-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_7329314-7462228

-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_27-snap.1774-T1
Valid prediction for GeneMark_model.102833_t
Valid prediction for GeneMark_model.102845_t
Valid prediction for CodingQuarry_transcript_41854-T1
Valid prediction for snap_scaffold_27-snap.1786-T1
Valid prediction for CodingQuarry_transcript_41857-T1
Valid prediction for GeneMark_model.102850_t
Valid prediction for snap_scaffold_27-snap.1759-T1
Valid prediction for GeneMark_model.102835_t
Valid prediction for GeneMark_model.102811_t
Valid prediction for GlimmerHMM_glimmerT_58986-T1
Couldn't classify 110648, 110727
Couldn't classify 113461, 113512
Sorry, prediction pasa_asmbl_36406.p1 fails validation.
(GTA)	 CC	110648-110727	GT	AGG
(AAT)	 AG	111635-111841	GT	AGG
(GAC)	 AG	112351-112489	GT	AGG
(TTC)	 AG	113138-113280	GT	GGG
(GCA)	 AG	113461-113512	GG	AAG
-recovered pasa_asmbl_36406.p1, internal, 111635, 111841
-recovered pasa_asmbl_36406.p1, internal, 112351, 112489
-recovered pasa_asmbl_36406.p1, internal, 113138, 113280
Valid prediction for Augustus_model.g39290.t1
Valid prediction for snap_scaffold_27-snap.1750-T1
Valid prediction for snap_scaffold_27-snap.1784-T1
Valid prediction for snap_scaffold_27-snap.1772-T1
Valid prediction for GlimmerHMM_glimmerT_58982-T1
Valid prediction for GeneMark_model.102847_t
Valid prediction for Augustus_model.g39300.t1
Valid prediction for GlimmerHMM_glimmerT_58985-T1
Valid prediction for snap_scaffold_27-snap.1757-T1
Valid prediction for snap_scaffold_27-snap.1787-T1
Couldn't classify 114870, 115187
Sorry, prediction pasa_asmbl_36407.p1 fails validation.
(GTG)	 AG	114870-115187	GT	AGG
(GTC)	 AG	115586-115912	GA	GAG
-recovered pasa_asmbl_36407.p1, terminal, 115586, 115912
-recovered pasa_asmbl_36407.p1, internal, 114870, 115187
Valid prediction for snap_scaffold_27-snap.1769-T1
Valid prediction for pasa_asmbl_36405.p1
Valid prediction for HiQ_model.g39301.t1
Valid prediction for GeneMark_model.102812_t
Valid prediction for snap_scaffold_27-snap.1762-T1
Valid prediction for snap_scaffold_27-snap.1756-T1
Valid prediction for snap_scaffold_27-snap.1768-T1
Valid prediction for GeneMark_model.102842_t
Valid prediction for snap_scaffold_27-snap.1760-T1
Valid prediction for snap_scaffold_27-snap.1751-T1
Valid prediction for snap_scaffold_27-snap.1782-T1
Valid prediction for snap_scaffold_27-snap.1778-T1
Valid prediction for GlimmerHMM_glimmerT_58974-T1
Valid prediction for GeneMark_model.102851_t
Valid prediction for GlimmerHMM_glimmerT_58983-T1
Valid prediction for GeneMark_model.102838_t
Valid prediction for HiQ_model.g39305.t1
Valid prediction for GeneMark_model.102819_t
Valid prediction for HiQ_model.g39294.t1
Valid prediction for pasa_asmbl_36411.p1
Valid prediction for CodingQuarry_transcript_41858-T1
Valid prediction for GlimmerHMM_glimmerT_58984-T1
Valid prediction for CodingQuarry_transcript_41856-T1
Valid prediction for GeneMark_model.102824_t
Valid prediction for GeneMark_model.102853_t
Valid prediction for GlimmerHMM_glimmerT_58987-T1
Valid prediction for snap_scaffold_27-snap.1765-T1
Valid prediction for GeneMark_model.102829_t
Valid prediction for GeneMark_model.102817_t
Valid prediction for GeneMark_model.102813_t
Valid prediction for snap_scaffold_27-snap.1790-T1
Valid prediction for GeneMark_model.102809_t
Valid prediction for GeneMark_model.102828_t
Valid prediction for snap_scaffold_27-snap.1754-T1
Valid prediction for GlimmerHMM_glimmerT_58972-T1
Couldn't classify 124008, 125159
Sorry, prediction pasa_asmbl_36410.p1 fails validation.
(CTG)	 TC	124008-125159	AG	AAA
Valid prediction for Augustus_model.g39304.t1
Valid prediction for GlimmerHMM_glimmerT_58976-T1
Valid prediction for Augustus_model.g39289.t1
Valid prediction for snap_scaffold_27-snap.1780-T1
Valid prediction for GlimmerHMM_glimmerT_58988-T1
Valid prediction for pasa_asmbl_36404.p1
Valid prediction for snap_scaffold_27-snap.1773-T1
Valid prediction for Augustus_model.g39302.t1
Valid prediction for GeneMark_model.102831_t
Valid prediction for GeneMark_model.102815_t
Valid prediction for GlimmerHMM_glimmerT_58968-T1
Valid prediction for snap_scaffold_27-snap.1767-T1
Valid prediction for GeneMark_model.102822_t
Valid prediction for GlimmerHMM_glimmerT_58969-T1
Valid prediction for snap_scaffold_27-snap.1789-T1
Valid prediction for pasa_asmbl_36408.p1
Valid prediction for HiQ_model.g39303.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 GeneMark_model.102814_t
Valid prediction for GlimmerHMM_glimmerT_58978-T1
Valid prediction for GeneMark_model.102818_t
Valid prediction for GeneMark_model.102834_t
Valid prediction for snap_scaffold_27-snap.1775-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.1779-T1
Valid prediction for pasa_asmbl_37060.p1
Couldn't classify 48752, 48809
Sorry, prediction pasa_asmbl_37062.p1 fails validation.
(GAT)	 GA	48752-48809	GT	AGG
(GCT)	 AG	49351-49664	GA	GAG
-recovered pasa_asmbl_37062.p1, terminal, 49351, 49664
Valid prediction for GlimmerHMM_glimmerT_58966-T1
Valid prediction for snap_scaffold_27-snap.1766-T1
Valid prediction for GeneMark_model.102841_t
Couldn't classify 40448, 40528
Couldn't classify 41313, 41635
Sorry, prediction pasa_asmbl_37064.p1 fails validation.
(CAA)	 AC	40448-40528	GT	GGG
(GTG)	 AG	40705-40909	GT	GGG
(GCT)	 AG	41313-41635	GC	AGG
-recovered pasa_asmbl_37064.p1, internal, 40705, 40909
-recovered pasa_asmbl_37064.p1, internal, 41313, 41635
Valid prediction for snap_scaffold_27-snap.1752-T1
Valid prediction for snap_scaffold_27-snap.1770-T1
Valid prediction for GeneMark_model.102839_t
Couldn't classify 58609, 58638
Sorry, prediction pasa_asmbl_37059.p1 fails validation.
(GTA)	 CG	58609-58638	GT	AGG
(AAC)	 AG	59297-59406	GT	TCG
(AGA)	 AG	59527-59626	GT	CGG
(CGA)	 AG	59971-60147	GT	AGG
(CTC)	 AG	60888-61029	GT	CGG
(TAA)	 AG	61425-61570	GT	ACG
(GCG)	 AG	61839-61919	GT	CGG
(CTG)	 AG	62020-62158	GT	AGG
(AGC)	 AG	62525-62655	GT	CGG
(GAC)	 AG	62766-62873	GT	AGG
(GCT)	 AG	63009-63073	GT	GGG
(TGT)	 AG	63354-63486	GT	TTG
(CTG)	 AG	63787-63933	GT	GAG
-recovered pasa_asmbl_37059.p1, terminal, 63787, 63933
-recovered pasa_asmbl_37059.p1, internal, 59297, 59406
-recovered pasa_asmbl_37059.p1, internal, 59527, 59626
-recovered pasa_asmbl_37059.p1, internal, 59971, 60147
-recovered pasa_asmbl_37059.p1, internal, 60888, 61029
-recovered pasa_asmbl_37059.p1, internal, 61425, 61570
-recovered pasa_asmbl_37059.p1, internal, 61839, 61919
-recovered pasa_asmbl_37059.p1, internal, 62020, 62158
-recovered pasa_asmbl_37059.p1, internal, 62525, 62655
-recovered pasa_asmbl_37059.p1, internal, 62766, 62873
-recovered pasa_asmbl_37059.p1, internal, 63009, 63073
-recovered pasa_asmbl_37059.p1, internal, 63354, 63486
-recovered pasa_asmbl_37059.p1, internal, 63787, 63933
Valid prediction for GlimmerHMM_glimmerT_58980-T1
Valid prediction for GeneMark_model.102816_t
Valid prediction for snap_scaffold_27-snap.1783-T1
Valid prediction for Augustus_model.g39295.t1
Valid prediction for GlimmerHMM_glimmerT_58977-T1
Valid prediction for GlimmerHMM_glimmerT_58973-T1
Valid prediction for snap_scaffold_27-snap.1788-T1
Valid prediction for snap_scaffold_27-snap.1758-T1
Valid prediction for GeneMark_model.102823_t
Valid prediction for GlimmerHMM_glimmerT_58981-T1
Valid prediction for GlimmerHMM_glimmerT_58967-T1
Valid prediction for GeneMark_model.102836_t
Valid prediction for snap_scaffold_27-snap.1781-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.1763-T1
Valid prediction for GeneMark_model.102844_t
Valid prediction for snap_scaffold_27-snap.1755-T1
Valid prediction for Augustus_model.g39287.t1
Valid prediction for GeneMark_model.102821_t
Valid prediction for GeneMark_model.102825_t
Valid prediction for snap_scaffold_27-snap.1776-T1
Valid prediction for GeneMark_model.102843_t
Valid prediction for GeneMark_model.102848_t
Valid prediction for snap_scaffold_27-snap.1777-T1
Valid prediction for GlimmerHMM_glimmerT_58965-T1
Valid prediction for GeneMark_model.102854_t
Valid prediction for snap_scaffold_27-snap.1761-T1
Valid prediction for HiQ_model.g39293.t1
Valid prediction for CodingQuarry_transcript_41855-T1
Valid prediction for GeneMark_model.102830_t
Valid prediction for GlimmerHMM_glimmerT_58971-T1
Valid prediction for snap_scaffold_27-snap.1771-T1
Valid prediction for GeneMark_model.102849_t
Valid prediction for snap_scaffold_27-snap.1764-T1
Valid prediction for snap_scaffold_27-snap.1753-T1
Valid prediction for GeneMark_model.102810_t
Valid prediction for Augustus_model.g39288.t1
Valid prediction for GeneMark_model.102827_t
Valid prediction for GeneMark_model.102846_t
Valid prediction for HiQ_model.g39296.t1
Valid prediction for GlimmerHMM_glimmerT_58979-T1
Valid prediction for Augustus_model.g39291.t1
Valid prediction for GeneMark_model.102837_t
Valid prediction for snap_scaffold_27-snap.1785-T1
Valid prediction for GlimmerHMM_glimmerT_58975-T1
Valid prediction for snap_scaffold_27-snap.1791-T1
Valid prediction for GlimmerHMM_glimmerT_58970-T1
Valid prediction for Augustus_model.g39299.t1
Valid prediction for Augustus_model.g39297.t1
Valid prediction for Augustus_model.g39298.t1
Valid prediction for Augustus_model.g39292.t1
Valid prediction for GeneMark_model.102832_t
Valid prediction for GlimmerHMM_glimmerT_58964-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14341, rend_intergenic: 11583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16781, rend_intergenic: 15945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19222, rend_intergenic: 17786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26263, rend_intergenic: 25359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32259, rend_intergenic: 26833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33165, rend_intergenic: 32506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36841, rend_intergenic: 35638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44694, rend_intergenic: 37855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49715, rend_intergenic: 44758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53601, rend_intergenic: 50025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62586, rend_intergenic: 54229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73412, rend_intergenic: 67211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89675, rend_intergenic: 86503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96940, rend_intergenic: 92371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100292, rend_intergenic: 98176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105461, rend_intergenic: 100329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115509, rend_intergenic: 111636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120580, rend_intergenic: 119468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129319, rend_intergenic: 126573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 132915
-exon list size: 718


building trellis

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75.3    
75.4    
75.6    
75.7    
75.8    
76.0    
76.1    
76.2    
76.4    
76.5    
76.7    
76.8    
76.9    
77.1    
77.2    
77.4    
77.5    
77.6    
77.8    
77.9    
78.1    
78.2    
78.3    
78.5    
78.6    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.6    
79.7    
79.9    
80.0    
80.1    
80.3    
80.4    
80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.4    
82.5    
82.6    
82.8    
82.9    
83.1    
83.2    
83.3    
83.5    
83.6    
83.8    
83.9    
84.0    
84.2    
84.3    
84.4    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.6    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.6    
89.7    
89.9    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
96.9    
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 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 14341, rend_intergenic: 11583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16781, rend_intergenic: 15945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19222, rend_intergenic: 17786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26263, rend_intergenic: 25359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32259, rend_intergenic: 26833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33165, rend_intergenic: 32506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36841, rend_intergenic: 35638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44694, rend_intergenic: 37855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49715, rend_intergenic: 44758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53601, rend_intergenic: 50025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62586, rend_intergenic: 54229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73412, rend_intergenic: 67211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89675, rend_intergenic: 86503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96940, rend_intergenic: 92371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100292, rend_intergenic: 98176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105461, rend_intergenic: 100329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115509, rend_intergenic: 111636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120580, rend_intergenic: 119468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129319, rend_intergenic: 126573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support