-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_4352923-4549735

-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_39058-T1
Valid prediction for Augustus_model.g26248.t1
Valid prediction for GeneMark_model.66883_t
Valid prediction for GeneMark_model.66890_t
Valid prediction for Augustus_model.g26240.t1
Valid prediction for GlimmerHMM_glimmerT_39066-T1
Valid prediction for snap_scaffold_16-snap.882-T1
Valid prediction for Augustus_model.g26249.t1
Valid prediction for GlimmerHMM_glimmerT_39072-T1
Valid prediction for GeneMark_model.66869_t
Valid prediction for GlimmerHMM_glimmerT_39054-T1
Valid prediction for GlimmerHMM_glimmerT_39084-T1
Valid prediction for GlimmerHMM_glimmerT_39080-T1
Valid prediction for snap_scaffold_16-snap.890-T1
Valid prediction for GlimmerHMM_glimmerT_39076-T1
Valid prediction for GlimmerHMM_glimmerT_39069-T1
Valid prediction for Augustus_model.g26244.t1
Valid prediction for GeneMark_model.66879_t
Valid prediction for snap_scaffold_16-snap.870-T1
Valid prediction for snap_scaffold_16-snap.865-T1
Valid prediction for GlimmerHMM_glimmerT_39074-T1
Valid prediction for snap_scaffold_16-snap.873-T1
Valid prediction for snap_scaffold_16-snap.869-T1
Valid prediction for snap_scaffold_16-snap.885-T1
Valid prediction for GeneMark_model.66906_t
Valid prediction for GlimmerHMM_glimmerT_39081-T1
Valid prediction for snap_scaffold_16-snap.852-T1
Valid prediction for Augustus_model.g26252.t1
Valid prediction for GlimmerHMM_glimmerT_39070-T1
Couldn't classify 65143, 65553
Sorry, prediction pasa_asmbl_16976.p1 fails validation.
(CAG)	 TA	65143-65553	AC	AAA
Valid prediction for GeneMark_model.66903_t
Valid prediction for GeneMark_model.66875_t
Valid prediction for GeneMark_model.66902_t
Valid prediction for Augustus_model.g26245.t1
Valid prediction for snap_scaffold_16-snap.886-T1
Valid prediction for snap_scaffold_16-snap.857-T1
Valid prediction for snap_scaffold_16-snap.888-T1
Valid prediction for GlimmerHMM_glimmerT_39068-T1
Valid prediction for snap_scaffold_16-snap.883-T1
Valid prediction for snap_scaffold_16-snap.881-T1
Valid prediction for GeneMark_model.66892_t
Valid prediction for snap_scaffold_16-snap.884-T1
Valid prediction for GeneMark_model.66901_t
Valid prediction for GlimmerHMM_glimmerT_39078-T1
Valid prediction for GeneMark_model.66908_t
Valid prediction for snap_scaffold_16-snap.855-T1
Valid prediction for snap_scaffold_16-snap.851-T1
Valid prediction for GeneMark_model.66898_t
Valid prediction for snap_scaffold_16-snap.859-T1
Valid prediction for GlimmerHMM_glimmerT_39077-T1
Valid prediction for GeneMark_model.66887_t
Valid prediction for GlimmerHMM_glimmerT_39060-T1
Valid prediction for snap_scaffold_16-snap.875-T1
Valid prediction for snap_scaffold_16-snap.871-T1
Valid prediction for snap_scaffold_16-snap.867-T1
Valid prediction for GlimmerHMM_glimmerT_39065-T1
Valid prediction for snap_scaffold_16-snap.880-T1
Valid prediction for GeneMark_model.66893_t
Valid prediction for snap_scaffold_16-snap.854-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g26253.t1
Valid prediction for GeneMark_model.66907_t
Valid prediction for GeneMark_model.66877_t
Valid prediction for Augustus_model.g26250.t1
Valid prediction for snap_scaffold_16-snap.889-T1
Valid prediction for pasa_asmbl_16977.p1
Valid prediction for GeneMark_model.66889_t
Valid prediction for GeneMark_model.66896_t
Valid prediction for GeneMark_model.66882_t
Valid prediction for Augustus_model.g26247.t1
Valid prediction for HiQ_model.g26251.t1
Valid prediction for snap_scaffold_16-snap.849-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_39079-T1
Valid prediction for GeneMark_model.66872_t
Valid prediction for snap_scaffold_16-snap.874-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.66881_t
Valid prediction for snap_scaffold_16-snap.887-T1
Valid prediction for GeneMark_model.66873_t
Valid prediction for snap_scaffold_16-snap.864-T1
Valid prediction for snap_scaffold_16-snap.863-T1
Couldn't classify 138921, 138983
Sorry, prediction pasa_asmbl_16236.p1 fails validation.
(ATG)	 CA	136572-136637	GT	TGG
(ATA)	 AG	136777-136883	GT	AGG
(GAT)	 AG	137521-137704	GT	TGG
(AAT)	 AG	138921-138983	AA	GGA
-recovered pasa_asmbl_16236.p1, initial, 136572, 136637
-recovered pasa_asmbl_16236.p1, internal, 136777, 136883
-recovered pasa_asmbl_16236.p1, internal, 137521, 137704
Valid prediction for GeneMark_model.66888_t
Valid prediction for GeneMark_model.66878_t
Valid prediction for CodingQuarry_transcript_19909-T1
Valid prediction for snap_scaffold_16-snap.862-T1
Valid prediction for Augustus_model.g26243.t1
Valid prediction for GlimmerHMM_glimmerT_39067-T1
Valid prediction for GlimmerHMM_glimmerT_39057-T1
Valid prediction for GeneMark_model.66891_t
Valid prediction for GlimmerHMM_glimmerT_39055-T1
Valid prediction for snap_scaffold_16-snap.879-T1
Valid prediction for GeneMark_model.66899_t
Valid prediction for snap_scaffold_16-snap.877-T1
Valid prediction for snap_scaffold_16-snap.860-T1
Valid prediction for GeneMark_model.66880_t
Valid prediction for snap_scaffold_16-snap.858-T1
Valid prediction for GeneMark_model.66894_t
Valid prediction for GlimmerHMM_glimmerT_39061-T1
Valid prediction for snap_scaffold_16-snap.850-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.872-T1
Valid prediction for GeneMark_model.66897_t
Valid prediction for GeneMark_model.66870_t
Valid prediction for GeneMark_model.66884_t
Valid prediction for Augustus_model.g26238.t1
Valid prediction for Augustus_model.g26236.t1
Valid prediction for GeneMark_model.66905_t
Valid prediction for GlimmerHMM_glimmerT_39075-T1
Valid prediction for GeneMark_model.66900_t
Valid prediction for Augustus_model.g26239.t1
Valid prediction for GeneMark_model.66876_t
Valid prediction for GlimmerHMM_glimmerT_39052-T1
Valid prediction for GlimmerHMM_glimmerT_39083-T1
Valid prediction for GlimmerHMM_glimmerT_39073-T1
Valid prediction for GeneMark_model.66886_t
Valid prediction for Augustus_model.g26242.t1
Valid prediction for snap_scaffold_16-snap.868-T1
Valid prediction for GlimmerHMM_glimmerT_39063-T1
Valid prediction for snap_scaffold_16-snap.876-T1
Valid prediction for Augustus_model.g26241.t1
Valid prediction for GlimmerHMM_glimmerT_39053-T1
Valid prediction for GlimmerHMM_glimmerT_39056-T1
Valid prediction for GeneMark_model.66874_t
Valid prediction for Augustus_model.g26237.t1
Valid prediction for GlimmerHMM_glimmerT_39064-T1
Valid prediction for GlimmerHMM_glimmerT_39071-T1
Valid prediction for snap_scaffold_16-snap.878-T1
Valid prediction for GeneMark_model.66885_t
Valid prediction for snap_scaffold_16-snap.853-T1
Valid prediction for GlimmerHMM_glimmerT_39082-T1
Valid prediction for snap_scaffold_16-snap.866-T1
Valid prediction for snap_scaffold_16-snap.856-T1
Valid prediction for GlimmerHMM_glimmerT_39062-T1
Valid prediction for Augustus_model.g26235.t1
Valid prediction for snap_scaffold_16-snap.861-T1
Valid prediction for GlimmerHMM_glimmerT_39059-T1
Valid prediction for GeneMark_model.66871_t
Valid prediction for GeneMark_model.66868_t
Valid prediction for GlimmerHMM_glimmerT_39051-T1
Valid prediction for GeneMark_model.66904_t
Valid prediction for Augustus_model.g26246.t1
Valid prediction for GeneMark_model.66895_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17492, rend_intergenic: 7867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19976, rend_intergenic: 19836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28554, rend_intergenic: 19985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31456, rend_intergenic: 29118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32496, rend_intergenic: 32055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39295, rend_intergenic: 32785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40696, rend_intergenic: 40048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46458, rend_intergenic: 41033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86768, rend_intergenic: 85565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103901, rend_intergenic: 101766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172746, rend_intergenic: 170867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 196813
-exon list size: 566


building trellis

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18.8    
19.0    
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26.2    
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27.8    
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28.2    
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29.8    
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33.3    
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33.6    
33.8    
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34.3    
34.5    
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34.9    
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36.8    
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38.0    
38.2    
38.4    
38.6    
38.7    
38.9    
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39.3    
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40.1    
40.3    
40.5    
40.7    
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41.0    
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41.9    
42.1    
42.3    
42.4    
42.6    
42.8    
43.0    
43.1    
43.3    
43.5    
43.7    
43.8    
44.0    
44.2    
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45.1    
45.2    
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45.6    
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47.0    
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47.5    
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47.9    
48.1    
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48.6    
48.8    
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49.1    
49.3    
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50.2    
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50.9    
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54.2    
54.4    
54.6    
54.8    
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55.1    
55.3    
55.5    
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55.8    
56.0    
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56.3    
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56.7    
56.9    
57.0    
57.2    
57.4    
57.6    
57.7    
57.9    
58.1    
58.3    
58.5    
58.6    
58.8    
59.0    
59.2    
59.3    
59.5    
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59.9    
60.0    
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61.1    
61.3    
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61.6    
61.8    
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62.3    
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64.1    
64.3    
64.4    
64.6    
64.8    
65.0    
65.1    
65.3    
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66.0    
66.2    
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66.9    
67.1    
67.3    
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67.6    
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68.0    
68.1    
68.3    
68.5    
68.7    
68.8    
69.0    
69.2    
69.4    
69.5    
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69.9    
70.1    
70.2    
70.4    
70.6    
70.8    
71.0    
71.1    
71.3    
71.5    
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71.8    
72.0    
72.2    
72.4    
72.5    
72.7    
72.9    
73.1    
73.2    
73.4    
73.6    
73.8    
73.9    
74.1    
74.3    
74.5    
74.6    
74.8    
75.0    
75.2    
75.4    
75.5    
75.7    
75.9    
76.1    
76.2    
76.4    
76.6    
76.8    
76.9    
77.1    
77.3    
77.5    
77.6    
77.8    
78.0    
78.2    
78.3    
78.5    
78.7    
78.9    
79.0    
79.2    
79.4    
79.6    
79.8    
79.9    
80.1    
80.3    
80.5    
80.6    
80.8    
81.0    
81.2    
81.3    
81.5    
81.7    
81.9    
82.0    
82.2    
82.4    
82.6    
82.7    
82.9    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.2    
84.3    
84.5    
84.7    
84.9    
85.0    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.3    
86.4    
86.6    
86.8    
87.0    
87.1    
87.3    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.3    
89.4    
89.6    
89.8    
90.0    
90.1    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
93.0    
93.1    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 17492, rend_intergenic: 7867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19976, rend_intergenic: 19836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28554, rend_intergenic: 19985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31456, rend_intergenic: 29118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32496, rend_intergenic: 32055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39295, rend_intergenic: 32785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40696, rend_intergenic: 40048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46458, rend_intergenic: 41033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86768, rend_intergenic: 85565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103901, rend_intergenic: 101766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172746, rend_intergenic: 170867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support