-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_10457292-10605297

-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.g26739.t1
Valid prediction for GeneMark_model.68174_t
Valid prediction for GlimmerHMM_glimmerT_39795-T1
Valid prediction for snap_scaffold_16-snap.1942-T1
Valid prediction for GeneMark_model.68188_t
Valid prediction for GeneMark_model.68166_t
Valid prediction for GeneMark_model.68193_t
Couldn't classify 7367, 7503
Sorry, prediction pasa_asmbl_17344.p1 fails validation.
(ATG)	 GC	5220-5418	GT	AGG
(GCC)	 AG	5554-5684	GT	AAG
(ATC)	 AG	5999-6158	GT	AGG
(GCA)	 AG	7367-7503	TG	GGT
-recovered pasa_asmbl_17344.p1, initial, 5220, 5418
-recovered pasa_asmbl_17344.p1, internal, 5554, 5684
-recovered pasa_asmbl_17344.p1, internal, 5999, 6158
Valid prediction for snap_scaffold_16-snap.1939-T1
Valid prediction for Augustus_model.g26736.t1
Valid prediction for GeneMark_model.68164_t
Couldn't classify 27754, 27966
Couldn't classify 30985, 31041
Sorry, prediction pasa_asmbl_17345.p1 fails validation.
(GTC)	 AG	27754-27966	GT	AGG
(ACG)	 AG	28157-28294	GT	AGG
(GTG)	 AG	29368-29496	GT	AGG
(ATG)	 AG	30985-31041	AG	ACA
-recovered pasa_asmbl_17345.p1, internal, 27754, 27966
-recovered pasa_asmbl_17345.p1, internal, 28157, 28294
-recovered pasa_asmbl_17345.p1, internal, 29368, 29496
Valid prediction for GeneMark_model.68156_t
Valid prediction for GlimmerHMM_glimmerT_39794-T1
Valid prediction for GeneMark_model.68167_t
Valid prediction for GeneMark_model.68182_t
Valid prediction for GeneMark_model.68177_t
Valid prediction for snap_scaffold_16-snap.1965-T1
Valid prediction for snap_scaffold_16-snap.1948-T1
Valid prediction for GlimmerHMM_glimmerT_39777-T1
Valid prediction for Augustus_model.g26738.t1
Valid prediction for GeneMark_model.68159_t
Valid prediction for GeneMark_model.68196_t
Valid prediction for GlimmerHMM_glimmerT_39784-T1
Valid prediction for GeneMark_model.68184_t
Valid prediction for HiQ_model.g26735.t1
Valid prediction for Augustus_model.g26740.t1
Valid prediction for snap_scaffold_16-snap.1941-T1
Valid prediction for GeneMark_model.68186_t
Couldn't classify 89240, 89259
Sorry, prediction pasa_asmbl_17349.p2 fails validation.
(GAT)	 TG	89240-89259	GT	GAG
(GAA)	 AG	89757-89856	GT	AGG
(TCT)	 AG	89998-90164	GT	GGG
(TAT)	 AG	90370-90507	GT	GGG
(GTA)	 AG	90907-91016	GT	TGG
(GCA)	 AG	91249-91457	GC	AGG
-recovered pasa_asmbl_17349.p2, terminal, 91249, 91457
-recovered pasa_asmbl_17349.p2, internal, 89757, 89856
-recovered pasa_asmbl_17349.p2, internal, 89998, 90164
-recovered pasa_asmbl_17349.p2, internal, 90370, 90507
-recovered pasa_asmbl_17349.p2, internal, 90907, 91016
-recovered pasa_asmbl_17349.p2, internal, 91249, 91457
Valid prediction for GlimmerHMM_glimmerT_39779-T1
Valid prediction for GeneMark_model.68169_t
Valid prediction for GlimmerHMM_glimmerT_39783-T1
Valid prediction for GeneMark_model.68191_t
Valid prediction for snap_scaffold_16-snap.1956-T1
Valid prediction for snap_scaffold_16-snap.1950-T1
Valid prediction for snap_scaffold_16-snap.1959-T1
Valid prediction for Augustus_model.g26745.t1
Valid prediction for Augustus_model.g26741.t1
Valid prediction for GlimmerHMM_glimmerT_39792-T1
Valid prediction for GeneMark_model.68162_t
Valid prediction for GeneMark_model.68190_t
Valid prediction for HiQ_model.g26748.t1
Valid prediction for snap_scaffold_16-snap.1937-T1
Valid prediction for GlimmerHMM_glimmerT_39789-T1
Valid prediction for GlimmerHMM_glimmerT_39797-T1
Valid prediction for GlimmerHMM_glimmerT_39772-T1
Couldn't classify 37531, 37878
Sorry, prediction pasa_asmbl_17347.p1 fails validation.
(CAG)	 CC	37531-37878	AG	TGA
Valid prediction for GeneMark_model.68173_t
Valid prediction for GlimmerHMM_glimmerT_39791-T1
Valid prediction for GeneMark_model.68183_t
Valid prediction for GlimmerHMM_glimmerT_39776-T1
Valid prediction for snap_scaffold_16-snap.1962-T1
Valid prediction for snap_scaffold_16-snap.1963-T1
Valid prediction for GeneMark_model.68180_t
Valid prediction for snap_scaffold_16-snap.1944-T1
Valid prediction for snap_scaffold_16-snap.1955-T1
Valid prediction for GlimmerHMM_glimmerT_39774-T1
Valid prediction for GlimmerHMM_glimmerT_39786-T1
Valid prediction for GlimmerHMM_glimmerT_39773-T1
Valid prediction for snap_scaffold_16-snap.1952-T1
Valid prediction for snap_scaffold_16-snap.1966-T1
Valid prediction for GlimmerHMM_glimmerT_39788-T1
Valid prediction for Augustus_model.g26751.t1
Valid prediction for Augustus_model.g26749.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.68192_t
Valid prediction for GeneMark_model.68157_t
Valid prediction for GeneMark_model.68172_t
Valid prediction for snap_scaffold_16-snap.1953-T1
Valid prediction for snap_scaffold_16-snap.1961-T1
Valid prediction for GeneMark_model.68179_t
Valid prediction for GeneMark_model.68161_t
Valid prediction for GlimmerHMM_glimmerT_39787-T1
Valid prediction for snap_scaffold_16-snap.1943-T1
Valid prediction for snap_scaffold_16-snap.1946-T1
Valid prediction for GeneMark_model.68195_t
Valid prediction for GeneMark_model.68181_t
Valid prediction for HiQ_model.g26752.t1
Valid prediction for GeneMark_model.68160_t
Valid prediction for GeneMark_model.68187_t
Valid prediction for GeneMark_model.68168_t
Valid prediction for GeneMark_model.68189_t
Valid prediction for snap_scaffold_16-snap.1945-T1
Valid prediction for snap_scaffold_16-snap.1964-T1
Valid prediction for GeneMark_model.68176_t
Valid prediction for GlimmerHMM_glimmerT_39790-T1
Valid prediction for GeneMark_model.68185_t
Valid prediction for pasa_asmbl_16494.p1
Valid prediction for snap_scaffold_16-snap.1938-T1
Valid prediction for snap_scaffold_16-snap.1951-T1
Valid prediction for Augustus_model.g26747.t1
Valid prediction for GlimmerHMM_glimmerT_39775-T1
Valid prediction for GlimmerHMM_glimmerT_39796-T1
Valid prediction for GlimmerHMM_glimmerT_39793-T1
Valid prediction for Augustus_model.g26753.t1
Valid prediction for snap_scaffold_16-snap.1954-T1
Valid prediction for GlimmerHMM_glimmerT_39782-T1
Valid prediction for GeneMark_model.68178_t
Valid prediction for snap_scaffold_16-snap.1960-T1
Valid prediction for snap_scaffold_16-snap.1957-T1
Valid prediction for snap_scaffold_16-snap.1940-T1
Valid prediction for Augustus_model.g26743.t1
Valid prediction for snap_scaffold_16-snap.1949-T1
Valid prediction for GeneMark_model.68170_t
Valid prediction for GlimmerHMM_glimmerT_39778-T1
Valid prediction for GlimmerHMM_glimmerT_39781-T1
Valid prediction for GeneMark_model.68163_t
Valid prediction for GeneMark_model.68171_t
Valid prediction for Augustus_model.g26746.t1
Valid prediction for Augustus_model.g26750.t1
Valid prediction for snap_scaffold_16-snap.1958-T1
Valid prediction for GeneMark_model.68197_t
Valid prediction for Augustus_model.g26744.t1
Valid prediction for Augustus_model.g26737.t1
Valid prediction for GeneMark_model.68194_t
Valid prediction for snap_scaffold_16-snap.1947-T1
Valid prediction for GeneMark_model.68175_t
Valid prediction for GlimmerHMM_glimmerT_39785-T1
Valid prediction for GeneMark_model.68165_t
Valid prediction for Augustus_model.g26742.t1
Valid prediction for GlimmerHMM_glimmerT_39780-T1
Valid prediction for GeneMark_model.68158_t
Valid prediction for CodingQuarry_transcript_20042-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 133131, rend_intergenic: 133128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18077, rend_intergenic: 15983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26066, rend_intergenic: 18206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41805, rend_intergenic: 29344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53344, rend_intergenic: 42394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53659, rend_intergenic: 53492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58916, rend_intergenic: 54886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63656, rend_intergenic: 61965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105323, rend_intergenic: 102115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117494, rend_intergenic: 115517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128257, rend_intergenic: 120993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132386, rend_intergenic: 128456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 148006
-exon list size: 536


building trellis

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2.8    
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3.2    
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3.9    
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6.9    
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8.0    
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8.7    
8.9    
9.1    
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10.6    
10.8    
11.0    
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12.8    
13.0    
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14.9    
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15.8    
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18.0    
18.2    
18.4    
18.6    
18.8    
19.0    
19.1    
19.3    
19.5    
19.7    
19.9    
20.1    
20.3    
20.4    
20.6    
20.8    
21.0    
21.2    
21.4    
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21.7    
21.9    
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22.9    
23.0    
23.2    
23.4    
23.6    
23.8    
24.0    
24.2    
24.3    
24.5    
24.7    
24.9    
25.1    
25.3    
25.5    
25.7    
25.8    
26.0    
26.2    
26.4    
26.6    
26.8    
27.0    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.6    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.1    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.1    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.8    
47.0    
47.2    
47.4    
47.6    
47.8    
48.0    
48.1    
48.3    
48.5    
48.7    
48.9    
49.1    
49.3    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.7    
50.9    
51.1    
51.3    
51.5    
51.7    
51.9    
52.0    
52.2    
52.4    
52.6    
52.8    
53.0    
53.2    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
55.9    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.2    
57.4    
57.6    
57.8    
58.0    
58.2    
58.4    
58.6    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
59.9    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.6    
62.8    
63.0    
63.2    
63.4    
63.6    
63.8    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.8    
68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.4    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.3    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.7    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 26 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 133131, rend_intergenic: 133128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18077, rend_intergenic: 15983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26066, rend_intergenic: 18206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41805, rend_intergenic: 29344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53344, rend_intergenic: 42394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53659, rend_intergenic: 53492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58916, rend_intergenic: 54886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63656, rend_intergenic: 61965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105323, rend_intergenic: 102115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117494, rend_intergenic: 115517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128257, rend_intergenic: 120993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132386, rend_intergenic: 128456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 133183 - 148006
-exon list size: 42


building trellis

2.3    
4.5    
6.8    
9.1    
11.4    
13.6    
15.9    
18.2    
20.5    
22.7    
25.0    
27.3    
29.5    
31.8    
34.1    
36.4    
38.6    
40.9    
43.2    
45.5    
47.7    
50.0    
52.3    
54.5    
56.8    
59.1    
61.4    
63.6    
65.9    
68.2    
70.5    
72.7    
75.0    
77.3    
79.5    
81.8    
84.1    
86.4    
88.6    
90.9    
93.2    
95.5    
97.7    
-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