-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_8849738-9087440

-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_35152-T1
Valid prediction for snap_scaffold_14-snap.1878-T1
Valid prediction for snap_scaffold_14-snap.1861-T1
Valid prediction for GeneMark_model.60261_t
Valid prediction for GlimmerHMM_glimmerT_35132-T1
Valid prediction for GeneMark_model.60227_t
Valid prediction for GlimmerHMM_glimmerT_35133-T1
Valid prediction for GeneMark_model.60199_t
Valid prediction for GeneMark_model.60205_t
Valid prediction for GeneMark_model.60211_t
Valid prediction for GeneMark_model.60217_t
Valid prediction for Augustus_model.g23635.t1
Valid prediction for snap_scaffold_14-snap.1889-T1
Valid prediction for GeneMark_model.60254_t
Valid prediction for Augustus_model.g23636.t1
Valid prediction for GeneMark_model.60247_t
Valid prediction for Augustus_model.g23638.t1
Valid prediction for GlimmerHMM_glimmerT_35138-T1
Valid prediction for GlimmerHMM_glimmerT_35145-T1
Valid prediction for snap_scaffold_14-snap.1858-T1
Valid prediction for GeneMark_model.60203_t
Valid prediction for snap_scaffold_14-snap.1869-T1
Valid prediction for GeneMark_model.60198_t
Valid prediction for snap_scaffold_14-snap.1887-T1
Valid prediction for GlimmerHMM_glimmerT_35139-T1
Valid prediction for GeneMark_model.60233_t
Valid prediction for GeneMark_model.60235_t
Valid prediction for GeneMark_model.60191_t
Valid prediction for GeneMark_model.60252_t
Valid prediction for snap_scaffold_14-snap.1879-T1
Valid prediction for GeneMark_model.60200_t
Valid prediction for GeneMark_model.60256_t
Valid prediction for snap_scaffold_14-snap.1870-T1
Valid prediction for GeneMark_model.60208_t
Valid prediction for GlimmerHMM_glimmerT_35140-T1
Valid prediction for GeneMark_model.60220_t
Valid prediction for GeneMark_model.60225_t
Valid prediction for snap_scaffold_14-snap.1860-T1
Valid prediction for snap_scaffold_14-snap.1851-T1
Valid prediction for snap_scaffold_14-snap.1884-T1
Valid prediction for Augustus_model.g23647.t1
Valid prediction for GeneMark_model.60232_t
Valid prediction for GlimmerHMM_glimmerT_35151-T1
Valid prediction for GlimmerHMM_glimmerT_35137-T1
Valid prediction for GeneMark_model.60188_t
Valid prediction for snap_scaffold_14-snap.1898-T1
Valid prediction for snap_scaffold_14-snap.1881-T1
Valid prediction for snap_scaffold_14-snap.1890-T1
Valid prediction for GeneMark_model.60218_t
Valid prediction for GeneMark_model.60264_t
Valid prediction for snap_scaffold_14-snap.1894-T1
Valid prediction for GlimmerHMM_glimmerT_35134-T1
Valid prediction for GeneMark_model.60222_t
Valid prediction for snap_scaffold_14-snap.1891-T1
Valid prediction for GlimmerHMM_glimmerT_35146-T1
Valid prediction for GeneMark_model.60263_t
Valid prediction for GeneMark_model.60250_t
Valid prediction for GeneMark_model.60259_t
Valid prediction for GeneMark_model.60239_t
Couldn't classify 218315, 218394
Sorry, prediction pasa_asmbl_12252.p1 fails validation.
(TCA)	 CC	218315-218394	GT	AAG
(AGG)	 AG	219115-219223	GT	AGG
(CTG)	 AG	219366-219440	GT	AGG
(AGT)	 AG	219673-219895	GT	TGG
(GTT)	 AG	220172-220344	GT	AGG
(GAA)	 AG	220587-220648	GT	AGG
(GTT)	 AG	220921-220978	GT	AGG
(GCT)	 AG	221872-221924	GT	GGG
(GGT)	 AG	222005-222044	GT	AGG
(GTT)	 AG	222235-222327	GT	AGG
(GAG)	 AG	222974-223024	AA	AGA
-recovered pasa_asmbl_12252.p1, terminal, 222974, 223024
-recovered pasa_asmbl_12252.p1, internal, 219115, 219223
-recovered pasa_asmbl_12252.p1, internal, 219366, 219440
-recovered pasa_asmbl_12252.p1, internal, 219673, 219895
-recovered pasa_asmbl_12252.p1, internal, 220172, 220344
-recovered pasa_asmbl_12252.p1, internal, 220587, 220648
-recovered pasa_asmbl_12252.p1, internal, 220921, 220978
-recovered pasa_asmbl_12252.p1, internal, 221872, 221924
-recovered pasa_asmbl_12252.p1, internal, 222005, 222044
-recovered pasa_asmbl_12252.p1, internal, 222235, 222327
Valid prediction for GeneMark_model.60255_t
Valid prediction for snap_scaffold_14-snap.1902-T1
Valid prediction for snap_scaffold_14-snap.1875-T1
Valid prediction for GlimmerHMM_glimmerT_35141-T1
Valid prediction for Augustus_model.g23637.t1
Valid prediction for snap_scaffold_14-snap.1867-T1
Valid prediction for GlimmerHMM_glimmerT_35131-T1
Valid prediction for GeneMark_model.60240_t
Valid prediction for GeneMark_model.60215_t
Valid prediction for snap_scaffold_14-snap.1901-T1
Valid prediction for HiQ_model.g23646.t1
Valid prediction for snap_scaffold_14-snap.1874-T1
Valid prediction for GlimmerHMM_glimmerT_35135-T1
Valid prediction for snap_scaffold_14-snap.1864-T1
Valid prediction for GeneMark_model.60204_t
Valid prediction for GeneMark_model.60257_t
Valid prediction for GeneMark_model.60193_t
Valid prediction for GeneMark_model.60242_t
Valid prediction for GeneMark_model.60195_t
Valid prediction for GeneMark_model.60237_t
Valid prediction for GeneMark_model.60266_t
Valid prediction for snap_scaffold_14-snap.1893-T1
Valid prediction for GeneMark_model.60196_t
Valid prediction for GeneMark_model.60244_t
Valid prediction for GlimmerHMM_glimmerT_35149-T1
Valid prediction for snap_scaffold_14-snap.1859-T1
Valid prediction for GeneMark_model.60230_t
Valid prediction for snap_scaffold_14-snap.1886-T1
Valid prediction for GeneMark_model.60201_t
Valid prediction for Augustus_model.g23639.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_14-snap.1895-T1
Valid prediction for GeneMark_model.60241_t
Valid prediction for HiQ_model.g23645.t1
Valid prediction for GeneMark_model.60260_t
Valid prediction for snap_scaffold_14-snap.1866-T1
Valid prediction for snap_scaffold_14-snap.1871-T1
Valid prediction for GeneMark_model.60221_t
Valid prediction for snap_scaffold_14-snap.1900-T1
Valid prediction for snap_scaffold_14-snap.1885-T1
Valid prediction for GeneMark_model.60206_t
Valid prediction for GeneMark_model.60194_t
Valid prediction for snap_scaffold_14-snap.1899-T1
Valid prediction for GeneMark_model.60267_t
Valid prediction for GlimmerHMM_glimmerT_35147-T1
Valid prediction for GeneMark_model.60197_t
Valid prediction for GeneMark_model.60213_t
Valid prediction for GeneMark_model.60192_t
Valid prediction for snap_scaffold_14-snap.1863-T1
Valid prediction for Augustus_model.g23643.t1
Valid prediction for GeneMark_model.60216_t
Valid prediction for snap_scaffold_14-snap.1888-T1
Valid prediction for snap_scaffold_14-snap.1892-T1
Valid prediction for snap_scaffold_14-snap.1877-T1
Valid prediction for snap_scaffold_14-snap.1873-T1
Valid prediction for snap_scaffold_14-snap.1855-T1
Valid prediction for GlimmerHMM_glimmerT_35142-T1
Valid prediction for GeneMark_model.60228_t
Valid prediction for snap_scaffold_14-snap.1883-T1
Valid prediction for Augustus_model.g23644.t1
Valid prediction for GlimmerHMM_glimmerT_35150-T1
Valid prediction for GeneMark_model.60224_t
Valid prediction for Augustus_model.g23634.t1
Valid prediction for GeneMark_model.60189_t
Valid prediction for GeneMark_model.60209_t
Valid prediction for GeneMark_model.60231_t
Valid prediction for GeneMark_model.60190_t
Valid prediction for GeneMark_model.60253_t
Valid prediction for GeneMark_model.60207_t
Valid prediction for GeneMark_model.60202_t
Valid prediction for GeneMark_model.60214_t
Valid prediction for GeneMark_model.60223_t
Valid prediction for snap_scaffold_14-snap.1880-T1
Valid prediction for GeneMark_model.60265_t
Valid prediction for GeneMark_model.60262_t
Valid prediction for GlimmerHMM_glimmerT_35136-T1
Valid prediction for GeneMark_model.60219_t
Valid prediction for snap_scaffold_14-snap.1862-T1
Valid prediction for GeneMark_model.60251_t
Valid prediction for snap_scaffold_14-snap.1853-T1
Valid prediction for Augustus_model.g23640.t1
Valid prediction for GlimmerHMM_glimmerT_35143-T1
Valid prediction for snap_scaffold_14-snap.1872-T1
Valid prediction for GeneMark_model.60249_t
Valid prediction for snap_scaffold_14-snap.1852-T1
Valid prediction for GeneMark_model.60234_t
Valid prediction for snap_scaffold_14-snap.1865-T1
Valid prediction for snap_scaffold_14-snap.1882-T1
Valid prediction for GlimmerHMM_glimmerT_35144-T1
Valid prediction for CodingQuarry_transcript_15736-T1
Valid prediction for GeneMark_model.60210_t
Valid prediction for GeneMark_model.60236_t
Valid prediction for GeneMark_model.60245_t
Valid prediction for GlimmerHMM_glimmerT_35148-T1
Valid prediction for GeneMark_model.60246_t
Valid prediction for snap_scaffold_14-snap.1897-T1
Valid prediction for snap_scaffold_14-snap.1856-T1
Valid prediction for snap_scaffold_14-snap.1854-T1
Valid prediction for GeneMark_model.60258_t
Valid prediction for snap_scaffold_14-snap.1896-T1
Valid prediction for GeneMark_model.60243_t
Valid prediction for snap_scaffold_14-snap.1876-T1
Valid prediction for GeneMark_model.60248_t
Valid prediction for snap_scaffold_14-snap.1868-T1
Valid prediction for GeneMark_model.60238_t
Valid prediction for GeneMark_model.60187_t
Valid prediction for Augustus_model.g23642.t1
Valid prediction for GeneMark_model.60229_t
Valid prediction for snap_scaffold_14-snap.1857-T1
Valid prediction for Augustus_model.g23641.t1
Valid prediction for GeneMark_model.60226_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18508, rend_intergenic: 6800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38949, rend_intergenic: 23454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41515, rend_intergenic: 39699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48003, rend_intergenic: 43473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65249, rend_intergenic: 58145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89978, rend_intergenic: 86440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93775, rend_intergenic: 90684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97710, rend_intergenic: 95301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108362, rend_intergenic: 107478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111487, rend_intergenic: 109492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117089, rend_intergenic: 112034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128036, rend_intergenic: 118640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138636, rend_intergenic: 131433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146476, rend_intergenic: 139588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171974, rend_intergenic: 147683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180902, rend_intergenic: 179629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200307, rend_intergenic: 185256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223024, rend_intergenic: 218969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224706, rend_intergenic: 223280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 237703
-exon list size: 821


building trellis

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72.8    
72.9    
73.0    
73.1    
73.3    
73.4    
73.5    
73.6    
73.8    
73.9    
74.0    
74.1    
74.2    
74.4    
74.5    
74.6    
74.7    
74.8    
75.0    
75.1    
75.2    
75.3    
75.5    
75.6    
75.7    
75.8    
75.9    
76.1    
76.2    
76.3    
76.4    
76.5    
76.7    
76.8    
76.9    
77.0    
77.2    
77.3    
77.4    
77.5    
77.6    
77.8    
77.9    
78.0    
78.1    
78.3    
78.4    
78.5    
78.6    
78.7    
78.9    
79.0    
79.1    
79.2    
79.3    
79.5    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
80.9    
81.0    
81.2    
81.3    
81.4    
81.5    
81.7    
81.8    
81.9    
82.0    
82.1    
82.3    
82.4    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.7    
83.8    
84.0    
84.1    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
84.9    
85.1    
85.2    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.0    
86.1    
86.3    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.7    
87.8    
88.0    
88.1    
88.2    
88.3    
88.5    
88.6    
88.7    
88.8    
88.9    
89.1    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
89.9    
90.0    
90.2    
90.3    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.3    
93.4    
93.6    
93.7    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.2    
96.4    
96.5    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.0    
99.1    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 55 predictions from path traversal
Error with prediction: snap lend_intergenic: 18508, rend_intergenic: 6800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38949, rend_intergenic: 23454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41515, rend_intergenic: 39699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48003, rend_intergenic: 43473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65249, rend_intergenic: 58145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89978, rend_intergenic: 86440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93775, rend_intergenic: 90684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97710, rend_intergenic: 95301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108362, rend_intergenic: 107478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111487, rend_intergenic: 109492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117089, rend_intergenic: 112034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128036, rend_intergenic: 118640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138636, rend_intergenic: 131433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146476, rend_intergenic: 139588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171974, rend_intergenic: 147683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180902, rend_intergenic: 179629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200307, rend_intergenic: 185256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223024, rend_intergenic: 218969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224706, rend_intergenic: 223280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 225527 - 237703
-exon list size: 32


building trellis

2.9    
5.9    
8.8    
11.8    
14.7    
17.6    
20.6    
23.5    
26.5    
29.4    
32.4    
35.3    
38.2    
41.2    
44.1    
47.1    
50.0    
52.9    
55.9    
58.8    
61.8    
64.7    
67.6    
70.6    
73.5    
76.5    
79.4    
82.4    
85.3    
88.2    
91.2    
94.1    
97.1    
-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 227592 - 237703
-exon list size: 28


building trellis

3.3    
6.7    
10.0    
13.3    
16.7    
20.0    
23.3    
26.7    
30.0    
33.3    
36.7    
40.0    
43.3    
46.7    
50.0    
53.3    
56.7    
60.0    
63.3    
66.7    
70.0    
73.3    
76.7    
80.0    
83.3    
86.7    
90.0    
93.3    
96.7    
-found 1 predictions from path traversal

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