-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_8176579-8489427

-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_5-snap.1599-T1
Valid prediction for GlimmerHMM_glimmerT_12280-T1
Valid prediction for GlimmerHMM_glimmerT_12301-T1
Valid prediction for snap_scaffold_5-snap.1567-T1
Valid prediction for GlimmerHMM_glimmerT_12297-T1
Valid prediction for Augustus_model.g8069.t1
Valid prediction for Augustus_model.g8070.t1
Valid prediction for snap_scaffold_5-snap.1569-T1
Valid prediction for snap_scaffold_5-snap.1577-T1
Valid prediction for snap_scaffold_5-snap.1572-T1
Valid prediction for snap_scaffold_5-snap.1573-T1
Valid prediction for snap_scaffold_5-snap.1562-T1
Valid prediction for Augustus_model.g8068.t1
Valid prediction for Augustus_model.g8067.t1
Valid prediction for GlimmerHMM_glimmerT_12272-T1
Valid prediction for Augustus_model.g8063.t1
Valid prediction for Augustus_model.g8062.t1
Valid prediction for GlimmerHMM_glimmerT_12285-T1
Valid prediction for Augustus_model.g8076.t1
Valid prediction for GlimmerHMM_glimmerT_12294-T1
Valid prediction for snap_scaffold_5-snap.1563-T1
Valid prediction for HiQ_model.g8072.t1
Valid prediction for snap_scaffold_5-snap.1594-T1
Couldn't classify 225669, 225855
Sorry, prediction pasa_asmbl_45545.p1 fails validation.
(TAT)	 AG	225669-225855	GT	TGG
(GCC)	 AG	225995-226110	GT	AGG
(GTG)	 AG	226792-226901	GT	GAG
(TGG)	 AG	227076-227218	GT	CAG
(ATT)	 AG	227331-227419	GT	CAG
(GTA)	 AG	227641-227765	GT	CAG
(AAG)	 AG	228112-228269	GT	GGG
(GTC)	 AG	228553-228704	CT	GAC
-recovered pasa_asmbl_45545.p1, terminal, 228553, 228704
-recovered pasa_asmbl_45545.p1, internal, 225669, 225855
-recovered pasa_asmbl_45545.p1, internal, 225995, 226110
-recovered pasa_asmbl_45545.p1, internal, 226792, 226901
-recovered pasa_asmbl_45545.p1, internal, 227076, 227218
-recovered pasa_asmbl_45545.p1, internal, 227331, 227419
-recovered pasa_asmbl_45545.p1, internal, 227641, 227765
-recovered pasa_asmbl_45545.p1, internal, 228112, 228269
Valid prediction for Augustus_model.g8064.t1
Valid prediction for snap_scaffold_5-snap.1589-T1
Valid prediction for GlimmerHMM_glimmerT_12281-T1
Valid prediction for GlimmerHMM_glimmerT_12293-T1
Valid prediction for snap_scaffold_5-snap.1574-T1
Valid prediction for GlimmerHMM_glimmerT_12275-T1
Valid prediction for GlimmerHMM_glimmerT_12284-T1
Valid prediction for GlimmerHMM_glimmerT_12288-T1
Valid prediction for snap_scaffold_5-snap.1583-T1
Valid prediction for snap_scaffold_5-snap.1587-T1
Valid prediction for CodingQuarry_transcript_52140-T1
Valid prediction for snap_scaffold_5-snap.1600-T1
Couldn't classify 187495, 187585
Sorry, prediction pasa_asmbl_45538.p1 fails validation.
(CCC)	 AG	187495-187585	GT	TGG
(TGA)	 AG	187772-187943	GT	AGG
(GTC)	 AG	189754-190014	GT	AGG
(GCT)	 AG	191513-191525	TG	GAT
-recovered pasa_asmbl_45538.p1, terminal, 191513, 191525
-recovered pasa_asmbl_45538.p1, internal, 187495, 187585
-recovered pasa_asmbl_45538.p1, internal, 187772, 187943
-recovered pasa_asmbl_45538.p1, internal, 189754, 190014
Valid prediction for HiQ_model.g8078.t1
Valid prediction for Augustus_model.g8075.t1
Valid prediction for snap_scaffold_5-snap.1592-T1
Valid prediction for GlimmerHMM_glimmerT_12298-T1
Valid prediction for GlimmerHMM_glimmerT_12282-T1
Valid prediction for GlimmerHMM_glimmerT_12283-T1
Valid prediction for snap_scaffold_5-snap.1565-T1
Valid prediction for Augustus_model.g8077.t1
Valid prediction for CodingQuarry_transcript_52139-T1
Valid prediction for pasa_asmbl_45543.p1
Valid prediction for GlimmerHMM_glimmerT_12290-T1
Valid prediction for snap_scaffold_5-snap.1570-T1
Valid prediction for Augustus_model.g8071.t1
Valid prediction for CodingQuarry_transcript_52141-T1
Valid prediction for snap_scaffold_5-snap.1585-T1
Valid prediction for snap_scaffold_5-snap.1576-T1
Valid prediction for snap_scaffold_5-snap.1590-T1
Valid prediction for snap_scaffold_5-snap.1598-T1
Valid prediction for GlimmerHMM_glimmerT_12291-T1
Valid prediction for snap_scaffold_5-snap.1597-T1
Valid prediction for snap_scaffold_5-snap.1581-T1
Valid prediction for GlimmerHMM_glimmerT_12287-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 snap_scaffold_5-snap.1584-T1
Valid prediction for GlimmerHMM_glimmerT_12302-T1
Valid prediction for snap_scaffold_5-snap.1578-T1
Valid prediction for snap_scaffold_5-snap.1610-T1
Valid prediction for snap_scaffold_5-snap.1595-T1
Valid prediction for snap_scaffold_5-snap.1601-T1
Valid prediction for Augustus_model.g8083.t1
Valid prediction for snap_scaffold_5-snap.1605-T1
Valid prediction for CodingQuarry_transcript_52142-T1
Valid prediction for GlimmerHMM_glimmerT_12273-T1
Valid prediction for snap_scaffold_5-snap.1586-T1
Valid prediction for GlimmerHMM_glimmerT_12303-T1
Valid prediction for GlimmerHMM_glimmerT_12296-T1
Valid prediction for GlimmerHMM_glimmerT_12295-T1
Valid prediction for GlimmerHMM_glimmerT_12277-T1
Valid prediction for Augustus_model.g8081.t1
Valid prediction for Augustus_model.g8074.t1
Valid prediction for snap_scaffold_5-snap.1593-T1
Valid prediction for snap_scaffold_5-snap.1566-T1
Valid prediction for Augustus_model.g8082.t1
Valid prediction for snap_scaffold_5-snap.1608-T1
Valid prediction for GlimmerHMM_glimmerT_12276-T1
Valid prediction for Augustus_model.g8085.t1
Valid prediction for snap_scaffold_5-snap.1588-T1
Valid prediction for snap_scaffold_5-snap.1609-T1
Valid prediction for snap_scaffold_5-snap.1602-T1
Valid prediction for GlimmerHMM_glimmerT_12299-T1
Valid prediction for Augustus_model.g8066.t1
Valid prediction for snap_scaffold_5-snap.1607-T1
Valid prediction for snap_scaffold_5-snap.1582-T1
Valid prediction for Augustus_model.g8065.t1
Valid prediction for Augustus_model.g8086.t1
Valid prediction for Augustus_model.g8084.t1
Valid prediction for GlimmerHMM_glimmerT_12274-T1
Couldn't classify 112140, 112332
Sorry, prediction pasa_asmbl_44203.p2 fails validation.
(GAC)	 CA	112140-112332	GT	AGG
(GTG)	 AG	112518-112627	AA	GAA
-recovered pasa_asmbl_44203.p2, terminal, 112518, 112627
Valid prediction for GlimmerHMM_glimmerT_12289-T1
Valid prediction for Augustus_model.g8080.t1
Valid prediction for snap_scaffold_5-snap.1564-T1
Valid prediction for snap_scaffold_5-snap.1596-T1
Valid prediction for snap_scaffold_5-snap.1579-T1
Valid prediction for snap_scaffold_5-snap.1603-T1
Valid prediction for GlimmerHMM_glimmerT_12292-T1
Valid prediction for snap_scaffold_5-snap.1580-T1
Valid prediction for snap_scaffold_5-snap.1568-T1
Couldn't classify 109515, 109626
Couldn't classify 111471, 111595
Sorry, prediction pasa_asmbl_44204.p1 fails validation.
(GAT)	 GG	109515-109626	GT	GGG
(AGA)	 AG	110374-110477	GT	GGG
(CAC)	 AG	110578-110664	GT	AGG
(TAT)	 AG	110782-110916	GT	AGG
(GTA)	 AG	111065-111142	GT	CTG
(GTG)	 AG	111251-111353	GT	ATG
(ATG)	 AG	111471-111595	GG	ATG
-recovered pasa_asmbl_44204.p1, internal, 110374, 110477
-recovered pasa_asmbl_44204.p1, internal, 110578, 110664
-recovered pasa_asmbl_44204.p1, internal, 110782, 110916
-recovered pasa_asmbl_44204.p1, internal, 111065, 111142
-recovered pasa_asmbl_44204.p1, internal, 111251, 111353
Valid prediction for Augustus_model.g8073.t1
Valid prediction for GlimmerHMM_glimmerT_12278-T1
Valid prediction for snap_scaffold_5-snap.1606-T1
Valid prediction for Augustus_model.g8079.t1
Valid prediction for GlimmerHMM_glimmerT_12279-T1
Valid prediction for snap_scaffold_5-snap.1604-T1
Valid prediction for snap_scaffold_5-snap.1591-T1
Valid prediction for snap_scaffold_5-snap.1575-T1
Valid prediction for GlimmerHMM_glimmerT_12286-T1
Valid prediction for GlimmerHMM_glimmerT_12300-T1
Valid prediction for snap_scaffold_5-snap.1571-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21321, rend_intergenic: 17103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43558, rend_intergenic: 42218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47405, rend_intergenic: 43564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61003, rend_intergenic: 50778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78556, rend_intergenic: 66284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93839, rend_intergenic: 92560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101452, rend_intergenic: 98342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126007, rend_intergenic: 112210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130320, rend_intergenic: 128886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135045, rend_intergenic: 132870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147554, rend_intergenic: 136468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151070, rend_intergenic: 147601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151535, rend_intergenic: 151202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155322, rend_intergenic: 152337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191647, rend_intergenic: 183655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 312849
-exon list size: 402


building trellis

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32.9    
33.2    
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33.7    
33.9    
34.2    
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34.9    
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35.4    
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36.1    
36.4    
36.6    
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37.6    
37.9    
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38.4    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
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41.3    
41.6    
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42.1    
42.3    
42.6    
42.8    
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43.6    
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44.1    
44.3    
44.6    
44.8    
45.0    
45.3    
45.5    
45.8    
46.0    
46.3    
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47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
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50.0    
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54.5    
54.7    
55.0    
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55.4    
55.7    
55.9    
56.2    
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56.9    
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58.4    
58.7    
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59.2    
59.4    
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60.1    
60.4    
60.6    
60.9    
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90.6    
90.8    
91.1    
91.3    
91.6    
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93.1    
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93.6    
93.8    
94.1    
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96.0    
96.3    
96.5    
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97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 21321, rend_intergenic: 17103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43558, rend_intergenic: 42218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47405, rend_intergenic: 43564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61003, rend_intergenic: 50778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78556, rend_intergenic: 66284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93839, rend_intergenic: 92560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101452, rend_intergenic: 98342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126007, rend_intergenic: 112210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130320, rend_intergenic: 128886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135045, rend_intergenic: 132870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147554, rend_intergenic: 136468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151070, rend_intergenic: 147601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151535, rend_intergenic: 151202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155322, rend_intergenic: 152337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191647, rend_intergenic: 183655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14735
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 2 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support