-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_10306426-10473584

-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_15740-T1
Valid prediction for GeneMark_model.26457_t
Valid prediction for GeneMark_model.26468_t
Valid prediction for GeneMark_model.26458_t
Valid prediction for snap_scaffold_6-snap.2228-T1
Valid prediction for GeneMark_model.26466_t
Valid prediction for GeneMark_model.26454_t
Valid prediction for CodingQuarry_transcript_55057-T1
Valid prediction for GeneMark_model.26476_t
Valid prediction for GeneMark_model.26471_t
Valid prediction for snap_scaffold_6-snap.2238-T1
Valid prediction for snap_scaffold_6-snap.2249-T1
Valid prediction for GlimmerHMM_glimmerT_15747-T1
Valid prediction for GeneMark_model.26459_t
Valid prediction for GlimmerHMM_glimmerT_15752-T1
Valid prediction for GlimmerHMM_glimmerT_15734-T1
Valid prediction for GeneMark_model.26462_t
Valid prediction for HiQ_model.g10533.t1
Valid prediction for snap_scaffold_6-snap.2254-T1
Valid prediction for pasa_asmbl_47218.p1
Valid prediction for GlimmerHMM_glimmerT_15742-T1
Valid prediction for snap_scaffold_6-snap.2243-T1
Valid prediction for GeneMark_model.26478_t
Valid prediction for pasa_asmbl_47219.p1
Valid prediction for snap_scaffold_6-snap.2250-T1
Valid prediction for snap_scaffold_6-snap.2230-T1
Valid prediction for GlimmerHMM_glimmerT_15738-T1
Valid prediction for GeneMark_model.26480_t
Valid prediction for GeneMark_model.26473_t
Valid prediction for GeneMark_model.26474_t
Valid prediction for snap_scaffold_6-snap.2226-T1
Valid prediction for Augustus_model.g10541.t1
Valid prediction for CodingQuarry_transcript_55056-T1
Valid prediction for GlimmerHMM_glimmerT_15736-T1
Valid prediction for GeneMark_model.26460_t
Valid prediction for snap_scaffold_6-snap.2240-T1
Valid prediction for GeneMark_model.26450_t
Valid prediction for HiQ_model.g10535.t1
Valid prediction for snap_scaffold_6-snap.2234-T1
Valid prediction for GeneMark_model.26456_t
Valid prediction for snap_scaffold_6-snap.2233-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: -)Couldn't classify 76621, 76638
Sorry, prediction pasa_asmbl_48635.p1 fails validation.
(GTT)	 AC	76621-76638	GT	AGG
(GTC)	 AG	76736-76828	GT	AGG
(GTG)	 AG	76988-77215	CC	GAC
-recovered pasa_asmbl_48635.p1, terminal, 76988, 77215
-recovered pasa_asmbl_48635.p1, internal, 76736, 76828
Valid prediction for GlimmerHMM_glimmerT_15750-T1
Valid prediction for snap_scaffold_6-snap.2236-T1
Valid prediction for GeneMark_model.26472_t
Valid prediction for GeneMark_model.26452_t
Valid prediction for Augustus_model.g10539.t1
Valid prediction for GlimmerHMM_glimmerT_15733-T1
Valid prediction for GlimmerHMM_glimmerT_15744-T1
Valid prediction for GeneMark_model.26461_t
Valid prediction for GlimmerHMM_glimmerT_15748-T1
Valid prediction for CodingQuarry_transcript_55059-T1
Valid prediction for GlimmerHMM_glimmerT_15735-T1
Valid prediction for snap_scaffold_6-snap.2246-T1
Valid prediction for snap_scaffold_6-snap.2253-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_15751-T1
Valid prediction for pasa_asmbl_48627.p1
Valid prediction for Augustus_model.g10534.t1
Valid prediction for CodingQuarry_transcript_55058-T1
Valid prediction for snap_scaffold_6-snap.2227-T1
Valid prediction for GeneMark_model.26463_t
Valid prediction for snap_scaffold_6-snap.2251-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for HiQ_model.g10531.t1
Couldn't classify 138085, 138444
Sorry, prediction pasa_asmbl_48622.p2 fails validation.
(CTG)	 GC	138085-138444	AC	GAA
Valid prediction for GeneMark_model.26449_t
Valid prediction for GeneMark_model.26467_t
Valid prediction for GeneMark_model.26481_t
Valid prediction for Augustus_model.g10537.t1
Valid prediction for GeneMark_model.26451_t
Valid prediction for snap_scaffold_6-snap.2244-T1
Valid prediction for GeneMark_model.26453_t
Valid prediction for GlimmerHMM_glimmerT_15737-T1
Valid prediction for GeneMark_model.26477_t
Valid prediction for snap_scaffold_6-snap.2239-T1
Valid prediction for snap_scaffold_6-snap.2237-T1
Valid prediction for CodingQuarry_transcript_55054-T1
Valid prediction for snap_scaffold_6-snap.2235-T1
Valid prediction for GeneMark_model.26479_t
Couldn't classify 82606, 82696
Couldn't classify 84463, 84503
Sorry, prediction pasa_asmbl_48633.p1 fails validation.
(CTG)	 AG	82606-82696	GT	AGG
(GTC)	 AG	82799-82902	GT	AGG
(TTG)	 AG	83003-83083	GT	AGG
(GAT)	 AG	83338-83475	GT	AGG
(GAA)	 AG	83572-83653	GT	AGG
(GAG)	 AG	83728-83844	GT	TGG
(ATG)	 AG	84056-84325	GT	TGG
(GCC)	 AG	84463-84503	CC	AAC
add_exon() Sorry, pasa_asmbl_48633.p1 84056-84325-initial-1 is invalid.
-recovered pasa_asmbl_48633.p1, initial, 84056, 84325
add_exon() Sorry, pasa_asmbl_48633.p1 83572-83653-terminal-3 is invalid.
-recovered pasa_asmbl_48633.p1, terminal, 83572, 83653
-recovered pasa_asmbl_48633.p1, internal, 82606, 82696
-recovered pasa_asmbl_48633.p1, internal, 82799, 82902
-recovered pasa_asmbl_48633.p1, internal, 83003, 83083
-recovered pasa_asmbl_48633.p1, internal, 83338, 83475
-recovered pasa_asmbl_48633.p1, internal, 83572, 83653
-recovered pasa_asmbl_48633.p1, internal, 83728, 83844
-recovered pasa_asmbl_48633.p1, internal, 84056, 84325
Valid prediction for snap_scaffold_6-snap.2242-T1
Valid prediction for GeneMark_model.26455_t
Valid prediction for GlimmerHMM_glimmerT_15739-T1
Valid prediction for Augustus_model.g10529.t1
Valid prediction for GeneMark_model.26482_t
Couldn't classify 155439, 155628
Sorry, prediction pasa_asmbl_48620.p1 fails validation.
(TCT)	 GG	155439-155628	GT	GGG
(GTC)	 AG	157866-157994	GT	CGG
(ACA)	 AG	158269-158350	GT	TGG
(CTG)	 AG	158719-158856	GT	TGG
(TTT)	 AG	160799-160916	GT	AGG
(ATC)	 AG	161949-162044	GT	GAG
(GAG)	 AG	162148-162244	GT	AGG
(TGG)	 AG	163831-163882	GT	AGG
(GAG)	 AG	164103-164259	GG	AGG
-recovered pasa_asmbl_48620.p1, terminal, 164103, 164259
-recovered pasa_asmbl_48620.p1, internal, 157866, 157994
-recovered pasa_asmbl_48620.p1, internal, 158269, 158350
-recovered pasa_asmbl_48620.p1, internal, 158719, 158856
-recovered pasa_asmbl_48620.p1, internal, 160799, 160916
-recovered pasa_asmbl_48620.p1, internal, 161949, 162044
-recovered pasa_asmbl_48620.p1, internal, 162148, 162244
-recovered pasa_asmbl_48620.p1, internal, 163831, 163882
Valid prediction for snap_scaffold_6-snap.2241-T1
Valid prediction for snap_scaffold_6-snap.2229-T1
Valid prediction for GlimmerHMM_glimmerT_15743-T1
Valid prediction for GlimmerHMM_glimmerT_15746-T1
Valid prediction for GeneMark_model.26469_t
Valid prediction for GeneMark_model.26464_t
Valid prediction for Augustus_model.g10543.t1
Valid prediction for Augustus_model.g10530.t1
Valid prediction for Augustus_model.g10528.t1
Valid prediction for Augustus_model.g10542.t1
Valid prediction for snap_scaffold_6-snap.2252-T1
Valid prediction for snap_scaffold_6-snap.2232-T1
Valid prediction for HiQ_model.g10536.t1
Valid prediction for Augustus_model.g10538.t1
Valid prediction for CodingQuarry_transcript_55055-T1
Valid prediction for snap_scaffold_6-snap.2245-T1
Valid prediction for GlimmerHMM_glimmerT_15741-T1
Valid prediction for snap_scaffold_6-snap.2248-T1
Valid prediction for snap_scaffold_6-snap.2247-T1
Valid prediction for GlimmerHMM_glimmerT_15745-T1
Valid prediction for GlimmerHMM_glimmerT_15749-T1
Valid prediction for GeneMark_model.26470_t
Valid prediction for HiQ_model.g10532.t1
Valid prediction for GeneMark_model.26475_t
Valid prediction for snap_scaffold_6-snap.2231-T1
Valid prediction for Augustus_model.g10540.t1
Couldn't classify 72555, 72656
Sorry, prediction pasa_asmbl_48637.p1 fails validation.
(GTG)	 GG	72555-72656	GT	AGG
(GTT)	 AG	72789-72963	GT	CGG
(GAA)	 AG	73305-73435	GT	AGG
(GTG)	 AG	73679-73858	GC	GAG
-recovered pasa_asmbl_48637.p1, terminal, 73679, 73858
-recovered pasa_asmbl_48637.p1, internal, 72789, 72963
-recovered pasa_asmbl_48637.p1, internal, 73305, 73435
-recovered pasa_asmbl_48637.p1, internal, 73679, 73858

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7277, rend_intergenic: 1829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12689, rend_intergenic: 7576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45151, rend_intergenic: 36054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47736, rend_intergenic: 45987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100059, rend_intergenic: 98923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125049, rend_intergenic: 120818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 167159
-exon list size: 431


building trellis

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1.2    
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1.6    
1.8    
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3.9    
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6.9    
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8.8    
9.0    
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10.9    
11.1    
11.3    
11.5    
11.8    
12.0    
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12.5    
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13.2    
13.4    
13.6    
13.9    
14.1    
14.3    
14.5    
14.8    
15.0    
15.2    
15.5    
15.7    
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16.4    
16.6    
16.9    
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17.6    
17.8    
18.0    
18.2    
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18.7    
18.9    
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19.6    
19.9    
20.1    
20.3    
20.6    
20.8    
21.0    
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21.9    
22.2    
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22.6    
22.9    
23.1    
23.3    
23.6    
23.8    
24.0    
24.2    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.9    
26.1    
26.3    
26.6    
26.8    
27.0    
27.3    
27.5    
27.7    
27.9    
28.2    
28.4    
28.6    
28.9    
29.1    
29.3    
29.6    
29.8    
30.0    
30.3    
30.5    
30.7    
30.9    
31.2    
31.4    
31.6    
31.9    
32.1    
32.3    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.2    
34.4    
34.6    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.3    
36.5    
36.7    
37.0    
37.2    
37.4    
37.6    
37.9    
38.1    
38.3    
38.6    
38.8    
39.0    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.9    
41.1    
41.3    
41.6    
41.8    
42.0    
42.3    
42.5    
42.7    
43.0    
43.2    
43.4    
43.6    
43.9    
44.1    
44.3    
44.6    
44.8    
45.0    
45.3    
45.5    
45.7    
46.0    
46.2    
46.4    
46.7    
46.9    
47.1    
47.3    
47.6    
47.8    
48.0    
48.3    
48.5    
48.7    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.3    
51.5    
51.7    
52.0    
52.2    
52.4    
52.7    
52.9    
53.1    
53.3    
53.6    
53.8    
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54.3    
54.5    
54.7    
55.0    
55.2    
55.4    
55.7    
55.9    
56.1    
56.4    
56.6    
56.8    
57.0    
57.3    
57.5    
57.7    
58.0    
58.2    
58.4    
58.7    
58.9    
59.1    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
60.7    
61.0    
61.2    
61.4    
61.7    
61.9    
62.1    
62.4    
62.6    
62.8    
63.0    
63.3    
63.5    
63.7    
64.0    
64.2    
64.4    
64.7    
64.9    
65.1    
65.4    
65.6    
65.8    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.7    
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68.1    
68.4    
68.6    
68.8    
69.1    
69.3    
69.5    
69.7    
70.0    
70.2    
70.4    
70.7    
70.9    
71.1    
71.4    
71.6    
71.8    
72.1    
72.3    
72.5    
72.7    
73.0    
73.2    
73.4    
73.7    
73.9    
74.1    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.8    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.4    
77.6    
77.8    
78.1    
78.3    
78.5    
78.8    
79.0    
79.2    
79.4    
79.7    
79.9    
80.1    
80.4    
80.6    
80.8    
81.1    
81.3    
81.5    
81.8    
82.0    
82.2    
82.4    
82.7    
82.9    
83.1    
83.4    
83.6    
83.8    
84.1    
84.3    
84.5    
84.8    
85.0    
85.2    
85.5    
85.7    
85.9    
86.1    
86.4    
86.6    
86.8    
87.1    
87.3    
87.5    
87.8    
88.0    
88.2    
88.5    
88.7    
88.9    
89.1    
89.4    
89.6    
89.8    
90.1    
90.3    
90.5    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.8    
96.1    
96.3    
96.5    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 7277, rend_intergenic: 1829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12689, rend_intergenic: 7576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45151, rend_intergenic: 36054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47736, rend_intergenic: 45987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100059, rend_intergenic: 98923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125049, rend_intergenic: 120818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support