-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_9204260-9530851

-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_6-snap.2061-T1
Valid prediction for GeneMark_model.26276_t
Valid prediction for GeneMark_model.26260_t
Valid prediction for snap_scaffold_6-snap.2038-T1
Valid prediction for snap_scaffold_6-snap.2041-T1
Valid prediction for GeneMark_model.26283_t
Valid prediction for GeneMark_model.26275_t
Valid prediction for GlimmerHMM_glimmerT_15600-T1
Valid prediction for GeneMark_model.26273_t
Valid prediction for GeneMark_model.26259_t
Valid prediction for GlimmerHMM_glimmerT_15615-T1
Valid prediction for GlimmerHMM_glimmerT_15614-T1
Valid prediction for snap_scaffold_6-snap.2040-T1
Couldn't classify 190454, 190897
Sorry, prediction pasa_asmbl_47164.p1 fails validation.
(ACA)	 CC	190454-190897	AG	AGA
Valid prediction for snap_scaffold_6-snap.2058-T1
Valid prediction for GeneMark_model.26258_t
Valid prediction for Augustus_model.g10414.t1
Valid prediction for snap_scaffold_6-snap.2042-T1
Valid prediction for Augustus_model.g10430.t1
Valid prediction for snap_scaffold_6-snap.2043-T1
Valid prediction for Augustus_model.g10434.t1
Valid prediction for Augustus_model.g10428.t1
Valid prediction for snap_scaffold_6-snap.2063-T1
Valid prediction for snap_scaffold_6-snap.2060-T1
Valid prediction for snap_scaffold_6-snap.2036-T1
Valid prediction for Augustus_model.g10417.t1
Valid prediction for snap_scaffold_6-snap.2051-T1
Valid prediction for GlimmerHMM_glimmerT_15622-T1
Valid prediction for GeneMark_model.26268_t
Valid prediction for GlimmerHMM_glimmerT_15612-T1
Valid prediction for GlimmerHMM_glimmerT_15602-T1
Valid prediction for Augustus_model.g10433.t1
Valid prediction for snap_scaffold_6-snap.2037-T1
Valid prediction for GeneMark_model.26265_t
Valid prediction for snap_scaffold_6-snap.2035-T1
Valid prediction for GeneMark_model.26279_t
Valid prediction for GlimmerHMM_glimmerT_15599-T1
Valid prediction for Augustus_model.g10416.t1
Valid prediction for GlimmerHMM_glimmerT_15603-T1
Valid prediction for GlimmerHMM_glimmerT_15613-T1
Valid prediction for GlimmerHMM_glimmerT_15606-T1
Valid prediction for GeneMark_model.26261_t
Valid prediction for snap_scaffold_6-snap.2064-T1
Valid prediction for Augustus_model.g10431.t1
Valid prediction for Augustus_model.g10418.t1
Valid prediction for GeneMark_model.26267_t
Valid prediction for Augustus_model.g10422.t1
Valid prediction for GlimmerHMM_glimmerT_15623-T1
Valid prediction for GlimmerHMM_glimmerT_15619-T1
Valid prediction for Augustus_model.g10413.t1
Valid prediction for GlimmerHMM_glimmerT_15608-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 snap_scaffold_6-snap.2048-T1
Valid prediction for GeneMark_model.26280_t
Valid prediction for snap_scaffold_6-snap.2044-T1
Valid prediction for pasa_asmbl_48553.p1
Valid prediction for snap_scaffold_6-snap.2062-T1
Couldn't classify 157275, 157349
Sorry, prediction pasa_asmbl_48557.p1 fails validation.
(ATG)	 GG	155631-155852	GT	AGG
(GAT)	 AG	157275-157349	AA	GGA
-recovered pasa_asmbl_48557.p1, initial, 155631, 155852
Valid prediction for GlimmerHMM_glimmerT_15620-T1
Valid prediction for Augustus_model.g10415.t1
Valid prediction for CodingQuarry_transcript_55021-T1
Valid prediction for snap_scaffold_6-snap.2045-T1
Valid prediction for GlimmerHMM_glimmerT_15611-T1
Valid prediction for snap_scaffold_6-snap.2055-T1
Valid prediction for GlimmerHMM_glimmerT_15607-T1
Valid prediction for snap_scaffold_6-snap.2039-T1
Valid prediction for GlimmerHMM_glimmerT_15621-T1
Valid prediction for Augustus_model.g10419.t1
Valid prediction for GlimmerHMM_glimmerT_15605-T1
Valid prediction for Augustus_model.g10421.t1
Valid prediction for snap_scaffold_6-snap.2046-T1
Couldn't classify 244158, 244236
Sorry, prediction pasa_asmbl_48548.p1 fails validation.
(CTC)	 AT	244158-244236	GT	AAG
(ATC)	 AG	244310-244546	GT	GGG
(GTT)	 AG	244656-244852	GT	AGG
(GCC)	 AG	244958-245215	GT	GGG
(GTA)	 AG	245408-245563	TG	GAT
-recovered pasa_asmbl_48548.p1, terminal, 245408, 245563
-recovered pasa_asmbl_48548.p1, internal, 244310, 244546
-recovered pasa_asmbl_48548.p1, internal, 244656, 244852
-recovered pasa_asmbl_48548.p1, internal, 244958, 245215
Valid prediction for GeneMark_model.26272_t
Valid prediction for GlimmerHMM_glimmerT_15609-T1
Valid prediction for GlimmerHMM_glimmerT_15616-T1
Valid prediction for HiQ_model.g10426.t1
Valid prediction for Augustus_model.g10423.t1
Valid prediction for snap_scaffold_6-snap.2057-T1
Valid prediction for Augustus_model.g10420.t1
Valid prediction for GeneMark_model.26257_t
Valid prediction for snap_scaffold_6-snap.2050-T1
Valid prediction for snap_scaffold_6-snap.2059-T1
Valid prediction for GeneMark_model.26269_t
Valid prediction for Augustus_model.g10429.t1
Valid prediction for GlimmerHMM_glimmerT_15610-T1
Valid prediction for GlimmerHMM_glimmerT_15617-T1
Valid prediction for GeneMark_model.26262_t
Valid prediction for GlimmerHMM_glimmerT_15604-T1
Valid prediction for snap_scaffold_6-snap.2065-T1
Valid prediction for Augustus_model.g10427.t1
Valid prediction for GeneMark_model.26271_t
Valid prediction for GlimmerHMM_glimmerT_15618-T1
Valid prediction for GeneMark_model.26277_t
Valid prediction for snap_scaffold_6-snap.2049-T1
Valid prediction for GeneMark_model.26281_t
Valid prediction for GeneMark_model.26270_t
Valid prediction for snap_scaffold_6-snap.2056-T1
Couldn't classify 241466, 241563
Couldn't classify 243806, 243940
Sorry, prediction pasa_asmbl_48549.p1 fails validation.
(TGT)	 AG	241466-241563	GT	AGG
(GTC)	 AG	242024-242141	GT	AGG
(ATA)	 AG	242279-242363	GT	AAG
(GAA)	 AG	242570-242736	GT	ATG
(ATA)	 AG	243612-243665	GT	AGG
(ACC)	 AG	243806-243940	AC	CCA
-recovered pasa_asmbl_48549.p1, internal, 241466, 241563
-recovered pasa_asmbl_48549.p1, internal, 242024, 242141
-recovered pasa_asmbl_48549.p1, internal, 242279, 242363
-recovered pasa_asmbl_48549.p1, internal, 242570, 242736
-recovered pasa_asmbl_48549.p1, internal, 243612, 243665
Valid prediction for GeneMark_model.26282_t
Valid prediction for GeneMark_model.26256_t
Valid prediction for Augustus_model.g10425.t1
Valid prediction for Augustus_model.g10424.t1
Valid prediction for snap_scaffold_6-snap.2054-T1
Valid prediction for snap_scaffold_6-snap.2053-T1
Valid prediction for GeneMark_model.26274_t
Valid prediction for snap_scaffold_6-snap.2047-T1
Valid prediction for GlimmerHMM_glimmerT_15601-T1
Valid prediction for snap_scaffold_6-snap.2052-T1
Valid prediction for Augustus_model.g10432.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 117030, rend_intergenic: 117027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 326592
-exon list size: 406


building trellis

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10.5    
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11.3    
11.5    
11.8    
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12.3    
12.5    
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13.5    
13.7    
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14.5    
14.7    
15.0    
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15.9    
16.2    
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17.2    
17.4    
17.6    
17.9    
18.1    
18.4    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.1    
20.3    
20.6    
20.8    
21.1    
21.3    
21.6    
21.8    
22.1    
22.3    
22.5    
22.8    
23.0    
23.3    
23.5    
23.8    
24.0    
24.3    
24.5    
24.8    
25.0    
25.2    
25.5    
25.7    
26.0    
26.2    
26.5    
26.7    
27.0    
27.2    
27.5    
27.7    
27.9    
28.2    
28.4    
28.7    
28.9    
29.2    
29.4    
29.7    
29.9    
30.1    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.4    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.6    
34.8    
35.0    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.8    
37.0    
37.3    
37.5    
37.7    
38.0    
38.2    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.7    
41.9    
42.2    
42.4    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.7    
52.9    
53.2    
53.4    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.1    
55.4    
55.6    
55.9    
56.1    
56.4    
56.6    
56.9    
57.1    
57.4    
57.6    
57.8    
58.1    
58.3    
58.6    
58.8    
59.1    
59.3    
59.6    
59.8    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.5    
61.8    
62.0    
62.3    
62.5    
62.7    
63.0    
63.2    
63.5    
63.7    
64.0    
64.2    
64.5    
64.7    
65.0    
65.2    
65.4    
65.7    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.6    
67.9    
68.1    
68.4    
68.6    
68.9    
69.1    
69.4    
69.6    
69.9    
70.1    
70.3    
70.6    
70.8    
71.1    
71.3    
71.6    
71.8    
72.1    
72.3    
72.5    
72.8    
73.0    
73.3    
73.5    
73.8    
74.0    
74.3    
74.5    
74.8    
75.0    
75.2    
75.5    
75.7    
76.0    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.7    
77.9    
78.2    
78.4    
78.7    
78.9    
79.2    
79.4    
79.7    
79.9    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.6    
81.9    
82.1    
82.4    
82.6    
82.8    
83.1    
83.3    
83.6    
83.8    
84.1    
84.3    
84.6    
84.8    
85.0    
85.3    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.0    
87.3    
87.5    
87.7    
88.0    
88.2    
88.5    
88.7    
89.0    
89.2    
89.5    
89.7    
90.0    
90.2    
90.4    
90.7    
90.9    
91.2    
91.4    
91.7    
91.9    
92.2    
92.4    
92.6    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.3    
95.6    
95.8    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 28 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 117030, rend_intergenic: 117027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 306398 - 326592
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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

-building DP trellis

-building trellis in range 306398 - 324330
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

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