-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_10255267-10436305

-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.92064_t
Valid prediction for snap_scaffold_23-snap.1990-T1
Valid prediction for GeneMark_model.92062_t
Valid prediction for snap_scaffold_23-snap.2012-T1
Valid prediction for snap_scaffold_23-snap.2021-T1
Valid prediction for Augustus_model.g35582.t1
Valid prediction for GeneMark_model.92079_t
Valid prediction for GlimmerHMM_glimmerT_52987-T1
Valid prediction for GlimmerHMM_glimmerT_52988-T1
Valid prediction for GeneMark_model.92027_t
Valid prediction for pasa_asmbl_31149.p1
Valid prediction for GeneMark_model.92085_t
Valid prediction for GlimmerHMM_glimmerT_52981-T1
Valid prediction for GeneMark_model.92038_t
Valid prediction for GeneMark_model.92083_t
Couldn't classify 88959, 89192
Sorry, prediction pasa_asmbl_31147.p1 fails validation.
(ATG)	 AC	86905-86974	GT	AGG
(GCT)	 AG	88583-88710	GT	AGG
(GCA)	 AG	88959-89192	TC	GGT
-recovered pasa_asmbl_31147.p1, initial, 86905, 86974
-recovered pasa_asmbl_31147.p1, internal, 88583, 88710
Valid prediction for Augustus_model.g35586.t1
Couldn't classify 157949, 158081
Couldn't classify 158640, 158785
Sorry, prediction pasa_asmbl_31154.p2 fails validation.
(CCA)	 GG	157949-158081	GT	GGG
(ACT)	 AG	158303-158461	GT	AGG
(ACG)	 AG	158640-158785	AC	CTA
-recovered pasa_asmbl_31154.p2, internal, 158303, 158461
Valid prediction for GlimmerHMM_glimmerT_52982-T1
Valid prediction for snap_scaffold_23-snap.2016-T1
Valid prediction for GeneMark_model.92043_t
Valid prediction for GeneMark_model.92060_t
Valid prediction for Augustus_model.g35590.t1
Valid prediction for Augustus_model.g35580.t1
Valid prediction for GlimmerHMM_glimmerT_52977-T1
Valid prediction for Augustus_model.g35581.t1
Valid prediction for GeneMark_model.92072_t
Valid prediction for snap_scaffold_23-snap.2018-T1
Valid prediction for Augustus_model.g35589.t1
Valid prediction for GeneMark_model.92082_t
Valid prediction for snap_scaffold_23-snap.2002-T1
Valid prediction for GeneMark_model.92025_t
Valid prediction for GeneMark_model.92024_t
Valid prediction for GeneMark_model.92058_t
Valid prediction for snap_scaffold_23-snap.2009-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.1993-T1
Valid prediction for CodingQuarry_transcript_35726-T1
Valid prediction for GeneMark_model.92041_t
Valid prediction for GlimmerHMM_glimmerT_52972-T1
Valid prediction for GeneMark_model.92056_t
Valid prediction for GeneMark_model.92044_t
Couldn't classify 147049, 147090
Couldn't classify 149732, 149814
Sorry, prediction pasa_asmbl_31151.p2 fails validation.
(AGG)	 AG	147049-147090	GT	AGG
(GGA)	 AG	147383-147461	GT	AAG
(ACG)	 AG	148001-148122	GT	GGG
(CAC)	 AG	148769-148850	GT	AAG
(CAG)	 AG	149732-149814	GA	GGG
-recovered pasa_asmbl_31151.p2, internal, 147049, 147090
-recovered pasa_asmbl_31151.p2, internal, 147383, 147461
-recovered pasa_asmbl_31151.p2, internal, 148001, 148122
-recovered pasa_asmbl_31151.p2, internal, 148769, 148850
Valid prediction for GeneMark_model.92080_t
Valid prediction for Augustus_model.g35578.t1
Valid prediction for CodingQuarry_transcript_35728-T1
Valid prediction for GeneMark_model.92035_t
Valid prediction for GeneMark_model.92077_t
Valid prediction for CodingQuarry_transcript_35727-T1
Valid prediction for GlimmerHMM_glimmerT_52984-T1
Valid prediction for snap_scaffold_23-snap.2008-T1
Valid prediction for snap_scaffold_23-snap.2005-T1
Valid prediction for GlimmerHMM_glimmerT_52973-T1
Valid prediction for GlimmerHMM_glimmerT_52986-T1
Valid prediction for GeneMark_model.92087_t
Valid prediction for snap_scaffold_23-snap.2006-T1
Valid prediction for GeneMark_model.92075_t
Valid prediction for snap_scaffold_23-snap.2001-T1
Valid prediction for GeneMark_model.92047_t
Valid prediction for snap_scaffold_23-snap.1991-T1
Valid prediction for GeneMark_model.92029_t
Valid prediction for GeneMark_model.92068_t
Couldn't classify 152058, 152163
Couldn't classify 156164, 156236
Sorry, prediction pasa_asmbl_31153.p1 fails validation.
(GCC)	 AC	152058-152163	GT	CGG
(GCT)	 AG	154131-154354	GT	AGG
(ACG)	 AG	155087-155276	GT	AGG
(CTC)	 AG	155610-155916	GT	ATG
(GAC)	 AG	156164-156236	AT	CCA
add_exon() Sorry, pasa_asmbl_31153.p1 155087-155276-terminal-3 is invalid.
-recovered pasa_asmbl_31153.p1, terminal, 155087, 155276
-recovered pasa_asmbl_31153.p1, internal, 154131, 154354
-recovered pasa_asmbl_31153.p1, internal, 155087, 155276
-recovered pasa_asmbl_31153.p1, internal, 155610, 155916
Valid prediction for snap_scaffold_23-snap.1997-T1
Valid prediction for GlimmerHMM_glimmerT_52971-T1
Valid prediction for snap_scaffold_23-snap.1996-T1
Valid prediction for GeneMark_model.92070_t
Valid prediction for GeneMark_model.92049_t
Valid prediction for pasa_asmbl_31142.p1
Valid prediction for GeneMark_model.92054_t
Valid prediction for snap_scaffold_23-snap.1999-T1
Valid prediction for GeneMark_model.92052_t
Valid prediction for GeneMark_model.92066_t
Valid prediction for GeneMark_model.92045_t
Valid prediction for Augustus_model.g35588.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.92086_t
Valid prediction for Augustus_model.g35584.t1
Valid prediction for GeneMark_model.92057_t
Valid prediction for GeneMark_model.92050_t
Valid prediction for GeneMark_model.92073_t
Valid prediction for snap_scaffold_23-snap.2007-T1
Valid prediction for HiQ_model.g35585.t1
Valid prediction for GeneMark_model.92084_t
Valid prediction for snap_scaffold_23-snap.2019-T1
Valid prediction for snap_scaffold_23-snap.2000-T1
Valid prediction for GeneMark_model.92067_t
Valid prediction for GeneMark_model.92055_t
Valid prediction for GeneMark_model.92071_t
Valid prediction for GeneMark_model.92032_t
Valid prediction for snap_scaffold_23-snap.1989-T1
Valid prediction for snap_scaffold_23-snap.2011-T1
Valid prediction for GlimmerHMM_glimmerT_52979-T1
Valid prediction for snap_scaffold_23-snap.2020-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.92046_t
Valid prediction for GlimmerHMM_glimmerT_52975-T1
Valid prediction for snap_scaffold_23-snap.1988-T1
Valid prediction for GeneMark_model.92030_t
Valid prediction for Augustus_model.g35591.t1
Valid prediction for pasa_asmbl_31858.p1
Valid prediction for GeneMark_model.92063_t
Valid prediction for GeneMark_model.92042_t
Valid prediction for Augustus_model.g35587.t1
Valid prediction for snap_scaffold_23-snap.2015-T1
Valid prediction for snap_scaffold_23-snap.2017-T1
Valid prediction for snap_scaffold_23-snap.2003-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.1998-T1
Valid prediction for GeneMark_model.92053_t
Valid prediction for GeneMark_model.92034_t
Valid prediction for GeneMark_model.92065_t
Valid prediction for GlimmerHMM_glimmerT_52980-T1
Valid prediction for CodingQuarry_transcript_35724-T1
Valid prediction for GeneMark_model.92026_t
Valid prediction for snap_scaffold_23-snap.2023-T1
Valid prediction for GlimmerHMM_glimmerT_52978-T1
Valid prediction for GeneMark_model.92069_t
Valid prediction for snap_scaffold_23-snap.2014-T1
Valid prediction for GeneMark_model.92059_t
Valid prediction for GeneMark_model.92028_t
Valid prediction for GeneMark_model.92074_t
Valid prediction for snap_scaffold_23-snap.2010-T1
Valid prediction for GeneMark_model.92048_t
Valid prediction for CodingQuarry_transcript_35725-T1
Valid prediction for snap_scaffold_23-snap.2022-T1
Valid prediction for snap_scaffold_23-snap.1992-T1
Valid prediction for snap_scaffold_23-snap.2004-T1
Sorry, intron length (7) is less than minimum required (10)
Couldn't classify 177063, 177926
Sorry, prediction pasa_asmbl_31856.p1 fails validation.
(GGT)	 CA	177063-177926	GA	GAG
Valid prediction for snap_scaffold_23-snap.2024-T1
Valid prediction for GlimmerHMM_glimmerT_52970-T1
Valid prediction for GeneMark_model.92036_t
Valid prediction for Augustus_model.g35583.t1
Valid prediction for snap_scaffold_23-snap.1995-T1
Valid prediction for GeneMark_model.92081_t
Valid prediction for Augustus_model.g35579.t1
Valid prediction for GlimmerHMM_glimmerT_52983-T1
Valid prediction for snap_scaffold_23-snap.1994-T1
Valid prediction for GlimmerHMM_glimmerT_52974-T1
Valid prediction for GeneMark_model.92051_t
Valid prediction for snap_scaffold_23-snap.2013-T1
Valid prediction for GeneMark_model.92076_t
Valid prediction for GeneMark_model.92040_t
Valid prediction for GlimmerHMM_glimmerT_52976-T1
Valid prediction for GeneMark_model.92078_t
Valid prediction for GeneMark_model.92061_t
Valid prediction for GlimmerHMM_glimmerT_52985-T1
Valid prediction for GeneMark_model.92039_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22725, rend_intergenic: 10066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27669, rend_intergenic: 22804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35202, rend_intergenic: 30281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42673, rend_intergenic: 39398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69830, rend_intergenic: 66895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78287, rend_intergenic: 72344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85923, rend_intergenic: 81294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90419, rend_intergenic: 87851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99689, rend_intergenic: 94226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120460, rend_intergenic: 102764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131258, rend_intergenic: 120525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134787, rend_intergenic: 131297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135798, rend_intergenic: 134794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154387, rend_intergenic: 135841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155269, rend_intergenic: 154809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161842, rend_intergenic: 155500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 181039
-exon list size: 832


building trellis

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77.6    
77.7    
77.8    
77.9    
78.1    
78.2    
78.3    
78.4    
78.5    
78.7    
78.8    
78.9    
79.0    
79.1    
79.3    
79.4    
79.5    
79.6    
79.7    
79.9    
80.0    
80.1    
80.2    
80.3    
80.5    
80.6    
80.7    
80.8    
80.9    
81.1    
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    
83.3    
83.5    
83.6    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.4    
84.5    
84.7    
84.8    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.6    
85.7    
85.9    
86.0    
86.1    
86.2    
86.3    
86.5    
86.6    
86.7    
86.8    
86.9    
87.1    
87.2    
87.3    
87.4    
87.5    
87.6    
87.8    
87.9    
88.0    
88.1    
88.2    
88.4    
88.5    
88.6    
88.7    
88.8    
89.0    
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    
91.2    
91.4    
91.5    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 22725, rend_intergenic: 10066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27669, rend_intergenic: 22804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35202, rend_intergenic: 30281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42673, rend_intergenic: 39398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69830, rend_intergenic: 66895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78287, rend_intergenic: 72344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85923, rend_intergenic: 81294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90419, rend_intergenic: 87851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99689, rend_intergenic: 94226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120460, rend_intergenic: 102764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131258, rend_intergenic: 120525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134787, rend_intergenic: 131297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135798, rend_intergenic: 134794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154387, rend_intergenic: 135841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155269, rend_intergenic: 154809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161842, rend_intergenic: 155500  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 161418 - 181039
-exon list size: 42


building trellis

2.3    
4.5    
6.8    
9.1    
11.4    
13.6    
15.9    
18.2    
20.5    
22.7    
25.0    
27.3    
29.5    
31.8    
34.1    
36.4    
38.6    
40.9    
43.2    
45.5    
47.7    
50.0    
52.3    
54.5    
56.8    
59.1    
61.4    
63.6    
65.9    
68.2    
70.5    
72.7    
75.0    
77.3    
79.5    
81.8    
84.1    
86.4    
88.6    
90.9    
93.2    
95.5    
97.7    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 167530 - 181039
-exon list size: 23


building trellis

4.0    
8.0    
12.0    
16.0    
20.0    
24.0    
28.0    
32.0    
36.0    
40.0    
44.0    
48.0    
52.0    
56.0    
60.0    
64.0    
68.0    
72.0    
76.0    
80.0    
84.0    
88.0    
92.0    
96.0    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 169221 - 181039
-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
GOT 5prime partial gene.

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