-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_18738629-18947523

-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.9294_t
Valid prediction for snap_scaffold_2-snap.3727-T1
Valid prediction for snap_scaffold_2-snap.3703-T1
Valid prediction for GeneMark_model.9308_t
Valid prediction for GeneMark_model.9304_t
Valid prediction for GlimmerHMM_glimmerT_5711-T1
Valid prediction for GeneMark_model.9279_t
Valid prediction for snap_scaffold_2-snap.3744-T1
Valid prediction for GlimmerHMM_glimmerT_5699-T1
Valid prediction for GlimmerHMM_glimmerT_5713-T1
Valid prediction for snap_scaffold_2-snap.3722-T1
Valid prediction for snap_scaffold_2-snap.3742-T1
Valid prediction for Augustus_model.g3852.t1
Valid prediction for snap_scaffold_2-snap.3741-T1
Valid prediction for snap_scaffold_2-snap.3717-T1
Valid prediction for GeneMark_model.9310_t
Valid prediction for GeneMark_model.9251_t
Valid prediction for GeneMark_model.9266_t
Valid prediction for Augustus_model.g3856.t1
Valid prediction for GeneMark_model.9283_t
Valid prediction for GlimmerHMM_glimmerT_5710-T1
Valid prediction for snap_scaffold_2-snap.3736-T1
Valid prediction for Augustus_model.g3853.t1
Valid prediction for GeneMark_model.9264_t
Valid prediction for snap_scaffold_2-snap.3701-T1
Valid prediction for snap_scaffold_2-snap.3731-T1
Valid prediction for GeneMark_model.9307_t
Valid prediction for GeneMark_model.9268_t
Valid prediction for GeneMark_model.9286_t
Valid prediction for GeneMark_model.9277_t
Valid prediction for snap_scaffold_2-snap.3700-T1
Valid prediction for GlimmerHMM_glimmerT_5716-T1
Valid prediction for snap_scaffold_2-snap.3720-T1
Valid prediction for Augustus_model.g3855.t1
Valid prediction for GeneMark_model.9302_t
Valid prediction for GeneMark_model.9272_t
Valid prediction for snap_scaffold_2-snap.3735-T1
Valid prediction for GeneMark_model.9312_t
Valid prediction for GlimmerHMM_glimmerT_5708-T1
Valid prediction for GeneMark_model.9274_t
Valid prediction for snap_scaffold_2-snap.3699-T1
Valid prediction for GeneMark_model.9282_t
Valid prediction for GeneMark_model.9289_t
Valid prediction for GeneMark_model.9255_t
Valid prediction for GeneMark_model.9296_t
Valid prediction for GeneMark_model.9269_t
Valid prediction for GeneMark_model.9314_t
Valid prediction for GeneMark_model.9253_t
Valid prediction for snap_scaffold_2-snap.3724-T1
Valid prediction for GlimmerHMM_glimmerT_5702-T1
Valid prediction for snap_scaffold_2-snap.3730-T1
Valid prediction for GlimmerHMM_glimmerT_5715-T1
Valid prediction for GlimmerHMM_glimmerT_5719-T1
Valid prediction for GeneMark_model.9257_t
Valid prediction for snap_scaffold_2-snap.3714-T1
Valid prediction for GeneMark_model.9281_t
Valid prediction for GeneMark_model.9259_t
Valid prediction for GeneMark_model.9299_t
Valid prediction for snap_scaffold_2-snap.3708-T1
Valid prediction for GeneMark_model.9292_t
Valid prediction for GeneMark_model.9305_t
Valid prediction for GeneMark_model.9252_t
Valid prediction for snap_scaffold_2-snap.3728-T1
Valid prediction for snap_scaffold_2-snap.3716-T1
Valid prediction for GlimmerHMM_glimmerT_5706-T1
Valid prediction for GeneMark_model.9288_t
Valid prediction for GlimmerHMM_glimmerT_5722-T1
Valid prediction for snap_scaffold_2-snap.3704-T1
Valid prediction for GlimmerHMM_glimmerT_5726-T1
Valid prediction for snap_scaffold_2-snap.3733-T1
Valid prediction for GlimmerHMM_glimmerT_5721-T1
Valid prediction for snap_scaffold_2-snap.3711-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.9263_t
Valid prediction for GeneMark_model.9297_t
Valid prediction for GlimmerHMM_glimmerT_5720-T1
Valid prediction for GeneMark_model.9284_t
Valid prediction for GeneMark_model.9287_t
Valid prediction for snap_scaffold_2-snap.3725-T1
Valid prediction for GeneMark_model.9291_t
Valid prediction for GlimmerHMM_glimmerT_5718-T1
Valid prediction for HiQ_model.g3857.t1
Valid prediction for snap_scaffold_2-snap.3697-T1
Valid prediction for snap_scaffold_2-snap.3702-T1
Valid prediction for GeneMark_model.9275_t
Valid prediction for GlimmerHMM_glimmerT_5717-T1
Valid prediction for GeneMark_model.9250_t
Valid prediction for GeneMark_model.9306_t
Valid prediction for GeneMark_model.9260_t
Valid prediction for snap_scaffold_2-snap.3726-T1
Valid prediction for snap_scaffold_2-snap.3713-T1
Valid prediction for GeneMark_model.9265_t
Valid prediction for GlimmerHMM_glimmerT_5703-T1
Valid prediction for GlimmerHMM_glimmerT_5705-T1
Valid prediction for snap_scaffold_2-snap.3732-T1
Valid prediction for GlimmerHMM_glimmerT_5712-T1
Valid prediction for GeneMark_model.9273_t
Valid prediction for CodingQuarry_transcript_28803-T1
Valid prediction for GlimmerHMM_glimmerT_5700-T1
Valid prediction for GeneMark_model.9278_t
Valid prediction for GeneMark_model.9254_t
Valid prediction for snap_scaffold_2-snap.3707-T1
Valid prediction for GeneMark_model.9313_t
Valid prediction for GeneMark_model.9295_t
Valid prediction for GlimmerHMM_glimmerT_5725-T1
Couldn't classify 178870, 179078
Sorry, prediction pasa_asmbl_23834.p1 fails validation.
(GGT)	 CA	178870-179078	GT	AGG
(ACG)	 AG	179588-179738	GT	TGG
(GAC)	 AG	182530-182727	GT	TGG
(GTT)	 AG	183147-183415	GT	AGG
(GTC)	 AG	183881-184017	GT	AGG
(GTG)	 AG	184891-185012	GT	GGG
(GTG)	 AG	187670-187849	GT	AGG
(GTT)	 AG	188057-188233	AG	GAA
add_exon() Sorry, pasa_asmbl_23834.p1 183881-184017-terminal-2 is invalid.
-recovered pasa_asmbl_23834.p1, terminal, 183881, 184017
-recovered pasa_asmbl_23834.p1, terminal, 188057, 188233
-recovered pasa_asmbl_23834.p1, internal, 179588, 179738
-recovered pasa_asmbl_23834.p1, internal, 182530, 182727
-recovered pasa_asmbl_23834.p1, internal, 183147, 183415
-recovered pasa_asmbl_23834.p1, internal, 183881, 184017
-recovered pasa_asmbl_23834.p1, internal, 184891, 185012
-recovered pasa_asmbl_23834.p1, internal, 187670, 187849
Valid prediction for GeneMark_model.9280_t
Valid prediction for GeneMark_model.9311_t
Valid prediction for GlimmerHMM_glimmerT_5701-T1
Valid prediction for snap_scaffold_2-snap.3729-T1
Valid prediction for snap_scaffold_2-snap.3740-T1
Valid prediction for snap_scaffold_2-snap.3698-T1
Valid prediction for snap_scaffold_2-snap.3705-T1
Valid prediction for GeneMark_model.9271_t
Valid prediction for GeneMark_model.9309_t
Valid prediction for snap_scaffold_2-snap.3719-T1
Couldn't classify 169810, 169962
Sorry, prediction pasa_asmbl_23842.p1 fails validation.
(ATG)	 AC	167978-168448	GT	AGG
(GAC)	 AG	169810-169962	TA	GCT
-recovered pasa_asmbl_23842.p1, initial, 167978, 168448
Valid prediction for GeneMark_model.9315_t
Valid prediction for GlimmerHMM_glimmerT_5724-T1
Couldn't classify 37192, 37638
Sorry, prediction pasa_asmbl_23847.p1 fails validation.
(CAT)	 CC	37192-37638	AC	AGA
Valid prediction for HiQ_model.g3851.t1
Valid prediction for snap_scaffold_2-snap.3745-T1
Valid prediction for GeneMark_model.9256_t
Valid prediction for snap_scaffold_2-snap.3715-T1
Valid prediction for snap_scaffold_2-snap.3721-T1
Valid prediction for Augustus_model.g3858.t1
Valid prediction for GlimmerHMM_glimmerT_5704-T1
Valid prediction for GeneMark_model.9262_t
Valid prediction for snap_scaffold_2-snap.3739-T1
Valid prediction for GlimmerHMM_glimmerT_5723-T1
Valid prediction for GeneMark_model.9293_t
Valid prediction for GlimmerHMM_glimmerT_5707-T1
Valid prediction for snap_scaffold_2-snap.3723-T1
Valid prediction for Augustus_model.g3854.t1
Valid prediction for snap_scaffold_2-snap.3738-T1
Valid prediction for GeneMark_model.9276_t
Valid prediction for Augustus_model.g3850.t1
Valid prediction for GlimmerHMM_glimmerT_5714-T1
Valid prediction for GeneMark_model.9258_t
Valid prediction for snap_scaffold_2-snap.3706-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GeneMark_model.9298_t
Valid prediction for GeneMark_model.9301_t
Valid prediction for GeneMark_model.9270_t
Valid prediction for snap_scaffold_2-snap.3718-T1
Valid prediction for GeneMark_model.9285_t
Valid prediction for snap_scaffold_2-snap.3734-T1
Valid prediction for snap_scaffold_2-snap.3743-T1
Valid prediction for snap_scaffold_2-snap.3712-T1
Valid prediction for GeneMark_model.9303_t
Valid prediction for snap_scaffold_2-snap.3737-T1
Valid prediction for snap_scaffold_2-snap.3709-T1
Valid prediction for GeneMark_model.9261_t
Valid prediction for GlimmerHMM_glimmerT_5709-T1
Valid prediction for snap_scaffold_2-snap.3710-T1
Valid prediction for GeneMark_model.9316_t
Valid prediction for snap_scaffold_2-snap.3746-T1
Valid prediction for GeneMark_model.9300_t
Valid prediction for CodingQuarry_transcript_28804-T1
Valid prediction for GeneMark_model.9267_t
Valid prediction for pasa_asmbl_23849.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13438, rend_intergenic: 11634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24009, rend_intergenic: 20663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26977, rend_intergenic: 24893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30062, rend_intergenic: 28552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52130, rend_intergenic: 49789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54693, rend_intergenic: 52716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56878, rend_intergenic: 54719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75624, rend_intergenic: 57599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81819, rend_intergenic: 76789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98024, rend_intergenic: 83869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111690, rend_intergenic: 99324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114297, rend_intergenic: 112168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115883, rend_intergenic: 114592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120408, rend_intergenic: 116919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124108, rend_intergenic: 121730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126014, rend_intergenic: 124414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128959, rend_intergenic: 126363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136725, rend_intergenic: 129432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137434, rend_intergenic: 137261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142652, rend_intergenic: 137832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149651, rend_intergenic: 142656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154018, rend_intergenic: 151913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166210, rend_intergenic: 154630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171992, rend_intergenic: 166553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189918, rend_intergenic: 182308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203402, rend_intergenic: 194640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208895
-exon list size: 794


building trellis

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69.3    
69.5    
69.6    
69.7    
69.8    
70.0    
70.1    
70.2    
70.4    
70.5    
70.6    
70.7    
70.9    
71.0    
71.1    
71.2    
71.4    
71.5    
71.6    
71.7    
71.9    
72.0    
72.1    
72.2    
72.4    
72.5    
72.6    
72.7    
72.9    
73.0    
73.1    
73.2    
73.4    
73.5    
73.6    
73.7    
73.9    
74.0    
74.1    
74.2    
74.4    
74.5    
74.6    
74.7    
74.9    
75.0    
75.1    
75.3    
75.4    
75.5    
75.6    
75.8    
75.9    
76.0    
76.1    
76.3    
76.4    
76.5    
76.6    
76.8    
76.9    
77.0    
77.1    
77.3    
77.4    
77.5    
77.6    
77.8    
77.9    
78.0    
78.1    
78.3    
78.4    
78.5    
78.6    
78.8    
78.9    
79.0    
79.1    
79.3    
79.4    
79.5    
79.6    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.5    
80.7    
80.8    
80.9    
81.0    
81.2    
81.3    
81.4    
81.5    
81.7    
81.8    
81.9    
82.0    
82.2    
82.3    
82.4    
82.5    
82.7    
82.8    
82.9    
83.0    
83.2    
83.3    
83.4    
83.5    
83.7    
83.8    
83.9    
84.0    
84.2    
84.3    
84.4    
84.5    
84.7    
84.8    
84.9    
85.1    
85.2    
85.3    
85.4    
85.6    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.4    
86.6    
86.7    
86.8    
86.9    
87.1    
87.2    
87.3    
87.4    
87.6    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.4    
88.6    
88.7    
88.8    
88.9    
89.1    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.3    
91.5    
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    
93.3    
93.5    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.2    
96.4    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.2    
98.4    
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 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 13438, rend_intergenic: 11634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24009, rend_intergenic: 20663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26977, rend_intergenic: 24893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30062, rend_intergenic: 28552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52130, rend_intergenic: 49789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54693, rend_intergenic: 52716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56878, rend_intergenic: 54719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75624, rend_intergenic: 57599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81819, rend_intergenic: 76789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98024, rend_intergenic: 83869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111690, rend_intergenic: 99324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114297, rend_intergenic: 112168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115883, rend_intergenic: 114592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120408, rend_intergenic: 116919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124108, rend_intergenic: 121730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126014, rend_intergenic: 124414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128959, rend_intergenic: 126363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136725, rend_intergenic: 129432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137434, rend_intergenic: 137261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142652, rend_intergenic: 137832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149651, rend_intergenic: 142656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154018, rend_intergenic: 151913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166210, rend_intergenic: 154630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171992, rend_intergenic: 166553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189918, rend_intergenic: 182308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203402, rend_intergenic: 194640  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

-building DP trellis

-building trellis in range 196407 - 208895
-exon list size: 24


building trellis

3.8    
7.7    
11.5    
15.4    
19.2    
23.1    
26.9    
30.8    
34.6    
38.5    
42.3    
46.2    
50.0    
53.8    
57.7    
61.5    
65.4    
69.2    
73.1    
76.9    
80.8    
84.6    
88.5    
92.3    
96.2    
-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