-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_15391280-15582342

-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_7-snap.2931-T1
Valid prediction for snap_scaffold_7-snap.2943-T1
Valid prediction for GeneMark_model.32023_t
Valid prediction for snap_scaffold_7-snap.2928-T1
Valid prediction for GeneMark_model.32021_t
Valid prediction for GeneMark_model.32019_t
Valid prediction for GlimmerHMM_glimmerT_19036-T1
Valid prediction for snap_scaffold_7-snap.2924-T1
Valid prediction for GeneMark_model.32014_t
Valid prediction for GeneMark_model.32001_t
Valid prediction for GeneMark_model.32009_t
Valid prediction for GeneMark_model.31999_t
Valid prediction for snap_scaffold_7-snap.2952-T1
Valid prediction for GeneMark_model.32018_t
Valid prediction for GeneMark_model.32010_t
Valid prediction for GeneMark_model.31996_t
Valid prediction for GeneMark_model.32016_t
Valid prediction for GeneMark_model.32012_t
Valid prediction for GeneMark_model.32027_t
Valid prediction for GeneMark_model.31993_t
Valid prediction for GeneMark_model.32013_t
Valid prediction for snap_scaffold_7-snap.2934-T1
Valid prediction for snap_scaffold_7-snap.2939-T1
Couldn't classify 10841, 11410
Sorry, prediction pasa_asmbl_51327.p2 fails validation.
(AGA)	 CT	10841-11410	TG	AGT
Valid prediction for snap_scaffold_7-snap.2949-T1
Valid prediction for Augustus_model.g12874.t1
Valid prediction for GeneMark_model.32008_t
Valid prediction for GeneMark_model.32004_t
Valid prediction for GeneMark_model.32030_t
Valid prediction for GeneMark_model.32007_t
Valid prediction for snap_scaffold_7-snap.2947-T1
Valid prediction for snap_scaffold_7-snap.2929-T1
Valid prediction for GlimmerHMM_glimmerT_19027-T1
Valid prediction for snap_scaffold_7-snap.2945-T1
Valid prediction for GeneMark_model.31998_t
Valid prediction for GlimmerHMM_glimmerT_19031-T1
Valid prediction for snap_scaffold_7-snap.2922-T1
Valid prediction for GeneMark_model.32025_t
Valid prediction for snap_scaffold_7-snap.2941-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_7-snap.2935-T1
Valid prediction for GeneMark_model.32031_t
Valid prediction for GlimmerHMM_glimmerT_19032-T1
Valid prediction for snap_scaffold_7-snap.2920-T1
Valid prediction for snap_scaffold_7-snap.2942-T1
Valid prediction for GeneMark_model.31995_t
Valid prediction for GlimmerHMM_glimmerT_19033-T1
Valid prediction for GlimmerHMM_glimmerT_19030-T1
Valid prediction for GlimmerHMM_glimmerT_19041-T1
Valid prediction for Augustus_model.g12877.t1
Valid prediction for Augustus_model.g12875.t1
Valid prediction for GlimmerHMM_glimmerT_19045-T1
Valid prediction for GlimmerHMM_glimmerT_19044-T1
Valid prediction for snap_scaffold_7-snap.2930-T1
Couldn't classify 25987, 26079
Sorry, prediction pasa_asmbl_50197.p1 fails validation.
(GCA)	 AG	25987-26079	GT	AGG
(CTC)	 AG	26314-26544	GT	CTG
(GAC)	 AG	26802-26949	GT	CGG
(GAA)	 AG	27272-27422	GT	AAG
(TGA)	 AG	27762-27870	GT	AAG
(AGG)	 AG	28654-28794	GT	AGG
(AGT)	 AG	29120-29302	GT	AGG
(GTG)	 AG	29786-29920	GT	AGG
(GAG)	 AG	30116-30295	GT	AGG
(CAC)	 AG	30845-30991	GT	GGG
(AAG)	 AG	32091-32156	GT	TGG
(GGT)	 AG	32453-32611	GT	AGG
(CCT)	 AG	32915-33073	CA	AAC
-recovered pasa_asmbl_50197.p1, terminal, 32915, 33073
-recovered pasa_asmbl_50197.p1, internal, 25987, 26079
-recovered pasa_asmbl_50197.p1, internal, 26314, 26544
-recovered pasa_asmbl_50197.p1, internal, 26802, 26949
-recovered pasa_asmbl_50197.p1, internal, 27272, 27422
-recovered pasa_asmbl_50197.p1, internal, 27762, 27870
-recovered pasa_asmbl_50197.p1, internal, 28654, 28794
-recovered pasa_asmbl_50197.p1, internal, 29120, 29302
-recovered pasa_asmbl_50197.p1, internal, 29786, 29920
-recovered pasa_asmbl_50197.p1, internal, 30116, 30295
-recovered pasa_asmbl_50197.p1, internal, 30845, 30991
-recovered pasa_asmbl_50197.p1, internal, 32091, 32156
-recovered pasa_asmbl_50197.p1, internal, 32453, 32611
Valid prediction for snap_scaffold_7-snap.2950-T1
Valid prediction for GlimmerHMM_glimmerT_19028-T1
Valid prediction for snap_scaffold_7-snap.2944-T1
Valid prediction for snap_scaffold_7-snap.2926-T1
Valid prediction for snap_scaffold_7-snap.2938-T1
Valid prediction for GlimmerHMM_glimmerT_19038-T1
Valid prediction for snap_scaffold_7-snap.2953-T1
Valid prediction for GeneMark_model.31997_t
Valid prediction for snap_scaffold_7-snap.2948-T1
Valid prediction for GeneMark_model.32017_t
Valid prediction for snap_scaffold_7-snap.2921-T1
Valid prediction for GeneMark_model.32024_t
Valid prediction for Augustus_model.g12881.t1
Couldn't classify 10736, 10817
Sorry, prediction pasa_asmbl_50201.p1 fails validation.
(CTG)	 AG	10736-10817	GT	AGG
(GTC)	 AG	11000-11096	GT	CAG
(TTG)	 AG	11201-11352	GT	CGG
(GGT)	 AG	11573-11710	GT	TGG
(GGG)	 AG	11875-12114	GT	AGG
(ACC)	 AG	12387-12595	GT	TGG
(ACA)	 AG	12713-12889	GT	GGG
(CTA)	 AG	14272-14342	GT	AGG
(TGC)	 AG	16126-16225	GT	AGG
(GTT)	 AG	16316-16369	GT	GGG
(AAA)	 AG	16474-16539	GT	ACG
(ATG)	 AG	16630-16698	GT	AGG
(GGT)	 AG	17004-17100	GT	GGG
(TAT)	 AG	17335-17405	TG	GAT
-recovered pasa_asmbl_50201.p1, initial, 16630, 16698
add_exon() Sorry, pasa_asmbl_50201.p1 10736-10817-terminal-3 is invalid.
-recovered pasa_asmbl_50201.p1, terminal, 10736, 10817
add_exon() Sorry, pasa_asmbl_50201.p1 11875-12114-terminal-1 is invalid.
-recovered pasa_asmbl_50201.p1, terminal, 11875, 12114
-recovered pasa_asmbl_50201.p1, terminal, 17335, 17405
-recovered pasa_asmbl_50201.p1, internal, 10736, 10817
-recovered pasa_asmbl_50201.p1, internal, 11000, 11096
-recovered pasa_asmbl_50201.p1, internal, 11201, 11352
-recovered pasa_asmbl_50201.p1, internal, 11573, 11710
-recovered pasa_asmbl_50201.p1, internal, 11875, 12114
-recovered pasa_asmbl_50201.p1, internal, 12387, 12595
-recovered pasa_asmbl_50201.p1, internal, 12713, 12889
-recovered pasa_asmbl_50201.p1, internal, 14272, 14342
-recovered pasa_asmbl_50201.p1, internal, 16126, 16225
-recovered pasa_asmbl_50201.p1, internal, 16316, 16369
-recovered pasa_asmbl_50201.p1, internal, 16474, 16539
-recovered pasa_asmbl_50201.p1, internal, 16630, 16698
-recovered pasa_asmbl_50201.p1, internal, 17004, 17100
Valid prediction for snap_scaffold_7-snap.2946-T1
Valid prediction for GlimmerHMM_glimmerT_19029-T1
Valid prediction for GeneMark_model.32011_t
Valid prediction for GeneMark_model.32029_t
Valid prediction for GlimmerHMM_glimmerT_19037-T1
Valid prediction for GeneMark_model.32020_t
Valid prediction for GeneMark_model.32028_t
Valid prediction for Augustus_model.g12878.t1
Valid prediction for snap_scaffold_7-snap.2932-T1
Valid prediction for GlimmerHMM_glimmerT_19042-T1
Valid prediction for snap_scaffold_7-snap.2951-T1
Valid prediction for Augustus_model.g12879.t1
Valid prediction for snap_scaffold_7-snap.2925-T1
Valid prediction for GlimmerHMM_glimmerT_19040-T1
Valid prediction for snap_scaffold_7-snap.2933-T1
Valid prediction for Augustus_model.g12876.t1
Couldn't classify 3442, 3639
Sorry, prediction pasa_asmbl_50204.p1 fails validation.
(CAT)	 AG	3442-3639	GT	TGG
(ACA)	 AG	3965-4141	GT	AGG
(CTG)	 AG	4437-4507	GT	AGG
(TGC)	 AG	5252-5351	GT	AGG
(GTT)	 AG	5442-5495	GT	GGG
(AAA)	 AG	5600-5665	GT	ATG
(ATG)	 AG	5763-5831	GT	AGG
(GGT)	 AG	6095-6191	GT	GAG
(TAT)	 AG	6314-6384	TG	GAT
-recovered pasa_asmbl_50204.p1, initial, 5763, 5831
-recovered pasa_asmbl_50204.p1, terminal, 6314, 6384
-recovered pasa_asmbl_50204.p1, internal, 3442, 3639
-recovered pasa_asmbl_50204.p1, internal, 3965, 4141
-recovered pasa_asmbl_50204.p1, internal, 4437, 4507
-recovered pasa_asmbl_50204.p1, internal, 5252, 5351
-recovered pasa_asmbl_50204.p1, internal, 5442, 5495
-recovered pasa_asmbl_50204.p1, internal, 5600, 5665
-recovered pasa_asmbl_50204.p1, internal, 5763, 5831
-recovered pasa_asmbl_50204.p1, internal, 6095, 6191
Valid prediction for GeneMark_model.32005_t
Valid prediction for GeneMark_model.32000_t
Valid prediction for snap_scaffold_7-snap.2937-T1
Couldn't classify 25710, 25768
Sorry, prediction pasa_asmbl_50199.p1 fails validation.
(ATG)	 CA	18599-18727	GT	AGG
(ACC)	 AG	21374-21488	GT	AGG
(GAG)	 AG	21645-21764	GT	GGG
(AGA)	 AG	22094-22180	GT	AGG
(AAA)	 AG	22301-22388	GT	AGG
(CTG)	 AG	22582-22660	GT	AGG
(GAC)	 AG	24026-24107	GT	AGG
(ACA)	 AG	25710-25768	TC	TCT
-recovered pasa_asmbl_50199.p1, initial, 18599, 18727
-recovered pasa_asmbl_50199.p1, internal, 21374, 21488
-recovered pasa_asmbl_50199.p1, internal, 21645, 21764
-recovered pasa_asmbl_50199.p1, internal, 22094, 22180
-recovered pasa_asmbl_50199.p1, internal, 22301, 22388
-recovered pasa_asmbl_50199.p1, internal, 22582, 22660
-recovered pasa_asmbl_50199.p1, internal, 24026, 24107
Valid prediction for CodingQuarry_transcript_57584-T1
Valid prediction for GlimmerHMM_glimmerT_19043-T1
Valid prediction for snap_scaffold_7-snap.2927-T1
Valid prediction for snap_scaffold_7-snap.2923-T1
Valid prediction for GlimmerHMM_glimmerT_19035-T1
Valid prediction for GlimmerHMM_glimmerT_19026-T1
Valid prediction for HiQ_model.g12880.t1
Valid prediction for GlimmerHMM_glimmerT_19039-T1
Valid prediction for GeneMark_model.32003_t
Valid prediction for snap_scaffold_7-snap.2936-T1
Valid prediction for GlimmerHMM_glimmerT_19034-T1
Valid prediction for GeneMark_model.32002_t
Valid prediction for GeneMark_model.32026_t
Valid prediction for GeneMark_model.32015_t
Valid prediction for GeneMark_model.32022_t
Valid prediction for GeneMark_model.32032_t
Valid prediction for Augustus_model.g12882.t1
Valid prediction for snap_scaffold_7-snap.2940-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29435, rend_intergenic: 24712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45253, rend_intergenic: 38534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53050, rend_intergenic: 50716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70442, rend_intergenic: 69281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71543, rend_intergenic: 70759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92696, rend_intergenic: 91070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102155, rend_intergenic: 99400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144956, rend_intergenic: 114596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155869, rend_intergenic: 147473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169930, rend_intergenic: 158921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189025, rend_intergenic: 184680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 191063
-exon list size: 615


building trellis

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91.6    
91.7    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 16 predictions from path traversal
Error with prediction: snap lend_intergenic: 29435, rend_intergenic: 24712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45253, rend_intergenic: 38534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53050, rend_intergenic: 50716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70442, rend_intergenic: 69281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71543, rend_intergenic: 70759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92696, rend_intergenic: 91070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102155, rend_intergenic: 99400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144956, rend_intergenic: 114596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155869, rend_intergenic: 147473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169930, rend_intergenic: 158921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189025, rend_intergenic: 184680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support