-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_12437313-12634219

-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_12-snap.2324-T1
Valid prediction for GlimmerHMM_glimmerT_30848-T1
Valid prediction for GeneMark_model.53217_t
Valid prediction for snap_scaffold_12-snap.2336-T1
Valid prediction for snap_scaffold_12-snap.2340-T1
Valid prediction for snap_scaffold_12-snap.2330-T1
Valid prediction for GeneMark_model.53242_t
Valid prediction for GlimmerHMM_glimmerT_30863-T1
Valid prediction for GlimmerHMM_glimmerT_30861-T1
Valid prediction for GlimmerHMM_glimmerT_30869-T1
Valid prediction for HiQ_model.g20596.t1
Valid prediction for HiQ_model.g20578.t1
Valid prediction for GeneMark_model.53203_t
Valid prediction for GeneMark_model.53223_t
Valid prediction for CodingQuarry_transcript_10397-T1
Valid prediction for GeneMark_model.53229_t
Valid prediction for GeneMark_model.53214_t
Valid prediction for GeneMark_model.53235_t
Valid prediction for Augustus_model.g20593.t1
Valid prediction for CodingQuarry_transcript_10398-T1
Valid prediction for snap_scaffold_12-snap.2320-T1
Valid prediction for GlimmerHMM_glimmerT_30866-T1
Couldn't classify 126047, 126199
Couldn't classify 129359, 129508
Sorry, prediction pasa_asmbl_8980.p1 fails validation.
(CAG)	 AG	126047-126199	GT	TGG
(GTG)	 AG	128142-128261	GT	AGG
(GAA)	 AG	129359-129508	CA	AGC
-recovered pasa_asmbl_8980.p1, internal, 126047, 126199
-recovered pasa_asmbl_8980.p1, internal, 128142, 128261
Valid prediction for GeneMark_model.53210_t
Valid prediction for GeneMark_model.53239_t
Valid prediction for GlimmerHMM_glimmerT_30851-T1
Valid prediction for GeneMark_model.53206_t
Valid prediction for Augustus_model.g20592.t1
Valid prediction for Augustus_model.g20599.t1
Valid prediction for GeneMark_model.53221_t
Valid prediction for GlimmerHMM_glimmerT_30850-T1
Valid prediction for GeneMark_model.53218_t
Valid prediction for snap_scaffold_12-snap.2312-T1
Valid prediction for CodingQuarry_transcript_10401-T1
Valid prediction for GeneMark_model.53237_t
Valid prediction for pasa_asmbl_8974.p1
Valid prediction for snap_scaffold_12-snap.2335-T1
Valid prediction for snap_scaffold_12-snap.2331-T1
Valid prediction for snap_scaffold_12-snap.2329-T1
Valid prediction for GeneMark_model.53219_t
Valid prediction for snap_scaffold_12-snap.2332-T1
Valid prediction for GlimmerHMM_glimmerT_30856-T1
Valid prediction for Augustus_model.g20589.t1
Valid prediction for GlimmerHMM_glimmerT_30868-T1
Valid prediction for Augustus_model.g20582.t1
Valid prediction for GlimmerHMM_glimmerT_30855-T1
Valid prediction for Augustus_model.g20581.t1
Valid prediction for GlimmerHMM_glimmerT_30859-T1
Valid prediction for snap_scaffold_12-snap.2313-T1
Valid prediction for GeneMark_model.53216_t
Valid prediction for Augustus_model.g20586.t1
Valid prediction for pasa_asmbl_8972.p1
Valid prediction for HiQ_model.g20580.t1
Valid prediction for GlimmerHMM_glimmerT_30846-T1
Valid prediction for Augustus_model.g20587.t1
Valid prediction for snap_scaffold_12-snap.2337-T1
Valid prediction for GeneMark_model.53212_t
Valid prediction for Augustus_model.g20594.t1
Valid prediction for snap_scaffold_12-snap.2325-T1
Valid prediction for GeneMark_model.53225_t
Valid prediction for GeneMark_model.53208_t
Valid prediction for snap_scaffold_12-snap.2341-T1
Valid prediction for snap_scaffold_12-snap.2317-T1
Valid prediction for snap_scaffold_12-snap.2344-T1
Valid prediction for Augustus_model.g20597.t1
Couldn't classify 169534, 169569
Sorry, prediction pasa_asmbl_8982.p2 fails validation.
(GGG)	 AT	169534-169569	GT	AGG
(GTG)	 AG	171967-172059	GT	AGG
(GTG)	 AG	172877-173033	GT	TGG
(AGA)	 AG	174202-174402	GT	AGG
(TCA)	 AG	176584-176744	CC	GAC
-recovered pasa_asmbl_8982.p2, terminal, 176584, 176744
-recovered pasa_asmbl_8982.p2, internal, 171967, 172059
-recovered pasa_asmbl_8982.p2, internal, 172877, 173033
-recovered pasa_asmbl_8982.p2, internal, 174202, 174402
Valid prediction for Augustus_model.g20585.t1
Valid prediction for Augustus_model.g20601.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 HiQ_model.g20591.t1
Valid prediction for GeneMark_model.53205_t
Valid prediction for GeneMark_model.53224_t
Valid prediction for Augustus_model.g20595.t1
Valid prediction for GeneMark_model.53241_t
Valid prediction for Augustus_model.g20579.t1
Valid prediction for snap_scaffold_12-snap.2321-T1
Valid prediction for snap_scaffold_12-snap.2345-T1
Valid prediction for GlimmerHMM_glimmerT_30862-T1
Valid prediction for GeneMark_model.53222_t
Valid prediction for snap_scaffold_12-snap.2322-T1
Valid prediction for GeneMark_model.53220_t
Valid prediction for GeneMark_model.53238_t
Valid prediction for GeneMark_model.53234_t
Valid prediction for Augustus_model.g20588.t1
Valid prediction for snap_scaffold_12-snap.2333-T1
Valid prediction for Augustus_model.g20584.t1
Valid prediction for GlimmerHMM_glimmerT_30864-T1
Valid prediction for snap_scaffold_12-snap.2319-T1
Valid prediction for GeneMark_model.53230_t
Valid prediction for Augustus_model.g20598.t1
Valid prediction for GlimmerHMM_glimmerT_30849-T1
Valid prediction for GeneMark_model.53211_t
Valid prediction for GeneMark_model.53209_t
Valid prediction for GlimmerHMM_glimmerT_30865-T1
Valid prediction for GeneMark_model.53213_t
Valid prediction for Augustus_model.g20583.t1
Valid prediction for snap_scaffold_12-snap.2318-T1
Valid prediction for snap_scaffold_12-snap.2334-T1
Valid prediction for GlimmerHMM_glimmerT_30857-T1
Valid prediction for GeneMark_model.53204_t
Valid prediction for snap_scaffold_12-snap.2327-T1
Valid prediction for snap_scaffold_12-snap.2342-T1
Valid prediction for Augustus_model.g20590.t1
Valid prediction for GeneMark_model.53232_t
Valid prediction for snap_scaffold_12-snap.2338-T1
Valid prediction for Augustus_model.g20600.t1
Valid prediction for GeneMark_model.53228_t
Valid prediction for GeneMark_model.53226_t
Valid prediction for GeneMark_model.53236_t
Couldn't classify 97794, 97920
Sorry, prediction pasa_asmbl_8020.p1 fails validation.
(ATG)	 AG	95582-95994	GT	AGG
(GTA)	 AG	97794-97920	CG	TCC
-recovered pasa_asmbl_8020.p1, initial, 95582, 95994
-recovered pasa_asmbl_8020.p1, internal, 95582, 95994
Valid prediction for GlimmerHMM_glimmerT_30854-T1
Valid prediction for GlimmerHMM_glimmerT_30847-T1
Valid prediction for GlimmerHMM_glimmerT_30860-T1
Valid prediction for snap_scaffold_12-snap.2326-T1
Valid prediction for GlimmerHMM_glimmerT_30852-T1
Valid prediction for CodingQuarry_transcript_10399-T1
Valid prediction for GlimmerHMM_glimmerT_30858-T1
Valid prediction for snap_scaffold_12-snap.2314-T1
Valid prediction for snap_scaffold_12-snap.2315-T1
Valid prediction for GeneMark_model.53207_t
Valid prediction for GeneMark_model.53227_t
Valid prediction for GeneMark_model.53240_t
Valid prediction for GlimmerHMM_glimmerT_30853-T1
Valid prediction for snap_scaffold_12-snap.2343-T1
Valid prediction for GeneMark_model.53215_t
Valid prediction for snap_scaffold_12-snap.2339-T1
Valid prediction for snap_scaffold_12-snap.2323-T1
Valid prediction for GeneMark_model.53231_t
Valid prediction for GlimmerHMM_glimmerT_30867-T1
Valid prediction for GeneMark_model.53233_t
Valid prediction for GlimmerHMM_glimmerT_30870-T1
Valid prediction for snap_scaffold_12-snap.2316-T1
Valid prediction for snap_scaffold_12-snap.2328-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13158, rend_intergenic: 8804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24783, rend_intergenic: 21287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29006, rend_intergenic: 25724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30163, rend_intergenic: 29010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42138, rend_intergenic: 38093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47137, rend_intergenic: 47070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169806, rend_intergenic: 163717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185578, rend_intergenic: 178068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 196907
-exon list size: 560


building trellis

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23.1    
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25.1    
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26.2    
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26.5    
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26.9    
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28.1    
28.3    
28.5    
28.6    
28.8    
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29.2    
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29.9    
30.1    
30.2    
30.4    
30.6    
30.8    
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31.1    
31.3    
31.5    
31.7    
31.9    
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32.2    
32.4    
32.6    
32.7    
32.9    
33.1    
33.3    
33.5    
33.6    
33.8    
34.0    
34.2    
34.3    
34.5    
34.7    
34.9    
35.1    
35.2    
35.4    
35.6    
35.8    
35.9    
36.1    
36.3    
36.5    
36.7    
36.8    
37.0    
37.2    
37.4    
37.5    
37.7    
37.9    
38.1    
38.3    
38.4    
38.6    
38.8    
39.0    
39.1    
39.3    
39.5    
39.7    
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40.2    
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40.6    
40.7    
40.9    
41.1    
41.3    
41.5    
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42.2    
42.3    
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44.0    
44.1    
44.3    
44.5    
44.7    
44.8    
45.0    
45.2    
45.4    
45.6    
45.7    
45.9    
46.1    
46.3    
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46.8    
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47.3    
47.5    
47.7    
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48.0    
48.2    
48.4    
48.6    
48.8    
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49.1    
49.3    
49.5    
49.6    
49.8    
50.0    
50.2    
50.4    
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51.2    
51.4    
51.6    
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52.5    
52.7    
52.8    
53.0    
53.2    
53.4    
53.6    
53.7    
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54.1    
54.3    
54.4    
54.6    
54.8    
55.0    
55.2    
55.3    
55.5    
55.7    
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56.0    
56.2    
56.4    
56.6    
56.8    
56.9    
57.1    
57.3    
57.5    
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57.8    
58.0    
58.2    
58.4    
58.5    
58.7    
58.9    
59.1    
59.3    
59.4    
59.6    
59.8    
60.0    
60.1    
60.3    
60.5    
60.7    
60.9    
61.0    
61.2    
61.4    
61.6    
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61.9    
62.1    
62.3    
62.5    
62.6    
62.8    
63.0    
63.2    
63.3    
63.5    
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64.1    
64.2    
64.4    
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64.8    
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65.1    
65.3    
65.5    
65.7    
65.8    
66.0    
66.2    
66.4    
66.5    
66.7    
66.9    
67.1    
67.3    
67.4    
67.6    
67.8    
68.0    
68.1    
68.3    
68.5    
68.7    
68.9    
69.0    
69.2    
69.4    
69.6    
69.8    
69.9    
70.1    
70.3    
70.5    
70.6    
70.8    
71.0    
71.2    
71.4    
71.5    
71.7    
71.9    
72.1    
72.2    
72.4    
72.6    
72.8    
73.0    
73.1    
73.3    
73.5    
73.7    
73.8    
74.0    
74.2    
74.4    
74.6    
74.7    
74.9    
75.1    
75.3    
75.4    
75.6    
75.8    
76.0    
76.2    
76.3    
76.5    
76.7    
76.9    
77.0    
77.2    
77.4    
77.6    
77.8    
77.9    
78.1    
78.3    
78.5    
78.6    
78.8    
79.0    
79.2    
79.4    
79.5    
79.7    
79.9    
80.1    
80.2    
80.4    
80.6    
80.8    
81.0    
81.1    
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    
85.1    
85.2    
85.4    
85.6    
85.8    
85.9    
86.1    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
89.7    
89.9    
90.0    
90.2    
90.4    
90.6    
90.7    
90.9    
91.1    
91.3    
91.5    
91.6    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.9    
98.0    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 13158, rend_intergenic: 8804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24783, rend_intergenic: 21287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29006, rend_intergenic: 25724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30163, rend_intergenic: 29010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42138, rend_intergenic: 38093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47137, rend_intergenic: 47070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169806, rend_intergenic: 163717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185578, rend_intergenic: 178068  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