-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_216799-395024

-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_28-snap.77-T1
Valid prediction for Augustus_model.g39497.t1
Valid prediction for GeneMark_model.103605_t
Valid prediction for GeneMark_model.103619_t
Valid prediction for GlimmerHMM_glimmerT_59345-T1
Valid prediction for HiQ_model.g39491.t1
Valid prediction for Augustus_model.g39486.t1
Valid prediction for GlimmerHMM_glimmerT_59351-T1
Valid prediction for snap_scaffold_28-snap.52-T1
Valid prediction for GlimmerHMM_glimmerT_59347-T1
Valid prediction for snap_scaffold_28-snap.72-T1
Valid prediction for snap_scaffold_28-snap.80-T1
Valid prediction for GlimmerHMM_glimmerT_59365-T1
Valid prediction for GeneMark_model.103607_t
Valid prediction for snap_scaffold_28-snap.56-T1
Valid prediction for GeneMark_model.103628_t
Valid prediction for CodingQuarry_transcript_43419-T1
Valid prediction for snap_scaffold_28-snap.44-T1
Valid prediction for CodingQuarry_transcript_43416-T1
Valid prediction for snap_scaffold_28-snap.74-T1
Valid prediction for GlimmerHMM_glimmerT_59361-T1
Valid prediction for GlimmerHMM_glimmerT_59350-T1
Valid prediction for GeneMark_model.103603_t
Valid prediction for GeneMark_model.103621_t
Valid prediction for GeneMark_model.103634_t
Valid prediction for GeneMark_model.103626_t
Valid prediction for CodingQuarry_transcript_43418-T1
Couldn't classify 23784, 23810
Sorry, prediction pasa_asmbl_37956.p1 fails validation.
(GCA)	 TT	23784-23810	GT	AGG
(AAC)	 AG	23910-24005	GT	AGG
(GGT)	 AG	24095-24244	GT	ACG
(GGT)	 AG	24352-24457	GT	GGG
(GTG)	 AG	24654-24787	GT	AGG
(AAC)	 AG	24965-25081	GT	AAG
-recovered pasa_asmbl_37956.p1, terminal, 24965, 25081
-recovered pasa_asmbl_37956.p1, internal, 23910, 24005
-recovered pasa_asmbl_37956.p1, internal, 24095, 24244
-recovered pasa_asmbl_37956.p1, internal, 24352, 24457
-recovered pasa_asmbl_37956.p1, internal, 24654, 24787
-recovered pasa_asmbl_37956.p1, internal, 24965, 25081
Valid prediction for Augustus_model.g39492.t1
Valid prediction for HiQ_model.g39490.t1
Valid prediction for Augustus_model.g39487.t1
Valid prediction for snap_scaffold_28-snap.47-T1
Valid prediction for Augustus_model.g39498.t1
Valid prediction for GeneMark_model.103613_t
Valid prediction for snap_scaffold_28-snap.58-T1
Valid prediction for GlimmerHMM_glimmerT_59349-T1
Valid prediction for CodingQuarry_transcript_43417-T1
Valid prediction for CodingQuarry_transcript_43414-T1
Valid prediction for GeneMark_model.103631_t
Valid prediction for GlimmerHMM_glimmerT_59353-T1
Valid prediction for CodingQuarry_transcript_43415-T1
Valid prediction for pasa_asmbl_37967.p1
Valid prediction for GlimmerHMM_glimmerT_59354-T1
Valid prediction for snap_scaffold_28-snap.55-T1
Valid prediction for GlimmerHMM_glimmerT_59352-T1
Valid prediction for Augustus_model.g39488.t1
Valid prediction for Augustus_model.g39484.t1
Valid prediction for snap_scaffold_28-snap.62-T1
Valid prediction for snap_scaffold_28-snap.79-T1
Valid prediction for snap_scaffold_28-snap.66-T1
Valid prediction for snap_scaffold_28-snap.64-T1
Valid prediction for GlimmerHMM_glimmerT_59369-T1
Valid prediction for snap_scaffold_28-snap.46-T1
Valid prediction for snap_scaffold_28-snap.71-T1
Valid prediction for snap_scaffold_28-snap.63-T1
Valid prediction for snap_scaffold_28-snap.53-T1
Valid prediction for GlimmerHMM_glimmerT_59366-T1
Valid prediction for Augustus_model.g39483.t1
Valid prediction for GlimmerHMM_glimmerT_59368-T1
Valid prediction for snap_scaffold_28-snap.65-T1
Valid prediction for GlimmerHMM_glimmerT_59344-T1
Valid prediction for GlimmerHMM_glimmerT_59364-T1
Valid prediction for Augustus_model.g39489.t1
Valid prediction for snap_scaffold_28-snap.78-T1
Valid prediction for GlimmerHMM_glimmerT_59357-T1
Valid prediction for Augustus_model.g39500.t1
Valid prediction for snap_scaffold_28-snap.61-T1
Valid prediction for GeneMark_model.103610_t
Valid prediction for GlimmerHMM_glimmerT_59355-T1
Couldn't classify 77000, 77038
Sorry, prediction pasa_asmbl_37961.p1 fails validation.
(GAG)	 AG	77000-77038	GT	AGG
(GCC)	 AG	77434-77726	GT	AGG
(ATG)	 AG	77837-78008	GT	AGG
(GAG)	 AG	78094-78279	GT	AGG
(ATT)	 AG	78468-78601	GT	AAG
(GTG)	 AG	78691-78739	GT	AGG
(GCA)	 AG	78820-78939	GT	TGG
(GTC)	 AG	79060-79158	GT	AGG
(TTG)	 AG	79257-79314	GT	GAG
(CAG)	 AG	79471-79707	GT	AGG
(GTG)	 AG	79795-79835	AA	AAA
-recovered pasa_asmbl_37961.p1, initial, 77837, 78008
-recovered pasa_asmbl_37961.p1, terminal, 79795, 79835
-recovered pasa_asmbl_37961.p1, internal, 77000, 77038
-recovered pasa_asmbl_37961.p1, internal, 77434, 77726
-recovered pasa_asmbl_37961.p1, internal, 77837, 78008
-recovered pasa_asmbl_37961.p1, internal, 78094, 78279
-recovered pasa_asmbl_37961.p1, internal, 78468, 78601
-recovered pasa_asmbl_37961.p1, internal, 78691, 78739
-recovered pasa_asmbl_37961.p1, internal, 78820, 78939
-recovered pasa_asmbl_37961.p1, internal, 79060, 79158
-recovered pasa_asmbl_37961.p1, internal, 79257, 79314
-recovered pasa_asmbl_37961.p1, internal, 79471, 79707
Valid prediction for Augustus_model.g39501.t1
Valid prediction for snap_scaffold_28-snap.51-T1
Valid prediction for GeneMark_model.103602_t
Valid prediction for GlimmerHMM_glimmerT_59343-T1
Valid prediction for GlimmerHMM_glimmerT_59348-T1
Valid prediction for HiQ_model.g39482.t1
Valid prediction for GeneMark_model.103612_t
Valid prediction for GeneMark_model.103614_t
Valid prediction for GeneMark_model.103618_t
Couldn't classify 10304, 10332
Sorry, prediction pasa_asmbl_37949.p1 fails validation.
(GAC)	 GA	10304-10332	GT	CGG
(TGT)	 AG	11991-12032	GT	AAG
(TTA)	 AG	12115-12205	GT	CTG
(GTT)	 AG	13468-13616	GT	CGG
(GGC)	 AG	13721-13829	GT	TGG
(CCT)	 AG	13913-14040	GT	AGG
(GCT)	 AG	14268-14367	GT	AGG
(GTG)	 AG	14960-15035	GT	TGG
(CGG)	 AG	15145-15230	GT	AGG
(GGA)	 AG	15388-15492	GT	AGG
(GTC)	 AG	15610-15685	GT	AGG
(ACT)	 AG	15764-15882	GT	AGG
(GCG)	 AG	15960-16043	GT	CTG
(ATC)	 AG	16788-16845	GT	AGG
(CTG)	 AG	16935-17116	GT	AGG
(TAT)	 AG	17184-17318	CA	GAC
-recovered pasa_asmbl_37949.p1, terminal, 17184, 17318
-recovered pasa_asmbl_37949.p1, internal, 11991, 12032
-recovered pasa_asmbl_37949.p1, internal, 12115, 12205
-recovered pasa_asmbl_37949.p1, internal, 13468, 13616
-recovered pasa_asmbl_37949.p1, internal, 13721, 13829
-recovered pasa_asmbl_37949.p1, internal, 13913, 14040
-recovered pasa_asmbl_37949.p1, internal, 14268, 14367
-recovered pasa_asmbl_37949.p1, internal, 14960, 15035
-recovered pasa_asmbl_37949.p1, internal, 15145, 15230
-recovered pasa_asmbl_37949.p1, internal, 15388, 15492
-recovered pasa_asmbl_37949.p1, internal, 15610, 15685
-recovered pasa_asmbl_37949.p1, internal, 15764, 15882
-recovered pasa_asmbl_37949.p1, internal, 15960, 16043
-recovered pasa_asmbl_37949.p1, internal, 16788, 16845
-recovered pasa_asmbl_37949.p1, internal, 16935, 17116
Valid prediction for GeneMark_model.103616_t
Valid prediction for snap_scaffold_28-snap.54-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_28-snap.48-T1
Valid prediction for GeneMark_model.103625_t
Valid prediction for CodingQuarry_transcript_43413-T1
Valid prediction for snap_scaffold_28-snap.50-T1
Valid prediction for GeneMark_model.103608_t
Valid prediction for GeneMark_model.103601_t
Valid prediction for snap_scaffold_28-snap.76-T1
Valid prediction for Augustus_model.g39499.t1
Valid prediction for Augustus_model.g39493.t1
Valid prediction for Augustus_model.g39495.t1
Valid prediction for HiQ_model.g39481.t1
Valid prediction for GlimmerHMM_glimmerT_59367-T1
Valid prediction for Augustus_model.g39496.t1
Valid prediction for GeneMark_model.103629_t
Valid prediction for snap_scaffold_28-snap.82-T1
Valid prediction for Augustus_model.g39494.t1
Valid prediction for GeneMark_model.103635_t
Valid prediction for GeneMark_model.103630_t
Valid prediction for GeneMark_model.103617_t
Valid prediction for GlimmerHMM_glimmerT_59356-T1
Valid prediction for GeneMark_model.103606_t
Valid prediction for pasa_asmbl_37224.p1
Valid prediction for GeneMark_model.103609_t
Valid prediction for GlimmerHMM_glimmerT_59363-T1
Valid prediction for snap_scaffold_28-snap.45-T1
Valid prediction for snap_scaffold_28-snap.75-T1
Valid prediction for GeneMark_model.103624_t
Valid prediction for GlimmerHMM_glimmerT_59342-T1
Valid prediction for snap_scaffold_28-snap.68-T1
Valid prediction for snap_scaffold_28-snap.81-T1
Valid prediction for GeneMark_model.103632_t
Valid prediction for GlimmerHMM_glimmerT_59360-T1
Valid prediction for Augustus_model.g39485.t1
Valid prediction for snap_scaffold_28-snap.49-T1
Valid prediction for GeneMark_model.103604_t
Valid prediction for snap_scaffold_28-snap.57-T1
Valid prediction for GeneMark_model.103623_t
Valid prediction for snap_scaffold_28-snap.70-T1
Valid prediction for GlimmerHMM_glimmerT_59362-T1
Valid prediction for GlimmerHMM_glimmerT_59359-T1
Valid prediction for snap_scaffold_28-snap.69-T1
Valid prediction for GeneMark_model.103611_t
Valid prediction for GeneMark_model.103633_t
Valid prediction for snap_scaffold_28-snap.73-T1
Valid prediction for GlimmerHMM_glimmerT_59358-T1
Valid prediction for CodingQuarry_transcript_43412-T1
Valid prediction for GeneMark_model.103615_t
Valid prediction for snap_scaffold_28-snap.67-T1
Valid prediction for GeneMark_model.103622_t
Valid prediction for snap_scaffold_28-snap.60-T1
Valid prediction for GeneMark_model.103627_t
Valid prediction for snap_scaffold_28-snap.59-T1
Valid prediction for GlimmerHMM_glimmerT_59346-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 61330, rend_intergenic: 57290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70671, rend_intergenic: 68305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117284, rend_intergenic: 115092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125453, rend_intergenic: 121779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 178226
-exon list size: 524


building trellis

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68.8    
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69.2    
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69.6    
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73.6    
73.8    
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74.3    
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74.7    
74.9    
75.1    
75.3    
75.5    
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75.9    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
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79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
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84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 61330, rend_intergenic: 57290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70671, rend_intergenic: 68305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117284, rend_intergenic: 115092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125453, rend_intergenic: 121779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support