-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_9066131-9279611

-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 GeneMark_model.75873_t
Valid prediction for GeneMark_model.75871_t
Valid prediction for GeneMark_model.75839_t
Valid prediction for GeneMark_model.75804_t
Valid prediction for snap_scaffold_18-snap.1957-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GeneMark_model.75824_t
Valid prediction for snap_scaffold_18-snap.1950-T1
Valid prediction for snap_scaffold_18-snap.1941-T1
Valid prediction for snap_scaffold_18-snap.1959-T1
Valid prediction for Augustus_model.g29414.t1
Valid prediction for GlimmerHMM_glimmerT_43905-T1
Valid prediction for GlimmerHMM_glimmerT_43913-T1
Valid prediction for GlimmerHMM_glimmerT_43893-T1
Valid prediction for GeneMark_model.75858_t
Valid prediction for GeneMark_model.75844_t
Valid prediction for GlimmerHMM_glimmerT_43898-T1
Valid prediction for Augustus_model.g29413.t1
Valid prediction for GeneMark_model.75802_t
Valid prediction for GeneMark_model.75840_t
Valid prediction for GlimmerHMM_glimmerT_43894-T1
Valid prediction for GlimmerHMM_glimmerT_43899-T1
Valid prediction for snap_scaffold_18-snap.1949-T1
Valid prediction for GeneMark_model.75848_t
Valid prediction for snap_scaffold_18-snap.1926-T1
Valid prediction for snap_scaffold_18-snap.1956-T1
Valid prediction for GeneMark_model.75867_t
Valid prediction for GeneMark_model.75834_t
Valid prediction for GeneMark_model.75851_t
Valid prediction for GeneMark_model.75832_t
Valid prediction for CodingQuarry_transcript_23818-T1
Valid prediction for snap_scaffold_18-snap.1934-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.75806_t
Valid prediction for GlimmerHMM_glimmerT_43886-T1
Valid prediction for GeneMark_model.75846_t
Valid prediction for GeneMark_model.75863_t
Valid prediction for GeneMark_model.75855_t
Valid prediction for snap_scaffold_18-snap.1925-T1
Valid prediction for GlimmerHMM_glimmerT_43889-T1
Valid prediction for pasa_asmbl_20906.p1
Valid prediction for CodingQuarry_transcript_23816-T1
Valid prediction for snap_scaffold_18-snap.1942-T1
Valid prediction for Augustus_model.g29410.t1
Valid prediction for snap_scaffold_18-snap.1937-T1
Valid prediction for GeneMark_model.75822_t
Valid prediction for GeneMark_model.75866_t
Valid prediction for CodingQuarry_transcript_23817-T1
Valid prediction for GlimmerHMM_glimmerT_43912-T1
Valid prediction for snap_scaffold_18-snap.1929-T1
Valid prediction for snap_scaffold_18-snap.1961-T1
Valid prediction for GeneMark_model.75808_t
Valid prediction for snap_scaffold_18-snap.1922-T1
Valid prediction for GeneMark_model.75869_t
Valid prediction for snap_scaffold_18-snap.1954-T1
Valid prediction for GeneMark_model.75826_t
Valid prediction for GlimmerHMM_glimmerT_43903-T1
Valid prediction for GlimmerHMM_glimmerT_43907-T1
Valid prediction for GeneMark_model.75799_t
Valid prediction for GlimmerHMM_glimmerT_43915-T1
Valid prediction for GeneMark_model.75819_t
Valid prediction for Augustus_model.g29401.t1
Valid prediction for Augustus_model.g29405.t1
Valid prediction for GeneMark_model.75853_t
Valid prediction for GeneMark_model.75810_t
Valid prediction for GlimmerHMM_glimmerT_43910-T1
Valid prediction for GeneMark_model.75820_t
Valid prediction for snap_scaffold_18-snap.1931-T1
Valid prediction for snap_scaffold_18-snap.1933-T1
Valid prediction for snap_scaffold_18-snap.1921-T1
Valid prediction for snap_scaffold_18-snap.1938-T1
Valid prediction for snap_scaffold_18-snap.1923-T1
Valid prediction for HiQ_model.g29407.t1
Valid prediction for pasa_asmbl_20900.p1
Valid prediction for GeneMark_model.75798_t
Valid prediction for GeneMark_model.75812_t
Valid prediction for GeneMark_model.75816_t
Valid prediction for GeneMark_model.75860_t
Valid prediction for snap_scaffold_18-snap.1917-T1
Valid prediction for Augustus_model.g29416.t1
Valid prediction for Augustus_model.g29408.t1
Valid prediction for GeneMark_model.75842_t
Valid prediction for GeneMark_model.75837_t
Valid prediction for GeneMark_model.75830_t
Valid prediction for snap_scaffold_18-snap.1951-T1
Valid prediction for GeneMark_model.75828_t
Valid prediction for snap_scaffold_18-snap.1947-T1
Valid prediction for GlimmerHMM_glimmerT_43896-T1
Valid prediction for snap_scaffold_18-snap.1927-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.75850_t
Valid prediction for GlimmerHMM_glimmerT_43918-T1
Valid prediction for snap_scaffold_18-snap.1944-T1
Valid prediction for Augustus_model.g29404.t1
Valid prediction for GeneMark_model.75807_t
Valid prediction for CodingQuarry_transcript_23821-T1
Valid prediction for GeneMark_model.75803_t
Valid prediction for Augustus_model.g29403.t1
Valid prediction for snap_scaffold_18-snap.1946-T1
Valid prediction for GeneMark_model.75814_t
Valid prediction for GeneMark_model.75841_t
Couldn't classify 160506, 160550
Sorry, prediction pasa_asmbl_20088.p1 fails validation.
(TCG)	 CA	160506-160550	GT	TGG
(AAG)	 AG	161117-161265	GT	GAG
(GCA)	 AG	163231-163315	GT	TGG
(ATG)	 AG	166313-166468	GA	GAG
add_exon() Sorry, pasa_asmbl_20088.p1 161117-161265-terminal-2 is invalid.
-recovered pasa_asmbl_20088.p1, terminal, 161117, 161265
-recovered pasa_asmbl_20088.p1, terminal, 166313, 166468
-recovered pasa_asmbl_20088.p1, internal, 161117, 161265
-recovered pasa_asmbl_20088.p1, internal, 163231, 163315
Valid prediction for GeneMark_model.75854_t
Valid prediction for snap_scaffold_18-snap.1939-T1
Valid prediction for GeneMark_model.75852_t
Valid prediction for snap_scaffold_18-snap.1919-T1
Valid prediction for snap_scaffold_18-snap.1920-T1
Valid prediction for snap_scaffold_18-snap.1940-T1
Valid prediction for GlimmerHMM_glimmerT_43901-T1
Valid prediction for GeneMark_model.75859_t
Valid prediction for GeneMark_model.75872_t
Valid prediction for GeneMark_model.75818_t
Valid prediction for GlimmerHMM_glimmerT_43892-T1
Valid prediction for Augustus_model.g29417.t1
Valid prediction for GeneMark_model.75831_t
Valid prediction for GlimmerHMM_glimmerT_43897-T1
Valid prediction for snap_scaffold_18-snap.1953-T1
Valid prediction for CodingQuarry_transcript_23820-T1
Valid prediction for Augustus_model.g29412.t1
Valid prediction for GlimmerHMM_glimmerT_43890-T1
Valid prediction for GeneMark_model.75809_t
Valid prediction for GeneMark_model.75870_t
Valid prediction for pasa_asmbl_20093.p1
Valid prediction for GeneMark_model.75849_t
Valid prediction for GeneMark_model.75861_t
Valid prediction for GlimmerHMM_glimmerT_43908-T1
Valid prediction for GlimmerHMM_glimmerT_43914-T1
Valid prediction for snap_scaffold_18-snap.1958-T1
Valid prediction for snap_scaffold_18-snap.1955-T1
Valid prediction for GeneMark_model.75811_t
Valid prediction for snap_scaffold_18-snap.1918-T1
Valid prediction for GeneMark_model.75825_t
Valid prediction for Augustus_model.g29402.t1
Valid prediction for GeneMark_model.75857_t
Valid prediction for GeneMark_model.75827_t
Valid prediction for GeneMark_model.75800_t
Valid prediction for snap_scaffold_18-snap.1960-T1
Valid prediction for CodingQuarry_transcript_23819-T1
Valid prediction for GlimmerHMM_glimmerT_43887-T1
Valid prediction for GeneMark_model.75865_t
Couldn't classify 92564, 93040
Sorry, prediction pasa_asmbl_20089.p1 fails validation.
(ATC)	 TC	92564-93040	AC	AGA
Valid prediction for Augustus_model.g29406.t1
Valid prediction for GlimmerHMM_glimmerT_43916-T1
Valid prediction for GeneMark_model.75862_t
Valid prediction for GlimmerHMM_glimmerT_43888-T1
Valid prediction for snap_scaffold_18-snap.1930-T1
Valid prediction for snap_scaffold_18-snap.1935-T1
Valid prediction for snap_scaffold_18-snap.1932-T1
Valid prediction for GeneMark_model.75856_t
Valid prediction for GeneMark_model.75845_t
Valid prediction for GeneMark_model.75821_t
Valid prediction for snap_scaffold_18-snap.1948-T1
Valid prediction for Augustus_model.g29398.t1
Valid prediction for GlimmerHMM_glimmerT_43911-T1
Valid prediction for GeneMark_model.75843_t
Valid prediction for GeneMark_model.75815_t
Couldn't classify 87387, 87530
Sorry, prediction pasa_asmbl_20090.p1 fails validation.
(ATG)	 CT	86650-86964	GT	AGG
(GTG)	 AG	87387-87530	AT	GCA
-recovered pasa_asmbl_20090.p1, initial, 86650, 86964
Valid prediction for GeneMark_model.75847_t
Valid prediction for GeneMark_model.75875_t
Valid prediction for GeneMark_model.75829_t
Valid prediction for GlimmerHMM_glimmerT_43909-T1
Valid prediction for GlimmerHMM_glimmerT_43891-T1
Valid prediction for GeneMark_model.75813_t
Valid prediction for GlimmerHMM_glimmerT_43904-T1
Valid prediction for snap_scaffold_18-snap.1924-T1
Valid prediction for GeneMark_model.75805_t
Valid prediction for GlimmerHMM_glimmerT_43895-T1
Valid prediction for Augustus_model.g29409.t1
Valid prediction for GlimmerHMM_glimmerT_43917-T1
Valid prediction for GlimmerHMM_glimmerT_43902-T1
Valid prediction for GeneMark_model.75835_t
Valid prediction for GeneMark_model.75868_t
Valid prediction for GeneMark_model.75833_t
Valid prediction for GeneMark_model.75838_t
Valid prediction for GlimmerHMM_glimmerT_43900-T1
Valid prediction for GeneMark_model.75801_t
Valid prediction for GeneMark_model.75876_t
Valid prediction for Augustus_model.g29415.t1
Valid prediction for GlimmerHMM_glimmerT_43906-T1
Valid prediction for snap_scaffold_18-snap.1945-T1
Valid prediction for snap_scaffold_18-snap.1936-T1
Valid prediction for Augustus_model.g29399.t1
Valid prediction for snap_scaffold_18-snap.1943-T1
Valid prediction for GeneMark_model.75874_t
Valid prediction for GeneMark_model.75823_t
Valid prediction for Augustus_model.g29411.t1
Valid prediction for snap_scaffold_18-snap.1928-T1
Valid prediction for snap_scaffold_18-snap.1952-T1
Valid prediction for GeneMark_model.75836_t
Valid prediction for Augustus_model.g29400.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23982, rend_intergenic: 3726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37903, rend_intergenic: 24062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41480, rend_intergenic: 38044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57398, rend_intergenic: 41997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68276, rend_intergenic: 60789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77522, rend_intergenic: 70292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93737, rend_intergenic: 77914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110220, rend_intergenic: 101783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111798, rend_intergenic: 110442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119016, rend_intergenic: 112235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138777, rend_intergenic: 135581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142646, rend_intergenic: 140874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189104, rend_intergenic: 171786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194710, rend_intergenic: 190022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 213481
-exon list size: 920


building trellis

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66.5    
66.6    
66.7    
66.8    
66.9    
67.0    
67.1    
67.2    
67.4    
67.5    
67.6    
67.7    
67.8    
67.9    
68.0    
68.1    
68.2    
68.3    
68.4    
68.5    
68.7    
68.8    
68.9    
69.0    
69.1    
69.2    
69.3    
69.4    
69.5    
69.6    
69.7    
69.8    
70.0    
70.1    
70.2    
70.3    
70.4    
70.5    
70.6    
70.7    
70.8    
70.9    
71.0    
71.1    
71.3    
71.4    
71.5    
71.6    
71.7    
71.8    
71.9    
72.0    
72.1    
72.2    
72.3    
72.5    
72.6    
72.7    
72.8    
72.9    
73.0    
73.1    
73.2    
73.3    
73.4    
73.5    
73.6    
73.8    
73.9    
74.0    
74.1    
74.2    
74.3    
74.4    
74.5    
74.6    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.4    
75.5    
75.6    
75.7    
75.8    
75.9    
76.0    
76.1    
76.2    
76.4    
76.5    
76.6    
76.7    
76.8    
76.9    
77.0    
77.1    
77.2    
77.3    
77.4    
77.5    
77.7    
77.8    
77.9    
78.0    
78.1    
78.2    
78.3    
78.4    
78.5    
78.6    
78.7    
78.9    
79.0    
79.1    
79.2    
79.3    
79.4    
79.5    
79.6    
79.7    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.5    
80.6    
80.7    
80.8    
80.9    
81.0    
81.1    
81.2    
81.3    
81.5    
81.6    
81.7    
81.8    
81.9    
82.0    
82.1    
82.2    
82.3    
82.4    
82.5    
82.6    
82.8    
82.9    
83.0    
83.1    
83.2    
83.3    
83.4    
83.5    
83.6    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.4    
84.5    
84.6    
84.7    
84.8    
84.9    
85.0    
85.1    
85.2    
85.4    
85.5    
85.6    
85.7    
85.8    
85.9    
86.0    
86.1    
86.2    
86.3    
86.4    
86.6    
86.7    
86.8    
86.9    
87.0    
87.1    
87.2    
87.3    
87.4    
87.5    
87.6    
87.7    
87.9    
88.0    
88.1    
88.2    
88.3    
88.4    
88.5    
88.6    
88.7    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.8    
89.9    
90.0    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.2    
91.3    
91.4    
91.5    
91.6    
91.8    
91.9    
92.0    
92.1    
92.2    
92.3    
92.4    
92.5    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.3    
93.4    
93.5    
93.6    
93.7    
93.8    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.6    
94.7    
94.8    
94.9    
95.0    
95.1    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
95.9    
96.0    
96.1    
96.2    
96.3    
96.4    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.2    
97.3    
97.4    
97.5    
97.6    
97.7    
97.8    
97.9    
98.0    
98.2    
98.3    
98.4    
98.5    
98.6    
98.7    
98.8    
98.9    
99.0    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.8    
99.9    
-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 23982, rend_intergenic: 3726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37903, rend_intergenic: 24062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41480, rend_intergenic: 38044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57398, rend_intergenic: 41997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68276, rend_intergenic: 60789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77522, rend_intergenic: 70292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93737, rend_intergenic: 77914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110220, rend_intergenic: 101783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111798, rend_intergenic: 110442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119016, rend_intergenic: 112235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138777, rend_intergenic: 135581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142646, rend_intergenic: 140874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189104, rend_intergenic: 171786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194710, rend_intergenic: 190022  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