-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_9526542-9754064

-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_6-snap.2070-T1
Valid prediction for GeneMark_model.26308_t
Valid prediction for GlimmerHMM_glimmerT_15626-T1
Valid prediction for GlimmerHMM_glimmerT_15637-T1
Valid prediction for GlimmerHMM_glimmerT_15633-T1
Valid prediction for HiQ_model.g10438.t1
Valid prediction for Augustus_model.g10447.t1
Valid prediction for Augustus_model.g10442.t1
Valid prediction for GeneMark_model.26287_t
Valid prediction for Augustus_model.g10444.t1
Valid prediction for Augustus_model.g10443.t1
Valid prediction for GlimmerHMM_glimmerT_15634-T1
Valid prediction for GlimmerHMM_glimmerT_15642-T1
Valid prediction for GeneMark_model.26294_t
Valid prediction for snap_scaffold_6-snap.2089-T1
Valid prediction for GeneMark_model.26327_t
Valid prediction for GeneMark_model.26312_t
Valid prediction for GlimmerHMM_glimmerT_15635-T1
Valid prediction for snap_scaffold_6-snap.2076-T1
Valid prediction for GeneMark_model.26301_t
Valid prediction for GeneMark_model.26293_t
Valid prediction for pasa_asmbl_47168.p1
Valid prediction for snap_scaffold_6-snap.2081-T1
Couldn't classify 57191, 57218
Sorry, prediction pasa_asmbl_47166.p1 fails validation.
(TAC)	 TG	57191-57218	GT	TGG
(GGA)	 AG	57942-58223	GT	TGG
(GTC)	 AG	58314-58522	GT	AGG
(CAA)	 AG	58679-58744	GT	AGG
(GAA)	 AG	58950-59055	GT	GGG
(AGA)	 AG	59136-59218	GT	TGG
(GCA)	 AG	59546-59656	TG	AAT
-recovered pasa_asmbl_47166.p1, terminal, 59546, 59656
-recovered pasa_asmbl_47166.p1, internal, 57942, 58223
-recovered pasa_asmbl_47166.p1, internal, 58314, 58522
-recovered pasa_asmbl_47166.p1, internal, 58679, 58744
-recovered pasa_asmbl_47166.p1, internal, 58950, 59055
-recovered pasa_asmbl_47166.p1, internal, 59136, 59218
Valid prediction for GeneMark_model.26321_t
Valid prediction for GlimmerHMM_glimmerT_15639-T1
Valid prediction for GeneMark_model.26289_t
Couldn't classify 141979, 142084
Sorry, prediction pasa_asmbl_47171.p2 fails validation.
(CGC)	 TG	141979-142084	GT	AGG
(GTG)	 AG	142735-142842	GT	GTG
(CAG)	 AG	144566-144708	TG	AGT
-recovered pasa_asmbl_47171.p2, terminal, 144566, 144708
-recovered pasa_asmbl_47171.p2, internal, 142735, 142842
Valid prediction for GlimmerHMM_glimmerT_15632-T1
Valid prediction for snap_scaffold_6-snap.2079-T1
Valid prediction for CodingQuarry_transcript_55022-T1
Valid prediction for GeneMark_model.26323_t
Valid prediction for Augustus_model.g10448.t1
Valid prediction for GeneMark_model.26303_t
Valid prediction for Augustus_model.g10446.t1
Valid prediction for snap_scaffold_6-snap.2074-T1
Valid prediction for GeneMark_model.26298_t
Valid prediction for snap_scaffold_6-snap.2068-T1
Valid prediction for GlimmerHMM_glimmerT_15630-T1
Valid prediction for GeneMark_model.26309_t
Valid prediction for GeneMark_model.26291_t
Valid prediction for HiQ_model.g10440.t1
Valid prediction for GeneMark_model.26317_t
Valid prediction for snap_scaffold_6-snap.2075-T1
Couldn't classify 74612, 74742
Couldn't classify 74892, 74936
Sorry, prediction CodingQuarry_transcript_55023-T1 fails validation.
(ATG)	 TC	72146-72157	GT	TGG
(GGA)	 AG	72489-72535	GT	AAG
(AAA)	 AG	72730-72802	GT	AGG
(GCC)	 AG	73195-73388	GT	AGG
(GTT)	 AG	73469-73639	GT	AGG
(GAG)	 AG	73777-73985	GT	AGG
(ACG)	 AG	74228-74387	GT	AGG
(CTC)	 AG	74469-74524	GT	AGG
(GAA)	 AG	74612-74742	GG	AAG
(AGA)	 TT	74892-74936	AG	GAA
-recovered CodingQuarry_transcript_55023-T1, initial, 72146, 72157
-recovered CodingQuarry_transcript_55023-T1, internal, 72489, 72535
-recovered CodingQuarry_transcript_55023-T1, internal, 72730, 72802
-recovered CodingQuarry_transcript_55023-T1, internal, 73195, 73388
-recovered CodingQuarry_transcript_55023-T1, internal, 73469, 73639
-recovered CodingQuarry_transcript_55023-T1, internal, 73777, 73985
-recovered CodingQuarry_transcript_55023-T1, internal, 74228, 74387
-recovered CodingQuarry_transcript_55023-T1, internal, 74469, 74524
Valid prediction for Augustus_model.g10445.t1
Valid prediction for GeneMark_model.26305_t
Valid prediction for GeneMark_model.26296_t
Valid prediction for GlimmerHMM_glimmerT_15628-T1
Valid prediction for GeneMark_model.26326_t

-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.26316_t
Valid prediction for GeneMark_model.26286_t
Valid prediction for GeneMark_model.26299_t
Valid prediction for GeneMark_model.26288_t
Valid prediction for GlimmerHMM_glimmerT_15643-T1
Valid prediction for HiQ_model.g10441.t1
Valid prediction for GlimmerHMM_glimmerT_15625-T1
Valid prediction for pasa_asmbl_48558.p1
Valid prediction for GeneMark_model.26313_t
Valid prediction for snap_scaffold_6-snap.2095-T1
Valid prediction for HiQ_model.g10437.t1
Valid prediction for GeneMark_model.26302_t
Valid prediction for GeneMark_model.26310_t
Valid prediction for snap_scaffold_6-snap.2084-T1
Valid prediction for Augustus_model.g10451.t1
Valid prediction for GeneMark_model.26292_t
Valid prediction for snap_scaffold_6-snap.2082-T1
Valid prediction for snap_scaffold_6-snap.2093-T1
Valid prediction for Augustus_model.g10435.t1
Valid prediction for snap_scaffold_6-snap.2083-T1
Valid prediction for GeneMark_model.26314_t
Valid prediction for GlimmerHMM_glimmerT_15629-T1
Valid prediction for GlimmerHMM_glimmerT_15640-T1
Valid prediction for snap_scaffold_6-snap.2069-T1
Valid prediction for GlimmerHMM_glimmerT_15638-T1
Valid prediction for GeneMark_model.26295_t
Valid prediction for GeneMark_model.26322_t
Valid prediction for snap_scaffold_6-snap.2096-T1
Valid prediction for GeneMark_model.26290_t
Valid prediction for Augustus_model.g10456.t1
Valid prediction for snap_scaffold_6-snap.2097-T1
Valid prediction for GeneMark_model.26320_t
Valid prediction for Augustus_model.g10452.t1
Valid prediction for Augustus_model.g10455.t1
Valid prediction for snap_scaffold_6-snap.2092-T1
Valid prediction for GlimmerHMM_glimmerT_15627-T1
Valid prediction for GeneMark_model.26297_t
Valid prediction for snap_scaffold_6-snap.2067-T1
Valid prediction for CodingQuarry_transcript_55026-T1
Valid prediction for snap_scaffold_6-snap.2094-T1
Valid prediction for snap_scaffold_6-snap.2085-T1
Valid prediction for GeneMark_model.26315_t
Valid prediction for pasa_asmbl_48562.p1
Valid prediction for snap_scaffold_6-snap.2073-T1
Valid prediction for Augustus_model.g10457.t1
Valid prediction for GlimmerHMM_glimmerT_15644-T1
Valid prediction for HiQ_model.g10436.t1
Valid prediction for GeneMark_model.26300_t
Valid prediction for CodingQuarry_transcript_55024-T1
Valid prediction for GeneMark_model.26311_t
Valid prediction for Augustus_model.g10454.t1
Valid prediction for Augustus_model.g10449.t1
Valid prediction for GlimmerHMM_glimmerT_15624-T1
Valid prediction for GlimmerHMM_glimmerT_15636-T1
Couldn't classify 56964, 56974
Sorry, prediction pasa_asmbl_48563.p1 fails validation.
(TTC)	 CC	56964-56974	GT	AGG
(GAA)	 AG	57176-57273	GT	ATG
(TCT)	 AG	57908-58212	TG	AGT
-recovered pasa_asmbl_48563.p1, terminal, 57908, 58212
-recovered pasa_asmbl_48563.p1, internal, 57176, 57273
Valid prediction for snap_scaffold_6-snap.2071-T1
Valid prediction for snap_scaffold_6-snap.2088-T1
Couldn't classify 55534, 55554
Couldn't classify 56869, 56918
Sorry, prediction pasa_asmbl_48564.p1 fails validation.
(GGG)	 AG	55534-55554	GT	AGG
(GTG)	 AG	55680-56343	GT	TGG
(CAG)	 AG	56452-56622	GT	AGG
(GTA)	 AG	56869-56918	GC	GCG
-recovered pasa_asmbl_48564.p1, internal, 55534, 55554
-recovered pasa_asmbl_48564.p1, internal, 55680, 56343
-recovered pasa_asmbl_48564.p1, internal, 56452, 56622
-recovered pasa_asmbl_48564.p1, internal, 56869, 56918
Valid prediction for snap_scaffold_6-snap.2077-T1
Valid prediction for Augustus_model.g10439.t1
Valid prediction for Augustus_model.g10453.t1
Valid prediction for GeneMark_model.26325_t
Valid prediction for snap_scaffold_6-snap.2091-T1
Valid prediction for GeneMark_model.26324_t
Valid prediction for GeneMark_model.26304_t
Valid prediction for Augustus_model.g10450.t1
Valid prediction for GeneMark_model.26318_t
Valid prediction for GlimmerHMM_glimmerT_15631-T1
Couldn't classify 38742, 39003
Sorry, prediction pasa_asmbl_48567.p1 fails validation.
(CAA)	 CG	38742-39003	GT	AGG
(TCG)	 AG	40141-40497	GT	TGG
(ATT)	 AG	40870-41178	GT	CGG
(GAG)	 AG	41520-41914	AG	AGA
-recovered pasa_asmbl_48567.p1, terminal, 41520, 41914
-recovered pasa_asmbl_48567.p1, internal, 40141, 40497
-recovered pasa_asmbl_48567.p1, internal, 40870, 41178
Valid prediction for snap_scaffold_6-snap.2090-T1
Valid prediction for snap_scaffold_6-snap.2087-T1
Valid prediction for snap_scaffold_6-snap.2066-T1
Couldn't classify 27089, 27311
Couldn't classify 27725, 28005
Sorry, prediction pasa_asmbl_48569.p1 fails validation.
(TTG)	 AC	27089-27311	GT	TGG
(TTC)	 AG	27483-27524	GT	TGG
(GTG)	 AG	27725-28005	GT	CGG
-recovered pasa_asmbl_48569.p1, internal, 27483, 27524
-recovered pasa_asmbl_48569.p1, internal, 27725, 28005
Valid prediction for GlimmerHMM_glimmerT_15641-T1
Valid prediction for snap_scaffold_6-snap.2086-T1
Valid prediction for snap_scaffold_6-snap.2080-T1
Valid prediction for pasa_asmbl_48559.p1
Valid prediction for snap_scaffold_6-snap.2078-T1
Valid prediction for GeneMark_model.26306_t
Valid prediction for GeneMark_model.26307_t
Valid prediction for snap_scaffold_6-snap.2072-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 76013, rend_intergenic: 73191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102051, rend_intergenic: 88523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119740, rend_intergenic: 105845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125342, rend_intergenic: 124956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127804, rend_intergenic: 125625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130241, rend_intergenic: 128281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155959, rend_intergenic: 133252  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 227523
-exon list size: 564


building trellis

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25.8    
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26.9    
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27.9    
28.1    
28.3    
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29.0    
29.2    
29.3    
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29.7    
29.9    
30.0    
30.2    
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30.6    
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30.9    
31.1    
31.3    
31.4    
31.6    
31.8    
32.0    
32.2    
32.3    
32.5    
32.7    
32.9    
33.0    
33.2    
33.4    
33.6    
33.7    
33.9    
34.1    
34.3    
34.5    
34.6    
34.8    
35.0    
35.2    
35.3    
35.5    
35.7    
35.9    
36.0    
36.2    
36.4    
36.6    
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37.1    
37.3    
37.5    
37.6    
37.8    
38.0    
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38.3    
38.5    
38.7    
38.9    
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39.6    
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39.9    
40.1    
40.3    
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40.6    
40.8    
41.0    
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41.3    
41.5    
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42.6    
42.8    
42.9    
43.1    
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43.5    
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44.9    
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47.3    
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48.1    
48.2    
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48.6    
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52.3    
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67.3    
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80.2    
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81.1    
81.3    
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82.7    
82.9    
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83.2    
83.4    
83.6    
83.7    
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84.3    
84.5    
84.6    
84.8    
85.0    
85.2    
85.3    
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85.9    
86.0    
86.2    
86.4    
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86.7    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.3    
88.5    
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88.9    
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89.2    
89.4    
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89.9    
90.1    
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90.5    
90.6    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.6    
92.8    
92.9    
93.1    
93.3    
93.5    
93.6    
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95.8    
95.9    
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96.5    
96.6    
96.8    
97.0    
97.2    
97.3    
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97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 76013, rend_intergenic: 73191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102051, rend_intergenic: 88523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119740, rend_intergenic: 105845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125342, rend_intergenic: 124956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127804, rend_intergenic: 125625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130241, rend_intergenic: 128281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155959, rend_intergenic: 133252  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support