-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_8859317-9069709

-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_43872-T1
Valid prediction for GlimmerHMM_glimmerT_43859-T1
Valid prediction for GeneMark_model.75796_t
Valid prediction for GlimmerHMM_glimmerT_43871-T1
Valid prediction for GlimmerHMM_glimmerT_43884-T1
Valid prediction for GeneMark_model.75761_t
Valid prediction for GeneMark_model.75741_t
Valid prediction for snap_scaffold_18-snap.1877-T1
Valid prediction for GeneMark_model.75733_t
Valid prediction for GeneMark_model.75735_t
Valid prediction for snap_scaffold_18-snap.1899-T1
Valid prediction for snap_scaffold_18-snap.1914-T1
Valid prediction for GeneMark_model.75752_t
Valid prediction for GeneMark_model.75780_t
Valid prediction for Augustus_model.g29396.t1
Valid prediction for GlimmerHMM_glimmerT_43875-T1
Valid prediction for GeneMark_model.75790_t
Valid prediction for GeneMark_model.75754_t
Valid prediction for snap_scaffold_18-snap.1915-T1
Valid prediction for GlimmerHMM_glimmerT_43870-T1
Valid prediction for snap_scaffold_18-snap.1885-T1
Valid prediction for GeneMark_model.75782_t
Valid prediction for GeneMark_model.75794_t
Valid prediction for GlimmerHMM_glimmerT_43866-T1
Valid prediction for GlimmerHMM_glimmerT_43867-T1
Valid prediction for GeneMark_model.75769_t
Valid prediction for snap_scaffold_18-snap.1870-T1
Valid prediction for snap_scaffold_18-snap.1890-T1
Valid prediction for snap_scaffold_18-snap.1884-T1
Valid prediction for GlimmerHMM_glimmerT_43873-T1
Valid prediction for snap_scaffold_18-snap.1881-T1
Valid prediction for GeneMark_model.75756_t
Valid prediction for Augustus_model.g29395.t1
Valid prediction for GeneMark_model.75748_t
Valid prediction for GeneMark_model.75774_t
Valid prediction for Augustus_model.g29391.t1
Valid prediction for GeneMark_model.75738_t
Valid prediction for GlimmerHMM_glimmerT_43878-T1
Valid prediction for GeneMark_model.75749_t
Valid prediction for GlimmerHMM_glimmerT_43883-T1
Valid prediction for GeneMark_model.75737_t
Valid prediction for snap_scaffold_18-snap.1871-T1
Valid prediction for GlimmerHMM_glimmerT_43863-T1
Valid prediction for GeneMark_model.75793_t
Valid prediction for snap_scaffold_18-snap.1872-T1
Valid prediction for snap_scaffold_18-snap.1886-T1
Valid prediction for snap_scaffold_18-snap.1910-T1
Valid prediction for snap_scaffold_18-snap.1908-T1
Valid prediction for GeneMark_model.75784_t
Valid prediction for GlimmerHMM_glimmerT_43880-T1
Valid prediction for GlimmerHMM_glimmerT_43861-T1
Valid prediction for GeneMark_model.75771_t
Valid prediction for GeneMark_model.75745_t
Valid prediction for GeneMark_model.75750_t
Valid prediction for GeneMark_model.75753_t
Valid prediction for GeneMark_model.75732_t
Valid prediction for GeneMark_model.75743_t
Valid prediction for GlimmerHMM_glimmerT_43865-T1
Valid prediction for GeneMark_model.75786_t
Valid prediction for snap_scaffold_18-snap.1893-T1
Valid prediction for GlimmerHMM_glimmerT_43881-T1
Couldn't classify 126, 152
Couldn't classify 1584, 1671
Sorry, prediction pasa_asmbl_20897.p1 fails validation.
(TGT)	 CG	126-152	GT	AGG
(GAG)	 AG	275-328	GT	AGG
(TCT)	 AG	515-589	GT	AGG
(GCA)	 AG	1038-1169	GT	TGG
(CCG)	 AG	1280-1389	GT	AGG
(TGT)	 AG	1584-1671	CT	GCC
-recovered pasa_asmbl_20897.p1, internal, 275, 328
-recovered pasa_asmbl_20897.p1, internal, 515, 589
-recovered pasa_asmbl_20897.p1, internal, 1038, 1169
-recovered pasa_asmbl_20897.p1, internal, 1280, 1389
Valid prediction for snap_scaffold_18-snap.1878-T1
Valid prediction for snap_scaffold_18-snap.1874-T1
Valid prediction for GeneMark_model.75760_t
Valid prediction for GeneMark_model.75777_t
Valid prediction for GeneMark_model.75758_t
Valid prediction for snap_scaffold_18-snap.1896-T1
Valid prediction for snap_scaffold_18-snap.1901-T1
Valid prediction for Augustus_model.g29388.t1
Valid prediction for snap_scaffold_18-snap.1888-T1
Valid prediction for snap_scaffold_18-snap.1905-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_18-snap.1895-T1
Valid prediction for HiQ_model.g29383.t1
Valid prediction for GeneMark_model.75746_t
Valid prediction for snap_scaffold_18-snap.1894-T1
Valid prediction for GlimmerHMM_glimmerT_43862-T1
Valid prediction for snap_scaffold_18-snap.1906-T1
Valid prediction for snap_scaffold_18-snap.1902-T1
Valid prediction for snap_scaffold_18-snap.1873-T1
Valid prediction for snap_scaffold_18-snap.1916-T1
Valid prediction for GeneMark_model.75773_t
Valid prediction for GeneMark_model.75772_t
Valid prediction for snap_scaffold_18-snap.1900-T1
Valid prediction for GeneMark_model.75764_t
Valid prediction for GlimmerHMM_glimmerT_43860-T1
Valid prediction for GlimmerHMM_glimmerT_43882-T1
Valid prediction for GeneMark_model.75747_t
Valid prediction for GlimmerHMM_glimmerT_43877-T1
Valid prediction for GeneMark_model.75744_t
Valid prediction for GeneMark_model.75785_t
Valid prediction for GeneMark_model.75740_t
Valid prediction for Augustus_model.g29386.t1
Valid prediction for snap_scaffold_18-snap.1883-T1
Valid prediction for HiQ_model.g29384.t1
Valid prediction for GlimmerHMM_glimmerT_43864-T1
Valid prediction for GlimmerHMM_glimmerT_43868-T1
Valid prediction for GeneMark_model.75770_t
Valid prediction for CodingQuarry_transcript_23815-T1
Valid prediction for GeneMark_model.75762_t
Valid prediction for GeneMark_model.75791_t
Valid prediction for GeneMark_model.75731_t
Valid prediction for snap_scaffold_18-snap.1898-T1
Valid prediction for snap_scaffold_18-snap.1911-T1
Couldn't classify 184394, 184536
Sorry, prediction pasa_asmbl_20071.p1 fails validation.
(GTG)	 GA	184394-184536	GT	AGG
(CAC)	 AG	185525-185921	GT	AGG
(GTG)	 AG	187552-187664	GT	AGG
(TCG)	 AG	188026-188293	GT	AGG
(GAG)	 AG	188792-188932	GT	AGG
(ATC)	 AG	190224-190267	GT	AGG
(CTC)	 AG	191154-191229	GT	AGG
(AGG)	 AG	191336-191476	GT	AGG
(GAA)	 AG	191645-191737	GT	CGG
(GAC)	 AG	193441-193509	GT	AGG
(GTG)	 AG	194673-194709	GT	TGG
(GCA)	 AG	196117-196130	TG	AAT
-recovered pasa_asmbl_20071.p1, terminal, 196117, 196130
-recovered pasa_asmbl_20071.p1, internal, 185525, 185921
-recovered pasa_asmbl_20071.p1, internal, 187552, 187664
-recovered pasa_asmbl_20071.p1, internal, 188026, 188293
-recovered pasa_asmbl_20071.p1, internal, 188792, 188932
-recovered pasa_asmbl_20071.p1, internal, 190224, 190267
-recovered pasa_asmbl_20071.p1, internal, 191154, 191229
-recovered pasa_asmbl_20071.p1, internal, 191336, 191476
-recovered pasa_asmbl_20071.p1, internal, 191645, 191737
-recovered pasa_asmbl_20071.p1, internal, 193441, 193509
-recovered pasa_asmbl_20071.p1, internal, 194673, 194709
Valid prediction for GeneMark_model.75736_t
Valid prediction for snap_scaffold_18-snap.1887-T1
Valid prediction for GeneMark_model.75776_t
Valid prediction for GlimmerHMM_glimmerT_43874-T1
Valid prediction for GeneMark_model.75792_t
Valid prediction for pasa_asmbl_20080.p1
Valid prediction for snap_scaffold_18-snap.1889-T1
Valid prediction for GeneMark_model.75789_t
Valid prediction for snap_scaffold_18-snap.1869-T1
Valid prediction for Augustus_model.g29393.t1
Valid prediction for snap_scaffold_18-snap.1897-T1
Valid prediction for snap_scaffold_18-snap.1875-T1
Valid prediction for Augustus_model.g29390.t1
Valid prediction for GeneMark_model.75788_t
Valid prediction for GlimmerHMM_glimmerT_43876-T1
Valid prediction for Augustus_model.g29397.t1
Valid prediction for Augustus_model.g29392.t1
Valid prediction for snap_scaffold_18-snap.1891-T1
Valid prediction for GeneMark_model.75734_t
Valid prediction for GlimmerHMM_glimmerT_43858-T1
Valid prediction for GeneMark_model.75778_t
Valid prediction for snap_scaffold_18-snap.1912-T1
Valid prediction for GeneMark_model.75775_t
Valid prediction for Augustus_model.g29389.t1
Valid prediction for snap_scaffold_18-snap.1909-T1
Valid prediction for snap_scaffold_18-snap.1904-T1
Valid prediction for GeneMark_model.75742_t
Valid prediction for GeneMark_model.75755_t
Valid prediction for snap_scaffold_18-snap.1879-T1
Valid prediction for snap_scaffold_18-snap.1903-T1
Valid prediction for snap_scaffold_18-snap.1880-T1
Valid prediction for GeneMark_model.75751_t
Valid prediction for GeneMark_model.75781_t
Valid prediction for snap_scaffold_18-snap.1907-T1
Valid prediction for snap_scaffold_18-snap.1892-T1
Valid prediction for snap_scaffold_18-snap.1868-T1
Valid prediction for GeneMark_model.75768_t
Valid prediction for GlimmerHMM_glimmerT_43869-T1
Valid prediction for snap_scaffold_18-snap.1882-T1
Valid prediction for GeneMark_model.75765_t
Valid prediction for Augustus_model.g29394.t1
Valid prediction for GeneMark_model.75739_t
Valid prediction for CodingQuarry_transcript_23813-T1
Valid prediction for GeneMark_model.75783_t
Valid prediction for GeneMark_model.75759_t
Valid prediction for GeneMark_model.75757_t
Valid prediction for snap_scaffold_18-snap.1876-T1
Valid prediction for snap_scaffold_18-snap.1913-T1
Valid prediction for GeneMark_model.75766_t
Valid prediction for Augustus_model.g29385.t1
Valid prediction for pasa_asmbl_20061.p1
Valid prediction for GeneMark_model.75767_t
Valid prediction for Augustus_model.g29387.t1
Valid prediction for GlimmerHMM_glimmerT_43879-T1
Valid prediction for CodingQuarry_transcript_23814-T1
Valid prediction for GeneMark_model.75779_t
Valid prediction for GeneMark_model.75795_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 155648, rend_intergenic: 155645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27908, rend_intergenic: 14340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34876, rend_intergenic: 31320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40508, rend_intergenic: 35030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44708, rend_intergenic: 41067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59657, rend_intergenic: 55033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108420, rend_intergenic: 104084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108933, rend_intergenic: 108778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111179, rend_intergenic: 108964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118694, rend_intergenic: 115467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123581, rend_intergenic: 122299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136303, rend_intergenic: 132564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141937, rend_intergenic: 137601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144402, rend_intergenic: 141954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147141, rend_intergenic: 144639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153838, rend_intergenic: 147340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180866, rend_intergenic: 180687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183379, rend_intergenic: 181385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194120, rend_intergenic: 184862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206006, rend_intergenic: 195221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 210393
-exon list size: 760


building trellis

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73.8    
73.9    
74.0    
74.1    
74.3    
74.4    
74.5    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.5    
75.6    
75.7    
75.9    
76.0    
76.1    
76.2    
76.4    
76.5    
76.6    
76.8    
76.9    
77.0    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
78.0    
78.1    
78.2    
78.3    
78.5    
78.6    
78.7    
78.9    
79.0    
79.1    
79.3    
79.4    
79.5    
79.7    
79.8    
79.9    
80.1    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.8    
81.9    
82.0    
82.2    
82.3    
82.4    
82.5    
82.7    
82.8    
82.9    
83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.9    
84.0    
84.1    
84.3    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.2    
85.3    
85.4    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.6    
86.7    
86.9    
87.0    
87.1    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.6    
89.8    
89.9    
90.0    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 41 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 155648, rend_intergenic: 155645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27908, rend_intergenic: 14340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34876, rend_intergenic: 31320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40508, rend_intergenic: 35030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44708, rend_intergenic: 41067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59657, rend_intergenic: 55033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108420, rend_intergenic: 104084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108933, rend_intergenic: 108778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111179, rend_intergenic: 108964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118694, rend_intergenic: 115467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123581, rend_intergenic: 122299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136303, rend_intergenic: 132564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141937, rend_intergenic: 137601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144402, rend_intergenic: 141954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147141, rend_intergenic: 144639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153838, rend_intergenic: 147340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180866, rend_intergenic: 180687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183379, rend_intergenic: 181385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194120, rend_intergenic: 184862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206006, rend_intergenic: 195221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support