-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_2648858-2867073

-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_10-snap.594-T1
Valid prediction for snap_scaffold_10-snap.578-T1
Valid prediction for snap_scaffold_10-snap.575-T1
Valid prediction for GeneMark_model.42416_t
Valid prediction for snap_scaffold_10-snap.598-T1
Valid prediction for snap_scaffold_10-snap.577-T1
Valid prediction for HiQ_model.g16637.t1
Valid prediction for GeneMark_model.42445_t
Valid prediction for HiQ_model.g16636.t1
Valid prediction for GlimmerHMM_glimmerT_24835-T1
Valid prediction for GlimmerHMM_glimmerT_24837-T1
Valid prediction for HiQ_model.g16650.t1
Valid prediction for GeneMark_model.42425_t
Valid prediction for GeneMark_model.42418_t
Valid prediction for snap_scaffold_10-snap.588-T1
Valid prediction for CodingQuarry_transcript_5302-T1
Valid prediction for snap_scaffold_10-snap.595-T1
Valid prediction for HiQ_model.g16644.t1
Couldn't classify 99907, 100024
Sorry, prediction pasa_asmbl_4285.p1 fails validation.
(CTG)	 CT	99907-100024	GT	AAG
(GGG)	 AG	101215-101490	GT	TGG
(TTC)	 AG	101701-102277	GT	AGG
(TAA)	 AG	102405-102590	GT	AGG
(TGG)	 AG	102766-102850	GT	AGG
(GTG)	 AG	102993-103151	GG	GAG
-recovered pasa_asmbl_4285.p1, terminal, 102993, 103151
-recovered pasa_asmbl_4285.p1, internal, 101215, 101490
-recovered pasa_asmbl_4285.p1, internal, 101701, 102277
-recovered pasa_asmbl_4285.p1, internal, 102405, 102590
-recovered pasa_asmbl_4285.p1, internal, 102766, 102850
Couldn't classify 70277, 70468
Sorry, prediction pasa_asmbl_4276.p1 fails validation.
(CAT)	 CA	70277-70468	GT	AGG
(ACT)	 AG	72633-72908	AG	AGA
-recovered pasa_asmbl_4276.p1, terminal, 72633, 72908
Valid prediction for Augustus_model.g16642.t1
Valid prediction for snap_scaffold_10-snap.568-T1
Valid prediction for snap_scaffold_10-snap.582-T1
Valid prediction for HiQ_model.g16635.t1
Valid prediction for GlimmerHMM_glimmerT_24831-T1
Valid prediction for snap_scaffold_10-snap.605-T1
Valid prediction for GeneMark_model.42437_t
Valid prediction for CodingQuarry_transcript_5295-T1
Valid prediction for GlimmerHMM_glimmerT_24836-T1
Valid prediction for GlimmerHMM_glimmerT_24851-T1
Valid prediction for snap_scaffold_10-snap.593-T1
Valid prediction for GeneMark_model.42430_t
Valid prediction for CodingQuarry_transcript_5294-T1
Valid prediction for snap_scaffold_10-snap.596-T1
Valid prediction for GlimmerHMM_glimmerT_24822-T1
Valid prediction for GlimmerHMM_glimmerT_24853-T1
Valid prediction for GlimmerHMM_glimmerT_24827-T1
Valid prediction for GeneMark_model.42448_t
Valid prediction for HiQ_model.g16643.t1
Valid prediction for snap_scaffold_10-snap.564-T1
Valid prediction for GeneMark_model.42433_t
Valid prediction for pasa_asmbl_4281.p1
Valid prediction for CodingQuarry_transcript_5296-T1
Valid prediction for GlimmerHMM_glimmerT_24838-T1
Valid prediction for CodingQuarry_transcript_5287-T1
Valid prediction for snap_scaffold_10-snap.576-T1
Valid prediction for GlimmerHMM_glimmerT_24847-T1
Valid prediction for CodingQuarry_transcript_5301-T1
Valid prediction for pasa_asmbl_4270.p1
Valid prediction for HiQ_model.g16652.t1
Valid prediction for snap_scaffold_10-snap.600-T1
Valid prediction for snap_scaffold_10-snap.580-T1
Valid prediction for Augustus_model.g16641.t1
Valid prediction for GlimmerHMM_glimmerT_24846-T1
Valid prediction for CodingQuarry_transcript_5298-T1
Valid prediction for snap_scaffold_10-snap.602-T1
Valid prediction for HiQ_model.g16646.t1
Valid prediction for GeneMark_model.42443_t
Valid prediction for pasa_asmbl_4273.p1
Valid prediction for GlimmerHMM_glimmerT_24844-T1
Valid prediction for GeneMark_model.42414_t
Valid prediction for GeneMark_model.42441_t
Valid prediction for GeneMark_model.42455_t
Valid prediction for GeneMark_model.42419_t
Valid prediction for CodingQuarry_transcript_5291-T1
Valid prediction for GeneMark_model.42457_t
Valid prediction for GeneMark_model.42423_t
Valid prediction for GeneMark_model.42426_t
Valid prediction for CodingQuarry_transcript_5304-T1
Valid prediction for snap_scaffold_10-snap.574-T1
Valid prediction for CodingQuarry_transcript_5292-T1
Valid prediction for pasa_asmbl_4288.p1
Valid prediction for snap_scaffold_10-snap.579-T1
Valid prediction for GlimmerHMM_glimmerT_24826-T1
Valid prediction for snap_scaffold_10-snap.566-T1
Valid prediction for snap_scaffold_10-snap.569-T1
Valid prediction for GlimmerHMM_glimmerT_24840-T1
Valid prediction for GeneMark_model.42458_t
Valid prediction for GeneMark_model.42432_t
Valid prediction for GeneMark_model.42452_t
Valid prediction for CodingQuarry_transcript_5293-T1
Valid prediction for pasa_asmbl_4284.p1
Valid prediction for GeneMark_model.42450_t
Couldn't classify 22815, 22857
Sorry, prediction pasa_asmbl_4269.p1 fails validation.
(GAG)	 TT	22815-22857	GT	AGG
(TAC)	 AG	23928-24149	GT	AGG
(GTG)	 AG	24237-24319	GT	AGG
(GGA)	 AG	24434-24655	GT	AGG
(GTG)	 AG	24818-25294	TG	AAT
-recovered pasa_asmbl_4269.p1, terminal, 24818, 25294
-recovered pasa_asmbl_4269.p1, internal, 23928, 24149
-recovered pasa_asmbl_4269.p1, internal, 24237, 24319
-recovered pasa_asmbl_4269.p1, internal, 24434, 24655
Valid prediction for snap_scaffold_10-snap.604-T1
Valid prediction for pasa_asmbl_4290.p1
Valid prediction for GeneMark_model.42427_t
Valid prediction for Augustus_model.g16647.t1
Valid prediction for GeneMark_model.42446_t
Valid prediction for pasa_asmbl_4266.p1
Valid prediction for GlimmerHMM_glimmerT_24824-T1
Valid prediction for GlimmerHMM_glimmerT_24833-T1
Valid prediction for CodingQuarry_transcript_5289-T1
Valid prediction for snap_scaffold_10-snap.603-T1
Valid prediction for snap_scaffold_10-snap.567-T1
Valid prediction for HiQ_model.g16633.t1
Valid prediction for snap_scaffold_10-snap.589-T1
Valid prediction for snap_scaffold_10-snap.583-T1
Valid prediction for HiQ_model.g16631.t1
Valid prediction for GeneMark_model.42439_t
Valid prediction for GlimmerHMM_glimmerT_24841-T1
Valid prediction for pasa_asmbl_4264.p1
Valid prediction for GeneMark_model.42429_t
Valid prediction for snap_scaffold_10-snap.599-T1
Valid prediction for snap_scaffold_10-snap.561-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 CodingQuarry_transcript_5300-T1
Valid prediction for GeneMark_model.42413_t
Valid prediction for Augustus_model.g16657.t1
Valid prediction for GlimmerHMM_glimmerT_24854-T1
Valid prediction for pasa_asmbl_3041.p1
Valid prediction for GlimmerHMM_glimmerT_24832-T1
Valid prediction for Augustus_model.g16649.t1
Valid prediction for GlimmerHMM_glimmerT_24823-T1
Valid prediction for GeneMark_model.42431_t
Valid prediction for HiQ_model.g16651.t1
Valid prediction for pasa_asmbl_3043.p1
Valid prediction for GeneMark_model.42442_t
Couldn't classify 180597, 180749
Sorry, prediction pasa_asmbl_3034.p2 fails validation.
(ATG)	 AT	179422-179445	GT	AGG
(CAG)	 AG	179604-179804	GT	AGG
(AAC)	 AG	180597-180749	AC	GGA
-recovered pasa_asmbl_3034.p2, initial, 179422, 179445
-recovered pasa_asmbl_3034.p2, internal, 179604, 179804
Valid prediction for CodingQuarry_transcript_5290-T1
Valid prediction for snap_scaffold_10-snap.592-T1
Valid prediction for GeneMark_model.42420_t
Valid prediction for snap_scaffold_10-snap.563-T1
Valid prediction for GlimmerHMM_glimmerT_24820-T1
Valid prediction for GlimmerHMM_glimmerT_24830-T1
Valid prediction for GeneMark_model.42438_t
Valid prediction for snap_scaffold_10-snap.572-T1
Valid prediction for GlimmerHMM_glimmerT_24821-T1
Valid prediction for CodingQuarry_transcript_5288-T1
Valid prediction for HiQ_model.g16634.t1
Valid prediction for GlimmerHMM_glimmerT_24852-T1
Valid prediction for snap_scaffold_10-snap.573-T1
Valid prediction for snap_scaffold_10-snap.606-T1
Valid prediction for pasa_asmbl_3046.p1
Valid prediction for CodingQuarry_transcript_5305-T1
Valid prediction for CodingQuarry_transcript_5299-T1
Valid prediction for GlimmerHMM_glimmerT_24834-T1
Valid prediction for snap_scaffold_10-snap.570-T1
Valid prediction for GeneMark_model.42417_t
Valid prediction for pasa_asmbl_3031.p1
Valid prediction for GeneMark_model.42459_t
Valid prediction for snap_scaffold_10-snap.581-T1
Valid prediction for snap_scaffold_10-snap.571-T1
Valid prediction for GlimmerHMM_glimmerT_24829-T1
Valid prediction for Augustus_model.g16630.t1
Valid prediction for GeneMark_model.42440_t
Valid prediction for GeneMark_model.42421_t
Valid prediction for Augustus_model.g16648.t1
Valid prediction for HiQ_model.g16632.t1
Valid prediction for GlimmerHMM_glimmerT_24850-T1
Valid prediction for GeneMark_model.42451_t
Valid prediction for snap_scaffold_10-snap.590-T1
Couldn't classify 194846, 194971
Sorry, prediction pasa_asmbl_3032.p1 fails validation.
(CTA)	 CC	194846-194971	GC	TGG
(ATA)	 AG	195129-195189	GT	AGG
(GAC)	 AG	195412-195539	GT	AGG
(GTA)	 AG	195630-195712	GT	GAG
(TCC)	 AG	195861-196052	GT	GGG
(GAT)	 AG	196263-196335	GT	AGG
(GTG)	 AG	196455-196617	GT	GGG
(CCA)	 AG	196779-196860	GT	TGG
(GTA)	 AG	197044-197110	AT	AAA
-recovered pasa_asmbl_3032.p1, terminal, 197044, 197110
-recovered pasa_asmbl_3032.p1, internal, 195129, 195189
-recovered pasa_asmbl_3032.p1, internal, 195412, 195539
-recovered pasa_asmbl_3032.p1, internal, 195630, 195712
-recovered pasa_asmbl_3032.p1, internal, 195861, 196052
-recovered pasa_asmbl_3032.p1, internal, 196263, 196335
-recovered pasa_asmbl_3032.p1, internal, 196455, 196617
-recovered pasa_asmbl_3032.p1, internal, 196779, 196860
Valid prediction for Augustus_model.g16656.t1
Valid prediction for Augustus_model.g16655.t1
Valid prediction for CodingQuarry_transcript_5297-T1
Valid prediction for GlimmerHMM_glimmerT_24848-T1
Valid prediction for GeneMark_model.42447_t
Valid prediction for snap_scaffold_10-snap.597-T1
Valid prediction for snap_scaffold_10-snap.586-T1
Valid prediction for GlimmerHMM_glimmerT_24828-T1
Valid prediction for snap_scaffold_10-snap.591-T1
Valid prediction for HiQ_model.g16638.t1
Valid prediction for CodingQuarry_transcript_5307-T1
Valid prediction for GlimmerHMM_glimmerT_24842-T1
Valid prediction for GlimmerHMM_glimmerT_24843-T1
Couldn't classify 60696, 60779
Couldn't classify 62974, 63012
Sorry, prediction pasa_asmbl_3053.p1 fails validation.
(GAG)	 AG	60696-60779	GT	GAG
(GGT)	 AG	61115-61168	GT	AGG
(GGA)	 AG	61323-61430	GT	TGG
(GGA)	 AG	61622-61675	GT	AGG
(GGT)	 AG	61776-61829	GT	AGG
(GGT)	 AG	62750-62806	GT	TCG
(GGT)	 AG	62974-63012	GA	GGG
-recovered pasa_asmbl_3053.p1, internal, 60696, 60779
-recovered pasa_asmbl_3053.p1, internal, 61115, 61168
-recovered pasa_asmbl_3053.p1, internal, 61323, 61430
-recovered pasa_asmbl_3053.p1, internal, 61622, 61675
-recovered pasa_asmbl_3053.p1, internal, 61776, 61829
-recovered pasa_asmbl_3053.p1, internal, 62750, 62806
Valid prediction for GeneMark_model.42436_t
Valid prediction for GeneMark_model.42444_t
Valid prediction for GeneMark_model.42415_t
Valid prediction for snap_scaffold_10-snap.585-T1
Valid prediction for GlimmerHMM_glimmerT_24825-T1
Couldn't classify 209507, 209579
Couldn't classify 211452, 211484
Sorry, prediction pasa_asmbl_4095.p1 fails validation.
(TTG)	 AT	209507-209579	GT	AGG
(GCT)	 AG	209941-210010	GT	TGG
(TCC)	 AG	210195-210308	GT	CGG
(GCC)	 AG	210563-210641	GT	AGG
(GAC)	 AG	211452-211484	CA	ACC
-recovered pasa_asmbl_4095.p1, internal, 209941, 210010
-recovered pasa_asmbl_4095.p1, internal, 210195, 210308
-recovered pasa_asmbl_4095.p1, internal, 210563, 210641
Valid prediction for HiQ_model.g16653.t1
Valid prediction for GeneMark_model.42435_t
Valid prediction for GeneMark_model.42449_t
Valid prediction for snap_scaffold_10-snap.565-T1
Valid prediction for GlimmerHMM_glimmerT_24845-T1
Valid prediction for GeneMark_model.42422_t
Valid prediction for snap_scaffold_10-snap.584-T1
Valid prediction for GeneMark_model.42424_t
Valid prediction for pasa_asmbl_3038.p1
Valid prediction for snap_scaffold_10-snap.607-T1
Couldn't classify 67495, 67548
Couldn't classify 68163, 68249
Sorry, prediction pasa_asmbl_3978.p1 fails validation.
(TGC)	 CC	67495-67548	GT	AGG
(TTG)	 AG	67813-68031	GT	GGG
(ATG)	 AG	68163-68249	CC	TGC
-recovered pasa_asmbl_3978.p1, internal, 67813, 68031
Valid prediction for GlimmerHMM_glimmerT_24849-T1
Couldn't classify 180888, 181006
Sorry, prediction pasa_asmbl_3033.p1 fails validation.
(TTG)	 CC	180888-181006	GT	AGG
(ACA)	 AG	181219-181326	GT	GGG
(GCG)	 AG	181878-182064	GA	GAG
-recovered pasa_asmbl_3033.p1, terminal, 181878, 182064
-recovered pasa_asmbl_3033.p1, internal, 181219, 181326
Valid prediction for snap_scaffold_10-snap.601-T1
Valid prediction for GeneMark_model.42454_t
Valid prediction for GeneMark_model.42453_t
Valid prediction for HiQ_model.g16654.t1
Valid prediction for snap_scaffold_10-snap.562-T1
Valid prediction for GeneMark_model.42434_t
Valid prediction for snap_scaffold_10-snap.587-T1
Valid prediction for snap_scaffold_10-snap.560-T1
Valid prediction for snap_scaffold_10-snap.559-T1
Valid prediction for Augustus_model.g16639.t1
Valid prediction for HiQ_model.g16645.t1
Valid prediction for CodingQuarry_transcript_5303-T1
Valid prediction for GeneMark_model.42456_t
Valid prediction for GlimmerHMM_glimmerT_24839-T1
Valid prediction for Augustus_model.g16640.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 164180, rend_intergenic: 149726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187766, rend_intergenic: 166080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203076, rend_intergenic: 188138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214367, rend_intergenic: 207672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 218216
-exon list size: 756


building trellis

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54.6    
54.7    
54.9    
55.0    
55.1    
55.3    
55.4    
55.5    
55.7    
55.8    
55.9    
56.1    
56.2    
56.3    
56.5    
56.6    
56.7    
56.9    
57.0    
57.1    
57.3    
57.4    
57.5    
57.7    
57.8    
57.9    
58.0    
58.2    
58.3    
58.4    
58.6    
58.7    
58.8    
59.0    
59.1    
59.2    
59.4    
59.5    
59.6    
59.8    
59.9    
60.0    
60.2    
60.3    
60.4    
60.6    
60.7    
60.8    
60.9    
61.1    
61.2    
61.3    
61.5    
61.6    
61.7    
61.9    
62.0    
62.1    
62.3    
62.4    
62.5    
62.7    
62.8    
62.9    
63.1    
63.2    
63.3    
63.5    
63.6    
63.7    
63.9    
64.0    
64.1    
64.2    
64.4    
64.5    
64.6    
64.8    
64.9    
65.0    
65.2    
65.3    
65.4    
65.6    
65.7    
65.8    
66.0    
66.1    
66.2    
66.4    
66.5    
66.6    
66.8    
66.9    
67.0    
67.2    
67.3    
67.4    
67.5    
67.7    
67.8    
67.9    
68.1    
68.2    
68.3    
68.5    
68.6    
68.7    
68.9    
69.0    
69.1    
69.3    
69.4    
69.5    
69.7    
69.8    
69.9    
70.1    
70.2    
70.3    
70.4    
70.6    
70.7    
70.8    
71.0    
71.1    
71.2    
71.4    
71.5    
71.6    
71.8    
71.9    
72.0    
72.2    
72.3    
72.4    
72.6    
72.7    
72.8    
73.0    
73.1    
73.2    
73.4    
73.5    
73.6    
73.7    
73.9    
74.0    
74.1    
74.3    
74.4    
74.5    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.5    
75.6    
75.7    
75.9    
76.0    
76.1    
76.3    
76.4    
76.5    
76.6    
76.8    
76.9    
77.0    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
78.0    
78.1    
78.2    
78.4    
78.5    
78.6    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.6    
79.7    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.7    
80.9    
81.0    
81.1    
81.3    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.3    
82.5    
82.6    
82.7    
82.8    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
85.0    
85.1    
85.2    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.1    
86.3    
86.4    
86.5    
86.7    
86.8    
86.9    
87.1    
87.2    
87.3    
87.5    
87.6    
87.7    
87.9    
88.0    
88.1    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.1    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.2    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 164180, rend_intergenic: 149726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187766, rend_intergenic: 166080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203076, rend_intergenic: 188138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214367, rend_intergenic: 207672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 207969 - 218216
-exon list size: 43


building trellis

2.2    
4.4    
6.7    
8.9    
11.1    
13.3    
15.6    
17.8    
20.0    
22.2    
24.4    
26.7    
28.9    
31.1    
33.3    
35.6    
37.8    
40.0    
42.2    
44.4    
46.7    
48.9    
51.1    
53.3    
55.6    
57.8    
60.0    
62.2    
64.4    
66.7    
68.9    
71.1    
73.3    
75.6    
77.8    
80.0    
82.2    
84.4    
86.7    
88.9    
91.1    
93.3    
95.6    
97.8    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support