-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_5114099-5293850

-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_14-snap.1060-T1
Valid prediction for GeneMark_model.59209_t
Valid prediction for snap_scaffold_14-snap.1037-T1
Valid prediction for GeneMark_model.59233_t
Valid prediction for GeneMark_model.59245_t
Valid prediction for snap_scaffold_14-snap.1019-T1
Valid prediction for snap_scaffold_14-snap.1024-T1
Couldn't classify 4946, 5605
Couldn't classify 5906, 5956
Sorry, prediction CodingQuarry_transcript_15592-T1 fails validation.
(ATG)	 TC	4946-5605	GA	ACG
(AGA)	 AT	5906-5956	CA	AGC
Valid prediction for snap_scaffold_14-snap.1039-T1
Valid prediction for snap_scaffold_14-snap.1031-T1
Valid prediction for GeneMark_model.59207_t
Valid prediction for snap_scaffold_14-snap.1036-T1
Valid prediction for Augustus_model.g23233.t1
Valid prediction for GeneMark_model.59203_t
Valid prediction for Augustus_model.g23236.t1
Valid prediction for snap_scaffold_14-snap.1043-T1
Valid prediction for GeneMark_model.59200_t
Valid prediction for GeneMark_model.59243_t
Valid prediction for GlimmerHMM_glimmerT_34565-T1
Valid prediction for snap_scaffold_14-snap.1032-T1
Valid prediction for GlimmerHMM_glimmerT_34562-T1
Valid prediction for GlimmerHMM_glimmerT_34558-T1
Valid prediction for Augustus_model.g23258.t1
Valid prediction for GeneMark_model.59255_t
Valid prediction for GeneMark_model.59217_t
Valid prediction for GeneMark_model.59254_t
Valid prediction for Augustus_model.g23253.t1
Valid prediction for GeneMark_model.59230_t
Valid prediction for Augustus_model.g23237.t1
Valid prediction for snap_scaffold_14-snap.1025-T1
Couldn't classify 36971, 37069
Couldn't classify 38595, 38658
Sorry, prediction pasa_asmbl_12752.p1 fails validation.
(GAG)	 GT	36971-37069	GT	AGG
(ACC)	 AG	38249-38403	GT	AGG
(ACT)	 AG	38595-38658	GC	AGG
-recovered pasa_asmbl_12752.p1, internal, 38249, 38403
-recovered pasa_asmbl_12752.p1, internal, 38595, 38658
Valid prediction for snap_scaffold_14-snap.1026-T1
Valid prediction for GeneMark_model.59248_t
Valid prediction for snap_scaffold_14-snap.1042-T1
Valid prediction for Augustus_model.g23247.t1
Valid prediction for GeneMark_model.59219_t
Valid prediction for snap_scaffold_14-snap.1041-T1
Valid prediction for snap_scaffold_14-snap.1051-T1
Valid prediction for snap_scaffold_14-snap.1053-T1
Valid prediction for GlimmerHMM_glimmerT_34578-T1
Valid prediction for GeneMark_model.59204_t
Valid prediction for GeneMark_model.59224_t
Valid prediction for snap_scaffold_14-snap.1021-T1
Valid prediction for snap_scaffold_14-snap.1048-T1
Couldn't classify 51796, 51937
Sorry, prediction pasa_asmbl_11986.p2 fails validation.
(GAG)	 CA	51796-51937	GT	CAG
(GCT)	 AG	52791-52951	GA	GAG
-recovered pasa_asmbl_11986.p2, terminal, 52791, 52951
Valid prediction for GeneMark_model.59206_t
Valid prediction for snap_scaffold_14-snap.1044-T1
Valid prediction for snap_scaffold_14-snap.1057-T1
Valid prediction for GlimmerHMM_glimmerT_34579-T1
Valid prediction for snap_scaffold_14-snap.1049-T1
Valid prediction for Augustus_model.g23232.t1
Valid prediction for Augustus_model.g23246.t1
Valid prediction for Augustus_model.g23250.t1
Valid prediction for GeneMark_model.59202_t
Valid prediction for GeneMark_model.59237_t
Couldn't classify 48073, 48303
Sorry, prediction pasa_asmbl_11983.p1 fails validation.
(ATG)	 AG	47800-47877	GT	GCG
(GTC)	 AG	48073-48303	AC	GTA
-recovered pasa_asmbl_11983.p1, initial, 47800, 47877
-recovered pasa_asmbl_11983.p1, internal, 47800, 47877
Valid prediction for GlimmerHMM_glimmerT_34572-T1
Valid prediction for GeneMark_model.59228_t
Valid prediction for GeneMark_model.59253_t
Valid prediction for GeneMark_model.59241_t
Valid prediction for GeneMark_model.59252_t
Valid prediction for snap_scaffold_14-snap.1022-T1
Valid prediction for GlimmerHMM_glimmerT_34583-T1
Valid prediction for GeneMark_model.59226_t
Valid prediction for snap_scaffold_14-snap.1061-T1
Valid prediction for GeneMark_model.59210_t
Valid prediction for GlimmerHMM_glimmerT_34574-T1
Valid prediction for Augustus_model.g23257.t1
Valid prediction for Augustus_model.g23255.t1
Valid prediction for GlimmerHMM_glimmerT_34564-T1
Valid prediction for GlimmerHMM_glimmerT_34576-T1
Valid prediction for GlimmerHMM_glimmerT_34588-T1
Valid prediction for GeneMark_model.59235_t
Valid prediction for GeneMark_model.59222_t
Valid prediction for GlimmerHMM_glimmerT_34575-T1
Valid prediction for GlimmerHMM_glimmerT_34568-T1
Valid prediction for Augustus_model.g23244.t1
Valid prediction for snap_scaffold_14-snap.1027-T1
Valid prediction for GlimmerHMM_glimmerT_34567-T1
Valid prediction for GeneMark_model.59212_t
Valid prediction for GlimmerHMM_glimmerT_34570-T1
Valid prediction for GeneMark_model.59199_t
Valid prediction for GlimmerHMM_glimmerT_34577-T1
Valid prediction for GeneMark_model.59214_t
Valid prediction for Augustus_model.g23248.t1
Valid prediction for snap_scaffold_14-snap.1065-T1
Valid prediction for GlimmerHMM_glimmerT_34590-T1
Valid prediction for Augustus_model.g23230.t1
Valid prediction for snap_scaffold_14-snap.1028-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.g23256.t1
Valid prediction for snap_scaffold_14-snap.1033-T1
Valid prediction for GeneMark_model.59225_t
Valid prediction for GlimmerHMM_glimmerT_34580-T1
Valid prediction for Augustus_model.g23240.t1
Valid prediction for snap_scaffold_14-snap.1058-T1
Valid prediction for snap_scaffold_14-snap.1030-T1
Valid prediction for GlimmerHMM_glimmerT_34589-T1
Valid prediction for snap_scaffold_14-snap.1045-T1
Valid prediction for GeneMark_model.59249_t
Valid prediction for GlimmerHMM_glimmerT_34584-T1
Couldn't classify 33169, 33789
Sorry, prediction pasa_asmbl_13057.p1 fails validation.
(AGG)	 TC	33169-33789	CG	GAC
Valid prediction for GlimmerHMM_glimmerT_34566-T1
Valid prediction for Augustus_model.g23243.t1
Valid prediction for snap_scaffold_14-snap.1038-T1
Valid prediction for GeneMark_model.59240_t
Valid prediction for snap_scaffold_14-snap.1062-T1
Valid prediction for snap_scaffold_14-snap.1059-T1
Valid prediction for snap_scaffold_14-snap.1052-T1
Valid prediction for snap_scaffold_14-snap.1055-T1
Valid prediction for Augustus_model.g23249.t1
Valid prediction for GeneMark_model.59213_t
Valid prediction for GeneMark_model.59218_t
Valid prediction for Augustus_model.g23254.t1
Valid prediction for GeneMark_model.59227_t
Valid prediction for GeneMark_model.59221_t
Valid prediction for GeneMark_model.59208_t
Valid prediction for GlimmerHMM_glimmerT_34587-T1
Valid prediction for GeneMark_model.59201_t
Valid prediction for snap_scaffold_14-snap.1064-T1
Valid prediction for snap_scaffold_14-snap.1050-T1
Couldn't classify 6958, 7031
Sorry, prediction pasa_asmbl_13793.p1 fails validation.
(CAG)	 CA	6958-7031	GT	AGG
(CCC)	 AG	9329-9561	GT	AGG
(GCG)	 AG	10967-11400	CC	AAC
-recovered pasa_asmbl_13793.p1, terminal, 10967, 11400
-recovered pasa_asmbl_13793.p1, internal, 9329, 9561
Valid prediction for snap_scaffold_14-snap.1040-T1
Valid prediction for snap_scaffold_14-snap.1020-T1
Valid prediction for Augustus_model.g23251.t1
Valid prediction for Augustus_model.g23234.t1
Valid prediction for snap_scaffold_14-snap.1034-T1
Valid prediction for snap_scaffold_14-snap.1056-T1
Valid prediction for GeneMark_model.59242_t
Valid prediction for GeneMark_model.59229_t
Valid prediction for GlimmerHMM_glimmerT_34561-T1
Valid prediction for GeneMark_model.59236_t
Valid prediction for GlimmerHMM_glimmerT_34563-T1
Valid prediction for snap_scaffold_14-snap.1047-T1
Valid prediction for GeneMark_model.59216_t
Valid prediction for GeneMark_model.59220_t
Valid prediction for GeneMark_model.59247_t
Valid prediction for GeneMark_model.59251_t
Valid prediction for snap_scaffold_14-snap.1023-T1
Valid prediction for GeneMark_model.59244_t
Valid prediction for GlimmerHMM_glimmerT_34581-T1
Valid prediction for Augustus_model.g23245.t1
Valid prediction for Augustus_model.g23231.t1
Valid prediction for Augustus_model.g23252.t1
Valid prediction for snap_scaffold_14-snap.1035-T1
Valid prediction for GeneMark_model.59205_t
Valid prediction for GlimmerHMM_glimmerT_34585-T1
Valid prediction for snap_scaffold_14-snap.1054-T1
Valid prediction for GlimmerHMM_glimmerT_34569-T1
Valid prediction for snap_scaffold_14-snap.1029-T1
Valid prediction for GlimmerHMM_glimmerT_34586-T1
Valid prediction for GlimmerHMM_glimmerT_34571-T1
Valid prediction for snap_scaffold_14-snap.1063-T1
Valid prediction for GlimmerHMM_glimmerT_34560-T1
Valid prediction for Augustus_model.g23235.t1
Valid prediction for Augustus_model.g23239.t1
Valid prediction for GlimmerHMM_glimmerT_34573-T1
Valid prediction for snap_scaffold_14-snap.1046-T1
Valid prediction for GeneMark_model.59231_t
Valid prediction for GeneMark_model.59234_t
Valid prediction for GeneMark_model.59246_t
Valid prediction for GeneMark_model.59215_t
Valid prediction for Augustus_model.g23242.t1
Valid prediction for Augustus_model.g23238.t1
Valid prediction for Augustus_model.g23241.t1
Valid prediction for GeneMark_model.59239_t
Valid prediction for GeneMark_model.59223_t
Valid prediction for GlimmerHMM_glimmerT_34559-T1
Valid prediction for GeneMark_model.59232_t
Valid prediction for GeneMark_model.59238_t
Valid prediction for GeneMark_model.59211_t
Valid prediction for GlimmerHMM_glimmerT_34582-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 27393, rend_intergenic: 19765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52951, rend_intergenic: 50739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62569, rend_intergenic: 55110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76852, rend_intergenic: 71258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78803, rend_intergenic: 77743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88853, rend_intergenic: 80287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115457, rend_intergenic: 108027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120490, rend_intergenic: 116736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127181, rend_intergenic: 123005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143176, rend_intergenic: 130828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149640, rend_intergenic: 148828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152474, rend_intergenic: 149699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157228, rend_intergenic: 152474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177289, rend_intergenic: 173931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179752
-exon list size: 738


building trellis

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84.1    
84.2    
84.3    
84.5    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.6    
87.7    
87.8    
88.0    
88.1    
88.2    
88.4    
88.5    
88.6    
88.8    
88.9    
89.1    
89.2    
89.3    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.3    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.6    
91.8    
91.9    
92.0    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 56 predictions from path traversal
Error with prediction: snap lend_intergenic: 27393, rend_intergenic: 19765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52951, rend_intergenic: 50739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62569, rend_intergenic: 55110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76852, rend_intergenic: 71258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78803, rend_intergenic: 77743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88853, rend_intergenic: 80287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115457, rend_intergenic: 108027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120490, rend_intergenic: 116736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127181, rend_intergenic: 123005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143176, rend_intergenic: 130828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149640, rend_intergenic: 148828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152474, rend_intergenic: 149699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157228, rend_intergenic: 152474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177289, rend_intergenic: 173931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support