-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_13669015-13880455

-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.g12752.t1
Valid prediction for GeneMark_model.31543_t
Valid prediction for GeneMark_model.31540_t
Valid prediction for CodingQuarry_transcript_57555-T1
Valid prediction for snap_scaffold_7-snap.2594-T1
Valid prediction for snap_scaffold_7-snap.2578-T1
Valid prediction for GlimmerHMM_glimmerT_18843-T1
Couldn't classify 26774, 26823
Sorry, prediction pasa_asmbl_51250.p1 fails validation.
(GCT)	 CA	26774-26823	GT	AGG
(CCT)	 AG	28938-29057	GT	AAG
(TAA)	 AG	29253-29355	GT	AGG
(ACC)	 AG	29499-29546	GT	AAG
(GTG)	 AG	29684-29752	GT	TGG
(GCC)	 AG	31211-31816	TG	GAT
-recovered pasa_asmbl_51250.p1, terminal, 28938, 29057
-recovered pasa_asmbl_51250.p1, terminal, 31211, 31816
-recovered pasa_asmbl_51250.p1, internal, 28938, 29057
-recovered pasa_asmbl_51250.p1, internal, 29253, 29355
-recovered pasa_asmbl_51250.p1, internal, 29499, 29546
-recovered pasa_asmbl_51250.p1, internal, 29684, 29752
Valid prediction for GeneMark_model.31564_t
Valid prediction for snap_scaffold_7-snap.2576-T1
Valid prediction for snap_scaffold_7-snap.2574-T1
Valid prediction for pasa_asmbl_51259.p3
Valid prediction for GeneMark_model.31562_t
Valid prediction for GeneMark_model.31535_t
Valid prediction for GlimmerHMM_glimmerT_18836-T1
Valid prediction for pasa_asmbl_51263.p1
Valid prediction for CodingQuarry_transcript_57557-T1
Valid prediction for snap_scaffold_7-snap.2610-T1
Valid prediction for GlimmerHMM_glimmerT_18838-T1
Valid prediction for GeneMark_model.31547_t
Valid prediction for GlimmerHMM_glimmerT_18848-T1
Valid prediction for GlimmerHMM_glimmerT_18846-T1
Valid prediction for Augustus_model.g12751.t1
Valid prediction for GlimmerHMM_glimmerT_18847-T1
Valid prediction for GeneMark_model.31533_t
Valid prediction for snap_scaffold_7-snap.2608-T1
Valid prediction for GlimmerHMM_glimmerT_18842-T1
Valid prediction for GeneMark_model.31563_t
Valid prediction for GlimmerHMM_glimmerT_18840-T1
Valid prediction for GeneMark_model.31541_t
Valid prediction for GlimmerHMM_glimmerT_18835-T1
Valid prediction for GeneMark_model.31558_t
Valid prediction for Augustus_model.g12753.t1
Valid prediction for GeneMark_model.31551_t
Valid prediction for GeneMark_model.31560_t
Valid prediction for snap_scaffold_7-snap.2593-T1
Valid prediction for snap_scaffold_7-snap.2585-T1
Couldn't classify 12591, 12683
Sorry, prediction GeneMark_model.31529_t fails validation.
(GAG)	 AG	12591-12683	GT	GCG
(CAA)	 AG	12866-12874	GT	GAG
(GCA)	 AG	13053-13064	GT	CAG
(AGG)	 AG	13092-13178	GT	GGG
(CAA)	 AG	13200-13217	GT	AGG
(AGG)	 AG	14294-14422	GT	AGG
(GAG)	 AG	16176-16199	GT	TGG
(GGA)	 AG	16812-16826	GT	CAG
(GCA)	 AG	16944-16952	GT	GGG
(CTC)	 AG	17216-17245	GT	AGG
(ATG)	 AG	17355-17358	GC	GAG
-recovered GeneMark_model.31529_t, initial, 17355, 17358
-recovered GeneMark_model.31529_t, terminal, 17355, 17358
-recovered GeneMark_model.31529_t, internal, 12591, 12683
-recovered GeneMark_model.31529_t, internal, 12866, 12874
-recovered GeneMark_model.31529_t, internal, 13053, 13064
-recovered GeneMark_model.31529_t, internal, 13092, 13178
-recovered GeneMark_model.31529_t, internal, 13200, 13217
-recovered GeneMark_model.31529_t, internal, 14294, 14422
-recovered GeneMark_model.31529_t, internal, 16176, 16199
-recovered GeneMark_model.31529_t, internal, 16812, 16826
-recovered GeneMark_model.31529_t, internal, 16944, 16952
-recovered GeneMark_model.31529_t, internal, 17216, 17245
-recovered GeneMark_model.31529_t, internal, 17355, 17358
Valid prediction for Augustus_model.g12745.t1
Valid prediction for snap_scaffold_7-snap.2590-T1
Valid prediction for GeneMark_model.31567_t
Valid prediction for GlimmerHMM_glimmerT_18833-T1
Valid prediction for snap_scaffold_7-snap.2603-T1
Valid prediction for GlimmerHMM_glimmerT_18844-T1
Valid prediction for snap_scaffold_7-snap.2586-T1
Valid prediction for Augustus_model.g12749.t1
Valid prediction for CodingQuarry_transcript_57556-T1
Valid prediction for GeneMark_model.31536_t
Valid prediction for GeneMark_model.31555_t
Valid prediction for snap_scaffold_7-snap.2604-T1
Valid prediction for GeneMark_model.31557_t
Valid prediction for snap_scaffold_7-snap.2601-T1
Valid prediction for GeneMark_model.31538_t
Valid prediction for snap_scaffold_7-snap.2572-T1
Valid prediction for GeneMark_model.31544_t
Valid prediction for HiQ_model.g12750.t1
Valid prediction for GeneMark_model.31531_t
Valid prediction for snap_scaffold_7-snap.2583-T1
Valid prediction for snap_scaffold_7-snap.2591-T1
Valid prediction for snap_scaffold_7-snap.2577-T1
Valid prediction for pasa_asmbl_50143.p1
Valid prediction for GeneMark_model.31549_t
Valid prediction for snap_scaffold_7-snap.2581-T1
Valid prediction for Augustus_model.g12747.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.31561_t
Valid prediction for GeneMark_model.31556_t
Valid prediction for GeneMark_model.31552_t
Valid prediction for snap_scaffold_7-snap.2587-T1
Valid prediction for snap_scaffold_7-snap.2589-T1
Valid prediction for snap_scaffold_7-snap.2579-T1
Valid prediction for GlimmerHMM_glimmerT_18837-T1
Valid prediction for Augustus_model.g12748.t1
Valid prediction for GlimmerHMM_glimmerT_18832-T1
Valid prediction for snap_scaffold_7-snap.2595-T1
Valid prediction for snap_scaffold_7-snap.2580-T1
Valid prediction for GeneMark_model.31553_t
Valid prediction for snap_scaffold_7-snap.2599-T1
Valid prediction for GeneMark_model.31542_t
Valid prediction for GeneMark_model.31559_t
Valid prediction for snap_scaffold_7-snap.2606-T1
Valid prediction for snap_scaffold_7-snap.2588-T1
Valid prediction for snap_scaffold_7-snap.2596-T1
Valid prediction for Augustus_model.g12746.t1
Valid prediction for Augustus_model.g12743.t1
Couldn't classify 6895, 7010
Sorry, prediction pasa_asmbl_50147.p1 fails validation.
(ATG)	 AT	2952-3642	GT	TTG
(ATG)	 AG	6308-6361	GC	AGG
(CAC)	 AG	6895-7010	GC	TGG
-recovered pasa_asmbl_50147.p1, initial, 2952, 3642
add_exon() Sorry, pasa_asmbl_50147.p1 6308-6361-initial-1 is invalid.
-recovered pasa_asmbl_50147.p1, initial, 6308, 6361
-recovered pasa_asmbl_50147.p1, internal, 6308, 6361
-recovered pasa_asmbl_50147.p1, internal, 6895, 7010
Valid prediction for GeneMark_model.31530_t
Valid prediction for CodingQuarry_transcript_57558-T1
Valid prediction for pasa_asmbl_50135.p1
Valid prediction for snap_scaffold_7-snap.2613-T1
Valid prediction for snap_scaffold_7-snap.2582-T1
Valid prediction for snap_scaffold_7-snap.2598-T1
Valid prediction for GlimmerHMM_glimmerT_18850-T1
Valid prediction for GeneMark_model.31569_t
Valid prediction for Augustus_model.g12755.t1
Valid prediction for GeneMark_model.31537_t
Valid prediction for GeneMark_model.31532_t
Valid prediction for snap_scaffold_7-snap.2592-T1
Valid prediction for GeneMark_model.31534_t
Valid prediction for snap_scaffold_7-snap.2609-T1
Valid prediction for snap_scaffold_7-snap.2607-T1
Valid prediction for snap_scaffold_7-snap.2575-T1
Valid prediction for GeneMark_model.31546_t
Couldn't classify 204218, 204382
Sorry, prediction GeneMark_model.31528_t fails validation.
(GGG)	 AG	204218-204382	GT	ATG
(GGA)	 AG	205094-205121	GT	ACG
(GAT)	 AG	207292-207448	GT	AGG
(GGG)	 AG	208280-208407	GC	AGG
-recovered GeneMark_model.31528_t, terminal, 208280, 208407
-recovered GeneMark_model.31528_t, internal, 204218, 204382
-recovered GeneMark_model.31528_t, internal, 205094, 205121
-recovered GeneMark_model.31528_t, internal, 207292, 207448
-recovered GeneMark_model.31528_t, internal, 208280, 208407
Valid prediction for snap_scaffold_7-snap.2584-T1
Valid prediction for GlimmerHMM_glimmerT_18834-T1
Valid prediction for snap_scaffold_7-snap.2614-T1
Valid prediction for GeneMark_model.31568_t
Valid prediction for GlimmerHMM_glimmerT_18839-T1
Valid prediction for snap_scaffold_7-snap.2602-T1
Valid prediction for GeneMark_model.31545_t
Valid prediction for GlimmerHMM_glimmerT_18845-T1
Valid prediction for Augustus_model.g12754.t1
Valid prediction for snap_scaffold_7-snap.2611-T1
Valid prediction for GeneMark_model.31550_t
Couldn't classify 7320, 8669
Sorry, prediction pasa_asmbl_50146.p1 fails validation.
(CCT)	 TC	7320-8669	GC	CTG
Valid prediction for GlimmerHMM_glimmerT_18841-T1
Valid prediction for GeneMark_model.31570_t
Valid prediction for GeneMark_model.31539_t
Valid prediction for snap_scaffold_7-snap.2612-T1
Valid prediction for snap_scaffold_7-snap.2597-T1
Valid prediction for GeneMark_model.31566_t
Valid prediction for snap_scaffold_7-snap.2605-T1
Valid prediction for GeneMark_model.31565_t
Valid prediction for snap_scaffold_7-snap.2600-T1
Valid prediction for GeneMark_model.31548_t
Valid prediction for Augustus_model.g12744.t1
Couldn't classify 206582, 206651
Sorry, prediction pasa_asmbl_50134.p1 fails validation.
(AAC)	 CA	206582-206651	GT	AGG
(TTC)	 AG	207027-207121	GT	AGG
(GAT)	 AG	207292-207448	GT	AGG
(GGG)	 AG	208280-208407	GC	AGG
-recovered pasa_asmbl_50134.p1, terminal, 208280, 208407
-recovered pasa_asmbl_50134.p1, internal, 207027, 207121
-recovered pasa_asmbl_50134.p1, internal, 207292, 207448
-recovered pasa_asmbl_50134.p1, internal, 208280, 208407
Valid prediction for GlimmerHMM_glimmerT_18849-T1
Valid prediction for snap_scaffold_7-snap.2573-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14976, rend_intergenic: 3035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18935, rend_intergenic: 16883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20667, rend_intergenic: 18968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27493, rend_intergenic: 21578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67646, rend_intergenic: 62721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70885, rend_intergenic: 70224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74912, rend_intergenic: 71140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81372, rend_intergenic: 79195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93737, rend_intergenic: 83265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98189, rend_intergenic: 94109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101393, rend_intergenic: 100349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110654, rend_intergenic: 101442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142331, rend_intergenic: 111348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152634, rend_intergenic: 149052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156502, rend_intergenic: 153434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162551, rend_intergenic: 158509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173183, rend_intergenic: 163841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176835, rend_intergenic: 173866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190818, rend_intergenic: 177773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 211441
-exon list size: 664


building trellis

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82.4    
82.6    
82.7    
82.9    
83.0    
83.2    
83.3    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
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    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
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 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 14976, rend_intergenic: 3035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18935, rend_intergenic: 16883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20667, rend_intergenic: 18968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27493, rend_intergenic: 21578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67646, rend_intergenic: 62721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70885, rend_intergenic: 70224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74912, rend_intergenic: 71140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81372, rend_intergenic: 79195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93737, rend_intergenic: 83265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98189, rend_intergenic: 94109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101393, rend_intergenic: 100349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110654, rend_intergenic: 101442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142331, rend_intergenic: 111348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152634, rend_intergenic: 149052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156502, rend_intergenic: 153434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162551, rend_intergenic: 158509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173183, rend_intergenic: 163841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176835, rend_intergenic: 173866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190818, rend_intergenic: 177773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support