-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_16975465-17203768

-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_1-snap.3031-T1
Valid prediction for Augustus_model.g1672.t1
Valid prediction for snap_scaffold_1-snap.3080-T1
Valid prediction for Augustus_model.g1674.t1
Valid prediction for snap_scaffold_1-snap.3036-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.3053-T1
Valid prediction for snap_scaffold_1-snap.3044-T1
Valid prediction for GlimmerHMM_glimmerT_2276-T1
Couldn't classify 74785, 74983
Sorry, prediction pasa_asmbl_2514.p1 fails validation.
(TTA)	 AC	74785-74983	GT	AGG
(TGT)	 AG	75477-75604	GT	TTG
(TGT)	 AG	75932-76073	GT	TGG
(ACA)	 AG	76350-76534	AG	AAA
-recovered pasa_asmbl_2514.p1, terminal, 76350, 76534
-recovered pasa_asmbl_2514.p1, internal, 75477, 75604
-recovered pasa_asmbl_2514.p1, internal, 75932, 76073
Valid prediction for snap_scaffold_1-snap.3042-T1
Valid prediction for GlimmerHMM_glimmerT_2271-T1
Valid prediction for snap_scaffold_1-snap.3054-T1
Valid prediction for snap_scaffold_1-snap.3051-T1
Valid prediction for GlimmerHMM_glimmerT_2280-T1
Valid prediction for GlimmerHMM_glimmerT_2261-T1
Valid prediction for snap_scaffold_1-snap.3062-T1
Valid prediction for Augustus_model.g1671.t1
Valid prediction for snap_scaffold_1-snap.3064-T1
Valid prediction for GlimmerHMM_glimmerT_2273-T1
Valid prediction for Augustus_model.g1675.t1
Valid prediction for Augustus_model.g1681.t1
Valid prediction for snap_scaffold_1-snap.3034-T1
Valid prediction for GlimmerHMM_glimmerT_2256-T1
Valid prediction for snap_scaffold_1-snap.3073-T1
Valid prediction for GlimmerHMM_glimmerT_2277-T1
Valid prediction for GlimmerHMM_glimmerT_2269-T1
Valid prediction for snap_scaffold_1-snap.3069-T1
Valid prediction for snap_scaffold_1-snap.3046-T1
Valid prediction for GlimmerHMM_glimmerT_2268-T1
Valid prediction for snap_scaffold_1-snap.3078-T1
Valid prediction for snap_scaffold_1-snap.3056-T1
Valid prediction for snap_scaffold_1-snap.3075-T1
Valid prediction for GlimmerHMM_glimmerT_2270-T1
Valid prediction for GlimmerHMM_glimmerT_2265-T1
Valid prediction for GlimmerHMM_glimmerT_2262-T1
Valid prediction for GlimmerHMM_glimmerT_2260-T1
Valid prediction for snap_scaffold_1-snap.3048-T1
Valid prediction for CodingQuarry_transcript_2971-T1
Valid prediction for snap_scaffold_1-snap.3059-T1
Valid prediction for snap_scaffold_1-snap.3043-T1
Valid prediction for snap_scaffold_1-snap.3039-T1
Valid prediction for GlimmerHMM_glimmerT_2254-T1
Valid prediction for GlimmerHMM_glimmerT_2259-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_1-snap.3050-T1
Valid prediction for GlimmerHMM_glimmerT_2279-T1
Valid prediction for snap_scaffold_1-snap.3033-T1
Valid prediction for snap_scaffold_1-snap.3041-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_2266-T1
Valid prediction for snap_scaffold_1-snap.3071-T1
Valid prediction for GlimmerHMM_glimmerT_2255-T1
Valid prediction for Augustus_model.g1685.t1
Valid prediction for GlimmerHMM_glimmerT_2253-T1
Valid prediction for snap_scaffold_1-snap.3070-T1
Valid prediction for Augustus_model.g1679.t1
Valid prediction for Augustus_model.g1680.t1
Valid prediction for snap_scaffold_1-snap.3065-T1
Valid prediction for snap_scaffold_1-snap.3077-T1
Valid prediction for GlimmerHMM_glimmerT_2283-T1
Valid prediction for snap_scaffold_1-snap.3074-T1
Valid prediction for snap_scaffold_1-snap.3045-T1
Valid prediction for GlimmerHMM_glimmerT_2252-T1
Valid prediction for GlimmerHMM_glimmerT_2258-T1
Valid prediction for Augustus_model.g1682.t1
Valid prediction for snap_scaffold_1-snap.3063-T1
Valid prediction for GlimmerHMM_glimmerT_2274-T1
Valid prediction for Augustus_model.g1677.t1
Valid prediction for snap_scaffold_1-snap.3068-T1
Valid prediction for GlimmerHMM_glimmerT_2278-T1
Valid prediction for GlimmerHMM_glimmerT_2272-T1
Valid prediction for snap_scaffold_1-snap.3049-T1
Valid prediction for Augustus_model.g1684.t1
Valid prediction for Augustus_model.g1676.t1
Valid prediction for snap_scaffold_1-snap.3032-T1
Valid prediction for snap_scaffold_1-snap.3061-T1
Valid prediction for snap_scaffold_1-snap.3058-T1
Valid prediction for GlimmerHMM_glimmerT_2267-T1
Valid prediction for snap_scaffold_1-snap.3037-T1
Valid prediction for snap_scaffold_1-snap.3047-T1
Valid prediction for Augustus_model.g1670.t1
Valid prediction for GlimmerHMM_glimmerT_2257-T1
Valid prediction for snap_scaffold_1-snap.3038-T1
Valid prediction for snap_scaffold_1-snap.3067-T1
Valid prediction for GlimmerHMM_glimmerT_2264-T1
Valid prediction for snap_scaffold_1-snap.3057-T1
Valid prediction for GlimmerHMM_glimmerT_2281-T1
Valid prediction for snap_scaffold_1-snap.3072-T1
Valid prediction for snap_scaffold_1-snap.3052-T1
Valid prediction for Augustus_model.g1678.t1
Valid prediction for GlimmerHMM_glimmerT_2282-T1
Valid prediction for snap_scaffold_1-snap.3055-T1
Valid prediction for Augustus_model.g1673.t1
Valid prediction for snap_scaffold_1-snap.3060-T1
Valid prediction for snap_scaffold_1-snap.3066-T1
Couldn't classify 134441, 134610
Couldn't classify 136701, 136938
Sorry, prediction pasa_asmbl_1027.p1 fails validation.
(CTG)	 AG	134441-134610	GT	TGG
(TTT)	 AG	136701-136938	AC	CCA
-recovered pasa_asmbl_1027.p1, internal, 134441, 134610
Valid prediction for snap_scaffold_1-snap.3079-T1
Valid prediction for GlimmerHMM_glimmerT_2263-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_2275-T1
Valid prediction for snap_scaffold_1-snap.3035-T1
Valid prediction for snap_scaffold_1-snap.3076-T1
Valid prediction for Augustus_model.g1683.t1
Valid prediction for snap_scaffold_1-snap.3040-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9466, rend_intergenic: 5170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22150, rend_intergenic: 20245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30290, rend_intergenic: 22504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35474, rend_intergenic: 31085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50371, rend_intergenic: 37209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69618, rend_intergenic: 50811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89068, rend_intergenic: 84713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91603, rend_intergenic: 89700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96653, rend_intergenic: 93754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100402, rend_intergenic: 96792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103816, rend_intergenic: 102890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105670, rend_intergenic: 105066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115314, rend_intergenic: 106315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119685, rend_intergenic: 115463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136667, rend_intergenic: 120297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156132, rend_intergenic: 152865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157842, rend_intergenic: 156662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162505, rend_intergenic: 159533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169790, rend_intergenic: 163447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186338, rend_intergenic: 170221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192606, rend_intergenic: 188187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199593, rend_intergenic: 196182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208926, rend_intergenic: 204654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213429, rend_intergenic: 208949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218323, rend_intergenic: 215417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221199, rend_intergenic: 218395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224470, rend_intergenic: 221355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 228304
-exon list size: 464


building trellis

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22.5    
22.7    
23.0    
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23.6    
23.8    
24.0    
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25.8    
26.0    
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26.4    
26.6    
26.8    
27.0    
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27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.8    
29.0    
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29.4    
29.6    
29.8    
30.0    
30.3    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
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    
37.6    
37.8    
38.0    
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38.4    
38.6    
38.8    
39.1    
39.3    
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40.3    
40.6    
40.8    
41.0    
41.2    
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41.6    
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42.1    
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43.1    
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44.0    
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44.6    
44.8    
45.1    
45.3    
45.5    
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45.9    
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46.4    
46.6    
46.8    
47.0    
47.2    
47.4    
47.6    
47.9    
48.1    
48.3    
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48.7    
48.9    
49.1    
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49.6    
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50.9    
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52.6    
52.8    
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53.9    
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55.8    
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84.3    
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85.2    
85.4    
85.6    
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87.1    
87.3    
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87.8    
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88.2    
88.4    
88.6    
88.8    
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89.3    
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90.1    
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90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.6    
93.8    
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94.2    
94.4    
94.6    
94.8    
95.1    
95.3    
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96.4    
96.6    
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97.0    
97.2    
97.4    
97.6    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 9466, rend_intergenic: 5170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22150, rend_intergenic: 20245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30290, rend_intergenic: 22504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35474, rend_intergenic: 31085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50371, rend_intergenic: 37209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69618, rend_intergenic: 50811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89068, rend_intergenic: 84713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91603, rend_intergenic: 89700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96653, rend_intergenic: 93754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100402, rend_intergenic: 96792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103816, rend_intergenic: 102890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105670, rend_intergenic: 105066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115314, rend_intergenic: 106315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119685, rend_intergenic: 115463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136667, rend_intergenic: 120297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156132, rend_intergenic: 152865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157842, rend_intergenic: 156662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162505, rend_intergenic: 159533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169790, rend_intergenic: 163447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186338, rend_intergenic: 170221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192606, rend_intergenic: 188187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199593, rend_intergenic: 196182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208926, rend_intergenic: 204654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213429, rend_intergenic: 208949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218323, rend_intergenic: 215417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221199, rend_intergenic: 218395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224470, rend_intergenic: 221355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support