-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_7047144-7234692

-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.g749.t1
Valid prediction for pasa_asmbl_1885.p1
Valid prediction for snap_scaffold_1-snap.1247-T1
Valid prediction for snap_scaffold_1-snap.1249-T1
Valid prediction for snap_scaffold_1-snap.1231-T1
Valid prediction for Augustus_model.g750.t1
Valid prediction for GeneMark_model.1247_t
Valid prediction for Augustus_model.g743.t1
Valid prediction for Augustus_model.g736.t1
Valid prediction for GeneMark_model.1263_t
Valid prediction for GlimmerHMM_glimmerT_1013-T1
Valid prediction for HiQ_model.g744.t1
Valid prediction for snap_scaffold_1-snap.1257-T1
Valid prediction for snap_scaffold_1-snap.1243-T1
Valid prediction for snap_scaffold_1-snap.1240-T1
Valid prediction for GlimmerHMM_glimmerT_1014-T1
Valid prediction for snap_scaffold_1-snap.1235-T1
Valid prediction for GlimmerHMM_glimmerT_1007-T1
Valid prediction for HiQ_model.g737.t1
Valid prediction for Augustus_model.g742.t1
Valid prediction for GlimmerHMM_glimmerT_998-T1
Valid prediction for GeneMark_model.1258_t
Valid prediction for Augustus_model.g738.t1
Valid prediction for snap_scaffold_1-snap.1251-T1
Valid prediction for Augustus_model.g740.t1
Valid prediction for GeneMark_model.1261_t
Valid prediction for GlimmerHMM_glimmerT_1010-T1
Valid prediction for snap_scaffold_1-snap.1255-T1
Valid prediction for GeneMark_model.1252_t
Couldn't classify 113762, 113941
Sorry, prediction pasa_asmbl_1879.p1 fails validation.
(GAA)	 CA	113762-113941	GT	AGG
(GAT)	 AG	114537-114626	GT	CAG
(CAC)	 AG	115060-115171	GT	TGG
(AAG)	 AG	115308-115438	GT	AGG
(GAA)	 AG	115736-115810	GA	AGG
-recovered pasa_asmbl_1879.p1, terminal, 115736, 115810
-recovered pasa_asmbl_1879.p1, internal, 114537, 114626
-recovered pasa_asmbl_1879.p1, internal, 115060, 115171
-recovered pasa_asmbl_1879.p1, internal, 115308, 115438
Valid prediction for snap_scaffold_1-snap.1262-T1
Valid prediction for GlimmerHMM_glimmerT_1023-T1
Valid prediction for snap_scaffold_1-snap.1253-T1
Valid prediction for GlimmerHMM_glimmerT_1016-T1
Valid prediction for GlimmerHMM_glimmerT_1022-T1
Valid prediction for GlimmerHMM_glimmerT_1025-T1
Valid prediction for snap_scaffold_1-snap.1229-T1
Valid prediction for pasa_asmbl_1880.p1
Valid prediction for Augustus_model.g748.t1
Valid prediction for Augustus_model.g754.t1
Valid prediction for GlimmerHMM_glimmerT_1012-T1
Valid prediction for GeneMark_model.1245_t
Valid prediction for GeneMark_model.1259_t
Valid prediction for GlimmerHMM_glimmerT_1021-T1
Valid prediction for Augustus_model.g753.t1
Couldn't classify 156199, 156229
Sorry, prediction pasa_asmbl_1883.p1 fails validation.
(ATG)	 AG	154350-154446	GT	AGG
(GTC)	 AG	154804-154915	GT	GGG
(AAT)	 AG	155173-155249	GT	GTG
(GTA)	 AG	155799-155925	GT	AGG
(GGT)	 AG	156199-156229	GC	CAG
-recovered pasa_asmbl_1883.p1, initial, 154350, 154446
-recovered pasa_asmbl_1883.p1, internal, 154350, 154446
-recovered pasa_asmbl_1883.p1, internal, 154804, 154915
-recovered pasa_asmbl_1883.p1, internal, 155173, 155249
-recovered pasa_asmbl_1883.p1, internal, 155799, 155925
-recovered pasa_asmbl_1883.p1, internal, 156199, 156229
Valid prediction for pasa_asmbl_1876.p1
Valid prediction for GlimmerHMM_glimmerT_1005-T1
Valid prediction for snap_scaffold_1-snap.1244-T1
Valid prediction for Augustus_model.g730.t1
Valid prediction for snap_scaffold_1-snap.1256-T1
Valid prediction for snap_scaffold_1-snap.1245-T1
Valid prediction for CodingQuarry_transcript_2677-T1
Valid prediction for GeneMark_model.1260_t
Valid prediction for GeneMark_model.1241_t
Valid prediction for GeneMark_model.1257_t
Valid prediction for snap_scaffold_1-snap.1248-T1
Valid prediction for GeneMark_model.1251_t
Valid prediction for GlimmerHMM_glimmerT_1004-T1
Valid prediction for snap_scaffold_1-snap.1239-T1
Valid prediction for Augustus_model.g746.t1
Valid prediction for GeneMark_model.1253_t
Valid prediction for snap_scaffold_1-snap.1260-T1
Valid prediction for GlimmerHMM_glimmerT_1018-T1
Valid prediction for CodingQuarry_transcript_2675-T1
Valid prediction for GeneMark_model.1244_t
Valid prediction for GlimmerHMM_glimmerT_1029-T1
Valid prediction for snap_scaffold_1-snap.1238-T1
Valid prediction for CodingQuarry_transcript_2678-T1
Valid prediction for GeneMark_model.1250_t
Valid prediction for snap_scaffold_1-snap.1252-T1
Valid prediction for GlimmerHMM_glimmerT_1024-T1
Valid prediction for GeneMark_model.1255_t
Valid prediction for GlimmerHMM_glimmerT_1000-T1
Valid prediction for snap_scaffold_1-snap.1232-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 Augustus_model.g752.t1
Valid prediction for Augustus_model.g733.t1
Valid prediction for GeneMark_model.1248_t
Valid prediction for GeneMark_model.1256_t
Valid prediction for snap_scaffold_1-snap.1227-T1
Valid prediction for GeneMark_model.1242_t
Valid prediction for GlimmerHMM_glimmerT_1019-T1
Valid prediction for GeneMark_model.1267_t
Valid prediction for Augustus_model.g731.t1
Valid prediction for GlimmerHMM_glimmerT_1011-T1
Valid prediction for GlimmerHMM_glimmerT_999-T1
Valid prediction for snap_scaffold_1-snap.1223-T1
Valid prediction for GeneMark_model.1246_t
Valid prediction for Augustus_model.g751.t1
Valid prediction for Augustus_model.g734.t1
Valid prediction for Augustus_model.g732.t1
Valid prediction for snap_scaffold_1-snap.1225-T1
Valid prediction for snap_scaffold_1-snap.1234-T1
Valid prediction for snap_scaffold_1-snap.1241-T1
Valid prediction for GlimmerHMM_glimmerT_1009-T1
Valid prediction for snap_scaffold_1-snap.1224-T1
Valid prediction for GlimmerHMM_glimmerT_1008-T1
Valid prediction for pasa_asmbl_420.p1
Valid prediction for snap_scaffold_1-snap.1230-T1
Valid prediction for GeneMark_model.1266_t
Valid prediction for GlimmerHMM_glimmerT_1026-T1
Valid prediction for GeneMark_model.1249_t
Valid prediction for Augustus_model.g735.t1
Valid prediction for GeneMark_model.1243_t
Valid prediction for GlimmerHMM_glimmerT_1017-T1
Valid prediction for GlimmerHMM_glimmerT_1027-T1
Valid prediction for snap_scaffold_1-snap.1246-T1
Valid prediction for Augustus_model.g747.t1
Valid prediction for GeneMark_model.1239_t
Valid prediction for snap_scaffold_1-snap.1221-T1
Valid prediction for snap_scaffold_1-snap.1258-T1
Valid prediction for snap_scaffold_1-snap.1263-T1
Valid prediction for snap_scaffold_1-snap.1233-T1
Valid prediction for GeneMark_model.1238_t
Valid prediction for GlimmerHMM_glimmerT_1006-T1
Valid prediction for snap_scaffold_1-snap.1228-T1
Valid prediction for GlimmerHMM_glimmerT_1015-T1
Valid prediction for GeneMark_model.1240_t
Valid prediction for snap_scaffold_1-snap.1259-T1
Valid prediction for GlimmerHMM_glimmerT_1020-T1
Valid prediction for snap_scaffold_1-snap.1236-T1
Valid prediction for CodingQuarry_transcript_2674-T1
Valid prediction for Augustus_model.g745.t1
Valid prediction for GlimmerHMM_glimmerT_1002-T1
Valid prediction for snap_scaffold_1-snap.1237-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_1028-T1
Valid prediction for GeneMark_model.1264_t
Valid prediction for snap_scaffold_1-snap.1261-T1
Valid prediction for GeneMark_model.1262_t
Valid prediction for Augustus_model.g739.t1
Valid prediction for GlimmerHMM_glimmerT_1001-T1
Valid prediction for CodingQuarry_transcript_2676-T1
Valid prediction for snap_scaffold_1-snap.1250-T1
Valid prediction for snap_scaffold_1-snap.1222-T1
Valid prediction for snap_scaffold_1-snap.1242-T1
Valid prediction for snap_scaffold_1-snap.1226-T1
Valid prediction for Augustus_model.g741.t1
Valid prediction for snap_scaffold_1-snap.1254-T1
Valid prediction for GeneMark_model.1254_t
Valid prediction for GlimmerHMM_glimmerT_1003-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 45193, rend_intergenic: 40691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90370, rend_intergenic: 74413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95294, rend_intergenic: 90722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104736, rend_intergenic: 100985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121121, rend_intergenic: 118258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139220, rend_intergenic: 135504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143653, rend_intergenic: 139756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151948, rend_intergenic: 149427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171088, rend_intergenic: 169411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175644, rend_intergenic: 173898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181684, rend_intergenic: 176342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187249, rend_intergenic: 183650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 187549
-exon list size: 580


building trellis

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48.8    
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49.3    
49.5    
49.7    
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55.8    
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85.1    
85.2    
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92.3    
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92.6    
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93.0    
93.1    
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95.2    
95.4    
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95.9    
96.0    
96.2    
96.4    
96.6    
96.7    
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98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 45193, rend_intergenic: 40691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90370, rend_intergenic: 74413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95294, rend_intergenic: 90722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104736, rend_intergenic: 100985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121121, rend_intergenic: 118258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139220, rend_intergenic: 135504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143653, rend_intergenic: 139756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151948, rend_intergenic: 149427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171088, rend_intergenic: 169411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175644, rend_intergenic: 173898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181684, rend_intergenic: 176342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187249, rend_intergenic: 183650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14038
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10249
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 1 - 10044
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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