-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_5517023-5790411

-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_17-snap.1149-T1
Valid prediction for GlimmerHMM_glimmerT_40321-T1
Couldn't classify 176232, 176283
Sorry, prediction CodingQuarry_transcript_21986-T1 fails validation.
(ATG)	 TT	175037-175159	GT	CCG
(GAT)	 CT	176232-176283	GT	AGG
(ACT)	 AG	176814-176870	GT	AAG
(GAC)	 AG	176985-177052	GT	AGG
(ACT)	 AG	177230-177352	GT	AGG
(GAT)	 AG	177602-177688	GC	AAG
-recovered CodingQuarry_transcript_21986-T1, initial, 175037, 175159
-recovered CodingQuarry_transcript_21986-T1, terminal, 177602, 177688
-recovered CodingQuarry_transcript_21986-T1, internal, 176814, 176870
-recovered CodingQuarry_transcript_21986-T1, internal, 176985, 177052
-recovered CodingQuarry_transcript_21986-T1, internal, 177230, 177352
-recovered CodingQuarry_transcript_21986-T1, internal, 177602, 177688
Valid prediction for GlimmerHMM_glimmerT_40346-T1
Valid prediction for snap_scaffold_17-snap.1162-T1
Valid prediction for snap_scaffold_17-snap.1174-T1
Valid prediction for pasa_asmbl_18825.p1
Valid prediction for GlimmerHMM_glimmerT_40337-T1
Valid prediction for GlimmerHMM_glimmerT_40334-T1
Valid prediction for snap_scaffold_17-snap.1165-T1
Valid prediction for Augustus_model.g26870.t1
Valid prediction for GlimmerHMM_glimmerT_40342-T1
Valid prediction for snap_scaffold_17-snap.1179-T1
Valid prediction for snap_scaffold_17-snap.1156-T1
Valid prediction for GlimmerHMM_glimmerT_40336-T1
Valid prediction for Augustus_model.g26868.t1
Valid prediction for snap_scaffold_17-snap.1173-T1
Valid prediction for GlimmerHMM_glimmerT_40353-T1
Valid prediction for snap_scaffold_17-snap.1142-T1
Valid prediction for pasa_asmbl_18829.p1
Valid prediction for snap_scaffold_17-snap.1159-T1
Valid prediction for snap_scaffold_17-snap.1180-T1
Valid prediction for Augustus_model.g26880.t1
Valid prediction for GlimmerHMM_glimmerT_40331-T1
Valid prediction for snap_scaffold_17-snap.1183-T1
Valid prediction for Augustus_model.g26872.t1
Valid prediction for GlimmerHMM_glimmerT_40333-T1
Valid prediction for snap_scaffold_17-snap.1161-T1
Valid prediction for snap_scaffold_17-snap.1181-T1
Valid prediction for GlimmerHMM_glimmerT_40343-T1
Valid prediction for CodingQuarry_transcript_21987-T1
Valid prediction for snap_scaffold_17-snap.1164-T1
Valid prediction for Augustus_model.g26881.t1
Valid prediction for GlimmerHMM_glimmerT_40344-T1
Valid prediction for Augustus_model.g26876.t1
Valid prediction for snap_scaffold_17-snap.1168-T1
Valid prediction for GlimmerHMM_glimmerT_40320-T1
Valid prediction for snap_scaffold_17-snap.1152-T1
Valid prediction for HiQ_model.g26878.t1
Valid prediction for snap_scaffold_17-snap.1151-T1
Valid prediction for snap_scaffold_17-snap.1148-T1
Valid prediction for snap_scaffold_17-snap.1167-T1
Valid prediction for Augustus_model.g26882.t1
Valid prediction for snap_scaffold_17-snap.1176-T1
Valid prediction for GlimmerHMM_glimmerT_40324-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_17-snap.1172-T1
Valid prediction for snap_scaffold_17-snap.1154-T1
Valid prediction for snap_scaffold_17-snap.1178-T1
Valid prediction for GlimmerHMM_glimmerT_40338-T1
Valid prediction for GlimmerHMM_glimmerT_40329-T1
Valid prediction for GlimmerHMM_glimmerT_40350-T1
Valid prediction for snap_scaffold_17-snap.1175-T1
Valid prediction for snap_scaffold_17-snap.1163-T1
Valid prediction for GlimmerHMM_glimmerT_40328-T1
Valid prediction for CodingQuarry_transcript_21988-T1
Valid prediction for GlimmerHMM_glimmerT_40340-T1
Valid prediction for GlimmerHMM_glimmerT_40341-T1
Valid prediction for snap_scaffold_17-snap.1140-T1
Valid prediction for snap_scaffold_17-snap.1171-T1
Valid prediction for GlimmerHMM_glimmerT_40325-T1
Valid prediction for GlimmerHMM_glimmerT_40339-T1
Valid prediction for snap_scaffold_17-snap.1158-T1
Valid prediction for Augustus_model.g26863.t1
Valid prediction for HiQ_model.g26871.t1
Valid prediction for GlimmerHMM_glimmerT_40322-T1
Valid prediction for snap_scaffold_17-snap.1184-T1
Valid prediction for CodingQuarry_transcript_21991-T1
Valid prediction for Augustus_model.g26862.t1
Valid prediction for GlimmerHMM_glimmerT_40351-T1
Valid prediction for GlimmerHMM_glimmerT_40323-T1
Valid prediction for snap_scaffold_17-snap.1153-T1
Valid prediction for Augustus_model.g26874.t1
Couldn't classify 58368, 58457
Sorry, prediction pasa_asmbl_17953.p1 fails validation.
(CAA)	 GT	58368-58457	GT	TGG
(GCA)	 AG	61358-61427	GT	AGG
(GTA)	 AG	61863-61942	GT	AGG
(AAA)	 AG	62948-63040	GT	TGG
(ATC)	 AG	64131-64313	GT	AGG
(CTC)	 AG	65105-65181	GT	TCG
(CCC)	 AG	65332-65489	GT	AGG
(ACA)	 AG	65719-65939	GC	GAG
-recovered pasa_asmbl_17953.p1, terminal, 65719, 65939
-recovered pasa_asmbl_17953.p1, internal, 61358, 61427
-recovered pasa_asmbl_17953.p1, internal, 61863, 61942
-recovered pasa_asmbl_17953.p1, internal, 62948, 63040
-recovered pasa_asmbl_17953.p1, internal, 64131, 64313
-recovered pasa_asmbl_17953.p1, internal, 65105, 65181
-recovered pasa_asmbl_17953.p1, internal, 65332, 65489
-recovered pasa_asmbl_17953.p1, internal, 65719, 65939
Valid prediction for GlimmerHMM_glimmerT_40327-T1
Valid prediction for Augustus_model.g26864.t1
Valid prediction for snap_scaffold_17-snap.1182-T1
Valid prediction for Augustus_model.g26877.t1
Valid prediction for snap_scaffold_17-snap.1143-T1
Valid prediction for Augustus_model.g26867.t1
Valid prediction for CodingQuarry_transcript_21989-T1
Valid prediction for GlimmerHMM_glimmerT_40348-T1
Valid prediction for GlimmerHMM_glimmerT_40330-T1
Valid prediction for GlimmerHMM_glimmerT_40347-T1
Valid prediction for snap_scaffold_17-snap.1145-T1
Valid prediction for pasa_asmbl_17950.p1
Valid prediction for GlimmerHMM_glimmerT_40332-T1
Valid prediction for snap_scaffold_17-snap.1170-T1
Valid prediction for GlimmerHMM_glimmerT_40345-T1
Valid prediction for snap_scaffold_17-snap.1157-T1
Valid prediction for Augustus_model.g26865.t1
Valid prediction for GlimmerHMM_glimmerT_40352-T1
Valid prediction for snap_scaffold_17-snap.1166-T1
Valid prediction for snap_scaffold_17-snap.1147-T1
Valid prediction for snap_scaffold_17-snap.1144-T1
Valid prediction for GlimmerHMM_glimmerT_40326-T1
Valid prediction for Augustus_model.g26869.t1
Valid prediction for snap_scaffold_17-snap.1146-T1
Valid prediction for HiQ_model.g26873.t1
Valid prediction for snap_scaffold_17-snap.1177-T1
Valid prediction for Augustus_model.g26879.t1
Valid prediction for snap_scaffold_17-snap.1169-T1
Valid prediction for snap_scaffold_17-snap.1141-T1
Valid prediction for HiQ_model.g26875.t1
Valid prediction for snap_scaffold_17-snap.1160-T1
Valid prediction for snap_scaffold_17-snap.1155-T1
Valid prediction for GlimmerHMM_glimmerT_40319-T1
Valid prediction for GlimmerHMM_glimmerT_40349-T1
Valid prediction for GlimmerHMM_glimmerT_40335-T1
Valid prediction for Augustus_model.g26866.t1
Valid prediction for snap_scaffold_17-snap.1150-T1
Couldn't classify 100635, 100773
Sorry, prediction pasa_asmbl_17945.p1 fails validation.
(GAC)	 AG	100635-100773	GT	GGG
(GTG)	 AG	101747-101925	GT	CGG
(AGT)	 AG	102393-102509	GT	TGG
(ACA)	 AG	102608-102658	TA	GAT
-recovered pasa_asmbl_17945.p1, terminal, 102608, 102658
-recovered pasa_asmbl_17945.p1, internal, 100635, 100773
-recovered pasa_asmbl_17945.p1, internal, 101747, 101925
-recovered pasa_asmbl_17945.p1, internal, 102393, 102509
Valid prediction for CodingQuarry_transcript_21990-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 83501, rend_intergenic: 77922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94112, rend_intergenic: 88869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102745, rend_intergenic: 99233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113582, rend_intergenic: 104572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125737, rend_intergenic: 122474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133777, rend_intergenic: 128195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145107, rend_intergenic: 140867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156039, rend_intergenic: 148272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173096, rend_intergenic: 171414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253845, rend_intergenic: 247264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 263078, rend_intergenic: 259610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 271952, rend_intergenic: 267835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 273389
-exon list size: 385


building trellis

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28.7    
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31.3    
31.5    
31.8    
32.0    
32.3    
32.6    
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33.1    
33.3    
33.6    
33.9    
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34.4    
34.6    
34.9    
35.1    
35.4    
35.7    
35.9    
36.2    
36.4    
36.7    
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38.5    
38.8    
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39.3    
39.5    
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40.3    
40.6    
40.8    
41.1    
41.3    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
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45.2    
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46.3    
46.5    
46.8    
47.0    
47.3    
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48.1    
48.3    
48.6    
48.8    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.2    
51.4    
51.7    
51.9    
52.2    
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54.3    
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55.6    
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56.1    
56.3    
56.6    
56.8    
57.1    
57.4    
57.6    
57.9    
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58.4    
58.7    
58.9    
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80.9    
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85.3    
85.5    
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86.0    
86.3    
86.6    
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87.3    
87.6    
87.9    
88.1    
88.4    
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88.9    
89.1    
89.4    
89.7    
89.9    
90.2    
90.4    
90.7    
91.0    
91.2    
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92.5    
92.8    
93.0    
93.3    
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94.1    
94.3    
94.6    
94.8    
95.1    
95.3    
95.6    
95.9    
96.1    
96.4    
96.6    
96.9    
97.2    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 83501, rend_intergenic: 77922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94112, rend_intergenic: 88869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102745, rend_intergenic: 99233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113582, rend_intergenic: 104572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125737, rend_intergenic: 122474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133777, rend_intergenic: 128195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145107, rend_intergenic: 140867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156039, rend_intergenic: 148272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173096, rend_intergenic: 171414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253845, rend_intergenic: 247264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 263078, rend_intergenic: 259610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 271952, rend_intergenic: 267835  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 1 - 17497
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 10029
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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