-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_4950772-5159921

-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 snap_scaffold_20-snap.1088-T1
Valid prediction for snap_scaffold_20-snap.1077-T1
Valid prediction for snap_scaffold_20-snap.1052-T1
Valid prediction for snap_scaffold_20-snap.1048-T1
Valid prediction for snap_scaffold_20-snap.1076-T1
Valid prediction for Augustus_model.g30499.t1
Couldn't classify 168723, 168820
Sorry, prediction pasa_asmbl_26605.p1 fails validation.
(ATG)	 CA	165962-166004	GT	AGG
(TGG)	 AG	166357-166447	GT	ATG
(CGT)	 AG	166739-166974	GT	AGG
(ATG)	 AG	168723-168820	GT	AGG
-recovered pasa_asmbl_26605.p1, initial, 165962, 166004
add_exon() Sorry, pasa_asmbl_26605.p1 168723-168820-initial-1 is invalid.
-recovered pasa_asmbl_26605.p1, initial, 168723, 168820
-recovered pasa_asmbl_26605.p1, internal, 166357, 166447
-recovered pasa_asmbl_26605.p1, internal, 166739, 166974
-recovered pasa_asmbl_26605.p1, internal, 168723, 168820
Valid prediction for Augustus_model.g30489.t1
Valid prediction for Augustus_model.g30488.t1
Valid prediction for snap_scaffold_20-snap.1062-T1
Valid prediction for snap_scaffold_20-snap.1072-T1
Couldn't classify 108106, 108426
Sorry, prediction pasa_asmbl_25755.p1 fails validation.
(CTT)	 CT	108106-108426	CC	AGC
Valid prediction for snap_scaffold_20-snap.1075-T1
Valid prediction for GlimmerHMM_glimmerT_45932-T1
Valid prediction for snap_scaffold_20-snap.1085-T1
Valid prediction for GlimmerHMM_glimmerT_45937-T1
Valid prediction for snap_scaffold_20-snap.1069-T1
Valid prediction for CodingQuarry_transcript_30499-T1
Valid prediction for snap_scaffold_20-snap.1081-T1
Valid prediction for pasa_asmbl_26601.p1
Valid prediction for HiQ_model.g30496.t1
Valid prediction for snap_scaffold_20-snap.1047-T1
Valid prediction for GlimmerHMM_glimmerT_45929-T1
Valid prediction for snap_scaffold_20-snap.1046-T1
Valid prediction for snap_scaffold_20-snap.1056-T1
Valid prediction for GlimmerHMM_glimmerT_45926-T1
Valid prediction for GlimmerHMM_glimmerT_45936-T1
Valid prediction for GlimmerHMM_glimmerT_45930-T1
Valid prediction for snap_scaffold_20-snap.1063-T1
Valid prediction for GlimmerHMM_glimmerT_45928-T1
Valid prediction for snap_scaffold_20-snap.1066-T1
Valid prediction for GlimmerHMM_glimmerT_45944-T1
Valid prediction for Augustus_model.g30501.t1
Valid prediction for snap_scaffold_20-snap.1050-T1
Valid prediction for snap_scaffold_20-snap.1067-T1
Valid prediction for GlimmerHMM_glimmerT_45941-T1
Valid prediction for snap_scaffold_20-snap.1054-T1
Valid prediction for snap_scaffold_20-snap.1053-T1
Valid prediction for Augustus_model.g30500.t1
Valid prediction for Augustus_model.g30487.t1
Valid prediction for GlimmerHMM_glimmerT_45939-T1
Valid prediction for snap_scaffold_20-snap.1083-T1
Valid prediction for snap_scaffold_20-snap.1089-T1
Valid prediction for snap_scaffold_20-snap.1058-T1
Valid prediction for HiQ_model.g30498.t1
Valid prediction for snap_scaffold_20-snap.1068-T1
Valid prediction for Augustus_model.g30492.t1
Valid prediction for GlimmerHMM_glimmerT_45946-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 Augustus_model.g30495.t1
Valid prediction for snap_scaffold_20-snap.1082-T1
Valid prediction for snap_scaffold_20-snap.1079-T1
Couldn't classify 85096, 85278
Sorry, prediction pasa_asmbl_25756.p1 fails validation.
(CCC)	 TT	85096-85278	GT	AGG
(GAA)	 AG	85593-85715	GT	ACG
(GTA)	 AG	85845-85917	GT	ATG
(ATG)	 AG	85996-86153	CC	GAC
-recovered pasa_asmbl_25756.p1, terminal, 85996, 86153
-recovered pasa_asmbl_25756.p1, internal, 85593, 85715
-recovered pasa_asmbl_25756.p1, internal, 85845, 85917
Valid prediction for GlimmerHMM_glimmerT_45927-T1
Valid prediction for snap_scaffold_20-snap.1049-T1
Valid prediction for Augustus_model.g30497.t1
Valid prediction for GlimmerHMM_glimmerT_45931-T1
Valid prediction for snap_scaffold_20-snap.1059-T1
Valid prediction for Augustus_model.g30491.t1
Couldn't classify 153962, 154000
Couldn't classify 154630, 155457
Sorry, prediction pasa_asmbl_25751.p1 fails validation.
(CTC)	 AT	153962-154000	GT	TGG
(GGA)	 AG	154087-154206	GT	ATG
(GTT)	 AG	154630-155457	TC	GCT
-recovered pasa_asmbl_25751.p1, internal, 154087, 154206
Valid prediction for snap_scaffold_20-snap.1080-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_20-snap.1065-T1
Valid prediction for Augustus_model.g30493.t1
Valid prediction for GlimmerHMM_glimmerT_45942-T1
Valid prediction for snap_scaffold_20-snap.1070-T1
Valid prediction for snap_scaffold_20-snap.1051-T1
Valid prediction for GlimmerHMM_glimmerT_45935-T1
Valid prediction for Augustus_model.g30494.t1
Valid prediction for CodingQuarry_transcript_30498-T1
Valid prediction for snap_scaffold_20-snap.1073-T1
Valid prediction for snap_scaffold_20-snap.1060-T1
Valid prediction for Augustus_model.g30486.t1
Valid prediction for GlimmerHMM_glimmerT_45940-T1
Valid prediction for snap_scaffold_20-snap.1061-T1
Valid prediction for GlimmerHMM_glimmerT_45945-T1
Valid prediction for GlimmerHMM_glimmerT_45938-T1
Couldn't classify 155677, 156015
Sorry, prediction pasa_asmbl_25750.p1 fails validation.
(GAG)	 AG	155677-156015	AG	CCA
Valid prediction for Augustus_model.g30490.t1
Valid prediction for snap_scaffold_20-snap.1057-T1
Valid prediction for snap_scaffold_20-snap.1055-T1
Couldn't classify 156232, 156606
Sorry, prediction pasa_asmbl_25749.p1 fails validation.
(CCG)	 GC	156232-156606	GA	GAG
Valid prediction for GlimmerHMM_glimmerT_45933-T1
Valid prediction for snap_scaffold_20-snap.1084-T1
Valid prediction for snap_scaffold_20-snap.1087-T1
Valid prediction for snap_scaffold_20-snap.1064-T1
Valid prediction for snap_scaffold_20-snap.1086-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_20-snap.1071-T1
Valid prediction for snap_scaffold_20-snap.1074-T1
Valid prediction for snap_scaffold_20-snap.1045-T1
Valid prediction for GlimmerHMM_glimmerT_45943-T1
Valid prediction for GlimmerHMM_glimmerT_45934-T1
Couldn't classify 152074, 152192
Couldn't classify 153170, 153488
Sorry, prediction pasa_asmbl_25752.p1 fails validation.
(GAG)	 CA	152074-152192	GT	AGG
(ACA)	 AG	153170-153488	AA	CCA
Valid prediction for snap_scaffold_20-snap.1078-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11156, rend_intergenic: 3047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40849, rend_intergenic: 36519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61551, rend_intergenic: 56962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64410, rend_intergenic: 62810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77916, rend_intergenic: 75428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87882, rend_intergenic: 78694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103576, rend_intergenic: 91191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115480, rend_intergenic: 112010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143653, rend_intergenic: 139093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173379, rend_intergenic: 167707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175759, rend_intergenic: 173444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185260, rend_intergenic: 180174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202963, rend_intergenic: 188533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 209150
-exon list size: 407


building trellis

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25.7    
25.9    
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26.4    
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26.9    
27.1    
27.4    
27.6    
27.9    
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28.6    
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29.1    
29.3    
29.6    
29.8    
30.1    
30.3    
30.6    
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31.3    
31.5    
31.8    
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32.3    
32.5    
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33.3    
33.5    
33.7    
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34.2    
34.5    
34.7    
35.0    
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35.9    
36.2    
36.4    
36.7    
36.9    
37.2    
37.4    
37.7    
37.9    
38.1    
38.4    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.6    
41.8    
42.1    
42.3    
42.5    
42.8    
43.0    
43.3    
43.5    
43.8    
44.0    
44.3    
44.5    
44.7    
45.0    
45.2    
45.5    
45.7    
46.0    
46.2    
46.5    
46.7    
46.9    
47.2    
47.4    
47.7    
47.9    
48.2    
48.4    
48.7    
48.9    
49.1    
49.4    
49.6    
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50.1    
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50.6    
50.9    
51.1    
51.3    
51.6    
51.8    
52.1    
52.3    
52.6    
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53.1    
53.3    
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54.0    
54.3    
54.5    
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55.3    
55.5    
55.7    
56.0    
56.2    
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56.7    
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57.9    
58.2    
58.4    
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58.9    
59.2    
59.4    
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59.9    
60.1    
60.4    
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69.2    
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79.5    
79.7    
80.0    
80.2    
80.4    
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80.9    
81.2    
81.4    
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81.9    
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82.6    
82.9    
83.1    
83.4    
83.6    
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84.4    
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86.3    
86.6    
86.8    
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87.3    
87.5    
87.8    
88.0    
88.3    
88.5    
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89.0    
89.2    
89.5    
89.7    
90.0    
90.2    
90.5    
90.7    
91.0    
91.2    
91.4    
91.7    
91.9    
92.2    
92.4    
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92.9    
93.2    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.8    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.6    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 11156, rend_intergenic: 3047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40849, rend_intergenic: 36519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61551, rend_intergenic: 56962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64410, rend_intergenic: 62810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77916, rend_intergenic: 75428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87882, rend_intergenic: 78694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103576, rend_intergenic: 91191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115480, rend_intergenic: 112010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143653, rend_intergenic: 139093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173379, rend_intergenic: 167707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175759, rend_intergenic: 173444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185260, rend_intergenic: 180174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202963, rend_intergenic: 188533  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