-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_3882379-4128030

-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_12013-T1
Valid prediction for GeneMark_model.20271_t
Valid prediction for snap_scaffold_5-snap.791-T1
Valid prediction for snap_scaffold_5-snap.778-T1
Valid prediction for snap_scaffold_5-snap.798-T1
Valid prediction for snap_scaffold_5-snap.767-T1
Valid prediction for GeneMark_model.20263_t
Couldn't classify 122228, 122372
Couldn't classify 123060, 123141
Sorry, prediction pasa_asmbl_43926.p1 fails validation.
(TGC)	 TG	122228-122372	GT	TGG
(GAA)	 AG	122675-122713	GT	ACG
(AGA)	 AG	122832-122904	GT	AGG
(CTT)	 AG	123060-123141	GG	CAG
-recovered pasa_asmbl_43926.p1, internal, 122675, 122713
-recovered pasa_asmbl_43926.p1, internal, 122832, 122904
Valid prediction for snap_scaffold_5-snap.779-T1
Valid prediction for snap_scaffold_5-snap.769-T1
Valid prediction for snap_scaffold_5-snap.806-T1
Valid prediction for GeneMark_model.20232_t
Valid prediction for GeneMark_model.20251_t
Valid prediction for GlimmerHMM_glimmerT_12015-T1
Valid prediction for GeneMark_model.20240_t
Valid prediction for snap_scaffold_5-snap.768-T1
Valid prediction for GeneMark_model.20269_t
Valid prediction for GeneMark_model.20257_t
Valid prediction for GeneMark_model.20253_t
Valid prediction for snap_scaffold_5-snap.805-T1
Valid prediction for HiQ_model.g7892.t1
Valid prediction for GlimmerHMM_glimmerT_12008-T1
Valid prediction for Augustus_model.g7900.t1
Valid prediction for snap_scaffold_5-snap.782-T1
Valid prediction for snap_scaffold_5-snap.795-T1
Valid prediction for snap_scaffold_5-snap.789-T1
Valid prediction for HiQ_model.g7895.t1
Valid prediction for snap_scaffold_5-snap.788-T1
Valid prediction for GlimmerHMM_glimmerT_12003-T1
Valid prediction for pasa_asmbl_43918.p1
Valid prediction for GeneMark_model.20234_t
Valid prediction for CodingQuarry_transcript_51891-T1
Valid prediction for GeneMark_model.20265_t
Valid prediction for snap_scaffold_5-snap.773-T1
Valid prediction for pasa_asmbl_45123.p1
Valid prediction for CodingQuarry_transcript_51894-T1
Valid prediction for GeneMark_model.20273_t
Valid prediction for GeneMark_model.20255_t
Valid prediction for GeneMark_model.20237_t
Valid prediction for snap_scaffold_5-snap.792-T1
Valid prediction for pasa_asmbl_43927.p1
Valid prediction for snap_scaffold_5-snap.802-T1
Valid prediction for GlimmerHMM_glimmerT_11998-T1
Valid prediction for GeneMark_model.20247_t
Valid prediction for GeneMark_model.20270_t
Valid prediction for GeneMark_model.20260_t
Valid prediction for CodingQuarry_transcript_51890-T1
Valid prediction for snap_scaffold_5-snap.807-T1
Valid prediction for GeneMark_model.20245_t
Valid prediction for pasa_asmbl_43929.p1
Valid prediction for CodingQuarry_transcript_51889-T1
Valid prediction for GlimmerHMM_glimmerT_12004-T1
Valid prediction for snap_scaffold_5-snap.803-T1
Valid prediction for GeneMark_model.20243_t
Valid prediction for GeneMark_model.20235_t
Valid prediction for GeneMark_model.20267_t
Valid prediction for HiQ_model.g7901.t1
Valid prediction for GlimmerHMM_glimmerT_12012-T1
Valid prediction for Augustus_model.g7903.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_5-snap.774-T1
Couldn't classify 1473, 1588
Couldn't classify 3746, 3981
Sorry, prediction pasa_asmbl_45339.p1 fails validation.
(ATC)	 AC	1473-1588	GT	AGG
(GGT)	 AG	1919-2034	GT	AGG
(CGG)	 AG	3746-3981	GA	GCG
-recovered pasa_asmbl_45339.p1, internal, 1919, 2034
Valid prediction for Augustus_model.g7904.t1
Valid prediction for GlimmerHMM_glimmerT_11999-T1
Valid prediction for GlimmerHMM_glimmerT_12009-T1
Valid prediction for GlimmerHMM_glimmerT_12016-T1
Valid prediction for GeneMark_model.20249_t
Valid prediction for snap_scaffold_5-snap.799-T1
Valid prediction for snap_scaffold_5-snap.786-T1
Valid prediction for GlimmerHMM_glimmerT_12001-T1
Valid prediction for GeneMark_model.20274_t
Couldn't classify 13017, 13116
Couldn't classify 18342, 18392
Sorry, prediction pasa_asmbl_46356.p1 fails validation.
(GAG)	 GT	13017-13116	GT	TGG
(TGT)	 AG	15450-15553	GT	AGG
(GGG)	 AG	15793-15842	GT	AAG
(GGA)	 AG	17637-17712	GT	AGG
(GGC)	 AG	18342-18392	AA	GCA
-recovered pasa_asmbl_46356.p1, internal, 15450, 15553
-recovered pasa_asmbl_46356.p1, internal, 15793, 15842
-recovered pasa_asmbl_46356.p1, internal, 17637, 17712
Valid prediction for snap_scaffold_5-snap.775-T1
Valid prediction for snap_scaffold_5-snap.785-T1
Valid prediction for Augustus_model.g7894.t1
Valid prediction for GeneMark_model.20246_t
Valid prediction for GeneMark_model.20242_t
Valid prediction for GeneMark_model.20244_t
Valid prediction for snap_scaffold_5-snap.809-T1
Valid prediction for GeneMark_model.20241_t
Valid prediction for snap_scaffold_5-snap.790-T1
Valid prediction for Augustus_model.g7907.t1
Valid prediction for GeneMark_model.20236_t
Valid prediction for snap_scaffold_5-snap.787-T1
Valid prediction for GeneMark_model.20268_t
Valid prediction for snap_scaffold_5-snap.784-T1
Valid prediction for GeneMark_model.20272_t
Valid prediction for snap_scaffold_5-snap.800-T1
Valid prediction for GlimmerHMM_glimmerT_12007-T1
Valid prediction for Augustus_model.g7893.t1
Valid prediction for snap_scaffold_5-snap.781-T1
Valid prediction for snap_scaffold_5-snap.808-T1
Valid prediction for snap_scaffold_5-snap.801-T1
Valid prediction for GeneMark_model.20250_t
Valid prediction for GeneMark_model.20264_t
Valid prediction for GeneMark_model.20258_t
Valid prediction for GlimmerHMM_glimmerT_12005-T1
Valid prediction for CodingQuarry_transcript_51893-T1
Couldn't classify 45703, 45750
Sorry, prediction pasa_asmbl_45333.p1 fails validation.
(TCA)	 AG	45703-45750	GT	AGG
(CTG)	 AG	46480-46655	GT	AGG
(GTG)	 AG	47002-47104	GT	AGG
(GGA)	 AG	47748-47815	GT	AGG
(GCT)	 AG	48357-48399	AA	AGA
-recovered pasa_asmbl_45333.p1, terminal, 48357, 48399
-recovered pasa_asmbl_45333.p1, internal, 45703, 45750
-recovered pasa_asmbl_45333.p1, internal, 46480, 46655
-recovered pasa_asmbl_45333.p1, internal, 47002, 47104
-recovered pasa_asmbl_45333.p1, internal, 47748, 47815
Valid prediction for Augustus_model.g7902.t1
Couldn't classify 30587, 30665
Couldn't classify 31648, 31764
Sorry, prediction pasa_asmbl_45336.p1 fails validation.
(GGG)	 AG	30587-30665	GT	AGG
(ACT)	 AG	31074-31252	GT	AGG
(ATC)	 AG	31648-31764	AC	ACA
-recovered pasa_asmbl_45336.p1, internal, 30587, 30665
-recovered pasa_asmbl_45336.p1, internal, 31074, 31252
Valid prediction for snap_scaffold_5-snap.804-T1
Couldn't classify 42168, 42263
Couldn't classify 45366, 45478
Sorry, prediction pasa_asmbl_45334.p2 fails validation.
(GAG)	 AC	42168-42263	GT	TGG
(AAA)	 AG	42994-43096	GT	CAG
(ACA)	 AG	44192-44335	GT	GGG
(CCT)	 AG	45366-45478	AG	TCA
-recovered pasa_asmbl_45334.p2, internal, 42994, 43096
-recovered pasa_asmbl_45334.p2, internal, 44192, 44335
Valid prediction for GeneMark_model.20266_t
Valid prediction for snap_scaffold_5-snap.771-T1
Couldn't classify 22404, 22547
Couldn't classify 27368, 27478
Sorry, prediction pasa_asmbl_45338.p1 fails validation.
(GTC)	 CA	22404-22547	GT	TGG
(ATT)	 AG	25165-25257	GT	AGG
(ATG)	 AG	27368-27478	CG	GAC
-recovered pasa_asmbl_45338.p1, internal, 25165, 25257
Valid prediction for HiQ_model.g7897.t1
Valid prediction for snap_scaffold_5-snap.770-T1
Valid prediction for GlimmerHMM_glimmerT_12018-T1
Couldn't classify 163735, 164094
Sorry, prediction pasa_asmbl_45323.p1 fails validation.
(GGA)	 CG	163735-164094	GA	AGG
Valid prediction for Augustus_model.g7898.t1
Valid prediction for Augustus_model.g7906.t1
Valid prediction for pasa_asmbl_45324.p1
Valid prediction for Augustus_model.g7896.t1
Valid prediction for Augustus_model.g7899.t1
Valid prediction for GlimmerHMM_glimmerT_12002-T1
Valid prediction for GeneMark_model.20233_t
Valid prediction for GlimmerHMM_glimmerT_12020-T1
Valid prediction for GlimmerHMM_glimmerT_12019-T1
Valid prediction for snap_scaffold_5-snap.797-T1
Valid prediction for GeneMark_model.20254_t
Valid prediction for GeneMark_model.20262_t
Valid prediction for GlimmerHMM_glimmerT_12000-T1
Valid prediction for snap_scaffold_5-snap.794-T1
Valid prediction for GlimmerHMM_glimmerT_12006-T1
Valid prediction for GeneMark_model.20259_t
Valid prediction for GeneMark_model.20248_t
Valid prediction for snap_scaffold_5-snap.776-T1
Valid prediction for GeneMark_model.20239_t
Valid prediction for snap_scaffold_5-snap.783-T1
Valid prediction for snap_scaffold_5-snap.780-T1
Valid prediction for pasa_asmbl_46413.p1
Valid prediction for GeneMark_model.20256_t
Valid prediction for GeneMark_model.20275_t
Couldn't classify 206169, 206253
Sorry, prediction pasa_asmbl_45318.p2 fails validation.
(TTC)	 GC	206169-206253	GT	AGG
(GGT)	 AG	206373-206677	GA	GAG
-recovered pasa_asmbl_45318.p2, terminal, 206373, 206677
Valid prediction for GlimmerHMM_glimmerT_12014-T1
Valid prediction for GlimmerHMM_glimmerT_12017-T1
Valid prediction for GeneMark_model.20261_t
Valid prediction for snap_scaffold_5-snap.777-T1
Valid prediction for Augustus_model.g7908.t1
Valid prediction for GlimmerHMM_glimmerT_12011-T1
Valid prediction for CodingQuarry_transcript_51896-T1
Valid prediction for snap_scaffold_5-snap.793-T1
Valid prediction for snap_scaffold_5-snap.796-T1
Valid prediction for GlimmerHMM_glimmerT_12010-T1
Valid prediction for snap_scaffold_5-snap.772-T1
Couldn't classify 189021, 189105
Couldn't classify 192049, 192114
Sorry, prediction pasa_asmbl_45321.p1 fails validation.
(GTA)	 AG	189021-189105	GT	TGG
(CAA)	 AG	189249-189355	GT	AGG
(GCC)	 AG	189639-189716	GT	AGG
(ACC)	 AG	190030-190087	GT	TGG
(TGA)	 AG	190347-190398	GT	AAG
(GGG)	 AG	190721-190780	GT	GTG
(GGG)	 AG	191006-191099	GT	ACG
(TTC)	 AG	191809-191856	GT	GGG
(ATT)	 AG	192049-192114	GG	GTG
-recovered pasa_asmbl_45321.p1, internal, 189021, 189105
-recovered pasa_asmbl_45321.p1, internal, 189249, 189355
-recovered pasa_asmbl_45321.p1, internal, 189639, 189716
-recovered pasa_asmbl_45321.p1, internal, 190030, 190087
-recovered pasa_asmbl_45321.p1, internal, 190347, 190398
-recovered pasa_asmbl_45321.p1, internal, 190721, 190780
-recovered pasa_asmbl_45321.p1, internal, 191006, 191099
-recovered pasa_asmbl_45321.p1, internal, 191809, 191856
Valid prediction for Augustus_model.g7905.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11137, rend_intergenic: 7477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34715, rend_intergenic: 32823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67113, rend_intergenic: 64909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128648, rend_intergenic: 119840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208460, rend_intergenic: 200924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211453, rend_intergenic: 210366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233353, rend_intergenic: 214282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238093, rend_intergenic: 233617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 245652
-exon list size: 656


building trellis

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86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.8    
88.9    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 11137, rend_intergenic: 7477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34715, rend_intergenic: 32823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67113, rend_intergenic: 64909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128648, rend_intergenic: 119840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208460, rend_intergenic: 200924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211453, rend_intergenic: 210366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233353, rend_intergenic: 214282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238093, rend_intergenic: 233617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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