-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_12128016-12355694

-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 Augustus_model.g3176.t1
Valid prediction for GeneMark_model.7575_t
Valid prediction for snap_scaffold_2-snap.2364-T1
Valid prediction for Augustus_model.g3173.t1
Valid prediction for GeneMark_model.7555_t
Valid prediction for Augustus_model.g3183.t1
Valid prediction for GeneMark_model.7566_t
Valid prediction for snap_scaffold_2-snap.2353-T1
Valid prediction for snap_scaffold_2-snap.2354-T1
Valid prediction for snap_scaffold_2-snap.2348-T1
Valid prediction for GeneMark_model.7548_t
Valid prediction for GlimmerHMM_glimmerT_4727-T1
Valid prediction for snap_scaffold_2-snap.2345-T1
Valid prediction for GlimmerHMM_glimmerT_4733-T1
Valid prediction for snap_scaffold_2-snap.2363-T1
Valid prediction for GlimmerHMM_glimmerT_4734-T1
Valid prediction for GeneMark_model.7579_t
Valid prediction for Augustus_model.g3178.t1
Valid prediction for GeneMark_model.7577_t
Valid prediction for GeneMark_model.7550_t
Valid prediction for GeneMark_model.7549_t
Valid prediction for snap_scaffold_2-snap.2361-T1
Valid prediction for snap_scaffold_2-snap.2360-T1
Valid prediction for GeneMark_model.7571_t
Valid prediction for snap_scaffold_2-snap.2371-T1
Valid prediction for snap_scaffold_2-snap.2370-T1
Valid prediction for GeneMark_model.7561_t
Valid prediction for snap_scaffold_2-snap.2362-T1
Valid prediction for Augustus_model.g3181.t1
Couldn't classify 195101, 195248
Couldn't classify 201034, 201134
Sorry, prediction pasa_asmbl_24819.p1 fails validation.
(GAG)	 CG	195101-195248	GT	CGG
(GGG)	 AG	198059-198142	GT	AGG
(GTG)	 AG	201034-201134	GT	TGG
-recovered pasa_asmbl_24819.p1, internal, 198059, 198142
-recovered pasa_asmbl_24819.p1, internal, 201034, 201134
Valid prediction for GlimmerHMM_glimmerT_4728-T1
Valid prediction for GeneMark_model.7582_t
Valid prediction for snap_scaffold_2-snap.2352-T1
Valid prediction for GeneMark_model.7542_t
Valid prediction for GeneMark_model.7541_t
Valid prediction for GlimmerHMM_glimmerT_4730-T1
Valid prediction for GeneMark_model.7568_t
Valid prediction for GlimmerHMM_glimmerT_4716-T1
Valid prediction for snap_scaffold_2-snap.2367-T1
Valid prediction for GeneMark_model.7543_t
Valid prediction for GlimmerHMM_glimmerT_4722-T1
Valid prediction for snap_scaffold_2-snap.2346-T1
Valid prediction for GeneMark_model.7560_t
Valid prediction for GeneMark_model.7554_t
Valid prediction for GeneMark_model.7558_t
Valid prediction for GlimmerHMM_glimmerT_4725-T1
Valid prediction for Augustus_model.g3180.t1
Valid prediction for GeneMark_model.7573_t
Valid prediction for GlimmerHMM_glimmerT_4729-T1
Couldn't classify 215310, 215498
Sorry, prediction pasa_asmbl_24822.p1 fails validation.
(GAT)	 GA	215310-215498	GT	CGG
(GGC)	 AG	217997-218144	GT	AGG
(AGG)	 AG	220391-220449	GT	AAG
(GAG)	 AG	221504-221662	GT	AGG
(GCT)	 AG	223931-223995	GT	AGG
(CAT)	 AG	226141-226411	CT	GAC
-recovered pasa_asmbl_24822.p1, terminal, 226141, 226411
-recovered pasa_asmbl_24822.p1, internal, 217997, 218144
-recovered pasa_asmbl_24822.p1, internal, 220391, 220449
-recovered pasa_asmbl_24822.p1, internal, 221504, 221662
-recovered pasa_asmbl_24822.p1, internal, 223931, 223995
Valid prediction for snap_scaffold_2-snap.2342-T1
Valid prediction for GeneMark_model.7545_t
Valid prediction for GeneMark_model.7564_t
Valid prediction for snap_scaffold_2-snap.2359-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.7557_t
Valid prediction for GlimmerHMM_glimmerT_4732-T1
Valid prediction for snap_scaffold_2-snap.2350-T1
Valid prediction for snap_scaffold_2-snap.2368-T1
Valid prediction for snap_scaffold_2-snap.2366-T1
Valid prediction for GeneMark_model.7559_t
Valid prediction for GlimmerHMM_glimmerT_4723-T1
Valid prediction for GeneMark_model.7583_t
Valid prediction for GlimmerHMM_glimmerT_4719-T1
Valid prediction for Augustus_model.g3175.t1
Valid prediction for Augustus_model.g3172.t1
Valid prediction for GeneMark_model.7553_t
Valid prediction for snap_scaffold_2-snap.2349-T1
Valid prediction for GeneMark_model.7540_t
Valid prediction for GlimmerHMM_glimmerT_4717-T1
Valid prediction for GlimmerHMM_glimmerT_4718-T1
Valid prediction for snap_scaffold_2-snap.2358-T1
Valid prediction for GeneMark_model.7570_t
Valid prediction for Augustus_model.g3177.t1
Valid prediction for snap_scaffold_2-snap.2357-T1
Valid prediction for GeneMark_model.7546_t
Valid prediction for GeneMark_model.7569_t
Valid prediction for GeneMark_model.7563_t
Valid prediction for snap_scaffold_2-snap.2341-T1
Valid prediction for GeneMark_model.7576_t
Valid prediction for GeneMark_model.7567_t
Valid prediction for GlimmerHMM_glimmerT_4731-T1
Valid prediction for Augustus_model.g3182.t1
Valid prediction for snap_scaffold_2-snap.2356-T1
Valid prediction for GlimmerHMM_glimmerT_4715-T1
Valid prediction for GeneMark_model.7580_t
Valid prediction for snap_scaffold_2-snap.2365-T1
Valid prediction for GeneMark_model.7574_t
Valid prediction for GlimmerHMM_glimmerT_4726-T1
Valid prediction for GeneMark_model.7565_t
Valid prediction for GeneMark_model.7544_t
Valid prediction for GeneMark_model.7562_t
Valid prediction for GlimmerHMM_glimmerT_4721-T1
Valid prediction for GeneMark_model.7581_t
Valid prediction for GeneMark_model.7572_t
Valid prediction for snap_scaffold_2-snap.2343-T1
Valid prediction for GeneMark_model.7552_t
Valid prediction for GeneMark_model.7547_t
Valid prediction for GeneMark_model.7584_t
Valid prediction for GlimmerHMM_glimmerT_4724-T1
Valid prediction for snap_scaffold_2-snap.2344-T1
Valid prediction for GeneMark_model.7556_t
Valid prediction for snap_scaffold_2-snap.2351-T1
Valid prediction for snap_scaffold_2-snap.2355-T1
Valid prediction for snap_scaffold_2-snap.2347-T1
Valid prediction for GlimmerHMM_glimmerT_4720-T1
Valid prediction for snap_scaffold_2-snap.2369-T1
Valid prediction for snap_scaffold_2-snap.2372-T1
Valid prediction for snap_scaffold_2-snap.2340-T1
Valid prediction for Augustus_model.g3179.t1
Valid prediction for Augustus_model.g3174.t1
Valid prediction for GeneMark_model.7578_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 129846, rend_intergenic: 128551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167525, rend_intergenic: 166051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205885, rend_intergenic: 199478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226411, rend_intergenic: 221308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 227679
-exon list size: 462


building trellis

0.2    
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0.9    
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18.3    
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18.8    
19.0    
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19.6    
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21.6    
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22.6    
22.8    
23.1    
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23.9    
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27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.7    
28.9    
29.1    
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29.5    
29.7    
30.0    
30.2    
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30.8    
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31.7    
31.9    
32.1    
32.3    
32.5    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.2    
36.4    
36.6    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
40.9    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.5    
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42.9    
43.1    
43.3    
43.5    
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44.0    
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44.6    
44.8    
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46.6    
46.8    
47.0    
47.2    
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47.6    
47.8    
48.1    
48.3    
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48.9    
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49.6    
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50.6    
50.9    
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51.9    
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52.8    
53.0    
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53.7    
53.9    
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55.6    
55.8    
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56.9    
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58.0    
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58.8    
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59.7    
59.9    
60.1    
60.3    
60.6    
60.8    
61.0    
61.2    
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61.6    
61.9    
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62.9    
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63.6    
63.8    
64.0    
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64.4    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
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66.4    
66.6    
66.8    
67.0    
67.2    
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69.0    
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69.6    
69.8    
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71.6    
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72.8    
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73.9    
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75.0    
75.2    
75.4    
75.6    
75.9    
76.1    
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76.9    
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77.6    
77.8    
78.0    
78.2    
78.4    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 129846, rend_intergenic: 128551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167525, rend_intergenic: 166051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205885, rend_intergenic: 199478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226411, rend_intergenic: 221308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support