-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_1370373-1521732

-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_14372-T1
Valid prediction for CodingQuarry_transcript_54778-T1
Couldn't classify 5338, 5380
Sorry, prediction pasa_asmbl_46654.p1 fails validation.
(CCC)	 CC	5338-5380	GT	TGG
(ATA)	 AG	5472-5581	GT	AGG
(ATC)	 AG	5892-6081	GT	GGG
(ATG)	 AG	6412-6500	GT	AGG
(GTC)	 AG	6947-7017	GT	AGG
(CTG)	 AG	7308-7479	GT	TGG
(GTC)	 AG	7973-8107	GT	TGG
(TGT)	 AG	8434-8568	GT	AGG
(ATC)	 AG	10180-10446	GT	AGG
(GGC)	 AG	10730-10908	GT	AGG
(GGG)	 AG	11370-11475	CA	AGC
add_exon() Sorry, pasa_asmbl_46654.p1 6412-6500-initial-1 is invalid.
-recovered pasa_asmbl_46654.p1, initial, 6412, 6500
-recovered pasa_asmbl_46654.p1, terminal, 11370, 11475
-recovered pasa_asmbl_46654.p1, internal, 5472, 5581
-recovered pasa_asmbl_46654.p1, internal, 5892, 6081
-recovered pasa_asmbl_46654.p1, internal, 6412, 6500
-recovered pasa_asmbl_46654.p1, internal, 6947, 7017
-recovered pasa_asmbl_46654.p1, internal, 7308, 7479
-recovered pasa_asmbl_46654.p1, internal, 7973, 8107
-recovered pasa_asmbl_46654.p1, internal, 8434, 8568
-recovered pasa_asmbl_46654.p1, internal, 10180, 10446
-recovered pasa_asmbl_46654.p1, internal, 10730, 10908
Valid prediction for snap_scaffold_6-snap.315-T1
Valid prediction for HiQ_model.g9586.t1
Valid prediction for GeneMark_model.24117_t
Valid prediction for GeneMark_model.24104_t
Valid prediction for snap_scaffold_6-snap.330-T1
Valid prediction for pasa_asmbl_46665.p1
Valid prediction for GlimmerHMM_glimmerT_14379-T1
Valid prediction for snap_scaffold_6-snap.307-T1
Valid prediction for snap_scaffold_6-snap.340-T1
Valid prediction for GeneMark_model.24150_t
Valid prediction for pasa_asmbl_46659.p1
Valid prediction for snap_scaffold_6-snap.305-T1
Valid prediction for Augustus_model.g9592.t1
Valid prediction for GeneMark_model.24151_t
Valid prediction for GeneMark_model.24110_t
Valid prediction for snap_scaffold_6-snap.312-T1
Valid prediction for GeneMark_model.24114_t
Valid prediction for GeneMark_model.24153_t
Valid prediction for GlimmerHMM_glimmerT_14377-T1
Couldn't classify 760, 760
Couldn't classify 5194, 5229
Sorry, prediction pasa_asmbl_47877.p1 fails validation.
(AGT)	 TA	760-760	GT	AAG
(TGT)	 AG	1856-1947	GT	CGG
(GCT)	 AG	3375-3524	GT	GGG
(ATG)	 AG	3714-3845	GT	CGG
(GTG)	 AG	4587-4715	GT	AGG
(GGG)	 AG	5194-5229	GA	TGG
-recovered pasa_asmbl_47877.p1, initial, 3714, 3845
-recovered pasa_asmbl_47877.p1, internal, 1856, 1947
-recovered pasa_asmbl_47877.p1, internal, 3375, 3524
-recovered pasa_asmbl_47877.p1, internal, 3714, 3845
-recovered pasa_asmbl_47877.p1, internal, 4587, 4715
Valid prediction for snap_scaffold_6-snap.327-T1
Valid prediction for GeneMark_model.24143_t
Valid prediction for pasa_asmbl_46656.p1
Valid prediction for snap_scaffold_6-snap.337-T1
Valid prediction for GeneMark_model.24160_t
Valid prediction for GeneMark_model.24124_t
Valid prediction for HiQ_model.g9593.t1
Valid prediction for GeneMark_model.24158_t
Valid prediction for GeneMark_model.24129_t
Valid prediction for pasa_asmbl_46669.p1
Valid prediction for GlimmerHMM_glimmerT_14381-T1
Valid prediction for HiQ_model.g9591.t1
Valid prediction for GeneMark_model.24116_t
Couldn't classify 4587, 4758
Couldn't classify 4783, 4838
Sorry, prediction CodingQuarry_transcript_54773-T1 fails validation.
(ATG)	 CC	1885-1947	GT	CGG
(GCT)	 AG	3375-3524	GT	GGG
(ATG)	 AG	3714-3845	GT	CGG
(GTG)	 AG	4587-4758	TG	TCT
(TGT)	 TG	4783-4838	GC	GAG
-recovered CodingQuarry_transcript_54773-T1, initial, 1885, 1947
-recovered CodingQuarry_transcript_54773-T1, initial, 3714, 3845
-recovered CodingQuarry_transcript_54773-T1, internal, 3375, 3524
-recovered CodingQuarry_transcript_54773-T1, internal, 3714, 3845
Valid prediction for snap_scaffold_6-snap.334-T1
Valid prediction for GlimmerHMM_glimmerT_14384-T1
Valid prediction for CodingQuarry_transcript_54779-T1
Valid prediction for GeneMark_model.24112_t
Valid prediction for snap_scaffold_6-snap.313-T1
Valid prediction for GlimmerHMM_glimmerT_14373-T1
Valid prediction for GlimmerHMM_glimmerT_14380-T1
Valid prediction for GeneMark_model.24145_t
Valid prediction for GeneMark_model.24108_t
Valid prediction for GeneMark_model.24102_t
Valid prediction for CodingQuarry_transcript_54775-T1
Valid prediction for GeneMark_model.24162_t
Valid prediction for GeneMark_model.24126_t
Valid prediction for snap_scaffold_6-snap.316-T1
Valid prediction for GeneMark_model.24138_t
Valid prediction for GeneMark_model.24121_t
Valid prediction for GeneMark_model.24128_t
Valid prediction for GlimmerHMM_glimmerT_14369-T1
Valid prediction for GeneMark_model.24148_t
Valid prediction for GeneMark_model.24131_t
Valid prediction for snap_scaffold_6-snap.336-T1
Valid prediction for snap_scaffold_6-snap.301-T1
Valid prediction for GeneMark_model.24119_t
Valid prediction for snap_scaffold_6-snap.331-T1
Couldn't classify 100740, 100762
Sorry, prediction HiQ_model.g9588.t1 fails validation.
(ATG)	 GG	91298-91412	GT	TTG
(TTT)	 AG	93340-93633	GT	AGG
(GCC)	 AG	94170-94306	GT	CTG
(GTA)	 AG	94715-94859	GT	AGG
(GTC)	 AG	95384-95644	GT	GGG
(AGC)	 AG	96197-96481	GT	AGG
(TCC)	 AG	96992-97288	GT	CGG
(AGC)	 AG	97385-97660	GT	AGG
(TGA)	 AG	97780-97912	GT	GTG
(GAA)	 AG	98037-98110	GT	TGG
(TCA)	 AG	98831-98884	GT	AGG
(AGT)	 AG	99346-99435	GT	AGG
(CTC)	 AG	99840-99896	GT	AGG
(GTG)	 AG	100740-100762	GT	GAG
-recovered HiQ_model.g9588.t1, initial, 91298, 91412
-recovered HiQ_model.g9588.t1, internal, 93340, 93633
-recovered HiQ_model.g9588.t1, internal, 94170, 94306
-recovered HiQ_model.g9588.t1, internal, 94715, 94859
-recovered HiQ_model.g9588.t1, internal, 95384, 95644
-recovered HiQ_model.g9588.t1, internal, 96197, 96481
-recovered HiQ_model.g9588.t1, internal, 96992, 97288
-recovered HiQ_model.g9588.t1, internal, 97385, 97660
-recovered HiQ_model.g9588.t1, internal, 97780, 97912
-recovered HiQ_model.g9588.t1, internal, 98037, 98110
-recovered HiQ_model.g9588.t1, internal, 98831, 98884
-recovered HiQ_model.g9588.t1, internal, 99346, 99435
-recovered HiQ_model.g9588.t1, internal, 99840, 99896
-recovered HiQ_model.g9588.t1, internal, 100740, 100762
Valid prediction for snap_scaffold_6-snap.320-T1
Valid prediction for GeneMark_model.24133_t
Valid prediction for snap_scaffold_6-snap.317-T1
Valid prediction for HiQ_model.g9590.t1
Valid prediction for HiQ_model.g9589.t1
Valid prediction for GlimmerHMM_glimmerT_14374-T1
Valid prediction for snap_scaffold_6-snap.328-T1
Valid prediction for GeneMark_model.24106_t
Valid prediction for snap_scaffold_6-snap.311-T1
Couldn't classify 122363, 122477
Couldn't classify 124556, 124610
Sorry, prediction CodingQuarry_transcript_54777-T1 fails validation.
(ATG)	 GA	121678-121780	GT	AAG
(CCT)	 AG	122363-122477	GA	CCG
(AGA)	 TA	124556-124610	TC	AGT
-recovered CodingQuarry_transcript_54777-T1, initial, 121678, 121780
Valid prediction for GlimmerHMM_glimmerT_14383-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_6-snap.339-T1
Valid prediction for snap_scaffold_6-snap.302-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GeneMark_model.24137_t
Valid prediction for GeneMark_model.24130_t
Valid prediction for GeneMark_model.24154_t
Valid prediction for snap_scaffold_6-snap.324-T1
Valid prediction for snap_scaffold_6-snap.335-T1
Valid prediction for GeneMark_model.24149_t
Valid prediction for GeneMark_model.24142_t
Valid prediction for GeneMark_model.24161_t
Valid prediction for Augustus_model.g9587.t1
Valid prediction for GlimmerHMM_glimmerT_14376-T1
Valid prediction for snap_scaffold_6-snap.319-T1
Valid prediction for GeneMark_model.24157_t
Valid prediction for snap_scaffold_6-snap.314-T1
Valid prediction for snap_scaffold_6-snap.329-T1
Valid prediction for GeneMark_model.24111_t
Valid prediction for GlimmerHMM_glimmerT_14382-T1
Valid prediction for snap_scaffold_6-snap.318-T1
Valid prediction for GeneMark_model.24146_t
Valid prediction for snap_scaffold_6-snap.310-T1
Valid prediction for snap_scaffold_6-snap.333-T1
Valid prediction for GeneMark_model.24132_t
Valid prediction for GeneMark_model.24123_t
Valid prediction for GeneMark_model.24109_t
Valid prediction for snap_scaffold_6-snap.338-T1
Valid prediction for GlimmerHMM_glimmerT_14378-T1
Valid prediction for snap_scaffold_6-snap.306-T1
Valid prediction for GlimmerHMM_glimmerT_14375-T1
Valid prediction for GeneMark_model.24127_t
Valid prediction for GeneMark_model.24105_t
Valid prediction for GeneMark_model.24125_t
Valid prediction for snap_scaffold_6-snap.323-T1
Valid prediction for snap_scaffold_6-snap.332-T1
Valid prediction for snap_scaffold_6-snap.309-T1
Valid prediction for GeneMark_model.24101_t
Valid prediction for snap_scaffold_6-snap.300-T1
Valid prediction for GeneMark_model.24140_t
Valid prediction for GeneMark_model.24115_t
Valid prediction for GeneMark_model.24155_t
Valid prediction for snap_scaffold_6-snap.303-T1
Valid prediction for GeneMark_model.24113_t
Valid prediction for GeneMark_model.24103_t
Valid prediction for snap_scaffold_6-snap.322-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.308-T1
Valid prediction for GeneMark_model.24159_t
Valid prediction for GeneMark_model.24144_t
Valid prediction for snap_scaffold_6-snap.325-T1
Valid prediction for snap_scaffold_6-snap.304-T1
Valid prediction for GlimmerHMM_glimmerT_14370-T1
Valid prediction for GeneMark_model.24147_t
Valid prediction for GeneMark_model.24118_t
Valid prediction for snap_scaffold_6-snap.326-T1
Valid prediction for GlimmerHMM_glimmerT_14371-T1
Valid prediction for GeneMark_model.24122_t
Valid prediction for GeneMark_model.24120_t
Valid prediction for GeneMark_model.24136_t
Valid prediction for GeneMark_model.24134_t
Valid prediction for snap_scaffold_6-snap.321-T1
Valid prediction for GeneMark_model.24156_t
Valid prediction for GeneMark_model.24139_t
Valid prediction for GeneMark_model.24135_t
Valid prediction for GeneMark_model.24107_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5409, rend_intergenic: 1885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11475, rend_intergenic: 5862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28281, rend_intergenic: 15170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33984, rend_intergenic: 28882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52026, rend_intergenic: 39985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56464, rend_intergenic: 52724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75255, rend_intergenic: 56637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78988, rend_intergenic: 77273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86054, rend_intergenic: 80890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108545, rend_intergenic: 86484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114358, rend_intergenic: 108744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118964, rend_intergenic: 115917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134356, rend_intergenic: 132404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148139, rend_intergenic: 135041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 151360
-exon list size: 695


building trellis

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75.3    
75.5    
75.6    
75.8    
75.9    
76.0    
76.2    
76.3    
76.5    
76.6    
76.8    
76.9    
77.0    
77.2    
77.3    
77.5    
77.6    
77.8    
77.9    
78.0    
78.2    
78.3    
78.5    
78.6    
78.8    
78.9    
79.1    
79.2    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.1    
81.2    
81.3    
81.5    
81.6    
81.8    
81.9    
82.1    
82.2    
82.4    
82.5    
82.6    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
87.9    
88.1    
88.2    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 44 predictions from path traversal
Error with prediction: snap lend_intergenic: 5409, rend_intergenic: 1885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11475, rend_intergenic: 5862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28281, rend_intergenic: 15170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33984, rend_intergenic: 28882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52026, rend_intergenic: 39985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56464, rend_intergenic: 52724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75255, rend_intergenic: 56637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78988, rend_intergenic: 77273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86054, rend_intergenic: 80890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108545, rend_intergenic: 86484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114358, rend_intergenic: 108744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118964, rend_intergenic: 115917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134356, rend_intergenic: 132404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148139, rend_intergenic: 135041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support