-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_13240768-13465002

-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_1742-T1
Valid prediction for snap_scaffold_1-snap.2308-T1
Valid prediction for snap_scaffold_1-snap.2288-T1
Valid prediction for GlimmerHMM_glimmerT_1753-T1
Valid prediction for GlimmerHMM_glimmerT_1734-T1
Valid prediction for GlimmerHMM_glimmerT_1739-T1
Valid prediction for snap_scaffold_1-snap.2269-T1
Valid prediction for snap_scaffold_1-snap.2271-T1
Valid prediction for Augustus_model.g1321.t1
Valid prediction for GlimmerHMM_glimmerT_1741-T1
Valid prediction for snap_scaffold_1-snap.2306-T1
Valid prediction for GlimmerHMM_glimmerT_1757-T1
Valid prediction for snap_scaffold_1-snap.2275-T1
Valid prediction for Augustus_model.g1322.t1
Valid prediction for Augustus_model.g1317.t1
Valid prediction for snap_scaffold_1-snap.2266-T1
Valid prediction for snap_scaffold_1-snap.2297-T1
Valid prediction for GlimmerHMM_glimmerT_1746-T1
Valid prediction for snap_scaffold_1-snap.2278-T1
Valid prediction for snap_scaffold_1-snap.2300-T1
Valid prediction for GlimmerHMM_glimmerT_1761-T1
Valid prediction for GlimmerHMM_glimmerT_1754-T1
Valid prediction for snap_scaffold_1-snap.2291-T1
Valid prediction for snap_scaffold_1-snap.2273-T1
Valid prediction for snap_scaffold_1-snap.2286-T1
Valid prediction for GlimmerHMM_glimmerT_1758-T1
Valid prediction for snap_scaffold_1-snap.2281-T1
Valid prediction for snap_scaffold_1-snap.2298-T1
Valid prediction for GlimmerHMM_glimmerT_1759-T1
Valid prediction for snap_scaffold_1-snap.2293-T1
Valid prediction for snap_scaffold_1-snap.2280-T1
Valid prediction for Augustus_model.g1315.t1
Valid prediction for snap_scaffold_1-snap.2295-T1
Valid prediction for snap_scaffold_1-snap.2302-T1
Valid prediction for Augustus_model.g1316.t1
Valid prediction for Augustus_model.g1319.t1
Valid prediction for snap_scaffold_1-snap.2283-T1
Valid prediction for snap_scaffold_1-snap.2276-T1
Valid prediction for GlimmerHMM_glimmerT_1748-T1
Valid prediction for GlimmerHMM_glimmerT_1751-T1
Valid prediction for GlimmerHMM_glimmerT_1737-T1
Valid prediction for GlimmerHMM_glimmerT_1750-T1
Valid prediction for snap_scaffold_1-snap.2304-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_1744-T1
Valid prediction for snap_scaffold_1-snap.2307-T1
Valid prediction for GlimmerHMM_glimmerT_1752-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 pasa_asmbl_802.p1
Valid prediction for snap_scaffold_1-snap.2274-T1
Valid prediction for Augustus_model.g1320.t1
Valid prediction for Augustus_model.g1323.t1
Valid prediction for snap_scaffold_1-snap.2279-T1
Valid prediction for snap_scaffold_1-snap.2267-T1
Valid prediction for GlimmerHMM_glimmerT_1762-T1
Valid prediction for GlimmerHMM_glimmerT_1743-T1
Valid prediction for snap_scaffold_1-snap.2309-T1
Valid prediction for snap_scaffold_1-snap.2284-T1
Valid prediction for snap_scaffold_1-snap.2277-T1
Valid prediction for snap_scaffold_1-snap.2268-T1
Valid prediction for snap_scaffold_1-snap.2270-T1
Valid prediction for GlimmerHMM_glimmerT_1760-T1
Valid prediction for snap_scaffold_1-snap.2272-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_1749-T1
Valid prediction for GlimmerHMM_glimmerT_1755-T1
Valid prediction for GlimmerHMM_glimmerT_1736-T1
Valid prediction for Augustus_model.g1314.t1
Valid prediction for snap_scaffold_1-snap.2299-T1
Valid prediction for snap_scaffold_1-snap.2287-T1
Valid prediction for snap_scaffold_1-snap.2265-T1
Valid prediction for GlimmerHMM_glimmerT_1756-T1
Valid prediction for GlimmerHMM_glimmerT_1740-T1
Valid prediction for GlimmerHMM_glimmerT_1738-T1
Valid prediction for snap_scaffold_1-snap.2294-T1
Valid prediction for snap_scaffold_1-snap.2303-T1
Valid prediction for GlimmerHMM_glimmerT_1745-T1
Valid prediction for snap_scaffold_1-snap.2282-T1
Valid prediction for pasa_asmbl_809.p1
Valid prediction for snap_scaffold_1-snap.2296-T1
Valid prediction for Augustus_model.g1318.t1
Valid prediction for snap_scaffold_1-snap.2285-T1
Couldn't classify 20728, 20763
Couldn't classify 23257, 23319
Sorry, prediction pasa_asmbl_805.p1 fails validation.
(CCA)	 CC	20728-20763	GT	AGG
(CTG)	 AG	21042-21215	GT	AGG
(GTG)	 AG	23068-23166	GT	AGG
(ACG)	 AG	23257-23319	GG	GGG
-recovered pasa_asmbl_805.p1, internal, 21042, 21215
-recovered pasa_asmbl_805.p1, internal, 23068, 23166
Valid prediction for HiQ_model.g1324.t1
Valid prediction for snap_scaffold_1-snap.2289-T1
Valid prediction for snap_scaffold_1-snap.2301-T1
Valid prediction for snap_scaffold_1-snap.2290-T1
Valid prediction for snap_scaffold_1-snap.2305-T1
Valid prediction for GlimmerHMM_glimmerT_1735-T1
Valid prediction for GlimmerHMM_glimmerT_1747-T1
Valid prediction for snap_scaffold_1-snap.2292-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13409, rend_intergenic: 5408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27764, rend_intergenic: 14411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31164, rend_intergenic: 28113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48293, rend_intergenic: 44135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57113, rend_intergenic: 51716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64883, rend_intergenic: 57829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78459, rend_intergenic: 67550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82529, rend_intergenic: 79915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90654, rend_intergenic: 83038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94309, rend_intergenic: 94118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117532, rend_intergenic: 97869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121684, rend_intergenic: 117624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123007, rend_intergenic: 121735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127149, rend_intergenic: 123237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135253, rend_intergenic: 134091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144165, rend_intergenic: 138191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146952, rend_intergenic: 144254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152519, rend_intergenic: 148096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166908, rend_intergenic: 162001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175096, rend_intergenic: 172129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188817, rend_intergenic: 185216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198526, rend_intergenic: 192952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216314, rend_intergenic: 198574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 103720, rend_intergenic: 103717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 224235
-exon list size: 378


building trellis

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33.7    
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38.7    
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44.7    
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48.7    
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51.6    
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73.7    
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75.0    
75.3    
75.5    
75.8    
76.1    
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76.6    
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77.1    
77.4    
77.6    
77.9    
78.2    
78.4    
78.7    
78.9    
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80.0    
80.3    
80.5    
80.8    
81.1    
81.3    
81.6    
81.8    
82.1    
82.4    
82.6    
82.9    
83.2    
83.4    
83.7    
83.9    
84.2    
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84.7    
85.0    
85.3    
85.5    
85.8    
86.1    
86.3    
86.6    
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87.1    
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87.6    
87.9    
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88.4    
88.7    
88.9    
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89.5    
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90.0    
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91.1    
91.3    
91.6    
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92.4    
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92.9    
93.2    
93.4    
93.7    
93.9    
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95.8    
96.1    
96.3    
96.6    
96.8    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 13409, rend_intergenic: 5408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27764, rend_intergenic: 14411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31164, rend_intergenic: 28113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48293, rend_intergenic: 44135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57113, rend_intergenic: 51716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64883, rend_intergenic: 57829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78459, rend_intergenic: 67550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82529, rend_intergenic: 79915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90654, rend_intergenic: 83038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94309, rend_intergenic: 94118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117532, rend_intergenic: 97869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121684, rend_intergenic: 117624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123007, rend_intergenic: 121735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127149, rend_intergenic: 123237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135253, rend_intergenic: 134091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144165, rend_intergenic: 138191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146952, rend_intergenic: 144254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152519, rend_intergenic: 148096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166908, rend_intergenic: 162001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175096, rend_intergenic: 172129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188817, rend_intergenic: 185216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198526, rend_intergenic: 192952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216314, rend_intergenic: 198574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 103720, rend_intergenic: 103717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 9 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10690
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support