-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_2916744-3173086

-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_17512-T1
Valid prediction for GeneMark_model.29571_t
Valid prediction for GeneMark_model.29498_t
Valid prediction for GeneMark_model.29517_t
Valid prediction for GeneMark_model.29509_t
Valid prediction for snap_scaffold_7-snap.717-T1
Valid prediction for pasa_asmbl_50556.p1
Valid prediction for snap_scaffold_7-snap.731-T1
Valid prediction for GeneMark_model.29544_t
Valid prediction for Augustus_model.g11728.t1
Valid prediction for snap_scaffold_7-snap.720-T1
Valid prediction for Augustus_model.g11726.t1
Valid prediction for GeneMark_model.29561_t
Valid prediction for snap_scaffold_7-snap.728-T1
Couldn't classify 22767, 22804
Couldn't classify 23192, 23336
Sorry, prediction pasa_asmbl_50550.p1 fails validation.
(CTG)	 TC	22767-22804	AT	TCA
(GTA)	 AC	23192-23336	GT	AGG
(GTG)	 AG	23430-23543	GT	CGG
(GGG)	 AG	23696-23778	GT	AGG
(GAA)	 AG	24119-24281	AC	AGA
-recovered pasa_asmbl_50550.p1, terminal, 24119, 24281
-recovered pasa_asmbl_50550.p1, internal, 23430, 23543
-recovered pasa_asmbl_50550.p1, internal, 23696, 23778
Valid prediction for snap_scaffold_7-snap.729-T1
Valid prediction for GlimmerHMM_glimmerT_17532-T1
Valid prediction for GeneMark_model.29540_t
Valid prediction for GeneMark_model.29528_t
Valid prediction for GeneMark_model.29566_t
Valid prediction for GlimmerHMM_glimmerT_17519-T1
Valid prediction for GeneMark_model.29569_t
Valid prediction for GeneMark_model.29558_t
Valid prediction for snap_scaffold_7-snap.706-T1
Valid prediction for snap_scaffold_7-snap.707-T1
Valid prediction for GeneMark_model.29554_t
Valid prediction for GeneMark_model.29508_t
Valid prediction for GeneMark_model.29546_t
Valid prediction for snap_scaffold_7-snap.714-T1
Valid prediction for GlimmerHMM_glimmerT_17521-T1
Valid prediction for GeneMark_model.29564_t
Valid prediction for snap_scaffold_7-snap.725-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_17517-T1
Valid prediction for snap_scaffold_7-snap.739-T1
Valid prediction for GeneMark_model.29511_t
Valid prediction for GeneMark_model.29532_t
Valid prediction for snap_scaffold_7-snap.715-T1
Couldn't classify 68467, 70845
Sorry, prediction pasa_asmbl_50555.p1 fails validation.
(ATC)	 CT	68467-70845	AA	AGA
Valid prediction for snap_scaffold_7-snap.752-T1
Valid prediction for GeneMark_model.29548_t
Valid prediction for Augustus_model.g11722.t1
Valid prediction for snap_scaffold_7-snap.722-T1
Valid prediction for snap_scaffold_7-snap.719-T1
Valid prediction for GeneMark_model.29538_t
Valid prediction for GeneMark_model.29502_t
Valid prediction for GeneMark_model.29534_t
Valid prediction for snap_scaffold_7-snap.705-T1
Valid prediction for snap_scaffold_7-snap.736-T1
Valid prediction for GeneMark_model.29519_t
Valid prediction for snap_scaffold_7-snap.741-T1
Valid prediction for GeneMark_model.29530_t
Valid prediction for GeneMark_model.29556_t
Valid prediction for GlimmerHMM_glimmerT_17539-T1
Valid prediction for GeneMark_model.29516_t
Couldn't classify 16521, 16667
Couldn't classify 18420, 18510
Sorry, prediction pasa_asmbl_50549.p1 fails validation.
(ATC)	 AC	16521-16667	GT	GGG
(CCC)	 AG	16891-17025	GT	AGG
(TTT)	 AG	17743-17885	GT	GAG
(GCT)	 AG	18420-18510	CA	ACC
-recovered pasa_asmbl_50549.p1, internal, 16891, 17025
-recovered pasa_asmbl_50549.p1, internal, 17743, 17885
Valid prediction for GlimmerHMM_glimmerT_17525-T1
Valid prediction for snap_scaffold_7-snap.724-T1
Valid prediction for GeneMark_model.29504_t
Valid prediction for GeneMark_model.29541_t
Valid prediction for snap_scaffold_7-snap.747-T1
Valid prediction for GeneMark_model.29494_t
Valid prediction for GlimmerHMM_glimmerT_17540-T1
Valid prediction for GlimmerHMM_glimmerT_17538-T1
Valid prediction for CodingQuarry_transcript_57301-T1
Valid prediction for GeneMark_model.29499_t
Valid prediction for snap_scaffold_7-snap.732-T1
Valid prediction for GeneMark_model.29536_t
Valid prediction for GeneMark_model.29506_t
Valid prediction for GeneMark_model.29493_t
Valid prediction for snap_scaffold_7-snap.744-T1
Couldn't classify 66838, 67275
Sorry, prediction pasa_asmbl_50554.p1 fails validation.
(GCA)	 TG	66838-67275	GA	AGG
Valid prediction for GeneMark_model.29526_t
Valid prediction for snap_scaffold_7-snap.712-T1
Valid prediction for GlimmerHMM_glimmerT_17515-T1
Valid prediction for GlimmerHMM_glimmerT_17527-T1
Valid prediction for GeneMark_model.29510_t
Valid prediction for GlimmerHMM_glimmerT_17531-T1
Valid prediction for GeneMark_model.29551_t
Valid prediction for HiQ_model.g11739.t1
Valid prediction for GeneMark_model.29492_t
Valid prediction for GlimmerHMM_glimmerT_17514-T1
Valid prediction for GlimmerHMM_glimmerT_17529-T1
Valid prediction for GeneMark_model.29496_t
Valid prediction for GeneMark_model.29525_t
Valid prediction for snap_scaffold_7-snap.726-T1
Valid prediction for snap_scaffold_7-snap.716-T1
Valid prediction for snap_scaffold_7-snap.723-T1
Valid prediction for Augustus_model.g11724.t1
Valid prediction for GeneMark_model.29513_t
Valid prediction for GeneMark_model.29543_t
Valid prediction for Augustus_model.g11727.t1
Valid prediction for GeneMark_model.29522_t
Valid prediction for snap_scaffold_7-snap.710-T1
Valid prediction for snap_scaffold_7-snap.749-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.718-T1
Valid prediction for Augustus_model.g11735.t1
Valid prediction for GeneMark_model.29537_t
Couldn't classify 28742, 28758
Couldn't classify 31190, 31328
Sorry, prediction pasa_asmbl_49595.p1 fails validation.
(TTC)	 CG	28742-28758	GT	AGG
(TAT)	 AG	28850-28958	GT	AGG
(GTT)	 AG	29266-29400	GT	TGG
(GAA)	 AG	30032-30222	GT	AAG
(ATT)	 AG	31190-31328	CA	TGC
-recovered pasa_asmbl_49595.p1, internal, 28850, 28958
-recovered pasa_asmbl_49595.p1, internal, 29266, 29400
-recovered pasa_asmbl_49595.p1, internal, 30032, 30222
Valid prediction for GlimmerHMM_glimmerT_17534-T1
Valid prediction for GlimmerHMM_glimmerT_17533-T1
Valid prediction for GeneMark_model.29553_t
Valid prediction for Augustus_model.g11729.t1
Valid prediction for snap_scaffold_7-snap.735-T1
Valid prediction for CodingQuarry_transcript_57298-T1
Valid prediction for GeneMark_model.29514_t
Valid prediction for GeneMark_model.29535_t
Valid prediction for GlimmerHMM_glimmerT_17530-T1
Valid prediction for GeneMark_model.29518_t
Valid prediction for GeneMark_model.29500_t
Valid prediction for GeneMark_model.29495_t
Valid prediction for snap_scaffold_7-snap.708-T1
Valid prediction for GeneMark_model.29533_t
Valid prediction for snap_scaffold_7-snap.737-T1
Valid prediction for Augustus_model.g11737.t1
Valid prediction for GlimmerHMM_glimmerT_17516-T1
Valid prediction for GeneMark_model.29557_t
Valid prediction for GeneMark_model.29505_t
Valid prediction for snap_scaffold_7-snap.753-T1
Valid prediction for pasa_asmbl_49596.p1
Valid prediction for snap_scaffold_7-snap.748-T1
Valid prediction for Augustus_model.g11723.t1
Valid prediction for Augustus_model.g11732.t1
Valid prediction for snap_scaffold_7-snap.713-T1
Valid prediction for GlimmerHMM_glimmerT_17513-T1
Valid prediction for snap_scaffold_7-snap.746-T1
Valid prediction for GlimmerHMM_glimmerT_17522-T1
Valid prediction for GlimmerHMM_glimmerT_17524-T1
Valid prediction for Augustus_model.g11730.t1
Valid prediction for GeneMark_model.29512_t
Valid prediction for GeneMark_model.29550_t
Valid prediction for GlimmerHMM_glimmerT_17528-T1
Valid prediction for GlimmerHMM_glimmerT_17537-T1
Valid prediction for snap_scaffold_7-snap.727-T1
Valid prediction for Augustus_model.g11734.t1
Valid prediction for snap_scaffold_7-snap.751-T1
Valid prediction for pasa_asmbl_49590.p1
Valid prediction for snap_scaffold_7-snap.738-T1
Valid prediction for snap_scaffold_7-snap.721-T1
Valid prediction for snap_scaffold_7-snap.750-T1
Valid prediction for GeneMark_model.29507_t
Valid prediction for GeneMark_model.29542_t
Couldn't classify 216482, 216805
Sorry, prediction pasa_asmbl_49588.p1 fails validation.
(CTT)	 CC	216482-216805	AT	GAA
Valid prediction for snap_scaffold_7-snap.733-T1
Valid prediction for HiQ_model.g11738.t1
Valid prediction for Augustus_model.g11733.t1
Couldn't classify 45016, 45069
Couldn't classify 53652, 53841
Sorry, prediction pasa_asmbl_49593.p1 fails validation.
(CCC)	 CA	45016-45069	GT	AGG
(CGT)	 AG	46323-46522	GT	AGG
(GTG)	 AG	46787-46913	GT	ACG
(GTG)	 AG	47563-47664	GT	AGG
(GCT)	 AG	48594-48737	GT	AGG
(ATT)	 AG	49788-49946	GT	AGG
(GAC)	 AG	50643-50809	GT	AGG
(TGT)	 AG	53652-53841	AG	GCA
-recovered pasa_asmbl_49593.p1, internal, 46323, 46522
-recovered pasa_asmbl_49593.p1, internal, 46787, 46913
-recovered pasa_asmbl_49593.p1, internal, 47563, 47664
-recovered pasa_asmbl_49593.p1, internal, 48594, 48737
-recovered pasa_asmbl_49593.p1, internal, 49788, 49946
-recovered pasa_asmbl_49593.p1, internal, 50643, 50809
Valid prediction for GeneMark_model.29565_t
Valid prediction for GeneMark_model.29521_t
Valid prediction for snap_scaffold_7-snap.743-T1
Valid prediction for GeneMark_model.29559_t
Couldn't classify 40425, 40552
Couldn't classify 44417, 44514
Sorry, prediction pasa_asmbl_49594.p1 fails validation.
(GCA)	 AA	40425-40552	GT	AGG
(TGT)	 AG	41479-41581	GT	AGG
(GTG)	 AG	41705-41924	GT	AGG
(GGT)	 AG	44417-44514	CC	TGC
-recovered pasa_asmbl_49594.p1, internal, 41479, 41581
-recovered pasa_asmbl_49594.p1, internal, 41705, 41924
Valid prediction for GeneMark_model.29531_t
Valid prediction for GeneMark_model.29547_t
Valid prediction for GeneMark_model.29555_t
Couldn't classify 34993, 35076
Sorry, prediction pasa_asmbl_50360.p1 fails validation.
(ATG)	 AC	33366-33422	GT	AGG
(ATT)	 AG	33874-34011	GT	TGG
(GTG)	 AG	34734-34880	GT	AGG
(ACG)	 AG	34993-35076	AG	TCA
-recovered pasa_asmbl_50360.p1, initial, 33366, 33422
-recovered pasa_asmbl_50360.p1, internal, 33874, 34011
-recovered pasa_asmbl_50360.p1, internal, 34734, 34880
Valid prediction for GlimmerHMM_glimmerT_17523-T1
Valid prediction for snap_scaffold_7-snap.730-T1
Valid prediction for GeneMark_model.29570_t
Valid prediction for snap_scaffold_7-snap.734-T1
Valid prediction for GeneMark_model.29552_t
Valid prediction for GeneMark_model.29501_t
Valid prediction for GeneMark_model.29497_t
Valid prediction for Augustus_model.g11736.t1
Valid prediction for GeneMark_model.29562_t
Valid prediction for GlimmerHMM_glimmerT_17536-T1
Valid prediction for Augustus_model.g11725.t1
Valid prediction for GeneMark_model.29520_t
Valid prediction for Augustus_model.g11731.t1
Valid prediction for GeneMark_model.29567_t
Valid prediction for GeneMark_model.29560_t
Valid prediction for GeneMark_model.29563_t
Valid prediction for GeneMark_model.29549_t
Valid prediction for CodingQuarry_transcript_57299-T1
Valid prediction for CodingQuarry_transcript_57300-T1
Valid prediction for snap_scaffold_7-snap.709-T1
Valid prediction for GlimmerHMM_glimmerT_17518-T1
Valid prediction for GeneMark_model.29568_t
Valid prediction for GeneMark_model.29524_t
Valid prediction for snap_scaffold_7-snap.711-T1
Valid prediction for GlimmerHMM_glimmerT_17535-T1
Valid prediction for GeneMark_model.29527_t
Valid prediction for GeneMark_model.29529_t
Valid prediction for snap_scaffold_7-snap.742-T1
Valid prediction for GlimmerHMM_glimmerT_17526-T1
Valid prediction for snap_scaffold_7-snap.745-T1
Valid prediction for GeneMark_model.29545_t
Valid prediction for snap_scaffold_7-snap.740-T1
Valid prediction for GlimmerHMM_glimmerT_17520-T1
Valid prediction for GeneMark_model.29539_t
Valid prediction for GeneMark_model.29523_t
Valid prediction for GlimmerHMM_glimmerT_17511-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 142456, rend_intergenic: 142453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23222, rend_intergenic: 16551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30184, rend_intergenic: 28371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87949, rend_intergenic: 78549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88306, rend_intergenic: 88171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109842, rend_intergenic: 89251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114270, rend_intergenic: 110571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122287, rend_intergenic: 114273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128058, rend_intergenic: 124154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137744, rend_intergenic: 128783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164887, rend_intergenic: 137759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169405, rend_intergenic: 165817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172963, rend_intergenic: 169656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181587, rend_intergenic: 177668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212713, rend_intergenic: 205260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222978, rend_intergenic: 218566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232194, rend_intergenic: 229655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 251062, rend_intergenic: 248234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 256343
-exon list size: 922


building trellis

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53.8    
53.9    
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54.7    
54.8    
54.9    
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55.8    
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57.8    
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58.8    
58.9    
59.0    
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60.0    
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61.8    
61.9    
62.0    
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62.8    
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63.0    
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63.7    
63.9    
64.0    
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64.6    
64.7    
64.8    
64.9    
65.0    
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65.6    
65.7    
65.8    
65.9    
66.0    
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66.8    
66.9    
67.0    
67.1    
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67.6    
67.7    
67.9    
68.0    
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68.6    
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68.8    
68.9    
69.0    
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69.8    
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70.0    
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71.0    
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73.9    
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74.8    
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75.0    
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76.0    
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76.9    
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77.9    
78.0    
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78.8    
78.9    
79.0    
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80.0    
80.1    
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80.8    
81.0    
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82.0    
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82.9    
83.0    
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87.0    
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87.6    
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88.0    
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88.2    
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88.6    
88.7    
88.9    
89.0    
89.1    
89.2    
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89.6    
89.7    
89.8    
89.9    
90.0    
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90.8    
90.9    
91.0    
91.1    
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91.6    
91.7    
91.8    
91.9    
92.0    
92.1    
92.2    
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92.7    
92.9    
93.0    
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93.9    
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95.0    
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96.0    
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96.8    
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98.8    
98.9    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.8    
99.9    
-found 45 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 142456, rend_intergenic: 142453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23222, rend_intergenic: 16551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30184, rend_intergenic: 28371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87949, rend_intergenic: 78549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88306, rend_intergenic: 88171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109842, rend_intergenic: 89251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114270, rend_intergenic: 110571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122287, rend_intergenic: 114273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128058, rend_intergenic: 124154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137744, rend_intergenic: 128783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164887, rend_intergenic: 137759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169405, rend_intergenic: 165817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172963, rend_intergenic: 169656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181587, rend_intergenic: 177668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212713, rend_intergenic: 205260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222978, rend_intergenic: 218566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232194, rend_intergenic: 229655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 251062, rend_intergenic: 248234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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

-building DP trellis

-building trellis in range 1 - 10074
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support