-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_11603868-11881884

-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_18-snap.2515-T1
Valid prediction for snap_scaffold_18-snap.2493-T1
Valid prediction for snap_scaffold_18-snap.2499-T1
Valid prediction for GlimmerHMM_glimmerT_44195-T1
Valid prediction for GeneMark_model.76683_t
Valid prediction for GeneMark_model.76688_t
Valid prediction for GeneMark_model.76670_t
Valid prediction for GeneMark_model.76716_t
Valid prediction for snap_scaffold_18-snap.2528-T1
Valid prediction for GeneMark_model.76673_t
Valid prediction for GeneMark_model.76678_t
Valid prediction for snap_scaffold_18-snap.2527-T1
Valid prediction for snap_scaffold_18-snap.2524-T1
Valid prediction for Augustus_model.g29589.t1
Valid prediction for GlimmerHMM_glimmerT_44197-T1
Valid prediction for GeneMark_model.76726_t
Valid prediction for GeneMark_model.76732_t
Valid prediction for snap_scaffold_18-snap.2518-T1
Valid prediction for GeneMark_model.76665_t
Valid prediction for GeneMark_model.76682_t
Valid prediction for GeneMark_model.76717_t
Valid prediction for snap_scaffold_18-snap.2490-T1
Valid prediction for GlimmerHMM_glimmerT_44205-T1
Valid prediction for GlimmerHMM_glimmerT_44204-T1
Valid prediction for snap_scaffold_18-snap.2496-T1
Valid prediction for GeneMark_model.76693_t
Valid prediction for GeneMark_model.76696_t
Valid prediction for Augustus_model.g29586.t1
Valid prediction for snap_scaffold_18-snap.2502-T1
Valid prediction for GeneMark_model.76684_t
Valid prediction for GeneMark_model.76679_t
Valid prediction for snap_scaffold_18-snap.2529-T1
Valid prediction for GlimmerHMM_glimmerT_44200-T1
Valid prediction for GeneMark_model.76692_t
Valid prediction for GlimmerHMM_glimmerT_44198-T1
Valid prediction for snap_scaffold_18-snap.2543-T1
Valid prediction for GeneMark_model.76735_t
Valid prediction for GeneMark_model.76738_t
Valid prediction for snap_scaffold_18-snap.2534-T1
Valid prediction for snap_scaffold_18-snap.2542-T1
Valid prediction for GeneMark_model.76663_t
Valid prediction for GeneMark_model.76720_t
Valid prediction for GeneMark_model.76701_t
Valid prediction for GlimmerHMM_glimmerT_44210-T1
Valid prediction for GlimmerHMM_glimmerT_44208-T1
Valid prediction for GeneMark_model.76710_t
Valid prediction for GeneMark_model.76687_t
Valid prediction for GeneMark_model.76708_t
Valid prediction for Augustus_model.g29584.t1
Valid prediction for snap_scaffold_18-snap.2537-T1
Valid prediction for GeneMark_model.76722_t
Valid prediction for Augustus_model.g29590.t1
Valid prediction for GlimmerHMM_glimmerT_44206-T1
Valid prediction for snap_scaffold_18-snap.2507-T1
Valid prediction for snap_scaffold_18-snap.2512-T1
Valid prediction for snap_scaffold_18-snap.2520-T1
Valid prediction for snap_scaffold_18-snap.2506-T1
Valid prediction for GeneMark_model.76677_t
Valid prediction for GeneMark_model.76689_t
Valid prediction for snap_scaffold_18-snap.2508-T1
Valid prediction for Augustus_model.g29587.t1
Valid prediction for GeneMark_model.76724_t
Valid prediction for GeneMark_model.76706_t
Valid prediction for snap_scaffold_18-snap.2504-T1
Valid prediction for GeneMark_model.76718_t
Couldn't classify 132930, 132962
Sorry, prediction GeneMark_model.76700_t fails validation.
(ATT)	 AG	132930-132962	GT	AGG
(GGG)	 AG	132984-132993	GT	GGG
(GGG)	 AG	133445-133459	GT	TGG
(GGG)	 AG	133488-133496	GT	GGG
(GGG)	 AG	133582-133592	GT	GTG
(AGA)	 AG	133623-133661	GT	GTG
(AGA)	 AG	135268-135384	GC	GAG
(AGA)	 AG	135415-135634	GT	AGG
(AGA)	 AG	135657-135733	GT	CTG
(AGG)	 AG	135937-136014	GC	AGG
(AGG)	 AG	136037-136088	AG	AAA
-recovered GeneMark_model.76700_t, terminal, 136037, 136088
-recovered GeneMark_model.76700_t, internal, 132930, 132962
-recovered GeneMark_model.76700_t, internal, 132984, 132993
-recovered GeneMark_model.76700_t, internal, 133445, 133459
-recovered GeneMark_model.76700_t, internal, 133488, 133496
-recovered GeneMark_model.76700_t, internal, 133582, 133592
-recovered GeneMark_model.76700_t, internal, 133623, 133661
-recovered GeneMark_model.76700_t, internal, 135268, 135384
-recovered GeneMark_model.76700_t, internal, 135415, 135634
-recovered GeneMark_model.76700_t, internal, 135657, 135733
-recovered GeneMark_model.76700_t, internal, 135937, 136014
Valid prediction for GeneMark_model.76667_t
Valid prediction for GeneMark_model.76675_t
Valid prediction for GlimmerHMM_glimmerT_44207-T1
Valid prediction for snap_scaffold_18-snap.2526-T1
Valid prediction for snap_scaffold_18-snap.2531-T1
Valid prediction for GeneMark_model.76729_t
Valid prediction for GlimmerHMM_glimmerT_44199-T1
Valid prediction for GeneMark_model.76690_t
Valid prediction for GeneMark_model.76714_t
Couldn't classify 158522, 158953
Sorry, prediction pasa_asmbl_20974.p1 fails validation.
(TTC)	 AG	158522-158953	AA	AGA
Valid prediction for Augustus_model.g29588.t1
Valid prediction for GeneMark_model.76703_t
Valid prediction for Augustus_model.g29591.t1
Valid prediction for snap_scaffold_18-snap.2521-T1
Valid prediction for GeneMark_model.76698_t
Valid prediction for GeneMark_model.76664_t
Valid prediction for snap_scaffold_18-snap.2498-T1
Valid prediction for snap_scaffold_18-snap.2495-T1
Valid prediction for snap_scaffold_18-snap.2513-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.76705_t
Valid prediction for snap_scaffold_18-snap.2511-T1
Valid prediction for snap_scaffold_18-snap.2523-T1
Valid prediction for GeneMark_model.76719_t
Valid prediction for GlimmerHMM_glimmerT_44202-T1
Valid prediction for GeneMark_model.76713_t
Valid prediction for GeneMark_model.76715_t
Valid prediction for GeneMark_model.76707_t
Valid prediction for snap_scaffold_18-snap.2544-T1
Valid prediction for GeneMark_model.76725_t
Valid prediction for snap_scaffold_18-snap.2500-T1
Valid prediction for GeneMark_model.76686_t
Valid prediction for GeneMark_model.76694_t
Valid prediction for snap_scaffold_18-snap.2516-T1
Valid prediction for snap_scaffold_18-snap.2491-T1
Valid prediction for GeneMark_model.76709_t
Valid prediction for GeneMark_model.76711_t
Valid prediction for snap_scaffold_18-snap.2492-T1
Valid prediction for Augustus_model.g29592.t1
Valid prediction for snap_scaffold_18-snap.2545-T1
Valid prediction for GeneMark_model.76704_t
Valid prediction for snap_scaffold_18-snap.2541-T1
Valid prediction for GeneMark_model.76695_t
Valid prediction for GlimmerHMM_glimmerT_44209-T1
Valid prediction for Augustus_model.g29583.t1
Couldn't classify 159040, 159045
Sorry, prediction GeneMark_model.76699_t fails validation.
(GAG)	 AG	159040-159045	GT	GAG
(TGC)	 AG	161008-161017	GT	CGG
(CTC)	 AG	161159-161295	GT	CTG
(GGG)	 AG	161445-161478	CC	GAC
-recovered GeneMark_model.76699_t, terminal, 161445, 161478
-recovered GeneMark_model.76699_t, internal, 159040, 159045
-recovered GeneMark_model.76699_t, internal, 161008, 161017
-recovered GeneMark_model.76699_t, internal, 161159, 161295
Valid prediction for snap_scaffold_18-snap.2539-T1
Valid prediction for Augustus_model.g29585.t1
Valid prediction for Augustus_model.g29582.t1
Valid prediction for snap_scaffold_18-snap.2503-T1
Valid prediction for Augustus_model.g29581.t1
Valid prediction for GeneMark_model.76681_t
Valid prediction for snap_scaffold_18-snap.2514-T1
Valid prediction for snap_scaffold_18-snap.2522-T1
Valid prediction for snap_scaffold_18-snap.2510-T1
Valid prediction for GeneMark_model.76674_t
Valid prediction for snap_scaffold_18-snap.2489-T1
Valid prediction for GeneMark_model.76669_t
Valid prediction for GeneMark_model.76680_t
Valid prediction for snap_scaffold_18-snap.2536-T1
Valid prediction for GeneMark_model.76662_t
Valid prediction for GeneMark_model.76691_t
Valid prediction for snap_scaffold_18-snap.2533-T1
Valid prediction for GeneMark_model.76685_t
Valid prediction for GeneMark_model.76737_t
Valid prediction for GeneMark_model.76668_t
Valid prediction for GlimmerHMM_glimmerT_44201-T1
Valid prediction for GeneMark_model.76702_t
Valid prediction for snap_scaffold_18-snap.2505-T1
Valid prediction for GlimmerHMM_glimmerT_44196-T1
Valid prediction for GeneMark_model.76666_t
Valid prediction for GeneMark_model.76697_t
Valid prediction for GlimmerHMM_glimmerT_44194-T1
Valid prediction for GeneMark_model.76672_t
Valid prediction for snap_scaffold_18-snap.2517-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.76676_t
Valid prediction for snap_scaffold_18-snap.2488-T1
Valid prediction for GlimmerHMM_glimmerT_44193-T1
Valid prediction for GeneMark_model.76734_t
Valid prediction for snap_scaffold_18-snap.2525-T1
Valid prediction for snap_scaffold_18-snap.2532-T1
Valid prediction for snap_scaffold_18-snap.2538-T1
Valid prediction for snap_scaffold_18-snap.2509-T1
Valid prediction for snap_scaffold_18-snap.2497-T1
Valid prediction for snap_scaffold_18-snap.2530-T1
Valid prediction for GeneMark_model.76733_t
Valid prediction for GeneMark_model.76728_t
Valid prediction for GeneMark_model.76723_t
Valid prediction for snap_scaffold_18-snap.2501-T1
Valid prediction for snap_scaffold_18-snap.2535-T1
Valid prediction for snap_scaffold_18-snap.2540-T1
Valid prediction for GeneMark_model.76730_t
Valid prediction for GeneMark_model.76671_t
Valid prediction for GlimmerHMM_glimmerT_44203-T1
Valid prediction for GeneMark_model.76731_t
Valid prediction for snap_scaffold_18-snap.2519-T1
Valid prediction for GeneMark_model.76727_t
Valid prediction for snap_scaffold_18-snap.2546-T1
Valid prediction for snap_scaffold_18-snap.2494-T1
Valid prediction for GeneMark_model.76736_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 68733, rend_intergenic: 68730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17892, rend_intergenic: 15662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24726, rend_intergenic: 21989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38618, rend_intergenic: 34192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45432, rend_intergenic: 42411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51178, rend_intergenic: 47225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62698, rend_intergenic: 59004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75545, rend_intergenic: 72027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81699, rend_intergenic: 75549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88703, rend_intergenic: 83447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136088, rend_intergenic: 101253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147781, rend_intergenic: 146662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154989, rend_intergenic: 147862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160425, rend_intergenic: 155283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170168, rend_intergenic: 164312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175475, rend_intergenic: 174137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181336, rend_intergenic: 179499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219140, rend_intergenic: 214402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221141, rend_intergenic: 220405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225453, rend_intergenic: 221857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233015, rend_intergenic: 228399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240414, rend_intergenic: 237914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 263586, rend_intergenic: 258799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 267811, rend_intergenic: 264054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 278017
-exon list size: 789


building trellis

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66.1    
66.2    
66.4    
66.5    
66.6    
66.8    
66.9    
67.0    
67.1    
67.3    
67.4    
67.5    
67.6    
67.8    
67.9    
68.0    
68.1    
68.3    
68.4    
68.5    
68.6    
68.8    
68.9    
69.0    
69.2    
69.3    
69.4    
69.5    
69.7    
69.8    
69.9    
70.0    
70.2    
70.3    
70.4    
70.5    
70.7    
70.8    
70.9    
71.0    
71.2    
71.3    
71.4    
71.6    
71.7    
71.8    
71.9    
72.1    
72.2    
72.3    
72.4    
72.6    
72.7    
72.8    
72.9    
73.1    
73.2    
73.3    
73.5    
73.6    
73.7    
73.8    
74.0    
74.1    
74.2    
74.3    
74.5    
74.6    
74.7    
74.8    
75.0    
75.1    
75.2    
75.3    
75.5    
75.6    
75.7    
75.9    
76.0    
76.1    
76.2    
76.4    
76.5    
76.6    
76.7    
76.9    
77.0    
77.1    
77.2    
77.4    
77.5    
77.6    
77.7    
77.9    
78.0    
78.1    
78.3    
78.4    
78.5    
78.6    
78.8    
78.9    
79.0    
79.1    
79.3    
79.4    
79.5    
79.6    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.5    
80.7    
80.8    
80.9    
81.0    
81.2    
81.3    
81.4    
81.5    
81.7    
81.8    
81.9    
82.0    
82.2    
82.3    
82.4    
82.6    
82.7    
82.8    
82.9    
83.1    
83.2    
83.3    
83.4    
83.6    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.5    
84.6    
84.7    
84.8    
85.0    
85.1    
85.2    
85.3    
85.5    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.3    
86.5    
86.6    
86.7    
86.9    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.7    
87.9    
88.0    
88.1    
88.2    
88.4    
88.5    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.6    
89.8    
89.9    
90.0    
90.1    
90.3    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.0    
92.2    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.6    
93.7    
93.8    
93.9    
94.1    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
94.9    
95.1    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.7    
98.9    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 42 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 68733, rend_intergenic: 68730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17892, rend_intergenic: 15662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24726, rend_intergenic: 21989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38618, rend_intergenic: 34192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45432, rend_intergenic: 42411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51178, rend_intergenic: 47225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62698, rend_intergenic: 59004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75545, rend_intergenic: 72027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81699, rend_intergenic: 75549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88703, rend_intergenic: 83447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136088, rend_intergenic: 101253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147781, rend_intergenic: 146662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154989, rend_intergenic: 147862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160425, rend_intergenic: 155283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170168, rend_intergenic: 164312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175475, rend_intergenic: 174137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181336, rend_intergenic: 179499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219140, rend_intergenic: 214402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221141, rend_intergenic: 220405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225453, rend_intergenic: 221857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233015, rend_intergenic: 228399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240414, rend_intergenic: 237914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 263586, rend_intergenic: 258799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 267811, rend_intergenic: 264054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 267359 - 278017
-exon list size: 37


building trellis

2.6    
5.1    
7.7    
10.3    
12.8    
15.4    
17.9    
20.5    
23.1    
25.6    
28.2    
30.8    
33.3    
35.9    
38.5    
41.0    
43.6    
46.2    
48.7    
51.3    
53.8    
56.4    
59.0    
61.5    
64.1    
66.7    
69.2    
71.8    
74.4    
76.9    
79.5    
82.1    
84.6    
87.2    
89.7    
92.3    
94.9    
97.4    
-found 4 predictions from path traversal

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