-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_11041677-11242127

-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 CodingQuarry_transcript_57633-T1
Valid prediction for snap_scaffold_7-snap.2114-T1
Valid prediction for Augustus_model.g12177.t1
Valid prediction for Augustus_model.g12170.t1
Valid prediction for CodingQuarry_transcript_57627-T1
Valid prediction for GlimmerHMM_glimmerT_18097-T1
Valid prediction for snap_scaffold_7-snap.2135-T1
Valid prediction for GlimmerHMM_glimmerT_18100-T1
Couldn't classify 75140, 75210
Sorry, prediction pasa_asmbl_50149.p1 fails validation.
(ACT)	 AG	75140-75210	GT	CGG
(ACA)	 AG	75412-75541	GT	AGG
(TCC)	 AG	75777-75863	GT	TTG
(AAA)	 AG	76005-76157	GT	AGG
(ATC)	 AG	76334-76516	GC	GAG
-recovered pasa_asmbl_50149.p1, terminal, 76334, 76516
-recovered pasa_asmbl_50149.p1, internal, 75140, 75210
-recovered pasa_asmbl_50149.p1, internal, 75412, 75541
-recovered pasa_asmbl_50149.p1, internal, 75777, 75863
-recovered pasa_asmbl_50149.p1, internal, 76005, 76157
-recovered pasa_asmbl_50149.p1, internal, 76334, 76516
Valid prediction for CodingQuarry_transcript_57630-T1
Valid prediction for snap_scaffold_7-snap.2101-T1
Valid prediction for Augustus_model.g12158.t1
Valid prediction for Augustus_model.g12174.t1
Valid prediction for snap_scaffold_7-snap.2123-T1
Valid prediction for snap_scaffold_7-snap.2105-T1
Valid prediction for GlimmerHMM_glimmerT_18102-T1
Valid prediction for GlimmerHMM_glimmerT_18106-T1
Valid prediction for Augustus_model.g12157.t1
Valid prediction for snap_scaffold_7-snap.2122-T1
Valid prediction for snap_scaffold_7-snap.2102-T1
Valid prediction for snap_scaffold_7-snap.2120-T1
Valid prediction for CodingQuarry_transcript_57629-T1
Valid prediction for snap_scaffold_7-snap.2127-T1
Valid prediction for GlimmerHMM_glimmerT_18112-T1
Valid prediction for Augustus_model.g12166.t1
Valid prediction for snap_scaffold_7-snap.2137-T1
Valid prediction for snap_scaffold_7-snap.2117-T1
Valid prediction for Augustus_model.g12180.t1
Valid prediction for GlimmerHMM_glimmerT_18108-T1
Valid prediction for snap_scaffold_7-snap.2107-T1
Valid prediction for GlimmerHMM_glimmerT_18101-T1
Valid prediction for snap_scaffold_7-snap.2110-T1
Valid prediction for snap_scaffold_7-snap.2131-T1
Valid prediction for snap_scaffold_7-snap.2130-T1
Valid prediction for snap_scaffold_7-snap.2129-T1
Valid prediction for GlimmerHMM_glimmerT_18099-T1
Valid prediction for snap_scaffold_7-snap.2109-T1
Valid prediction for snap_scaffold_7-snap.2106-T1
Valid prediction for CodingQuarry_transcript_57631-T1
Valid prediction for HiQ_model.g12169.t1
Valid prediction for GlimmerHMM_glimmerT_18093-T1
Couldn't classify 70602, 70761
Couldn't classify 71445, 71486
Sorry, prediction pasa_asmbl_50587.p1 fails validation.
(GCC)	 AG	70602-70761	GT	AGG
(CTG)	 AG	70913-71049	GT	GTG
(GAG)	 AG	71243-71356	GT	CTG
(AGT)	 AG	71445-71486	GG	ACG
-recovered pasa_asmbl_50587.p1, internal, 70602, 70761
-recovered pasa_asmbl_50587.p1, internal, 70913, 71049
-recovered pasa_asmbl_50587.p1, internal, 71243, 71356
Valid prediction for pasa_asmbl_50160.p1
Valid prediction for snap_scaffold_7-snap.2116-T1
Valid prediction for Augustus_model.g12168.t1
Valid prediction for pasa_asmbl_50152.p1
Valid prediction for snap_scaffold_7-snap.2125-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.2113-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 GlimmerHMM_glimmerT_18096-T1
Valid prediction for pasa_asmbl_51150.p1
Valid prediction for snap_scaffold_7-snap.2121-T1
Valid prediction for Augustus_model.g12173.t1
Valid prediction for GlimmerHMM_glimmerT_18114-T1
Valid prediction for Augustus_model.g12162.t1
Valid prediction for Augustus_model.g12178.t1
Valid prediction for snap_scaffold_7-snap.2133-T1
Valid prediction for GlimmerHMM_glimmerT_18105-T1
Valid prediction for snap_scaffold_7-snap.2103-T1
Valid prediction for GlimmerHMM_glimmerT_18092-T1
Valid prediction for snap_scaffold_7-snap.2141-T1
Valid prediction for snap_scaffold_7-snap.2139-T1
Valid prediction for snap_scaffold_7-snap.2136-T1
Valid prediction for snap_scaffold_7-snap.2126-T1
Valid prediction for snap_scaffold_7-snap.2140-T1
Valid prediction for CodingQuarry_transcript_57632-T1
Valid prediction for snap_scaffold_7-snap.2119-T1
Valid prediction for snap_scaffold_7-snap.2112-T1
Couldn't classify 187146, 187307
Couldn't classify 187475, 187627
Sorry, prediction pasa_asmbl_51149.p2 fails validation.
(TGT)	 CA	187146-187307	GT	TGG
(GAT)	 AG	187475-187627	GC	GGG
-recovered pasa_asmbl_51149.p2, internal, 187475, 187627
Valid prediction for Augustus_model.g12165.t1
Valid prediction for Augustus_model.g12161.t1
Valid prediction for GlimmerHMM_glimmerT_18094-T1
Valid prediction for GlimmerHMM_glimmerT_18103-T1
Valid prediction for GlimmerHMM_glimmerT_18098-T1
Valid prediction for GlimmerHMM_glimmerT_18107-T1
Valid prediction for GlimmerHMM_glimmerT_18115-T1
Valid prediction for HiQ_model.g12159.t1
Valid prediction for snap_scaffold_7-snap.2115-T1
Valid prediction for Augustus_model.g12163.t1
Valid prediction for GlimmerHMM_glimmerT_18104-T1
Valid prediction for Augustus_model.g12175.t1
Valid prediction for Augustus_model.g12160.t1
Valid prediction for Augustus_model.g12176.t1
Valid prediction for GlimmerHMM_glimmerT_18110-T1
Valid prediction for Augustus_model.g12171.t1
Valid prediction for GlimmerHMM_glimmerT_18113-T1
Valid prediction for GlimmerHMM_glimmerT_18095-T1
Valid prediction for GlimmerHMM_glimmerT_18111-T1
Valid prediction for HiQ_model.g12167.t1
Couldn't classify 190206, 190499
Sorry, prediction pasa_asmbl_51148.p1 fails validation.
(GTG)	 TA	190206-190499	GT	AGG
(CAA)	 AG	190758-191948	AC	AAA
-recovered pasa_asmbl_51148.p1, terminal, 190758, 191948
Valid prediction for snap_scaffold_7-snap.2132-T1
Valid prediction for CodingQuarry_transcript_57628-T1
Valid prediction for Augustus_model.g12181.t1
Valid prediction for snap_scaffold_7-snap.2128-T1
Valid prediction for snap_scaffold_7-snap.2108-T1
Valid prediction for GlimmerHMM_glimmerT_18109-T1
Valid prediction for snap_scaffold_7-snap.2104-T1
Valid prediction for pasa_asmbl_51154.p1
Valid prediction for snap_scaffold_7-snap.2138-T1
Valid prediction for Augustus_model.g12164.t1
Valid prediction for snap_scaffold_7-snap.2124-T1
Valid prediction for snap_scaffold_7-snap.2111-T1
Valid prediction for Augustus_model.g12172.t1
Valid prediction for snap_scaffold_7-snap.2118-T1
Valid prediction for Augustus_model.g12179.t1
Valid prediction for snap_scaffold_7-snap.2134-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 35156, rend_intergenic: 17278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35379, rend_intergenic: 35313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42901, rend_intergenic: 35936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45547, rend_intergenic: 42992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49642, rend_intergenic: 45743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54319, rend_intergenic: 50051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58871, rend_intergenic: 54376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76516, rend_intergenic: 61449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117705, rend_intergenic: 110911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119791, rend_intergenic: 117715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127500, rend_intergenic: 120623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136955, rend_intergenic: 128115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141073, rend_intergenic: 136960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154970, rend_intergenic: 147676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163313, rend_intergenic: 161913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166335, rend_intergenic: 163355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 200451
-exon list size: 475


building trellis

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17.0    
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17.8    
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20.8    
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22.6    
22.9    
23.1    
23.3    
23.5    
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23.9    
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25.8    
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26.6    
26.8    
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27.5    
27.7    
27.9    
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28.7    
28.9    
29.1    
29.4    
29.6    
29.8    
30.0    
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30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.7    
31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.1    
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42.6    
42.8    
43.0    
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44.0    
44.2    
44.4    
44.7    
44.9    
45.1    
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45.5    
45.7    
45.9    
46.1    
46.3    
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46.8    
47.0    
47.2    
47.4    
47.6    
47.8    
48.0    
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48.4    
48.6    
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49.9    
50.1    
50.3    
50.5    
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60.6    
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64.4    
64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
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66.0    
66.2    
66.5    
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67.1    
67.3    
67.5    
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68.1    
68.3    
68.6    
68.8    
69.0    
69.2    
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69.6    
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77.6    
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78.4    
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78.8    
79.0    
79.2    
79.5    
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80.1    
80.3    
80.5    
80.7    
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81.1    
81.3    
81.6    
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82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
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86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 35156, rend_intergenic: 17278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35379, rend_intergenic: 35313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42901, rend_intergenic: 35936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45547, rend_intergenic: 42992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49642, rend_intergenic: 45743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54319, rend_intergenic: 50051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58871, rend_intergenic: 54376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76516, rend_intergenic: 61449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117705, rend_intergenic: 110911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119791, rend_intergenic: 117715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127500, rend_intergenic: 120623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136955, rend_intergenic: 128115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141073, rend_intergenic: 136960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154970, rend_intergenic: 147676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163313, rend_intergenic: 161913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166335, rend_intergenic: 163355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support