-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_17721763-17839023

-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_16884-T1
Valid prediction for pasa_asmbl_47726.p1
Valid prediction for snap_scaffold_6-snap.3773-T1
Valid prediction for GeneMark_model.28262_t
Valid prediction for snap_scaffold_6-snap.3759-T1
Valid prediction for HiQ_model.g11354.t1
Valid prediction for GlimmerHMM_glimmerT_16886-T1
Couldn't classify 105276, 105866
Sorry, prediction pasa_asmbl_47723.p1 fails validation.
(CCC)	 GG	105276-105866	GT	GAG
Couldn't classify 102712, 102801
Couldn't classify 105004, 105062
Sorry, prediction pasa_asmbl_47722.p2 fails validation.
(AAG)	 TG	102712-102801	GT	AGG
(GTG)	 AG	103455-103653	GT	GGG
(ATG)	 AG	104490-104570	GT	AAG
(TGG)	 AG	105004-105062	CT	CCC
-recovered pasa_asmbl_47722.p2, initial, 104490, 104570
-recovered pasa_asmbl_47722.p2, internal, 103455, 103653
-recovered pasa_asmbl_47722.p2, internal, 104490, 104570
Valid prediction for snap_scaffold_6-snap.3771-T1
Valid prediction for Augustus_model.g11352.t1
Valid prediction for GeneMark_model.28271_t
Valid prediction for CodingQuarry_transcript_55264-T1
Valid prediction for Augustus_model.g11349.t1
Valid prediction for snap_scaffold_6-snap.3775-T1
Valid prediction for GeneMark_model.28265_t
Valid prediction for GlimmerHMM_glimmerT_16875-T1
Valid prediction for GeneMark_model.28253_t
Valid prediction for GlimmerHMM_glimmerT_16876-T1
Valid prediction for GlimmerHMM_glimmerT_16887-T1
Valid prediction for GlimmerHMM_glimmerT_16869-T1
Valid prediction for GeneMark_model.28273_t
Valid prediction for snap_scaffold_6-snap.3755-T1
Valid prediction for Augustus_model.g11351.t1
Valid prediction for GeneMark_model.28269_t
Valid prediction for snap_scaffold_6-snap.3770-T1
Valid prediction for GeneMark_model.28254_t
Valid prediction for GlimmerHMM_glimmerT_16874-T1
Valid prediction for GeneMark_model.28242_t
Valid prediction for CodingQuarry_transcript_55266-T1
Valid prediction for GlimmerHMM_glimmerT_16871-T1
Valid prediction for snap_scaffold_6-snap.3760-T1
Valid prediction for CodingQuarry_transcript_55265-T1
Valid prediction for GeneMark_model.28244_t
Valid prediction for GeneMark_model.28267_t
Valid prediction for Augustus_model.g11353.t1
Valid prediction for GeneMark_model.28256_t
Valid prediction for HiQ_model.g11350.t1
Valid prediction for snap_scaffold_6-snap.3763-T1
Valid prediction for snap_scaffold_6-snap.3757-T1
Valid prediction for GlimmerHMM_glimmerT_16885-T1
Valid prediction for GeneMark_model.28274_t
Valid prediction for GeneMark_model.28248_t
Valid prediction for GeneMark_model.28258_t
Valid prediction for GlimmerHMM_glimmerT_16881-T1
Couldn't classify 88228, 88287
Couldn't classify 91302, 91346
Sorry, prediction pasa_asmbl_47721.p1 fails validation.
(CTC)	 AC	88228-88287	GT	AGG
(ATG)	 AG	89554-89694	GT	AAG
(GCT)	 AG	89930-90067	GT	GAG
(TCT)	 AG	91302-91346	GG	AGG
-recovered pasa_asmbl_47721.p1, initial, 89554, 89694
-recovered pasa_asmbl_47721.p1, internal, 89554, 89694
-recovered pasa_asmbl_47721.p1, internal, 89930, 90067
Valid prediction for GeneMark_model.28251_t
Valid prediction for GeneMark_model.28240_t
Valid prediction for Augustus_model.g11346.t1
Valid prediction for snap_scaffold_6-snap.3772-T1
Valid prediction for snap_scaffold_6-snap.3765-T1
Valid prediction for snap_scaffold_6-snap.3752-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g11343.t1
Valid prediction for snap_scaffold_6-snap.3768-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GeneMark_model.28272_t
Valid prediction for Augustus_model.g11344.t1
Valid prediction for snap_scaffold_6-snap.3774-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_6-snap.3764-T1
Valid prediction for snap_scaffold_6-snap.3761-T1
Valid prediction for snap_scaffold_6-snap.3762-T1
Valid prediction for snap_scaffold_6-snap.3767-T1
Valid prediction for GeneMark_model.28246_t
Valid prediction for GlimmerHMM_glimmerT_16872-T1
Valid prediction for snap_scaffold_6-snap.3758-T1
Valid prediction for pasa_asmbl_49132.p1
Valid prediction for GeneMark_model.28257_t
Valid prediction for GeneMark_model.28252_t
Valid prediction for GlimmerHMM_glimmerT_16877-T1
Valid prediction for pasa_asmbl_49138.p1
Valid prediction for snap_scaffold_6-snap.3766-T1
Valid prediction for GlimmerHMM_glimmerT_16882-T1
Valid prediction for GeneMark_model.28247_t
Valid prediction for GeneMark_model.28259_t
Valid prediction for GeneMark_model.28243_t
Valid prediction for GeneMark_model.28263_t
Valid prediction for GlimmerHMM_glimmerT_16880-T1
Valid prediction for GlimmerHMM_glimmerT_16878-T1
Valid prediction for GeneMark_model.28245_t
Valid prediction for GeneMark_model.28261_t
Valid prediction for snap_scaffold_6-snap.3753-T1
Valid prediction for GlimmerHMM_glimmerT_16870-T1
Valid prediction for snap_scaffold_6-snap.3756-T1
Valid prediction for Augustus_model.g11345.t1
Valid prediction for GeneMark_model.28255_t
Valid prediction for GlimmerHMM_glimmerT_16883-T1
Couldn't classify 94656, 94709
Sorry, prediction GlimmerHMM_glimmerT_16873-T1 fails validation.
(ATG)	 AG	83996-84122	GT	AAG
(ACA)	 AG	88105-88277	GT	AGG
(AGT)	 AG	94656-94709	NN	ANN
-recovered GlimmerHMM_glimmerT_16873-T1, initial, 83996, 84122
-recovered GlimmerHMM_glimmerT_16873-T1, internal, 83996, 84122
-recovered GlimmerHMM_glimmerT_16873-T1, internal, 88105, 88277
Valid prediction for GeneMark_model.28270_t
Valid prediction for GeneMark_model.28264_t
Valid prediction for GeneMark_model.28241_t
Valid prediction for HiQ_model.g11355.t1
Valid prediction for GeneMark_model.28268_t
Valid prediction for GeneMark_model.28266_t
Valid prediction for CodingQuarry_transcript_55263-T1
Valid prediction for GeneMark_model.28250_t
Valid prediction for snap_scaffold_6-snap.3769-T1
Valid prediction for GeneMark_model.28249_t
Valid prediction for snap_scaffold_6-snap.3754-T1
Valid prediction for GlimmerHMM_glimmerT_16879-T1
Valid prediction for Augustus_model.g11347.t1
Valid prediction for Augustus_model.g11348.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16434, rend_intergenic: 2732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21272, rend_intergenic: 16630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36783, rend_intergenic: 28949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37824, rend_intergenic: 37213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45485, rend_intergenic: 40367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58931, rend_intergenic: 46689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65346, rend_intergenic: 59317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71265, rend_intergenic: 68684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72222, rend_intergenic: 71521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87079, rend_intergenic: 80354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94938, rend_intergenic: 88742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 117261
-exon list size: 547


building trellis

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28.8    
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29.1    
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30.8    
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31.3    
31.5    
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32.6    
32.8    
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33.2    
33.3    
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33.9    
34.1    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.3    
35.5    
35.7    
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36.1    
36.2    
36.4    
36.6    
36.8    
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37.7    
37.9    
38.1    
38.3    
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38.6    
38.8    
39.0    
39.2    
39.3    
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39.7    
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40.1    
40.3    
40.4    
40.6    
40.8    
41.0    
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41.3    
41.5    
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42.1    
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42.8    
43.0    
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43.4    
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44.1    
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45.0    
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58.8    
59.0    
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60.3    
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64.3    
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66.1    
66.3    
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66.7    
66.8    
67.0    
67.2    
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67.6    
67.8    
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68.9    
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69.2    
69.4    
69.6    
69.8    
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71.2    
71.4    
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73.2    
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73.6    
73.8    
74.0    
74.1    
74.3    
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74.7    
74.9    
75.0    
75.2    
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75.6    
75.8    
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76.1    
76.3    
76.5    
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77.2    
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77.6    
77.8    
78.0    
78.1    
78.3    
78.5    
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78.9    
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80.1    
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82.1    
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82.9    
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83.2    
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83.6    
83.8    
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84.9    
85.1    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.3    
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86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
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89.6    
89.8    
90.0    
90.2    
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90.7    
90.9    
91.1    
91.3    
91.4    
91.6    
91.8    
92.0    
92.2    
92.3    
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92.7    
92.9    
93.1    
93.3    
93.4    
93.6    
93.8    
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94.2    
94.4    
94.5    
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94.9    
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95.8    
96.0    
96.2    
96.4    
96.5    
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97.1    
97.3    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 16434, rend_intergenic: 2732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21272, rend_intergenic: 16630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36783, rend_intergenic: 28949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37824, rend_intergenic: 37213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45485, rend_intergenic: 40367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58931, rend_intergenic: 46689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65346, rend_intergenic: 59317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71265, rend_intergenic: 68684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72222, rend_intergenic: 71521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87079, rend_intergenic: 80354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94938, rend_intergenic: 88742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support