-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_7253049-7528262

-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_40535-T1
Valid prediction for snap_scaffold_17-snap.1455-T1
Valid prediction for CodingQuarry_transcript_22032-T1
Valid prediction for snap_scaffold_17-snap.1471-T1
Valid prediction for CodingQuarry_transcript_22031-T1
Valid prediction for Augustus_model.g27015.t1
Valid prediction for Augustus_model.g27022.t1
Valid prediction for snap_scaffold_17-snap.1473-T1
Valid prediction for GlimmerHMM_glimmerT_40558-T1
Couldn't classify 117231, 117526
Sorry, prediction pasa_asmbl_18903.p1 fails validation.
(ATG)	 AC	115058-115066	GT	AGG
(ATC)	 AG	115180-115423	GT	GAG
(AGC)	 AG	117231-117526	CC	TGC
-recovered pasa_asmbl_18903.p1, initial, 115058, 115066
-recovered pasa_asmbl_18903.p1, terminal, 115180, 115423
-recovered pasa_asmbl_18903.p1, internal, 115180, 115423
Valid prediction for Augustus_model.g27024.t1
Valid prediction for snap_scaffold_17-snap.1457-T1
Valid prediction for snap_scaffold_17-snap.1477-T1
Valid prediction for GlimmerHMM_glimmerT_40542-T1
Valid prediction for Augustus_model.g27028.t1
Valid prediction for GlimmerHMM_glimmerT_40541-T1
Valid prediction for snap_scaffold_17-snap.1442-T1
Valid prediction for snap_scaffold_17-snap.1459-T1
Valid prediction for Augustus_model.g27034.t1
Valid prediction for snap_scaffold_17-snap.1449-T1
Valid prediction for snap_scaffold_17-snap.1451-T1
Valid prediction for GlimmerHMM_glimmerT_40543-T1
Valid prediction for snap_scaffold_17-snap.1461-T1
Valid prediction for GlimmerHMM_glimmerT_40538-T1
Valid prediction for snap_scaffold_17-snap.1434-T1
Valid prediction for Augustus_model.g27023.t1
Valid prediction for snap_scaffold_17-snap.1462-T1
Valid prediction for Augustus_model.g27020.t1
Valid prediction for Augustus_model.g27016.t1
Valid prediction for Augustus_model.g27017.t1
Valid prediction for snap_scaffold_17-snap.1446-T1
Valid prediction for Augustus_model.g27021.t1
Valid prediction for pasa_asmbl_18906.p1
Valid prediction for GlimmerHMM_glimmerT_40554-T1
Couldn't classify 173982, 174128
Sorry, prediction pasa_asmbl_18905.p1 fails validation.
(GTG)	 GC	173982-174128	GT	AGG
(TTG)	 AG	174277-174366	GT	AGG
(AAG)	 AG	174591-174686	CA	GAC
-recovered pasa_asmbl_18905.p1, terminal, 174591, 174686
-recovered pasa_asmbl_18905.p1, internal, 174277, 174366
Valid prediction for snap_scaffold_17-snap.1467-T1
Valid prediction for snap_scaffold_17-snap.1474-T1
Valid prediction for Augustus_model.g27025.t1
Valid prediction for GlimmerHMM_glimmerT_40556-T1
Valid prediction for snap_scaffold_17-snap.1453-T1
Valid prediction for Augustus_model.g27018.t1
Valid prediction for GlimmerHMM_glimmerT_40537-T1
Valid prediction for snap_scaffold_17-snap.1465-T1
Valid prediction for snap_scaffold_17-snap.1464-T1
Valid prediction for snap_scaffold_17-snap.1432-T1
Couldn't classify 247175, 247292
Sorry, prediction pasa_asmbl_18909.p1 fails validation.
(ATA)	 AG	247175-247292	GT	AGG
(GCG)	 AG	247520-247686	GT	AGG
(TCC)	 AG	248677-248809	GT	AGG
(CCG)	 AG	250258-250421	AG	AAA
-recovered pasa_asmbl_18909.p1, terminal, 250258, 250421
-recovered pasa_asmbl_18909.p1, internal, 247175, 247292
-recovered pasa_asmbl_18909.p1, internal, 247520, 247686
-recovered pasa_asmbl_18909.p1, internal, 248677, 248809
Valid prediction for GlimmerHMM_glimmerT_40532-T1
Valid prediction for GlimmerHMM_glimmerT_40550-T1
Valid prediction for GlimmerHMM_glimmerT_40531-T1
Valid prediction for GlimmerHMM_glimmerT_40547-T1
Valid prediction for GlimmerHMM_glimmerT_40534-T1
Valid prediction for HiQ_model.g27031.t1
Valid prediction for GlimmerHMM_glimmerT_40553-T1
Valid prediction for Augustus_model.g27032.t1
Valid prediction for GlimmerHMM_glimmerT_40539-T1
Valid prediction for snap_scaffold_17-snap.1469-T1
Valid prediction for snap_scaffold_17-snap.1437-T1
Valid prediction for snap_scaffold_17-snap.1440-T1
Valid prediction for snap_scaffold_17-snap.1466-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 GlimmerHMM_glimmerT_40552-T1
Valid prediction for GlimmerHMM_glimmerT_40546-T1
Valid prediction for Augustus_model.g27027.t1
Valid prediction for GlimmerHMM_glimmerT_40555-T1
Valid prediction for snap_scaffold_17-snap.1476-T1
Valid prediction for GlimmerHMM_glimmerT_40548-T1
Valid prediction for snap_scaffold_17-snap.1468-T1
Valid prediction for snap_scaffold_17-snap.1450-T1
Valid prediction for snap_scaffold_17-snap.1436-T1
Valid prediction for snap_scaffold_17-snap.1463-T1
Valid prediction for CodingQuarry_transcript_22030-T1
Valid prediction for Augustus_model.g27026.t1
Valid prediction for GlimmerHMM_glimmerT_40549-T1
Valid prediction for snap_scaffold_17-snap.1431-T1
Valid prediction for snap_scaffold_17-snap.1444-T1
Valid prediction for Augustus_model.g27033.t1
Valid prediction for snap_scaffold_17-snap.1448-T1
Valid prediction for GlimmerHMM_glimmerT_40557-T1
Valid prediction for HiQ_model.g27019.t1
Valid prediction for GlimmerHMM_glimmerT_40540-T1
Valid prediction for snap_scaffold_17-snap.1475-T1
Valid prediction for GlimmerHMM_glimmerT_40545-T1
Valid prediction for GlimmerHMM_glimmerT_40530-T1
Valid prediction for snap_scaffold_17-snap.1458-T1
Valid prediction for snap_scaffold_17-snap.1438-T1
Valid prediction for snap_scaffold_17-snap.1441-T1
Valid prediction for snap_scaffold_17-snap.1460-T1
Valid prediction for GlimmerHMM_glimmerT_40529-T1
Valid prediction for GlimmerHMM_glimmerT_40559-T1
Valid prediction for GlimmerHMM_glimmerT_40544-T1
Valid prediction for snap_scaffold_17-snap.1454-T1
Valid prediction for snap_scaffold_17-snap.1435-T1
Valid prediction for snap_scaffold_17-snap.1443-T1
Valid prediction for snap_scaffold_17-snap.1452-T1
Valid prediction for snap_scaffold_17-snap.1470-T1
Valid prediction for GlimmerHMM_glimmerT_40536-T1
Valid prediction for Augustus_model.g27029.t1
Valid prediction for snap_scaffold_17-snap.1433-T1
Valid prediction for GlimmerHMM_glimmerT_40551-T1
Valid prediction for snap_scaffold_17-snap.1472-T1
Valid prediction for snap_scaffold_17-snap.1439-T1
Valid prediction for snap_scaffold_17-snap.1447-T1
Valid prediction for GlimmerHMM_glimmerT_40533-T1
Valid prediction for snap_scaffold_17-snap.1456-T1
Valid prediction for snap_scaffold_17-snap.1445-T1
Valid prediction for Augustus_model.g27030.t1
Valid prediction for pasa_asmbl_18054.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7877, rend_intergenic: 5137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8898, rend_intergenic: 8150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22229, rend_intergenic: 9186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26056, rend_intergenic: 23113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79033, rend_intergenic: 39814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87121, rend_intergenic: 80225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100885, rend_intergenic: 91861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106677, rend_intergenic: 104210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119460, rend_intergenic: 110763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135350, rend_intergenic: 133908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137209, rend_intergenic: 136817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152376, rend_intergenic: 148905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160569, rend_intergenic: 155832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187498, rend_intergenic: 175990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189451, rend_intergenic: 187506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200644, rend_intergenic: 190408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203552, rend_intergenic: 201047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210671, rend_intergenic: 203580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231437, rend_intergenic: 228858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239984, rend_intergenic: 233017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 250421, rend_intergenic: 240642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 267298, rend_intergenic: 259509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 268617, rend_intergenic: 267690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 275214
-exon list size: 469


building trellis

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23.6    
23.8    
24.0    
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24.8    
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25.3    
25.5    
25.7    
25.9    
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26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.9    
39.1    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.6    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.4    
52.7    
52.9    
53.1    
53.3    
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53.9    
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54.4    
54.6    
54.8    
55.0    
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55.8    
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58.6    
58.8    
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59.2    
59.4    
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59.9    
60.1    
60.3    
60.5    
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61.4    
61.6    
61.8    
62.0    
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63.3    
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64.1    
64.3    
64.5    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
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66.7    
66.9    
67.1    
67.3    
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68.2    
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68.6    
68.8    
69.0    
69.2    
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73.0    
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73.9    
74.1    
74.3    
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75.6    
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76.0    
76.2    
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76.6    
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77.1    
77.3    
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77.9    
78.1    
78.3    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
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82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
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83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 7877, rend_intergenic: 5137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8898, rend_intergenic: 8150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22229, rend_intergenic: 9186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26056, rend_intergenic: 23113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79033, rend_intergenic: 39814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87121, rend_intergenic: 80225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100885, rend_intergenic: 91861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106677, rend_intergenic: 104210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119460, rend_intergenic: 110763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135350, rend_intergenic: 133908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137209, rend_intergenic: 136817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152376, rend_intergenic: 148905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160569, rend_intergenic: 155832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187498, rend_intergenic: 175990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189451, rend_intergenic: 187506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200644, rend_intergenic: 190408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203552, rend_intergenic: 201047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210671, rend_intergenic: 203580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231437, rend_intergenic: 228858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239984, rend_intergenic: 233017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 250421, rend_intergenic: 240642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 267298, rend_intergenic: 259509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 268617, rend_intergenic: 267690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support