-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_10341708-10536122

-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_32989-T1
Couldn't classify 99367, 99551
Sorry, prediction pasa_asmbl_11226.p2 fails validation.
(GGA)	 CA	99367-99551	GT	AAG
(TGG)	 AG	100268-100323	GT	TGG
(AGA)	 AG	100748-100869	GG	AAG
-recovered pasa_asmbl_11226.p2, terminal, 100748, 100869
-recovered pasa_asmbl_11226.p2, internal, 100268, 100323
Valid prediction for GlimmerHMM_glimmerT_33006-T1
Valid prediction for snap_scaffold_13-snap.1898-T1
Valid prediction for GeneMark_model.56301_t
Valid prediction for snap_scaffold_13-snap.1934-T1
Valid prediction for Augustus_model.g22161.t1
Valid prediction for GeneMark_model.56276_t
Valid prediction for snap_scaffold_13-snap.1911-T1
Valid prediction for snap_scaffold_13-snap.1930-T1
Valid prediction for GlimmerHMM_glimmerT_32986-T1
Valid prediction for GlimmerHMM_glimmerT_32988-T1
Valid prediction for GeneMark_model.56270_t
Valid prediction for GeneMark_model.56309_t
Valid prediction for GlimmerHMM_glimmerT_32990-T1
Valid prediction for GeneMark_model.56305_t
Valid prediction for snap_scaffold_13-snap.1907-T1
Valid prediction for Augustus_model.g22156.t1
Valid prediction for GeneMark_model.56297_t
Valid prediction for GeneMark_model.56286_t
Valid prediction for snap_scaffold_13-snap.1924-T1
Valid prediction for GeneMark_model.56283_t
Valid prediction for GlimmerHMM_glimmerT_33005-T1
Valid prediction for GeneMark_model.56268_t
Valid prediction for GeneMark_model.56263_t
Valid prediction for snap_scaffold_13-snap.1908-T1
Valid prediction for GeneMark_model.56277_t
Valid prediction for GeneMark_model.56289_t
Valid prediction for GeneMark_model.56272_t
Valid prediction for GeneMark_model.56257_t
Valid prediction for Augustus_model.g22159.t1
Valid prediction for GlimmerHMM_glimmerT_32997-T1
Couldn't classify 94899, 95024
Sorry, prediction pasa_asmbl_11225.p2 fails validation.
(ATG)	 GT	91562-91591	GT	AAG
(ACG)	 AG	91750-91792	GT	TGG
(CCC)	 AG	93770-93891	GT	AGG
(AGA)	 AG	94899-95024	TT	GGT
-recovered pasa_asmbl_11225.p2, initial, 91562, 91591
-recovered pasa_asmbl_11225.p2, internal, 91750, 91792
-recovered pasa_asmbl_11225.p2, internal, 93770, 93891
Valid prediction for Augustus_model.g22162.t1
Valid prediction for GeneMark_model.56253_t
Valid prediction for GlimmerHMM_glimmerT_33000-T1
Valid prediction for GlimmerHMM_glimmerT_33004-T1
Valid prediction for GlimmerHMM_glimmerT_32977-T1
Valid prediction for Augustus_model.g22167.t1
Valid prediction for GlimmerHMM_glimmerT_32996-T1
Valid prediction for GeneMark_model.56259_t
Valid prediction for GlimmerHMM_glimmerT_32978-T1
Valid prediction for snap_scaffold_13-snap.1932-T1
Valid prediction for snap_scaffold_13-snap.1913-T1
Valid prediction for GeneMark_model.56249_t
Valid prediction for snap_scaffold_13-snap.1904-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.1922-T1
Valid prediction for GeneMark_model.56307_t
Valid prediction for GlimmerHMM_glimmerT_32980-T1
Valid prediction for GeneMark_model.56252_t
Valid prediction for GeneMark_model.56274_t
Valid prediction for GeneMark_model.56303_t
Valid prediction for GeneMark_model.56279_t
Valid prediction for snap_scaffold_13-snap.1937-T1
Valid prediction for snap_scaffold_13-snap.1928-T1
Valid prediction for GeneMark_model.56256_t
Valid prediction for GeneMark_model.56251_t
Valid prediction for Augustus_model.g22163.t1
Valid prediction for snap_scaffold_13-snap.1901-T1
Valid prediction for Augustus_model.g22170.t1
Valid prediction for GeneMark_model.56313_t
Valid prediction for Augustus_model.g22157.t1
Valid prediction for snap_scaffold_13-snap.1914-T1
Valid prediction for GeneMark_model.56296_t
Valid prediction for snap_scaffold_13-snap.1933-T1
Valid prediction for GeneMark_model.56266_t
Valid prediction for snap_scaffold_13-snap.1917-T1
Valid prediction for GeneMark_model.56281_t
Valid prediction for snap_scaffold_13-snap.1936-T1
Valid prediction for Augustus_model.g22160.t1
Valid prediction for snap_scaffold_13-snap.1912-T1
Valid prediction for snap_scaffold_13-snap.1925-T1
Valid prediction for GlimmerHMM_glimmerT_32987-T1
Valid prediction for GeneMark_model.56308_t
Valid prediction for GlimmerHMM_glimmerT_32992-T1
Valid prediction for GeneMark_model.56255_t
Valid prediction for GeneMark_model.56293_t
Valid prediction for GeneMark_model.56295_t
Valid prediction for GlimmerHMM_glimmerT_32984-T1
Valid prediction for GeneMark_model.56311_t

-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_13-snap.1905-T1
Valid prediction for snap_scaffold_13-snap.1910-T1
Valid prediction for snap_scaffold_13-snap.1902-T1
Valid prediction for GeneMark_model.56291_t
Valid prediction for GlimmerHMM_glimmerT_33002-T1
Valid prediction for snap_scaffold_13-snap.1926-T1
Valid prediction for GeneMark_model.56306_t
Valid prediction for GeneMark_model.56269_t
Valid prediction for GeneMark_model.56284_t
Valid prediction for snap_scaffold_13-snap.1935-T1
Valid prediction for GeneMark_model.56280_t
Valid prediction for snap_scaffold_13-snap.1919-T1
Valid prediction for GeneMark_model.56250_t
Valid prediction for GlimmerHMM_glimmerT_32979-T1
Valid prediction for GeneMark_model.56271_t
Valid prediction for GlimmerHMM_glimmerT_32994-T1
Valid prediction for GlimmerHMM_glimmerT_33003-T1
Valid prediction for snap_scaffold_13-snap.1906-T1
Valid prediction for snap_scaffold_13-snap.1903-T1
Valid prediction for GeneMark_model.56302_t
Valid prediction for snap_scaffold_13-snap.1918-T1
Valid prediction for snap_scaffold_13-snap.1915-T1
Valid prediction for GlimmerHMM_glimmerT_32998-T1
Valid prediction for GeneMark_model.56292_t
Valid prediction for GeneMark_model.56261_t
Valid prediction for GeneMark_model.56304_t
Valid prediction for Augustus_model.g22158.t1
Valid prediction for GlimmerHMM_glimmerT_32993-T1
Valid prediction for GlimmerHMM_glimmerT_32995-T1
Valid prediction for GeneMark_model.56278_t
Valid prediction for snap_scaffold_13-snap.1916-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_32985-T1
Valid prediction for snap_scaffold_13-snap.1931-T1
Valid prediction for GeneMark_model.56264_t
Valid prediction for GeneMark_model.56254_t
Valid prediction for snap_scaffold_13-snap.1938-T1
Valid prediction for GlimmerHMM_glimmerT_33001-T1
Valid prediction for GeneMark_model.56294_t
Valid prediction for GlimmerHMM_glimmerT_32983-T1
Valid prediction for GeneMark_model.56275_t
Valid prediction for snap_scaffold_13-snap.1900-T1
Valid prediction for GeneMark_model.56300_t
Valid prediction for snap_scaffold_13-snap.1909-T1
Valid prediction for GeneMark_model.56287_t
Valid prediction for GeneMark_model.56273_t
Valid prediction for GeneMark_model.56258_t
Valid prediction for Augustus_model.g22168.t1
Valid prediction for GeneMark_model.56282_t
Valid prediction for snap_scaffold_13-snap.1920-T1
Valid prediction for Augustus_model.g22164.t1
Valid prediction for snap_scaffold_13-snap.1897-T1
Valid prediction for GeneMark_model.56288_t
Valid prediction for snap_scaffold_13-snap.1921-T1
Valid prediction for GlimmerHMM_glimmerT_32982-T1
Valid prediction for GlimmerHMM_glimmerT_32991-T1
Valid prediction for GlimmerHMM_glimmerT_32981-T1
Valid prediction for Augustus_model.g22169.t1
Valid prediction for GeneMark_model.56267_t
Valid prediction for Augustus_model.g22166.t1
Valid prediction for GeneMark_model.56265_t
Valid prediction for GlimmerHMM_glimmerT_32999-T1
Valid prediction for snap_scaffold_13-snap.1899-T1
Valid prediction for GlimmerHMM_glimmerT_32976-T1
Valid prediction for Augustus_model.g22165.t1
Valid prediction for GeneMark_model.56260_t
Valid prediction for GeneMark_model.56298_t
Valid prediction for GeneMark_model.56312_t
Valid prediction for snap_scaffold_13-snap.1923-T1
Valid prediction for snap_scaffold_13-snap.1929-T1
Valid prediction for GeneMark_model.56262_t
Valid prediction for GeneMark_model.56285_t
Valid prediction for GeneMark_model.56310_t
Valid prediction for GeneMark_model.56290_t
Valid prediction for snap_scaffold_13-snap.1927-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15033, rend_intergenic: 5914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22840, rend_intergenic: 20936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35340, rend_intergenic: 22872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41390, rend_intergenic: 35626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49656, rend_intergenic: 41413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56162, rend_intergenic: 55196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72700, rend_intergenic: 61511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85116, rend_intergenic: 73072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105890, rend_intergenic: 95979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110983, rend_intergenic: 106231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159033, rend_intergenic: 158524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166321, rend_intergenic: 165913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175612, rend_intergenic: 171596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193446, rend_intergenic: 180776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 194415
-exon list size: 781


building trellis

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90.0    
90.2    
90.3    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.7    
93.9    
94.0    
94.1    
94.3    
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    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 15033, rend_intergenic: 5914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22840, rend_intergenic: 20936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35340, rend_intergenic: 22872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41390, rend_intergenic: 35626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49656, rend_intergenic: 41413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56162, rend_intergenic: 55196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72700, rend_intergenic: 61511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85116, rend_intergenic: 73072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105890, rend_intergenic: 95979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110983, rend_intergenic: 106231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159033, rend_intergenic: 158524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166321, rend_intergenic: 165913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175612, rend_intergenic: 171596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193446, rend_intergenic: 180776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 20917
-exon list size: 54


building trellis

1.8    
3.6    
5.4    
7.1    
8.9    
10.7    
12.5    
14.3    
16.1    
17.9    
19.6    
21.4    
23.2    
25.0    
26.8    
28.6    
30.4    
32.1    
33.9    
35.7    
37.5    
39.3    
41.1    
42.9    
44.6    
46.4    
48.2    
50.0    
51.8    
53.6    
55.4    
57.1    
58.9    
60.7    
62.5    
64.3    
66.1    
67.9    
69.6    
71.4    
73.2    
75.0    
76.8    
78.6    
80.4    
82.1    
83.9    
85.7    
87.5    
89.3    
91.1    
92.9    
94.6    
96.4    
98.2    
-found 5 predictions from path traversal

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