T1
Valid prediction for snap_scaffold_23-snap.1206-T1
Valid prediction for snap_scaffold_23-snap.1208-T1
Valid prediction for HiQ_model.g34242.t1
Valid prediction for snap_scaffold_23-snap.1202-T1
Valid prediction for Augustus_model.g34247.t1
Valid prediction for GlimmerHMM_glimmerT_51181-T1
Valid prediction for snap_scaffold_23-snap.1180-T1
Valid prediction for snap_scaffold_23-snap.1181-T1
Valid prediction for GlimmerHMM_glimmerT_51190-T1
Valid prediction for GlimmerHMM_glimmerT_51184-T1
Valid prediction for Augustus_model.g34232.t1
Valid prediction for snap_scaffold_23-snap.1212-T1
Valid prediction for snap_scaffold_23-snap.1178-T1
Valid prediction for snap_scaffold_23-snap.1186-T1
Valid prediction for GlimmerHMM_glimmerT_51171-T1
Valid prediction for Augustus_model.g34236.t1
Valid prediction for GlimmerHMM_glimmerT_51177-T1
Valid prediction for snap_scaffold_23-snap.1194-T1
Valid prediction for snap_scaffold_23-snap.1210-T1
Valid prediction for Augustus_model.g34230.t1
Valid prediction for snap_scaffold_23-snap.1215-T1
Valid prediction for snap_scaffold_23-snap.1185-T1
Valid prediction for GlimmerHMM_glimmerT_51183-T1
Valid prediction for pasa_asmbl_30980.p1
Valid prediction for snap_scaffold_23-snap.1199-T1
Valid prediction for snap_scaffold_23-snap.1197-T1
Valid prediction for snap_scaffold_23-snap.1205-T1
Valid prediction for snap_scaffold_23-snap.1200-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13789, rend_intergenic: 10148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21394, rend_intergenic: 15310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26884, rend_intergenic: 22055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51336, rend_intergenic: 44048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111012, rend_intergenic: 106126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123789, rend_intergenic: 111014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128680, rend_intergenic: 126222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129897, rend_intergenic: 129205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147683, rend_intergenic: 130266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185541, rend_intergenic: 181317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192912, rend_intergenic: 192149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196436, rend_intergenic: 193390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 200103
-exon list size: 463


building trellis

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23.9    
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25.8    
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26.9    
27.1    
27.3    
27.5    
27.7    
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28.2    
28.4    
28.6    
28.8    
29.0    
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29.7    
29.9    
30.1    
30.3    
30.5    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
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    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.7    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.2    
45.4    
45.6    
45.8    
46.0    
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46.9    
47.1    
47.3    
47.5    
47.7    
48.0    
48.2    
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48.8    
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50.8    
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51.6    
51.8    
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60.6    
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63.9    
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66.9    
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68.8    
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71.8    
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79.8    
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80.2    
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80.6    
80.9    
81.1    
81.3    
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81.9    
82.2    
82.4    
82.6    
82.8    
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84.9    
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85.4    
85.6    
85.8    
86.0    
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86.5    
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86.9    
87.1    
87.3    
87.5    
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88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 13789, rend_intergenic: 10148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21394, rend_intergenic: 15310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26884, rend_intergenic: 22055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51336, rend_intergenic: 44048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111012, rend_intergenic: 106126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123789, rend_intergenic: 111014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128680, rend_intergenic: 126222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129897, rend_intergenic: 129205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147683, rend_intergenic: 130266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185541, rend_intergenic: 181317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192912, rend_intergenic: 192149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196436, rend_intergenic: 193390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support