-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_6995250-7223748

-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 GeneMark_model.21097_t
Valid prediction for snap_scaffold_5-snap.1436-T1
Valid prediction for snap_scaffold_5-snap.1442-T1
Valid prediction for GeneMark_model.21119_t
Valid prediction for GeneMark_model.21121_t
Valid prediction for snap_scaffold_5-snap.1425-T1
Valid prediction for Augustus_model.g8222.t1
Valid prediction for snap_scaffold_5-snap.1405-T1
Valid prediction for snap_scaffold_5-snap.1434-T1
Valid prediction for GeneMark_model.21117_t
Valid prediction for GeneMark_model.21145_t
Valid prediction for Augustus_model.g8212.t1
Valid prediction for GeneMark_model.21110_t
Valid prediction for GlimmerHMM_glimmerT_12420-T1
Valid prediction for GlimmerHMM_glimmerT_12417-T1
Valid prediction for GeneMark_model.21113_t
Valid prediction for GeneMark_model.21094_t
Valid prediction for snap_scaffold_5-snap.1419-T1
Valid prediction for GlimmerHMM_glimmerT_12407-T1
Valid prediction for GlimmerHMM_glimmerT_12421-T1
Valid prediction for snap_scaffold_5-snap.1445-T1
Valid prediction for snap_scaffold_5-snap.1424-T1
Valid prediction for GeneMark_model.21091_t
Valid prediction for snap_scaffold_5-snap.1409-T1
Valid prediction for snap_scaffold_5-snap.1439-T1
Valid prediction for GeneMark_model.21124_t
Valid prediction for Augustus_model.g8213.t1
Valid prediction for GeneMark_model.21139_t
Valid prediction for snap_scaffold_5-snap.1430-T1
Valid prediction for GeneMark_model.21108_t
Valid prediction for GlimmerHMM_glimmerT_12413-T1
Valid prediction for GeneMark_model.21101_t
Valid prediction for GlimmerHMM_glimmerT_12404-T1
Valid prediction for GlimmerHMM_glimmerT_12412-T1
Valid prediction for GlimmerHMM_glimmerT_12409-T1
Valid prediction for Augustus_model.g8223.t1
Valid prediction for GeneMark_model.21130_t
Valid prediction for snap_scaffold_5-snap.1416-T1
Valid prediction for GeneMark_model.21103_t
Valid prediction for GeneMark_model.21144_t
Valid prediction for Augustus_model.g8220.t1
Valid prediction for GeneMark_model.21138_t
Valid prediction for Augustus_model.g8215.t1
Valid prediction for GlimmerHMM_glimmerT_12423-T1
Valid prediction for GlimmerHMM_glimmerT_12406-T1
Valid prediction for GeneMark_model.21089_t
Valid prediction for snap_scaffold_5-snap.1411-T1
Valid prediction for GeneMark_model.21141_t
Valid prediction for GlimmerHMM_glimmerT_12415-T1
Valid prediction for snap_scaffold_5-snap.1415-T1
Valid prediction for Augustus_model.g8216.t1
Valid prediction for GeneMark_model.21133_t
Valid prediction for snap_scaffold_5-snap.1446-T1
Valid prediction for GeneMark_model.21147_t
Valid prediction for GlimmerHMM_glimmerT_12416-T1
Valid prediction for GeneMark_model.21115_t
Valid prediction for GeneMark_model.21099_t
Valid prediction for snap_scaffold_5-snap.1444-T1
Valid prediction for snap_scaffold_5-snap.1440-T1
Valid prediction for snap_scaffold_5-snap.1433-T1
Valid prediction for snap_scaffold_5-snap.1438-T1
Valid prediction for snap_scaffold_5-snap.1449-T1
Valid prediction for GeneMark_model.21128_t
Valid prediction for snap_scaffold_5-snap.1412-T1
Valid prediction for snap_scaffold_5-snap.1422-T1
Valid prediction for GeneMark_model.21126_t
Couldn't classify 33484, 33733
Sorry, prediction pasa_asmbl_44138.p1 fails validation.
(TGT)	 CT	33484-33733	GT	CAG
(ACC)	 AG	34079-34155	GT	AGG
(CAG)	 AG	34301-34447	GT	AGG
(GTG)	 AG	34568-34706	GT	CGG
(ACC)	 AG	35882-36846	TC	AAT
-recovered pasa_asmbl_44138.p1, terminal, 35882, 36846
-recovered pasa_asmbl_44138.p1, internal, 34079, 34155
-recovered pasa_asmbl_44138.p1, internal, 34301, 34447
-recovered pasa_asmbl_44138.p1, internal, 34568, 34706
Valid prediction for Augustus_model.g8214.t1
Valid prediction for GlimmerHMM_glimmerT_12419-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.21149_t
Valid prediction for snap_scaffold_5-snap.1435-T1
Valid prediction for GeneMark_model.21092_t
Valid prediction for GlimmerHMM_glimmerT_12411-T1
Valid prediction for snap_scaffold_5-snap.1421-T1
Valid prediction for GeneMark_model.21127_t
Valid prediction for GeneMark_model.21120_t
Valid prediction for GeneMark_model.21095_t
Valid prediction for Augustus_model.g8225.t1
Valid prediction for snap_scaffold_5-snap.1432-T1
Valid prediction for GeneMark_model.21096_t
Valid prediction for snap_scaffold_5-snap.1431-T1
Valid prediction for GeneMark_model.21098_t
Valid prediction for snap_scaffold_5-snap.1414-T1
Valid prediction for snap_scaffold_5-snap.1407-T1
Valid prediction for Augustus_model.g8219.t1
Valid prediction for GeneMark_model.21106_t
Valid prediction for GeneMark_model.21129_t
Valid prediction for pasa_asmbl_45550.p1
Valid prediction for GeneMark_model.21125_t
Valid prediction for GeneMark_model.21122_t
Valid prediction for snap_scaffold_5-snap.1448-T1
Valid prediction for GeneMark_model.21131_t
Valid prediction for GeneMark_model.21100_t
Valid prediction for CodingQuarry_transcript_51986-T1
Valid prediction for GeneMark_model.21102_t
Valid prediction for snap_scaffold_5-snap.1404-T1
Valid prediction for GeneMark_model.21090_t
Valid prediction for Augustus_model.g8217.t1
Valid prediction for GeneMark_model.21093_t
Valid prediction for snap_scaffold_5-snap.1450-T1
Valid prediction for GeneMark_model.21123_t
Valid prediction for snap_scaffold_5-snap.1410-T1
Valid prediction for GeneMark_model.21105_t
Valid prediction for GeneMark_model.21143_t
Valid prediction for Augustus_model.g8218.t1
Valid prediction for snap_scaffold_5-snap.1429-T1
Valid prediction for snap_scaffold_5-snap.1420-T1
Valid prediction for GeneMark_model.21107_t
Valid prediction for snap_scaffold_5-snap.1441-T1
Valid prediction for GeneMark_model.21132_t
Valid prediction for GeneMark_model.21137_t
Valid prediction for GeneMark_model.21118_t
Valid prediction for GeneMark_model.21142_t
Valid prediction for snap_scaffold_5-snap.1428-T1
Valid prediction for Augustus_model.g8226.t1
Valid prediction for snap_scaffold_5-snap.1447-T1
Valid prediction for GlimmerHMM_glimmerT_12424-T1
Valid prediction for GlimmerHMM_glimmerT_12422-T1
Valid prediction for snap_scaffold_5-snap.1443-T1
Valid prediction for snap_scaffold_5-snap.1406-T1
Valid prediction for GlimmerHMM_glimmerT_12408-T1
Valid prediction for GeneMark_model.21140_t
Valid prediction for CodingQuarry_transcript_51987-T1
Valid prediction for snap_scaffold_5-snap.1427-T1
Valid prediction for snap_scaffold_5-snap.1417-T1
Valid prediction for GeneMark_model.21111_t
Valid prediction for snap_scaffold_5-snap.1423-T1
Valid prediction for GeneMark_model.21136_t
Valid prediction for snap_scaffold_5-snap.1437-T1
Valid prediction for GlimmerHMM_glimmerT_12410-T1
Valid prediction for GeneMark_model.21148_t
Valid prediction for GlimmerHMM_glimmerT_12405-T1
Valid prediction for snap_scaffold_5-snap.1408-T1
Valid prediction for GeneMark_model.21104_t
Valid prediction for GlimmerHMM_glimmerT_12414-T1
Valid prediction for GlimmerHMM_glimmerT_12418-T1
Valid prediction for snap_scaffold_5-snap.1413-T1
Valid prediction for GeneMark_model.21146_t
Valid prediction for snap_scaffold_5-snap.1426-T1
Valid prediction for GeneMark_model.21109_t
Valid prediction for GeneMark_model.21112_t
Valid prediction for GeneMark_model.21114_t
Valid prediction for Augustus_model.g8221.t1
Valid prediction for GeneMark_model.21116_t
Valid prediction for Augustus_model.g8224.t1
Couldn't classify 112403, 112531
Sorry, prediction pasa_asmbl_45549.p1 fails validation.
(TTC)	 CC	112403-112531	GT	AGG
(GAG)	 AG	112704-112846	GT	AAG
(GGT)	 AG	113013-113197	GT	AGG
(GCT)	 AG	113662-113750	GT	AGG
(GCG)	 AG	113892-114032	GT	AGG
(GTG)	 AG	114187-114498	GT	AGG
(GTG)	 AG	114656-114958	AT	AGA
add_exon() Sorry, pasa_asmbl_45549.p1 113013-113197-terminal-2 is invalid.
-recovered pasa_asmbl_45549.p1, terminal, 113013, 113197
-recovered pasa_asmbl_45549.p1, terminal, 114656, 114958
-recovered pasa_asmbl_45549.p1, internal, 112704, 112846
-recovered pasa_asmbl_45549.p1, internal, 113013, 113197
-recovered pasa_asmbl_45549.p1, internal, 113662, 113750
-recovered pasa_asmbl_45549.p1, internal, 113892, 114032
-recovered pasa_asmbl_45549.p1, internal, 114187, 114498
Valid prediction for GeneMark_model.21134_t
Valid prediction for snap_scaffold_5-snap.1418-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25536, rend_intergenic: 10804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37618, rend_intergenic: 25918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56090, rend_intergenic: 47437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64493, rend_intergenic: 59078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68617, rend_intergenic: 65692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72479, rend_intergenic: 70071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78303, rend_intergenic: 72747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84926, rend_intergenic: 82945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91601, rend_intergenic: 90837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100487, rend_intergenic: 92077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105053, rend_intergenic: 102461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116169, rend_intergenic: 113124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142362, rend_intergenic: 142138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153102, rend_intergenic: 148624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 228499
-exon list size: 716


building trellis

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95.3    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 25536, rend_intergenic: 10804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37618, rend_intergenic: 25918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56090, rend_intergenic: 47437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64493, rend_intergenic: 59078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68617, rend_intergenic: 65692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72479, rend_intergenic: 70071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78303, rend_intergenic: 72747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84926, rend_intergenic: 82945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91601, rend_intergenic: 90837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100487, rend_intergenic: 92077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105053, rend_intergenic: 102461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116169, rend_intergenic: 113124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142362, rend_intergenic: 142138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153102, rend_intergenic: 148624  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