-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_11024807-11205706

-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 GeneMark_model.21799_t
Valid prediction for Augustus_model.g8594.t1
Couldn't classify 69746, 70093
Sorry, prediction pasa_asmbl_44405.p1 fails validation.
(AAT)	 AG	69746-70093	CA	GAC
Valid prediction for snap_scaffold_5-snap.2060-T1
Valid prediction for HiQ_model.g8588.t1
Valid prediction for GeneMark_model.21795_t
Valid prediction for GeneMark_model.21816_t
Valid prediction for GlimmerHMM_glimmerT_12899-T1
Couldn't classify 71408, 75859
Sorry, prediction pasa_asmbl_44406.p1 fails validation.
(ACA)	 GC	71408-75859	TT	AAT
Couldn't classify 49836, 50045
Sorry, prediction pasa_asmbl_44397.p1 fails validation.
(CAT)	 GA	49836-50045	GT	AGG
(AAA)	 AG	50538-50651	GT	GGG
(ACA)	 AG	50872-50964	GT	AGG
(AAC)	 AG	51096-51183	GT	AGG
(GTA)	 AG	51269-51324	GT	AGG
(ATG)	 AG	51423-51500	GT	GTG
(GGT)	 AG	51675-51790	GT	AGG
(GGC)	 AG	51878-52356	GT	TGG
(CAT)	 AG	52537-52668	GT	TGG
(ACC)	 AG	52826-52975	GT	AGG
(GTA)	 AG	53082-53588	GT	TGG
(GAA)	 AG	53688-54194	GT	AGG
(CTG)	 AG	54320-54483	GT	AGG
(ATG)	 AG	54567-54647	GT	AGG
(ATT)	 AG	54757-54835	GT	AGG
(AGC)	 AG	54940-55179	GT	AGG
(CCA)	 AG	55322-55500	CC	AAC
-recovered pasa_asmbl_44397.p1, initial, 51423, 51500
-recovered pasa_asmbl_44397.p1, initial, 54567, 54647
add_exon() Sorry, pasa_asmbl_44397.p1 52826-52975-terminal-1 is invalid.
-recovered pasa_asmbl_44397.p1, terminal, 52826, 52975
add_exon() Sorry, pasa_asmbl_44397.p1 54757-54835-terminal-3 is invalid.
-recovered pasa_asmbl_44397.p1, terminal, 54757, 54835
-recovered pasa_asmbl_44397.p1, terminal, 55322, 55500
-recovered pasa_asmbl_44397.p1, internal, 50538, 50651
-recovered pasa_asmbl_44397.p1, internal, 50872, 50964
-recovered pasa_asmbl_44397.p1, internal, 51096, 51183
-recovered pasa_asmbl_44397.p1, internal, 51269, 51324
-recovered pasa_asmbl_44397.p1, internal, 51423, 51500
-recovered pasa_asmbl_44397.p1, internal, 51675, 51790
-recovered pasa_asmbl_44397.p1, internal, 51878, 52356
-recovered pasa_asmbl_44397.p1, internal, 52537, 52668
-recovered pasa_asmbl_44397.p1, internal, 52826, 52975
-recovered pasa_asmbl_44397.p1, internal, 53082, 53588
-recovered pasa_asmbl_44397.p1, internal, 53688, 54194
-recovered pasa_asmbl_44397.p1, internal, 54320, 54483
-recovered pasa_asmbl_44397.p1, internal, 54567, 54647
-recovered pasa_asmbl_44397.p1, internal, 54757, 54835
-recovered pasa_asmbl_44397.p1, internal, 54940, 55179
Valid prediction for snap_scaffold_5-snap.2081-T1
Valid prediction for snap_scaffold_5-snap.2065-T1
Valid prediction for GlimmerHMM_glimmerT_12895-T1
Valid prediction for GeneMark_model.21807_t
Valid prediction for GeneMark_model.21794_t
Valid prediction for GlimmerHMM_glimmerT_12886-T1
Valid prediction for GlimmerHMM_glimmerT_12896-T1
Valid prediction for snap_scaffold_5-snap.2078-T1
Valid prediction for snap_scaffold_5-snap.2064-T1
Valid prediction for snap_scaffold_5-snap.2074-T1
Valid prediction for GlimmerHMM_glimmerT_12892-T1
Valid prediction for snap_scaffold_5-snap.2068-T1
Valid prediction for GeneMark_model.21811_t
Valid prediction for snap_scaffold_5-snap.2056-T1
Valid prediction for GeneMark_model.21782_t
Valid prediction for GeneMark_model.21783_t
Valid prediction for snap_scaffold_5-snap.2058-T1
Valid prediction for Augustus_model.g8590.t1
Couldn't classify 58750, 59039
Couldn't classify 59878, 59913
Sorry, prediction pasa_asmbl_44402.p1 fails validation.
(GCT)	 CT	58750-59039	GT	AGG
(GTT)	 AG	59145-59391	GT	AGG
(GAG)	 AG	59496-59726	GT	AGG
(GGT)	 AG	59878-59913	GA	CAG
-recovered pasa_asmbl_44402.p1, internal, 59145, 59391
-recovered pasa_asmbl_44402.p1, internal, 59496, 59726
Valid prediction for snap_scaffold_5-snap.2082-T1
Valid prediction for GeneMark_model.21808_t
Valid prediction for GlimmerHMM_glimmerT_12889-T1
Couldn't classify 68100, 68226
Couldn't classify 68337, 68773
Sorry, prediction pasa_asmbl_44404.p1 fails validation.
(TAC)	 CT	68100-68226	GT	AGG
(GAC)	 AG	68337-68773	AC	CCA
Valid prediction for GeneMark_model.21798_t
Valid prediction for GeneMark_model.21804_t
Valid prediction for snap_scaffold_5-snap.2076-T1
Valid prediction for GeneMark_model.21801_t
Valid prediction for Augustus_model.g8589.t1
Valid prediction for Augustus_model.g8591.t1
Valid prediction for GlimmerHMM_glimmerT_12901-T1
Valid prediction for Augustus_model.g8597.t1
Couldn't classify 57992, 58344
Sorry, prediction pasa_asmbl_44401.p1 fails validation.
(ATG)	 CC	57826-57880	GT	CGG
(AGG)	 AG	57992-58344	CC	ACC
-recovered pasa_asmbl_44401.p1, initial, 57826, 57880
Valid prediction for snap_scaffold_5-snap.2066-T1
Valid prediction for GeneMark_model.21814_t
Valid prediction for GeneMark_model.21791_t
Valid prediction for GeneMark_model.21785_t
Valid prediction for GlimmerHMM_glimmerT_12902-T1
Valid prediction for snap_scaffold_5-snap.2059-T1
Valid prediction for GlimmerHMM_glimmerT_12891-T1
Valid prediction for snap_scaffold_5-snap.2075-T1
Valid prediction for GeneMark_model.21789_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 CodingQuarry_transcript_52121-T1
Valid prediction for GeneMark_model.21788_t
Valid prediction for GeneMark_model.21793_t
Valid prediction for snap_scaffold_5-snap.2085-T1
Valid prediction for snap_scaffold_5-snap.2077-T1
Valid prediction for GeneMark_model.21806_t
Valid prediction for GeneMark_model.21780_t
Valid prediction for GlimmerHMM_glimmerT_12900-T1
Valid prediction for GeneMark_model.21809_t
Valid prediction for snap_scaffold_5-snap.2067-T1
Valid prediction for snap_scaffold_5-snap.2057-T1
Valid prediction for GeneMark_model.21786_t
Valid prediction for HiQ_model.g8587.t1
Valid prediction for GlimmerHMM_glimmerT_12893-T1
Valid prediction for GlimmerHMM_glimmerT_12898-T1
Valid prediction for snap_scaffold_5-snap.2063-T1
Valid prediction for GlimmerHMM_glimmerT_12890-T1
Valid prediction for snap_scaffold_5-snap.2061-T1
Valid prediction for snap_scaffold_5-snap.2084-T1
Valid prediction for snap_scaffold_5-snap.2072-T1
Valid prediction for Augustus_model.g8592.t1
Valid prediction for GeneMark_model.21812_t
Valid prediction for GeneMark_model.21802_t
Valid prediction for GeneMark_model.21800_t
Valid prediction for GlimmerHMM_glimmerT_12888-T1
Valid prediction for snap_scaffold_5-snap.2062-T1
Valid prediction for HiQ_model.g8593.t1
Valid prediction for GeneMark_model.21787_t
Valid prediction for GeneMark_model.21796_t
Valid prediction for snap_scaffold_5-snap.2070-T1
Valid prediction for snap_scaffold_5-snap.2083-T1
Valid prediction for snap_scaffold_5-snap.2069-T1
Valid prediction for GeneMark_model.21813_t
Valid prediction for snap_scaffold_5-snap.2080-T1
Valid prediction for GlimmerHMM_glimmerT_12894-T1
Valid prediction for pasa_asmbl_45785.p1
Valid prediction for GeneMark_model.21792_t
Valid prediction for GlimmerHMM_glimmerT_12897-T1
Valid prediction for CodingQuarry_transcript_52118-T1
Valid prediction for GeneMark_model.21784_t
Valid prediction for GeneMark_model.21781_t
Valid prediction for snap_scaffold_5-snap.2073-T1
Valid prediction for GlimmerHMM_glimmerT_12887-T1
Valid prediction for GeneMark_model.21803_t
Valid prediction for Augustus_model.g8596.t1
Valid prediction for GeneMark_model.21797_t
Valid prediction for GeneMark_model.21790_t
Valid prediction for Augustus_model.g8595.t1
Valid prediction for GeneMark_model.21805_t
Valid prediction for pasa_asmbl_45786.p1
Valid prediction for snap_scaffold_5-snap.2071-T1
Valid prediction for snap_scaffold_5-snap.2079-T1
Valid prediction for GeneMark_model.21815_t
Valid prediction for GeneMark_model.21810_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7558, rend_intergenic: 3876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21754, rend_intergenic: 8515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54527, rend_intergenic: 48378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155137, rend_intergenic: 151253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163787, rend_intergenic: 159730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166806, rend_intergenic: 165338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 180900
-exon list size: 484


building trellis

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31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
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34.4    
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34.8    
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35.8    
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36.6    
36.8    
37.0    
37.2    
37.4    
37.7    
37.9    
38.1    
38.3    
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38.7    
38.9    
39.1    
39.3    
39.5    
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39.9    
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40.3    
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40.7    
40.9    
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48.6    
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82.9    
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83.3    
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84.4    
84.6    
84.8    
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85.2    
85.4    
85.6    
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86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
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87.9    
88.1    
88.3    
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88.7    
88.9    
89.1    
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91.4    
91.6    
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92.6    
92.8    
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93.2    
93.4    
93.6    
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97.9    
98.1    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 7558, rend_intergenic: 3876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21754, rend_intergenic: 8515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54527, rend_intergenic: 48378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155137, rend_intergenic: 151253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163787, rend_intergenic: 159730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166806, rend_intergenic: 165338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support