-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_2208885-2406721

-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 Augustus_model.g225.t1
Valid prediction for GeneMark_model.343_t
Valid prediction for GeneMark_model.348_t
Valid prediction for snap_scaffold_1-snap.387-T1
Valid prediction for snap_scaffold_1-snap.390-T1
Valid prediction for GeneMark_model.328_t
Valid prediction for snap_scaffold_1-snap.371-T1
Valid prediction for Augustus_model.g227.t1
Valid prediction for Augustus_model.g226.t1
Valid prediction for Augustus_model.g238.t1
Valid prediction for snap_scaffold_1-snap.392-T1
Valid prediction for GeneMark_model.340_t
Valid prediction for GlimmerHMM_glimmerT_300-T1
Valid prediction for GlimmerHMM_glimmerT_313-T1
Valid prediction for Augustus_model.g237.t1
Valid prediction for snap_scaffold_1-snap.391-T1
Valid prediction for GlimmerHMM_glimmerT_310-T1
Valid prediction for Augustus_model.g235.t1
Valid prediction for GeneMark_model.325_t
Valid prediction for snap_scaffold_1-snap.370-T1
Valid prediction for snap_scaffold_1-snap.389-T1
Valid prediction for Augustus_model.g224.t1
Valid prediction for GeneMark_model.352_t
Valid prediction for GlimmerHMM_glimmerT_297-T1
Valid prediction for snap_scaffold_1-snap.374-T1
Valid prediction for GeneMark_model.350_t
Valid prediction for GlimmerHMM_glimmerT_307-T1
Valid prediction for Augustus_model.g229.t1
Valid prediction for GlimmerHMM_glimmerT_295-T1
Valid prediction for GlimmerHMM_glimmerT_305-T1
Valid prediction for GeneMark_model.336_t
Valid prediction for GlimmerHMM_glimmerT_294-T1
Valid prediction for GlimmerHMM_glimmerT_308-T1
Valid prediction for GeneMark_model.346_t
Valid prediction for snap_scaffold_1-snap.372-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.338_t
Valid prediction for GeneMark_model.335_t
Valid prediction for GeneMark_model.333_t
Valid prediction for snap_scaffold_1-snap.395-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.384-T1
Valid prediction for GeneMark_model.353_t
Valid prediction for Augustus_model.g233.t1
Valid prediction for Augustus_model.g234.t1
Valid prediction for Augustus_model.g236.t1
Valid prediction for GlimmerHMM_glimmerT_299-T1
Couldn't classify 21668, 21781
Couldn't classify 22840, 23012
Sorry, prediction pasa_asmbl_117.p1 fails validation.
(CCC)	 AG	21668-21781	GT	GGG
(GTG)	 AG	22115-22325	GT	AGG
(TCC)	 AG	22554-22676	GT	AGG
(TGA)	 AG	22840-23012	GG	AAG
-recovered pasa_asmbl_117.p1, internal, 21668, 21781
-recovered pasa_asmbl_117.p1, internal, 22115, 22325
-recovered pasa_asmbl_117.p1, internal, 22554, 22676
Valid prediction for Augustus_model.g231.t1
Valid prediction for Augustus_model.g239.t1
Valid prediction for Augustus_model.g232.t1
Valid prediction for GlimmerHMM_glimmerT_293-T1
Valid prediction for snap_scaffold_1-snap.380-T1
Valid prediction for Augustus_model.g245.t1
Valid prediction for snap_scaffold_1-snap.393-T1
Valid prediction for GeneMark_model.334_t
Valid prediction for snap_scaffold_1-snap.394-T1
Valid prediction for GlimmerHMM_glimmerT_314-T1
Valid prediction for GlimmerHMM_glimmerT_303-T1
Valid prediction for snap_scaffold_1-snap.386-T1
Valid prediction for snap_scaffold_1-snap.375-T1
Valid prediction for snap_scaffold_1-snap.383-T1
Valid prediction for snap_scaffold_1-snap.378-T1
Valid prediction for GlimmerHMM_glimmerT_306-T1
Valid prediction for GlimmerHMM_glimmerT_304-T1
Valid prediction for snap_scaffold_1-snap.379-T1
Valid prediction for snap_scaffold_1-snap.369-T1
Valid prediction for snap_scaffold_1-snap.373-T1
Valid prediction for GlimmerHMM_glimmerT_309-T1
Valid prediction for Augustus_model.g230.t1
Valid prediction for Augustus_model.g223.t1
Valid prediction for GlimmerHMM_glimmerT_301-T1
Couldn't classify 8593, 8690
Sorry, prediction pasa_asmbl_120.p1 fails validation.
(ATG)	 AG	2684-2777	GT	TCG
(TGA)	 AG	5627-5732	GT	ATG
(CTT)	 AG	8239-8435	GT	CAG
(AGG)	 AG	8593-8690	CC	CGC
-recovered pasa_asmbl_120.p1, initial, 2684, 2777
-recovered pasa_asmbl_120.p1, internal, 2684, 2777
-recovered pasa_asmbl_120.p1, internal, 5627, 5732
-recovered pasa_asmbl_120.p1, internal, 8239, 8435
Valid prediction for GeneMark_model.327_t
Valid prediction for GeneMark_model.341_t
Valid prediction for GeneMark_model.324_t
Valid prediction for snap_scaffold_1-snap.382-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.381-T1
Valid prediction for Augustus_model.g243.t1
Valid prediction for GlimmerHMM_glimmerT_298-T1
Valid prediction for Augustus_model.g242.t1
Valid prediction for GlimmerHMM_glimmerT_302-T1
Couldn't classify 20192, 20291
Couldn't classify 21189, 21350
Sorry, prediction pasa_asmbl_118.p1 fails validation.
(CGT)	 GC	20192-20291	GC	AGG
(AGT)	 AG	20484-20681	GT	CCG
(CCC)	 AG	20868-20938	GT	AGG
(CCT)	 AG	21189-21350	AT	CCA
-recovered pasa_asmbl_118.p1, internal, 20484, 20681
-recovered pasa_asmbl_118.p1, internal, 20868, 20938
Valid prediction for GeneMark_model.344_t
Valid prediction for GlimmerHMM_glimmerT_312-T1
Valid prediction for GeneMark_model.330_t
Valid prediction for GeneMark_model.339_t
Valid prediction for Augustus_model.g228.t1
Valid prediction for GeneMark_model.351_t
Valid prediction for Augustus_model.g241.t1
Valid prediction for GeneMark_model.342_t
Valid prediction for snap_scaffold_1-snap.385-T1
Valid prediction for CodingQuarry_transcript_2547-T1
Valid prediction for GeneMark_model.331_t
Valid prediction for GeneMark_model.345_t
Valid prediction for Augustus_model.g244.t1
Valid prediction for Augustus_model.g240.t1
Valid prediction for snap_scaffold_1-snap.376-T1
Valid prediction for GeneMark_model.332_t
Valid prediction for snap_scaffold_1-snap.388-T1
Valid prediction for GeneMark_model.349_t
Valid prediction for GeneMark_model.337_t
Valid prediction for GlimmerHMM_glimmerT_292-T1
Valid prediction for snap_scaffold_1-snap.377-T1
Valid prediction for GeneMark_model.329_t
Valid prediction for GeneMark_model.326_t
Valid prediction for GlimmerHMM_glimmerT_315-T1
Valid prediction for GeneMark_model.347_t
Valid prediction for GlimmerHMM_glimmerT_311-T1
Valid prediction for GlimmerHMM_glimmerT_296-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 110068, rend_intergenic: 109674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192630, rend_intergenic: 188162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 197837
-exon list size: 420


building trellis

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30.3    
30.6    
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33.2    
33.4    
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34.6    
34.8    
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35.8    
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37.7    
37.9    
38.2    
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38.6    
38.9    
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39.6    
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42.9    
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43.6    
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45.0    
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54.0    
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57.6    
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58.1    
58.3    
58.5    
58.8    
59.0    
59.2    
59.5    
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61.4    
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62.6    
62.8    
63.0    
63.3    
63.5    
63.7    
64.0    
64.2    
64.5    
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65.2    
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65.6    
65.9    
66.1    
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66.6    
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68.0    
68.2    
68.5    
68.7    
69.0    
69.2    
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70.4    
70.6    
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73.0    
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82.9    
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83.4    
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84.4    
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84.8    
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85.5    
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86.0    
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88.6    
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89.3    
89.6    
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90.0    
90.3    
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90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.2    
92.4    
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92.9    
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93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.8    
95.0    
95.3    
95.5    
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96.0    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 110068, rend_intergenic: 109674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192630, rend_intergenic: 188162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 14181
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 1 - 10294