-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_152353-352426

-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.37270_t
Valid prediction for GeneMark_model.37253_t
Valid prediction for GeneMark_model.37299_t
Valid prediction for snap_scaffold_9-snap.48-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GeneMark_model.37247_t
Valid prediction for GlimmerHMM_glimmerT_21931-T1
Valid prediction for snap_scaffold_9-snap.47-T1
Valid prediction for GeneMark_model.37276_t
Valid prediction for GlimmerHMM_glimmerT_21933-T1
Valid prediction for GeneMark_model.37263_t
Valid prediction for GlimmerHMM_glimmerT_21949-T1
Valid prediction for GeneMark_model.37283_t
Valid prediction for GeneMark_model.37304_t
Valid prediction for GeneMark_model.37268_t
Valid prediction for GeneMark_model.37286_t
Valid prediction for GeneMark_model.37264_t
Valid prediction for Augustus_model.g14694.t1
Valid prediction for snap_scaffold_9-snap.45-T1
Valid prediction for GeneMark_model.37295_t
Valid prediction for GlimmerHMM_glimmerT_21946-T1
Valid prediction for GlimmerHMM_glimmerT_21929-T1
Valid prediction for Augustus_model.g14693.t1
Valid prediction for snap_scaffold_9-snap.58-T1
Valid prediction for GlimmerHMM_glimmerT_21941-T1
Valid prediction for snap_scaffold_9-snap.61-T1
Valid prediction for GeneMark_model.37311_t
Couldn't classify 198707, 198946
Couldn't classify 199275, 199343
Sorry, prediction pasa_asmbl_54742.p2 fails validation.
(GAG)	 AC	198707-198946	GT	AGG
(GTG)	 AG	199275-199343	AA	GTA
Valid prediction for snap_scaffold_9-snap.68-T1
Valid prediction for GeneMark_model.37261_t
Valid prediction for snap_scaffold_9-snap.59-T1
Valid prediction for GeneMark_model.37310_t
Valid prediction for snap_scaffold_9-snap.55-T1
Valid prediction for GeneMark_model.37282_t
Valid prediction for GeneMark_model.37306_t
Valid prediction for GeneMark_model.37289_t
Valid prediction for GeneMark_model.37309_t
Valid prediction for snap_scaffold_9-snap.42-T1
Valid prediction for GeneMark_model.37293_t
Valid prediction for GeneMark_model.37302_t
Valid prediction for GeneMark_model.37307_t
Valid prediction for snap_scaffold_9-snap.62-T1
Valid prediction for snap_scaffold_9-snap.40-T1
Valid prediction for GeneMark_model.37272_t
Valid prediction for GeneMark_model.37313_t
Valid prediction for GeneMark_model.37251_t
Valid prediction for snap_scaffold_9-snap.66-T1
Valid prediction for Augustus_model.g14695.t1
Valid prediction for GlimmerHMM_glimmerT_21935-T1
Valid prediction for snap_scaffold_9-snap.43-T1
Valid prediction for snap_scaffold_9-snap.50-T1
Valid prediction for GeneMark_model.37249_t
Valid prediction for GeneMark_model.37287_t
Valid prediction for GeneMark_model.37266_t
Valid prediction for GeneMark_model.37252_t
Valid prediction for GeneMark_model.37273_t
Valid prediction for GeneMark_model.37256_t
Valid prediction for GlimmerHMM_glimmerT_21940-T1
Valid prediction for GeneMark_model.37258_t
Valid prediction for GlimmerHMM_glimmerT_21932-T1
Valid prediction for GeneMark_model.37278_t
Valid prediction for GlimmerHMM_glimmerT_21944-T1
Valid prediction for GlimmerHMM_glimmerT_21945-T1
Valid prediction for GeneMark_model.37275_t
Valid prediction for snap_scaffold_9-snap.52-T1
Valid prediction for GlimmerHMM_glimmerT_21942-T1
Valid prediction for GeneMark_model.37280_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_9-snap.46-T1
Valid prediction for GeneMark_model.37301_t
Valid prediction for GeneMark_model.37255_t
Valid prediction for snap_scaffold_9-snap.74-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.37254_t
Valid prediction for snap_scaffold_9-snap.65-T1
Valid prediction for GeneMark_model.37279_t
Valid prediction for GlimmerHMM_glimmerT_21939-T1
Valid prediction for snap_scaffold_9-snap.72-T1
Valid prediction for GeneMark_model.37260_t
Valid prediction for GeneMark_model.37246_t
Valid prediction for GeneMark_model.37265_t
Valid prediction for GeneMark_model.37281_t
Valid prediction for snap_scaffold_9-snap.51-T1
Valid prediction for GlimmerHMM_glimmerT_21943-T1
Valid prediction for snap_scaffold_9-snap.71-T1
Valid prediction for GeneMark_model.37312_t
Valid prediction for GlimmerHMM_glimmerT_21934-T1
Valid prediction for snap_scaffold_9-snap.67-T1
Valid prediction for snap_scaffold_9-snap.49-T1
Valid prediction for GeneMark_model.37248_t
Valid prediction for GlimmerHMM_glimmerT_21950-T1
Valid prediction for GeneMark_model.37267_t
Valid prediction for GlimmerHMM_glimmerT_21936-T1
Valid prediction for GeneMark_model.37305_t
Valid prediction for snap_scaffold_9-snap.75-T1
Valid prediction for GeneMark_model.37298_t
Valid prediction for snap_scaffold_9-snap.39-T1
Valid prediction for GeneMark_model.37292_t
Valid prediction for snap_scaffold_9-snap.69-T1
Valid prediction for GeneMark_model.37269_t
Valid prediction for GeneMark_model.37308_t
Valid prediction for GeneMark_model.37297_t
Valid prediction for GlimmerHMM_glimmerT_21938-T1
Valid prediction for GeneMark_model.37300_t
Valid prediction for snap_scaffold_9-snap.56-T1
Valid prediction for snap_scaffold_9-snap.76-T1
Valid prediction for snap_scaffold_9-snap.54-T1
Valid prediction for GeneMark_model.37296_t
Valid prediction for GlimmerHMM_glimmerT_21937-T1
Valid prediction for snap_scaffold_9-snap.41-T1
Valid prediction for GeneMark_model.37259_t
Valid prediction for GeneMark_model.37315_t
Valid prediction for GeneMark_model.37257_t
Valid prediction for snap_scaffold_9-snap.64-T1
Valid prediction for GeneMark_model.37250_t
Valid prediction for GeneMark_model.37291_t
Valid prediction for GlimmerHMM_glimmerT_21930-T1
Valid prediction for GeneMark_model.37285_t
Valid prediction for GeneMark_model.37284_t
Valid prediction for snap_scaffold_9-snap.60-T1
Valid prediction for snap_scaffold_9-snap.53-T1
Valid prediction for GeneMark_model.37277_t
Valid prediction for GeneMark_model.37294_t
Valid prediction for GeneMark_model.37290_t
Valid prediction for snap_scaffold_9-snap.44-T1
Valid prediction for GeneMark_model.37262_t
Valid prediction for snap_scaffold_9-snap.70-T1
Valid prediction for GlimmerHMM_glimmerT_21947-T1
Valid prediction for GeneMark_model.37303_t
Valid prediction for GlimmerHMM_glimmerT_21948-T1
Valid prediction for GeneMark_model.37288_t
Valid prediction for GeneMark_model.37274_t
Valid prediction for GeneMark_model.37314_t
Valid prediction for snap_scaffold_9-snap.57-T1
Valid prediction for snap_scaffold_9-snap.63-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25671, rend_intergenic: 15203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40654, rend_intergenic: 26483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41725, rend_intergenic: 40736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45009, rend_intergenic: 42034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52447, rend_intergenic: 46473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63604, rend_intergenic: 62707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67844, rend_intergenic: 63875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72147, rend_intergenic: 70743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82190, rend_intergenic: 72512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86358, rend_intergenic: 82491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95243, rend_intergenic: 87151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96949, rend_intergenic: 95320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108163, rend_intergenic: 99665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147124, rend_intergenic: 121847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149532, rend_intergenic: 147194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152046, rend_intergenic: 152043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156743, rend_intergenic: 152560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179871, rend_intergenic: 156755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 200074
-exon list size: 848


building trellis

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92.1    
92.2    
92.4    
92.5    
92.6    
92.7    
92.8    
92.9    
93.1    
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    
94.9    
95.1    
95.2    
95.3    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.1    
96.2    
96.4    
96.5    
96.6    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 25671, rend_intergenic: 15203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40654, rend_intergenic: 26483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41725, rend_intergenic: 40736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45009, rend_intergenic: 42034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52447, rend_intergenic: 46473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63604, rend_intergenic: 62707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67844, rend_intergenic: 63875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72147, rend_intergenic: 70743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82190, rend_intergenic: 72512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86358, rend_intergenic: 82491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95243, rend_intergenic: 87151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96949, rend_intergenic: 95320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108163, rend_intergenic: 99665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147124, rend_intergenic: 121847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149532, rend_intergenic: 147194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152046, rend_intergenic: 152043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156743, rend_intergenic: 152560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179871, rend_intergenic: 156755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 17750
-exon list size: 35


building trellis

2.7    
5.4    
8.1    
10.8    
13.5    
16.2    
18.9    
21.6    
24.3    
27.0    
29.7    
32.4    
35.1    
37.8    
40.5    
43.2    
45.9    
48.6    
51.4    
54.1    
56.8    
59.5    
62.2    
64.9    
67.6    
70.3    
73.0    
75.7    
78.4    
81.1    
83.8    
86.5    
89.2    
91.9    
94.6    
97.3    
-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

-building DP trellis

-building trellis in range 188780 - 200074
-exon list size: 28


building trellis

3.3    
6.7    
10.0    
13.3    
16.7    
20.0    
23.3    
26.7    
30.0    
33.3    
36.7    
40.0    
43.3    
46.7    
50.0    
53.3    
56.7    
60.0    
63.3    
66.7    
70.0    
73.3    
76.7    
80.0    
83.3    
86.7    
90.0    
93.3    
96.7    
-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