-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_10252560-10466374

-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.g26728.t1
Valid prediction for CodingQuarry_transcript_20041-T1
Valid prediction for Augustus_model.g26725.t1
Valid prediction for GeneMark_model.68154_t
Valid prediction for GeneMark_model.68127_t
Valid prediction for snap_scaffold_16-snap.1918-T1
Valid prediction for GlimmerHMM_glimmerT_39751-T1
Couldn't classify 188328, 188942
Sorry, prediction pasa_asmbl_17331.p1 fails validation.
(GGC)	 CC	188328-188942	GT	CCG
(GGT)	 AG	189034-189114	TC	GAT
-recovered pasa_asmbl_17331.p1, terminal, 189034, 189114
Valid prediction for GlimmerHMM_glimmerT_39765-T1
Valid prediction for snap_scaffold_16-snap.1905-T1
Valid prediction for Augustus_model.g26720.t1
Valid prediction for snap_scaffold_16-snap.1932-T1
Valid prediction for snap_scaffold_16-snap.1901-T1
Valid prediction for snap_scaffold_16-snap.1937-T1
Valid prediction for GeneMark_model.68121_t
Valid prediction for snap_scaffold_16-snap.1923-T1
Valid prediction for pasa_asmbl_17338.p1
Valid prediction for GlimmerHMM_glimmerT_39750-T1
Valid prediction for GlimmerHMM_glimmerT_39761-T1
Valid prediction for GeneMark_model.68153_t
Valid prediction for HiQ_model.g26733.t1
Valid prediction for GlimmerHMM_glimmerT_39749-T1
Valid prediction for GeneMark_model.68130_t
Valid prediction for GeneMark_model.68133_t
Valid prediction for GeneMark_model.68135_t
Valid prediction for snap_scaffold_16-snap.1907-T1
Valid prediction for snap_scaffold_16-snap.1911-T1
Valid prediction for GeneMark_model.68129_t
Valid prediction for GeneMark_model.68145_t
Valid prediction for GeneMark_model.68140_t
Valid prediction for GeneMark_model.68143_t
Valid prediction for snap_scaffold_16-snap.1924-T1
Valid prediction for GeneMark_model.68148_t
Valid prediction for GlimmerHMM_glimmerT_39771-T1
Valid prediction for GlimmerHMM_glimmerT_39759-T1
Valid prediction for GlimmerHMM_glimmerT_39746-T1
Valid prediction for GeneMark_model.68125_t
Valid prediction for Augustus_model.g26730.t1
Valid prediction for GlimmerHMM_glimmerT_39754-T1
Valid prediction for GeneMark_model.68131_t
Valid prediction for GeneMark_model.68151_t
Couldn't classify 212099, 212235
Sorry, prediction pasa_asmbl_17344.p1 fails validation.
(ATG)	 GC	209952-210150	GT	AGG
(GCC)	 AG	210286-210416	GT	AAG
(ATC)	 AG	210731-210890	GT	AGG
(GCA)	 AG	212099-212235	TG	GGT
-recovered pasa_asmbl_17344.p1, initial, 209952, 210150
-recovered pasa_asmbl_17344.p1, internal, 210286, 210416
-recovered pasa_asmbl_17344.p1, internal, 210731, 210890
Valid prediction for snap_scaffold_16-snap.1931-T1
Valid prediction for GeneMark_model.68118_t
Valid prediction for snap_scaffold_16-snap.1936-T1
Valid prediction for snap_scaffold_16-snap.1935-T1
Valid prediction for Augustus_model.g26717.t1
Valid prediction for snap_scaffold_16-snap.1900-T1
Valid prediction for GlimmerHMM_glimmerT_39752-T1
Valid prediction for Augustus_model.g26732.t1
Couldn't classify 54118, 54393
Couldn't classify 54625, 54669
Sorry, prediction pasa_asmbl_17586.p1 fails validation.
(GAC)	 AC	54118-54393	GT	TGG
(CTC)	 AG	54625-54669	CC	CCC
Valid prediction for snap_scaffold_16-snap.1921-T1
Valid prediction for GlimmerHMM_glimmerT_39770-T1
Valid prediction for snap_scaffold_16-snap.1912-T1
Valid prediction for snap_scaffold_16-snap.1897-T1
Valid prediction for snap_scaffold_16-snap.1896-T1
Valid prediction for GlimmerHMM_glimmerT_39772-T1
Valid prediction for snap_scaffold_16-snap.1927-T1
Valid prediction for snap_scaffold_16-snap.1909-T1
Valid prediction for GeneMark_model.68138_t
Valid prediction for Augustus_model.g26734.t1
Valid prediction for GeneMark_model.68123_t
Valid prediction for GlimmerHMM_glimmerT_39755-T1
Valid prediction for snap_scaffold_16-snap.1934-T1
Couldn't classify 167847, 168616
Sorry, prediction pasa_asmbl_17328.p2 fails validation.
(ATG)	 GA	165182-165560	GT	AGG
(GTA)	 AG	167847-168616	TA	GGT
-recovered pasa_asmbl_17328.p2, initial, 165182, 165560
Valid prediction for GlimmerHMM_glimmerT_39768-T1
Valid prediction for GlimmerHMM_glimmerT_39769-T1
Valid prediction for snap_scaffold_16-snap.1929-T1
Valid prediction for HiQ_model.g26735.t1
Valid prediction for Augustus_model.g26721.t1
Valid prediction for snap_scaffold_16-snap.1933-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.68146_t
Valid prediction for snap_scaffold_16-snap.1903-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.1925-T1
Valid prediction for GlimmerHMM_glimmerT_39764-T1
Valid prediction for GeneMark_model.68144_t
Valid prediction for GlimmerHMM_glimmerT_39767-T1
Valid prediction for snap_scaffold_16-snap.1915-T1
Valid prediction for GeneMark_model.68119_t
Valid prediction for Augustus_model.g26727.t1
Valid prediction for GeneMark_model.68128_t
Valid prediction for Augustus_model.g26723.t1
Valid prediction for GlimmerHMM_glimmerT_39757-T1
Valid prediction for snap_scaffold_16-snap.1919-T1
Valid prediction for GeneMark_model.68132_t
Valid prediction for GeneMark_model.68142_t
Valid prediction for snap_scaffold_16-snap.1898-T1
Valid prediction for GlimmerHMM_glimmerT_39753-T1
Valid prediction for snap_scaffold_16-snap.1902-T1
Valid prediction for GeneMark_model.68147_t
Valid prediction for GlimmerHMM_glimmerT_39758-T1
Valid prediction for Augustus_model.g26726.t1
Valid prediction for GeneMark_model.68141_t
Valid prediction for GeneMark_model.68134_t
Valid prediction for snap_scaffold_16-snap.1916-T1
Valid prediction for snap_scaffold_16-snap.1910-T1
Valid prediction for snap_scaffold_16-snap.1928-T1
Valid prediction for Augustus_model.g26718.t1
Valid prediction for GlimmerHMM_glimmerT_39756-T1
Valid prediction for Augustus_model.g26719.t1
Couldn't classify 181961, 183469
Sorry, prediction pasa_asmbl_16491.p1 fails validation.
(CTG)	 CA	181961-183469	GG	GAG
Valid prediction for snap_scaffold_16-snap.1899-T1
Valid prediction for GlimmerHMM_glimmerT_39762-T1
Valid prediction for GlimmerHMM_glimmerT_39763-T1
Valid prediction for snap_scaffold_16-snap.1917-T1
Valid prediction for GeneMark_model.68136_t
Valid prediction for GlimmerHMM_glimmerT_39748-T1
Valid prediction for GeneMark_model.68137_t
Valid prediction for GeneMark_model.68152_t
Valid prediction for GlimmerHMM_glimmerT_39766-T1
Valid prediction for snap_scaffold_16-snap.1904-T1
Valid prediction for GeneMark_model.68126_t
Valid prediction for GeneMark_model.68155_t
Valid prediction for snap_scaffold_16-snap.1920-T1
Valid prediction for snap_scaffold_16-snap.1908-T1
Valid prediction for Augustus_model.g26729.t1
Valid prediction for Augustus_model.g26724.t1
Valid prediction for GlimmerHMM_glimmerT_39747-T1
Valid prediction for Augustus_model.g26722.t1
Valid prediction for snap_scaffold_16-snap.1922-T1
Valid prediction for snap_scaffold_16-snap.1926-T1
Valid prediction for GeneMark_model.68150_t
Valid prediction for snap_scaffold_16-snap.1913-T1
Valid prediction for GlimmerHMM_glimmerT_39760-T1
Valid prediction for snap_scaffold_16-snap.1930-T1
Valid prediction for snap_scaffold_16-snap.1914-T1
Valid prediction for GeneMark_model.68124_t
Valid prediction for Augustus_model.g26731.t1
Valid prediction for snap_scaffold_16-snap.1906-T1
Valid prediction for GeneMark_model.68139_t
Valid prediction for GeneMark_model.68122_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 61479, rend_intergenic: 46382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72586, rend_intergenic: 70807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77298, rend_intergenic: 74430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81952, rend_intergenic: 80257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117301, rend_intergenic: 116290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122663, rend_intergenic: 119904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169436, rend_intergenic: 167911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175345, rend_intergenic: 170058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176744, rend_intergenic: 175720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186500, rend_intergenic: 177565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 213815
-exon list size: 565


building trellis

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5.8    
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6.7    
6.9    
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8.1    
8.3    
8.5    
8.6    
8.8    
9.0    
9.2    
9.3    
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9.9    
10.1    
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10.9    
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12.3    
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18.9    
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20.8    
21.0    
21.2    
21.3    
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22.6    
22.8    
22.9    
23.1    
23.3    
23.5    
23.6    
23.8    
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24.2    
24.3    
24.5    
24.7    
24.9    
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25.2    
25.4    
25.6    
25.7    
25.9    
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26.3    
26.5    
26.6    
26.8    
27.0    
27.2    
27.3    
27.5    
27.7    
27.9    
28.0    
28.2    
28.4    
28.6    
28.7    
28.9    
29.1    
29.3    
29.5    
29.6    
29.8    
30.0    
30.2    
30.3    
30.5    
30.7    
30.9    
31.0    
31.2    
31.4    
31.6    
31.7    
31.9    
32.1    
32.3    
32.5    
32.6    
32.8    
33.0    
33.2    
33.3    
33.5    
33.7    
33.9    
34.0    
34.2    
34.4    
34.6    
34.7    
34.9    
35.1    
35.3    
35.4    
35.6    
35.8    
36.0    
36.2    
36.3    
36.5    
36.7    
36.9    
37.0    
37.2    
37.4    
37.6    
37.7    
37.9    
38.1    
38.3    
38.4    
38.6    
38.8    
39.0    
39.2    
39.3    
39.5    
39.7    
39.9    
40.0    
40.2    
40.4    
40.6    
40.7    
40.9    
41.1    
41.3    
41.4    
41.6    
41.8    
42.0    
42.2    
42.3    
42.5    
42.7    
42.9    
43.0    
43.2    
43.4    
43.6    
43.7    
43.9    
44.1    
44.3    
44.4    
44.6    
44.8    
45.0    
45.1    
45.3    
45.5    
45.7    
45.9    
46.0    
46.2    
46.4    
46.6    
46.7    
46.9    
47.1    
47.3    
47.4    
47.6    
47.8    
48.0    
48.1    
48.3    
48.5    
48.7    
48.9    
49.0    
49.2    
49.4    
49.6    
49.7    
49.9    
50.1    
50.3    
50.4    
50.6    
50.8    
51.0    
51.1    
51.3    
51.5    
51.7    
51.9    
52.0    
52.2    
52.4    
52.6    
52.7    
52.9    
53.1    
53.3    
53.4    
53.6    
53.8    
54.0    
54.1    
54.3    
54.5    
54.7    
54.9    
55.0    
55.2    
55.4    
55.6    
55.7    
55.9    
56.1    
56.3    
56.4    
56.6    
56.8    
57.0    
57.1    
57.3    
57.5    
57.7    
57.8    
58.0    
58.2    
58.4    
58.6    
58.7    
58.9    
59.1    
59.3    
59.4    
59.6    
59.8    
60.0    
60.1    
60.3    
60.5    
60.7    
60.8    
61.0    
61.2    
61.4    
61.6    
61.7    
61.9    
62.1    
62.3    
62.4    
62.6    
62.8    
63.0    
63.1    
63.3    
63.5    
63.7    
63.8    
64.0    
64.2    
64.4    
64.6    
64.7    
64.9    
65.1    
65.3    
65.4    
65.6    
65.8    
66.0    
66.1    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.4    
67.5    
67.7    
67.9    
68.1    
68.3    
68.4    
68.6    
68.8    
69.0    
69.1    
69.3    
69.5    
69.7    
69.8    
70.0    
70.2    
70.4    
70.5    
70.7    
70.9    
71.1    
71.3    
71.4    
71.6    
71.8    
72.0    
72.1    
72.3    
72.5    
72.7    
72.8    
73.0    
73.2    
73.4    
73.5    
73.7    
73.9    
74.1    
74.3    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.8    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.1    
77.2    
77.4    
77.6    
77.8    
78.0    
78.1    
78.3    
78.5    
78.7    
78.8    
79.0    
79.2    
79.4    
79.5    
79.7    
79.9    
80.1    
80.2    
80.4    
80.6    
80.8    
81.0    
81.1    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.4    
82.5    
82.7    
82.9    
83.1    
83.2    
83.4    
83.6    
83.8    
84.0    
84.1    
84.3    
84.5    
84.7    
84.8    
85.0    
85.2    
85.4    
85.5    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.5    
87.7    
87.8    
88.0    
88.2    
88.4    
88.5    
88.7    
88.9    
89.1    
89.2    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.1    
92.2    
92.4    
92.6    
92.8    
92.9    
93.1    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 61479, rend_intergenic: 46382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72586, rend_intergenic: 70807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77298, rend_intergenic: 74430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81952, rend_intergenic: 80257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117301, rend_intergenic: 116290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122663, rend_intergenic: 119904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169436, rend_intergenic: 167911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175345, rend_intergenic: 170058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176744, rend_intergenic: 175720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186500, rend_intergenic: 177565  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 1 - 24490
-exon list size: 19


building trellis

4.8    
9.5    
14.3    
19.0    
23.8    
28.6    
33.3    
38.1    
42.9    
47.6    
52.4    
57.1    
61.9    
66.7    
71.4    
76.2    
81.0    
85.7    
90.5    
95.2    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 7107 - 24490
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-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 10730 - 24490
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-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