-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_200519-382313

-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_3086-T1
Valid prediction for GeneMark_model.5022_t
Valid prediction for GeneMark_model.4986_t
Valid prediction for GlimmerHMM_glimmerT_3095-T1
Valid prediction for GlimmerHMM_glimmerT_3098-T1
Valid prediction for GeneMark_model.4992_t
Valid prediction for snap_scaffold_2-snap.70-T1
Valid prediction for GeneMark_model.4999_t
Valid prediction for GeneMark_model.5023_t
Valid prediction for GlimmerHMM_glimmerT_3090-T1
Valid prediction for GlimmerHMM_glimmerT_3093-T1
Valid prediction for GlimmerHMM_glimmerT_3102-T1
Valid prediction for snap_scaffold_2-snap.57-T1
Valid prediction for GeneMark_model.4994_t
Valid prediction for snap_scaffold_2-snap.56-T1
Valid prediction for snap_scaffold_2-snap.54-T1
Valid prediction for GeneMark_model.4984_t
Valid prediction for GeneMark_model.5000_t
Valid prediction for GeneMark_model.4996_t
Valid prediction for GlimmerHMM_glimmerT_3091-T1
Valid prediction for GlimmerHMM_glimmerT_3087-T1
Valid prediction for snap_scaffold_2-snap.51-T1
Valid prediction for snap_scaffold_2-snap.71-T1
Valid prediction for Augustus_model.g2105.t1
Valid prediction for GeneMark_model.4989_t
Valid prediction for snap_scaffold_2-snap.80-T1
Valid prediction for Augustus_model.g2099.t1
Valid prediction for snap_scaffold_2-snap.64-T1
Valid prediction for snap_scaffold_2-snap.53-T1
Valid prediction for GlimmerHMM_glimmerT_3103-T1
Valid prediction for GlimmerHMM_glimmerT_3099-T1
Valid prediction for GeneMark_model.5019_t
Valid prediction for GeneMark_model.5020_t
Valid prediction for GeneMark_model.4993_t
Valid prediction for GeneMark_model.5008_t
Valid prediction for snap_scaffold_2-snap.76-T1
Valid prediction for GeneMark_model.5029_t
Valid prediction for snap_scaffold_2-snap.79-T1
Valid prediction for snap_scaffold_2-snap.68-T1
Valid prediction for snap_scaffold_2-snap.49-T1
Valid prediction for GeneMark_model.5007_t
Valid prediction for GeneMark_model.5005_t
Valid prediction for snap_scaffold_2-snap.81-T1
Valid prediction for snap_scaffold_2-snap.60-T1
Valid prediction for snap_scaffold_2-snap.67-T1
Valid prediction for GeneMark_model.5017_t
Valid prediction for snap_scaffold_2-snap.47-T1
Valid prediction for snap_scaffold_2-snap.73-T1
Valid prediction for GeneMark_model.5003_t
Valid prediction for GeneMark_model.5026_t
Valid prediction for GeneMark_model.5010_t
Valid prediction for GeneMark_model.5015_t
Valid prediction for snap_scaffold_2-snap.75-T1
Valid prediction for snap_scaffold_2-snap.66-T1
Valid prediction for GeneMark_model.4988_t
Valid prediction for snap_scaffold_2-snap.48-T1
Valid prediction for GeneMark_model.5012_t
Valid prediction for snap_scaffold_2-snap.59-T1
Valid prediction for GeneMark_model.4990_t
Valid prediction for GeneMark_model.4997_t
Valid prediction for GeneMark_model.5030_t
Valid prediction for GlimmerHMM_glimmerT_3089-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.5004_t
Valid prediction for GlimmerHMM_glimmerT_3101-T1
Valid prediction for GeneMark_model.4987_t
Couldn't classify 77377, 77676
Sorry, prediction pasa_asmbl_22827.p1 fails validation.
(ATG)	 TT	77377-77676	GG	CGG
Valid prediction for snap_scaffold_2-snap.83-T1
Valid prediction for snap_scaffold_2-snap.78-T1
Valid prediction for GeneMark_model.4991_t
Couldn't classify 95831, 95885
Couldn't classify 99024, 99074
Sorry, prediction pasa_asmbl_22824.p1 fails validation.
(TCC)	 AC	95831-95885	GT	AGG
(TGT)	 AG	96276-96379	GT	AGG
(GTG)	 AG	97369-97467	GT	AGG
(TAT)	 AG	98303-98374	GT	AGG
(GTG)	 AG	99024-99074	TC	CCT
-recovered pasa_asmbl_22824.p1, internal, 96276, 96379
-recovered pasa_asmbl_22824.p1, internal, 97369, 97467
-recovered pasa_asmbl_22824.p1, internal, 98303, 98374
Valid prediction for GeneMark_model.4995_t
Valid prediction for Augustus_model.g2098.t1
Valid prediction for snap_scaffold_2-snap.82-T1
Valid prediction for Augustus_model.g2106.t1
Valid prediction for snap_scaffold_2-snap.62-T1
Valid prediction for GeneMark_model.5027_t
Valid prediction for GeneMark_model.5024_t
Valid prediction for GlimmerHMM_glimmerT_3104-T1
Valid prediction for GeneMark_model.5018_t
Valid prediction for snap_scaffold_2-snap.55-T1
Valid prediction for snap_scaffold_2-snap.72-T1
Valid prediction for Augustus_model.g2097.t1
Valid prediction for Augustus_model.g2100.t1
Valid prediction for Augustus_model.g2103.t1
Valid prediction for snap_scaffold_2-snap.50-T1
Valid prediction for snap_scaffold_2-snap.74-T1
Valid prediction for GlimmerHMM_glimmerT_3088-T1
Valid prediction for GlimmerHMM_glimmerT_3084-T1
Valid prediction for GlimmerHMM_glimmerT_3085-T1
Valid prediction for GeneMark_model.5009_t
Valid prediction for GeneMark_model.5028_t
Valid prediction for GlimmerHMM_glimmerT_3096-T1
Valid prediction for GeneMark_model.5016_t
Valid prediction for GeneMark_model.4985_t
Valid prediction for GlimmerHMM_glimmerT_3100-T1
Valid prediction for snap_scaffold_2-snap.58-T1
Valid prediction for GeneMark_model.5001_t
Couldn't classify 74221, 74529
Couldn't classify 74878, 75033
Sorry, prediction pasa_asmbl_22828.p1 fails validation.
(TCT)	 GC	74221-74529	GT	AGG
(GAG)	 AG	74878-75033	GC	GCG
-recovered pasa_asmbl_22828.p1, internal, 74878, 75033
Valid prediction for Augustus_model.g2104.t1
Valid prediction for GeneMark_model.5011_t
Valid prediction for snap_scaffold_2-snap.52-T1
Valid prediction for GlimmerHMM_glimmerT_3092-T1
Valid prediction for GeneMark_model.5021_t
Valid prediction for snap_scaffold_2-snap.65-T1
Valid prediction for GlimmerHMM_glimmerT_3094-T1
Valid prediction for snap_scaffold_2-snap.77-T1
Valid prediction for GlimmerHMM_glimmerT_3097-T1
Valid prediction for GeneMark_model.5002_t
Valid prediction for snap_scaffold_2-snap.61-T1
Valid prediction for snap_scaffold_2-snap.69-T1
Valid prediction for GeneMark_model.4998_t
Valid prediction for GeneMark_model.5006_t
Valid prediction for Augustus_model.g2101.t1
Valid prediction for GeneMark_model.5013_t
Valid prediction for GlimmerHMM_glimmerT_3105-T1
Valid prediction for Augustus_model.g2102.t1
Valid prediction for snap_scaffold_2-snap.63-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15578, rend_intergenic: 13889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19675, rend_intergenic: 16198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29388, rend_intergenic: 20081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36969, rend_intergenic: 31911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39105, rend_intergenic: 38937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43757, rend_intergenic: 39131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48783, rend_intergenic: 47343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53701, rend_intergenic: 49237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76954, rend_intergenic: 70303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97412, rend_intergenic: 80379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111091, rend_intergenic: 100026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119449, rend_intergenic: 111983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121620, rend_intergenic: 120323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122384, rend_intergenic: 122280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138215, rend_intergenic: 123954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158704, rend_intergenic: 151341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170239, rend_intergenic: 167007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 181795
-exon list size: 696


building trellis

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-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 15578, rend_intergenic: 13889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19675, rend_intergenic: 16198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29388, rend_intergenic: 20081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36969, rend_intergenic: 31911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39105, rend_intergenic: 38937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43757, rend_intergenic: 39131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48783, rend_intergenic: 47343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53701, rend_intergenic: 49237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76954, rend_intergenic: 70303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97412, rend_intergenic: 80379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111091, rend_intergenic: 100026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119449, rend_intergenic: 111983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121620, rend_intergenic: 120323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122384, rend_intergenic: 122280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138215, rend_intergenic: 123954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158704, rend_intergenic: 151341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170239, rend_intergenic: 167007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 158807 - 181795
-exon list size: 47


building trellis

2.0    
4.1    
6.1    
8.2    
10.2    
12.2    
14.3    
16.3    
18.4    
20.4    
22.4    
24.5    
26.5    
28.6    
30.6    
32.7    
34.7    
36.7    
38.8    
40.8    
42.9    
44.9    
46.9    
49.0    
51.0    
53.1    
55.1    
57.1    
59.2    
61.2    
63.3    
65.3    
67.3    
69.4    
71.4    
73.5    
75.5    
77.6    
79.6    
81.6    
83.7    
85.7    
87.8    
89.8    
91.8    
93.9    
95.9    
98.0    
-found 6 predictions from path traversal

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