-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_15746464-15881384

-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.27663_t
Valid prediction for GlimmerHMM_glimmerT_16561-T1
Valid prediction for GeneMark_model.27677_t
Valid prediction for snap_scaffold_6-snap.3322-T1
Valid prediction for GlimmerHMM_glimmerT_16564-T1
Valid prediction for GlimmerHMM_glimmerT_16550-T1
Valid prediction for snap_scaffold_6-snap.3315-T1
Valid prediction for GlimmerHMM_glimmerT_16548-T1
Valid prediction for GeneMark_model.27680_t
Valid prediction for GlimmerHMM_glimmerT_16560-T1
Valid prediction for snap_scaffold_6-snap.3309-T1
Valid prediction for Augustus_model.g11149.t1
Valid prediction for snap_scaffold_6-snap.3311-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_16556-T1
Valid prediction for Augustus_model.g11153.t1
Valid prediction for GlimmerHMM_glimmerT_16557-T1
Valid prediction for GlimmerHMM_glimmerT_16549-T1
Valid prediction for Augustus_model.g11158.t1
Valid prediction for GlimmerHMM_glimmerT_16559-T1
Valid prediction for GeneMark_model.27675_t
Valid prediction for HiQ_model.g11163.t1
Valid prediction for GeneMark_model.27664_t
Valid prediction for HiQ_model.g11165.t1
Couldn't classify 127162, 127324
Couldn't classify 127789, 127841
Sorry, prediction CodingQuarry_transcript_55222-T1 fails validation.
(ATG)	 TC	125405-125434	GT	CTG
(GGT)	 AG	125545-125598	GT	TCG
(GGC)	 AG	125727-125780	GT	CTG
(GGA)	 AG	126096-126149	GT	AGG
(GGA)	 AG	126257-126310	GT	AGG
(GGC)	 AG	126506-126550	GT	GAG
(GGT)	 AG	126725-126823	GT	AGG
(GGT)	 AG	126933-127040	GT	GAG
(GGA)	 AG	127162-127324	TG	TGT
(GTG)	 TA	127789-127841	GT	CCG
(GGC)	 AG	128071-128178	GT	AGG
(GGA)	 AG	128334-128387	GT	CTG
(GGT)	 AG	128682-128735	GT	CTG
(GGC)	 AG	128904-129065	GT	CTG
(GGT)	 AG	129603-129710	GT	CTG
(GGA)	 AG	129845-129952	GT	AGG
(GGA)	 AG	130066-130119	GT	AGG
(GGA)	 AG	130276-130383	GT	CTG
(GGT)	 AG	130578-130631	GT	CTG
(GGA)	 AG	130857-130964	GT	CCG
(GGA)	 AG	131136-131189	GT	GAG
(GGA)	 AG	131335-131442	GT	CTG
(GGA)	 AG	131610-131892	GT	CGG
(GCG)	 AG	132047-132237	GT	AGG
(TTC)	 AG	132713-132955	GT	CGG
(TCG)	 AG	133177-133323	AA	AAA
-recovered CodingQuarry_transcript_55222-T1, initial, 125405, 125434
-recovered CodingQuarry_transcript_55222-T1, terminal, 133177, 133323
-recovered CodingQuarry_transcript_55222-T1, internal, 125545, 125598
-recovered CodingQuarry_transcript_55222-T1, internal, 125727, 125780
-recovered CodingQuarry_transcript_55222-T1, internal, 126096, 126149
-recovered CodingQuarry_transcript_55222-T1, internal, 126257, 126310
-recovered CodingQuarry_transcript_55222-T1, internal, 126506, 126550
-recovered CodingQuarry_transcript_55222-T1, internal, 126725, 126823
-recovered CodingQuarry_transcript_55222-T1, internal, 126933, 127040
-recovered CodingQuarry_transcript_55222-T1, internal, 128071, 128178
-recovered CodingQuarry_transcript_55222-T1, internal, 128334, 128387
-recovered CodingQuarry_transcript_55222-T1, internal, 128682, 128735
-recovered CodingQuarry_transcript_55222-T1, internal, 128904, 129065
-recovered CodingQuarry_transcript_55222-T1, internal, 129603, 129710
-recovered CodingQuarry_transcript_55222-T1, internal, 129845, 129952
-recovered CodingQuarry_transcript_55222-T1, internal, 130066, 130119
-recovered CodingQuarry_transcript_55222-T1, internal, 130276, 130383
-recovered CodingQuarry_transcript_55222-T1, internal, 130578, 130631
-recovered CodingQuarry_transcript_55222-T1, internal, 130857, 130964
-recovered CodingQuarry_transcript_55222-T1, internal, 131136, 131189
-recovered CodingQuarry_transcript_55222-T1, internal, 131335, 131442
-recovered CodingQuarry_transcript_55222-T1, internal, 131610, 131892
-recovered CodingQuarry_transcript_55222-T1, internal, 132047, 132237
-recovered CodingQuarry_transcript_55222-T1, internal, 132713, 132955
Valid prediction for snap_scaffold_6-snap.3299-T1
Valid prediction for GlimmerHMM_glimmerT_16553-T1
Valid prediction for snap_scaffold_6-snap.3332-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.3331-T1
Valid prediction for snap_scaffold_6-snap.3302-T1
Valid prediction for GeneMark_model.27684_t
Valid prediction for GeneMark_model.27666_t
Valid prediction for snap_scaffold_6-snap.3301-T1
Valid prediction for GlimmerHMM_glimmerT_16545-T1
Valid prediction for snap_scaffold_6-snap.3306-T1
Valid prediction for GeneMark_model.27672_t
Valid prediction for snap_scaffold_6-snap.3321-T1
Valid prediction for GeneMark_model.27692_t
Valid prediction for HiQ_model.g11155.t1
Valid prediction for Augustus_model.g11159.t1
Valid prediction for GeneMark_model.27686_t
Valid prediction for snap_scaffold_6-snap.3329-T1
Valid prediction for GeneMark_model.27671_t
Couldn't classify 118635, 118688
Sorry, prediction pasa_asmbl_47613.p1 fails validation.
(ATG)	 AC	113024-113105	GT	TCG
(GCG)	 AG	114431-114622	GT	TGG
(GGT)	 AG	115231-115256	GT	AGG
(GGA)	 AG	115462-115497	GT	GAG
(GGT)	 AG	116410-116502	GT	GAG
(AAC)	 AG	117441-117509	GT	TGG
(GGT)	 AG	117889-117933	GT	GCG
(GGC)	 AG	118635-118688	GT	CTG
-recovered pasa_asmbl_47613.p1, initial, 113024, 113105
-recovered pasa_asmbl_47613.p1, internal, 114431, 114622
-recovered pasa_asmbl_47613.p1, internal, 115231, 115256
-recovered pasa_asmbl_47613.p1, internal, 115462, 115497
-recovered pasa_asmbl_47613.p1, internal, 116410, 116502
-recovered pasa_asmbl_47613.p1, internal, 117441, 117509
-recovered pasa_asmbl_47613.p1, internal, 117889, 117933
-recovered pasa_asmbl_47613.p1, internal, 118635, 118688
Valid prediction for GlimmerHMM_glimmerT_16565-T1
Valid prediction for Augustus_model.g11157.t1
Valid prediction for GeneMark_model.27689_t
Valid prediction for GlimmerHMM_glimmerT_16552-T1
Valid prediction for Augustus_model.g11156.t1
Valid prediction for GeneMark_model.27678_t
Valid prediction for snap_scaffold_6-snap.3317-T1
Valid prediction for snap_scaffold_6-snap.3320-T1
Valid prediction for snap_scaffold_6-snap.3313-T1
Valid prediction for Augustus_model.g11164.t1
Valid prediction for GeneMark_model.27687_t
Valid prediction for pasa_asmbl_47611.p1
Valid prediction for GeneMark_model.27668_t
Valid prediction for snap_scaffold_6-snap.3327-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.3304-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.3324-T1
Valid prediction for GeneMark_model.27691_t
Valid prediction for snap_scaffold_6-snap.3303-T1
Valid prediction for CodingQuarry_transcript_55220-T1
Valid prediction for GeneMark_model.27676_t
Valid prediction for snap_scaffold_6-snap.3300-T1
Valid prediction for GeneMark_model.27667_t
Valid prediction for GlimmerHMM_glimmerT_16551-T1
Valid prediction for snap_scaffold_6-snap.3330-T1
Valid prediction for snap_scaffold_6-snap.3305-T1
Valid prediction for snap_scaffold_6-snap.3314-T1
Valid prediction for Augustus_model.g11151.t1
Valid prediction for GlimmerHMM_glimmerT_16563-T1
Valid prediction for snap_scaffold_6-snap.3325-T1
Valid prediction for snap_scaffold_6-snap.3333-T1
Valid prediction for GlimmerHMM_glimmerT_16555-T1
Valid prediction for snap_scaffold_6-snap.3316-T1
Valid prediction for GeneMark_model.27670_t
Valid prediction for GlimmerHMM_glimmerT_16547-T1
Valid prediction for snap_scaffold_6-snap.3328-T1
Valid prediction for GeneMark_model.27683_t
Valid prediction for GeneMark_model.27662_t
Valid prediction for GlimmerHMM_glimmerT_16554-T1
Valid prediction for GeneMark_model.27681_t
Valid prediction for GeneMark_model.27665_t
Valid prediction for snap_scaffold_6-snap.3323-T1
Valid prediction for GeneMark_model.27685_t
Valid prediction for Augustus_model.g11154.t1
Valid prediction for Augustus_model.g11161.t1
Valid prediction for Augustus_model.g11152.t1
Valid prediction for snap_scaffold_6-snap.3326-T1
Valid prediction for snap_scaffold_6-snap.3307-T1
Valid prediction for GeneMark_model.27688_t
Valid prediction for GlimmerHMM_glimmerT_16558-T1
Valid prediction for GeneMark_model.27669_t
Valid prediction for snap_scaffold_6-snap.3312-T1
Valid prediction for Augustus_model.g11150.t1
Valid prediction for CodingQuarry_transcript_55221-T1
Valid prediction for snap_scaffold_6-snap.3319-T1
Valid prediction for Augustus_model.g11160.t1
Valid prediction for snap_scaffold_6-snap.3308-T1
Valid prediction for GeneMark_model.27674_t
Valid prediction for GeneMark_model.27690_t
Valid prediction for snap_scaffold_6-snap.3298-T1
Valid prediction for Augustus_model.g11162.t1
Valid prediction for GeneMark_model.27679_t
Valid prediction for snap_scaffold_6-snap.3318-T1
Valid prediction for snap_scaffold_6-snap.3310-T1
Couldn't classify 121770, 121826
Sorry, prediction pasa_asmbl_49021.p1 fails validation.
(ATG)	 AG	116276-116393	GT	CGG
(GTT)	 AG	117052-117193	GT	TGG
(GTA)	 AG	118865-118936	GT	ACG
(GTT)	 AG	119020-119204	GT	CAG
(CGC)	 AG	120090-120179	GT	AGG
(ACG)	 AG	120377-120454	GT	CGG
(CCA)	 AG	120705-120781	GT	AGG
(AAC)	 AG	120899-120997	GT	AGG
(ATG)	 AG	121770-121826	AT	ACA
-recovered pasa_asmbl_49021.p1, initial, 116276, 116393
-recovered pasa_asmbl_49021.p1, internal, 116276, 116393
-recovered pasa_asmbl_49021.p1, internal, 117052, 117193
-recovered pasa_asmbl_49021.p1, internal, 118865, 118936
-recovered pasa_asmbl_49021.p1, internal, 119020, 119204
-recovered pasa_asmbl_49021.p1, internal, 120090, 120179
-recovered pasa_asmbl_49021.p1, internal, 120377, 120454
-recovered pasa_asmbl_49021.p1, internal, 120705, 120781
-recovered pasa_asmbl_49021.p1, internal, 120899, 120997
Valid prediction for GlimmerHMM_glimmerT_16546-T1
Valid prediction for GlimmerHMM_glimmerT_16562-T1
Valid prediction for GeneMark_model.27673_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 3982, rend_intergenic: 1894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10884, rend_intergenic: 6825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15925, rend_intergenic: 12037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29181, rend_intergenic: 26361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32088, rend_intergenic: 29725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42361, rend_intergenic: 36397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54112, rend_intergenic: 50539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59754, rend_intergenic: 58741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61551, rend_intergenic: 59878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62681, rend_intergenic: 61785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65901, rend_intergenic: 62803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68394, rend_intergenic: 65903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83511, rend_intergenic: 68767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92049, rend_intergenic: 84008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104670, rend_intergenic: 100332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133323, rend_intergenic: 124632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 134921
-exon list size: 720


building trellis

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72.4    
72.6    
72.7    
72.9    
73.0    
73.1    
73.3    
73.4    
73.5    
73.7    
73.8    
74.0    
74.1    
74.2    
74.4    
74.5    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.5    
75.6    
75.8    
75.9    
76.0    
76.2    
76.3    
76.5    
76.6    
76.7    
76.9    
77.0    
77.1    
77.3    
77.4    
77.6    
77.7    
77.8    
78.0    
78.1    
78.3    
78.4    
78.5    
78.7    
78.8    
78.9    
79.1    
79.2    
79.4    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.7    
80.9    
81.0    
81.2    
81.3    
81.4    
81.6    
81.7    
81.9    
82.0    
82.1    
82.3    
82.4    
82.5    
82.7    
82.8    
83.0    
83.1    
83.2    
83.4    
83.5    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.0    
85.2    
85.3    
85.5    
85.6    
85.7    
85.9    
86.0    
86.1    
86.3    
86.4    
86.6    
86.7    
86.8    
87.0    
87.1    
87.3    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.2    
88.4    
88.5    
88.6    
88.8    
88.9    
89.1    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.0    
90.2    
90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
96.0    
96.1    
96.3    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 3982, rend_intergenic: 1894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10884, rend_intergenic: 6825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15925, rend_intergenic: 12037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29181, rend_intergenic: 26361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32088, rend_intergenic: 29725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42361, rend_intergenic: 36397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54112, rend_intergenic: 50539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59754, rend_intergenic: 58741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61551, rend_intergenic: 59878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62681, rend_intergenic: 61785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65901, rend_intergenic: 62803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68394, rend_intergenic: 65903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83511, rend_intergenic: 68767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92049, rend_intergenic: 84008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104670, rend_intergenic: 100332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133323, rend_intergenic: 124632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support