-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_12597089-12773969

-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 Augustus_model.g22383.t1
Valid prediction for GeneMark_model.56857_t
Valid prediction for snap_scaffold_13-snap.2391-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.56826_t
Couldn't classify 128823, 128930
Couldn't classify 130320, 130352
Sorry, prediction pasa_asmbl_11336.p1 fails validation.
(ACG)	 GA	128823-128930	GT	AGG
(GCG)	 AG	129565-129711	GC	AGG
(GTC)	 AG	129915-130015	GT	AAG
(GGA)	 AG	130102-130168	GT	AGG
(AAA)	 AG	130320-130352	AG	AGA
-recovered pasa_asmbl_11336.p1, internal, 129565, 129711
-recovered pasa_asmbl_11336.p1, internal, 129915, 130015
-recovered pasa_asmbl_11336.p1, internal, 130102, 130168
Valid prediction for Augustus_model.g22384.t1
Valid prediction for GlimmerHMM_glimmerT_33301-T1
Valid prediction for GeneMark_model.56830_t
Valid prediction for GeneMark_model.56832_t
Valid prediction for GeneMark_model.56840_t
Valid prediction for GeneMark_model.56856_t
Valid prediction for GlimmerHMM_glimmerT_33288-T1
Valid prediction for snap_scaffold_13-snap.2366-T1
Valid prediction for snap_scaffold_13-snap.2377-T1
Couldn't classify 154343, 154454
Couldn't classify 156824, 157113
Sorry, prediction pasa_asmbl_11338.p2 fails validation.
(AGG)	 AC	154343-154454	GT	AGG
(GCT)	 AG	155128-155319	GT	AGG
(GTT)	 AG	155729-155886	GT	AGG
(GAG)	 AG	156371-156494	GT	CTG
(CTT)	 AG	156824-157113	TT	ACT
-recovered pasa_asmbl_11338.p2, internal, 155128, 155319
-recovered pasa_asmbl_11338.p2, internal, 155729, 155886
-recovered pasa_asmbl_11338.p2, internal, 156371, 156494
Valid prediction for GeneMark_model.56854_t
Valid prediction for GeneMark_model.56835_t
Valid prediction for GeneMark_model.56866_t
Valid prediction for GeneMark_model.56852_t
Valid prediction for GlimmerHMM_glimmerT_33294-T1
Valid prediction for snap_scaffold_13-snap.2385-T1
Valid prediction for snap_scaffold_13-snap.2367-T1
Valid prediction for Augustus_model.g22382.t1
Valid prediction for GeneMark_model.56827_t
Valid prediction for GeneMark_model.56865_t
Couldn't classify 157969, 158105
Sorry, prediction pasa_asmbl_11579.p1 fails validation.
(GTG)	 AG	157969-158105	GT	AAG
(GCT)	 AG	158671-158791	GT	AGG
(GCA)	 AG	159210-159692	GT	AGG
(TCC)	 AG	160369-160560	GT	TGG
(GTG)	 AG	161116-161229	AA	GAA
-recovered pasa_asmbl_11579.p1, terminal, 161116, 161229
-recovered pasa_asmbl_11579.p1, internal, 157969, 158105
-recovered pasa_asmbl_11579.p1, internal, 158671, 158791
-recovered pasa_asmbl_11579.p1, internal, 159210, 159692
-recovered pasa_asmbl_11579.p1, internal, 160369, 160560
Valid prediction for GeneMark_model.56834_t
Valid prediction for GeneMark_model.56851_t
Valid prediction for snap_scaffold_13-snap.2379-T1
Valid prediction for snap_scaffold_13-snap.2372-T1
Valid prediction for GeneMark_model.56861_t
Valid prediction for GeneMark_model.56863_t
Valid prediction for GlimmerHMM_glimmerT_33285-T1
Valid prediction for snap_scaffold_13-snap.2381-T1
Valid prediction for GlimmerHMM_glimmerT_33297-T1
Valid prediction for GeneMark_model.56859_t
Valid prediction for snap_scaffold_13-snap.2368-T1
Valid prediction for GeneMark_model.56846_t
Valid prediction for Augustus_model.g22386.t1
Valid prediction for snap_scaffold_13-snap.2371-T1
Valid prediction for GlimmerHMM_glimmerT_33300-T1
Valid prediction for snap_scaffold_13-snap.2395-T1
Valid prediction for GeneMark_model.56844_t
Valid prediction for Augustus_model.g22385.t1
Valid prediction for Augustus_model.g22381.t1
Valid prediction for GeneMark_model.56848_t
Valid prediction for GlimmerHMM_glimmerT_33281-T1
Valid prediction for GlimmerHMM_glimmerT_33283-T1
Valid prediction for GlimmerHMM_glimmerT_33287-T1
Valid prediction for GlimmerHMM_glimmerT_33289-T1
Valid prediction for snap_scaffold_13-snap.2388-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g22377.t1
Valid prediction for GlimmerHMM_glimmerT_33292-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 GlimmerHMM_glimmerT_33290-T1
Valid prediction for GlimmerHMM_glimmerT_33282-T1
Valid prediction for snap_scaffold_13-snap.2393-T1
Valid prediction for GeneMark_model.56836_t
Valid prediction for GeneMark_model.56862_t
Valid prediction for GlimmerHMM_glimmerT_33298-T1
Valid prediction for GeneMark_model.56867_t
Valid prediction for snap_scaffold_13-snap.2389-T1
Valid prediction for GeneMark_model.56864_t
Valid prediction for snap_scaffold_13-snap.2376-T1
Valid prediction for GeneMark_model.56860_t
Valid prediction for snap_scaffold_13-snap.2390-T1
Valid prediction for Augustus_model.g22379.t1
Valid prediction for snap_scaffold_13-snap.2380-T1
Valid prediction for snap_scaffold_13-snap.2374-T1
Valid prediction for snap_scaffold_13-snap.2375-T1
Valid prediction for Augustus_model.g22378.t1
Valid prediction for snap_scaffold_13-snap.2382-T1
Valid prediction for GeneMark_model.56838_t
Valid prediction for Augustus_model.g22380.t1
Valid prediction for snap_scaffold_13-snap.2370-T1
Valid prediction for GlimmerHMM_glimmerT_33293-T1
Valid prediction for GeneMark_model.56849_t
Valid prediction for snap_scaffold_13-snap.2386-T1
Valid prediction for GeneMark_model.56843_t
Valid prediction for GlimmerHMM_glimmerT_33296-T1
Valid prediction for GeneMark_model.56855_t
Valid prediction for GeneMark_model.56853_t
Valid prediction for GlimmerHMM_glimmerT_33302-T1
Valid prediction for snap_scaffold_13-snap.2373-T1
Valid prediction for GeneMark_model.56842_t
Valid prediction for snap_scaffold_13-snap.2384-T1
Valid prediction for GeneMark_model.56845_t
Valid prediction for snap_scaffold_13-snap.2383-T1
Valid prediction for GeneMark_model.56837_t
Valid prediction for snap_scaffold_13-snap.2394-T1
Valid prediction for GeneMark_model.56831_t
Valid prediction for GlimmerHMM_glimmerT_33295-T1
Valid prediction for GlimmerHMM_glimmerT_33291-T1
Valid prediction for snap_scaffold_13-snap.2392-T1
Valid prediction for snap_scaffold_13-snap.2378-T1
Valid prediction for snap_scaffold_13-snap.2387-T1
Valid prediction for GeneMark_model.56858_t
Valid prediction for GeneMark_model.56841_t
Valid prediction for GeneMark_model.56850_t
Valid prediction for GeneMark_model.56828_t
Valid prediction for GlimmerHMM_glimmerT_33299-T1
Valid prediction for GlimmerHMM_glimmerT_33286-T1
Valid prediction for GeneMark_model.56839_t
Valid prediction for GeneMark_model.56847_t
Valid prediction for GlimmerHMM_glimmerT_33284-T1
Valid prediction for snap_scaffold_13-snap.2369-T1
Valid prediction for GeneMark_model.56829_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 77181, rend_intergenic: 72415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99866, rend_intergenic: 98419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125946, rend_intergenic: 123305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144980, rend_intergenic: 132811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148199, rend_intergenic: 145760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161229, rend_intergenic: 151132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173171, rend_intergenic: 166021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176881
-exon list size: 514


building trellis

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25.8    
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27.9    
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29.3    
29.5    
29.7    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
32.9    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.1    
39.3    
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40.9    
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41.3    
41.5    
41.7    
41.9    
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42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
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45.2    
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46.5    
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46.9    
47.1    
47.3    
47.5    
47.7    
47.9    
48.1    
48.3    
48.4    
48.6    
48.8    
49.0    
49.2    
49.4    
49.6    
49.8    
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50.4    
50.6    
50.8    
51.0    
51.2    
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51.9    
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52.9    
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53.3    
53.5    
53.7    
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54.7    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.4    
56.6    
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58.5    
58.7    
58.9    
59.1    
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59.9    
60.1    
60.3    
60.5    
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60.9    
61.0    
61.2    
61.4    
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62.6    
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63.0    
63.2    
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63.6    
63.8    
64.0    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
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65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.1    
67.2    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.3    
70.5    
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70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 77181, rend_intergenic: 72415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99866, rend_intergenic: 98419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125946, rend_intergenic: 123305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144980, rend_intergenic: 132811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148199, rend_intergenic: 145760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161229, rend_intergenic: 151132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173171, rend_intergenic: 166021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support