-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_3349635-3463323

-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 GeneMark_model.63044_t
Valid prediction for snap_scaffold_15-snap.746-T1
Valid prediction for GeneMark_model.63050_t
Valid prediction for GeneMark_model.63063_t
Valid prediction for GeneMark_model.63059_t
Valid prediction for GeneMark_model.63071_t
Couldn't classify 57824, 57941
Couldn't classify 58766, 58873
Sorry, prediction pasa_asmbl_14877.p1 fails validation.
(GAC)	 AT	57824-57941	GT	TGG
(AGC)	 AG	58037-58112	GT	AGG
(AGT)	 AG	58215-58316	GT	AGG
(GTG)	 AG	58524-58635	GT	CGG
(GTG)	 AG	58766-58873	CC	AGC
-recovered pasa_asmbl_14877.p1, internal, 58037, 58112
-recovered pasa_asmbl_14877.p1, internal, 58215, 58316
-recovered pasa_asmbl_14877.p1, internal, 58524, 58635
Valid prediction for GeneMark_model.63067_t
Valid prediction for GlimmerHMM_glimmerT_36637-T1
Valid prediction for GlimmerHMM_glimmerT_36635-T1
Valid prediction for GlimmerHMM_glimmerT_36648-T1
Valid prediction for GeneMark_model.63061_t
Valid prediction for Augustus_model.g24604.t1
Valid prediction for GlimmerHMM_glimmerT_36625-T1
Valid prediction for GeneMark_model.63073_t
Couldn't classify 71668, 71824
Couldn't classify 76666, 76772
Sorry, prediction pasa_asmbl_14902.p1 fails validation.
(TCA)	 TG	71668-71824	GT	TGG
(ACA)	 AG	74792-74914	GT	GGG
(ACT)	 AG	76666-76772	AA	ACA
-recovered pasa_asmbl_14902.p1, internal, 74792, 74914
Valid prediction for GeneMark_model.63042_t
Valid prediction for snap_scaffold_15-snap.739-T1
Valid prediction for GlimmerHMM_glimmerT_36630-T1
Valid prediction for CodingQuarry_transcript_17915-T1
Valid prediction for snap_scaffold_15-snap.734-T1
Valid prediction for Augustus_model.g24607.t1
Valid prediction for snap_scaffold_15-snap.741-T1
Valid prediction for HiQ_model.g24597.t1
Valid prediction for GlimmerHMM_glimmerT_36650-T1
Valid prediction for GlimmerHMM_glimmerT_36629-T1
Valid prediction for snap_scaffold_15-snap.750-T1
Valid prediction for GeneMark_model.63058_t
Valid prediction for GlimmerHMM_glimmerT_36638-T1
Couldn't classify 22280, 22489
Sorry, prediction pasa_asmbl_14039.p1 fails validation.
(CAC)	 TC	22280-22489	GT	AGG
(AGG)	 AG	23619-23739	GT	CGG
(GGC)	 AG	24446-24636	AC	AGA
-recovered pasa_asmbl_14039.p1, terminal, 24446, 24636
-recovered pasa_asmbl_14039.p1, internal, 23619, 23739
Valid prediction for snap_scaffold_15-snap.735-T1
Couldn't classify 13316, 13648
Sorry, prediction pasa_asmbl_15097.p1 fails validation.
(CCC)	 TG	13316-13648	AG	GAA
Valid prediction for snap_scaffold_15-snap.727-T1
Valid prediction for Augustus_model.g24601.t1
Valid prediction for snap_scaffold_15-snap.730-T1
Valid prediction for snap_scaffold_15-snap.744-T1
Valid prediction for GeneMark_model.63057_t
Valid prediction for snap_scaffold_15-snap.742-T1
Valid prediction for GlimmerHMM_glimmerT_36639-T1
Valid prediction for GeneMark_model.63047_t
Valid prediction for snap_scaffold_15-snap.743-T1
Valid prediction for GlimmerHMM_glimmerT_36645-T1
Valid prediction for GlimmerHMM_glimmerT_36636-T1
Valid prediction for snap_scaffold_15-snap.751-T1
Valid prediction for GeneMark_model.63053_t
Valid prediction for Augustus_model.g24602.t1
Valid prediction for snap_scaffold_15-snap.733-T1
Valid prediction for Augustus_model.g24610.t1
Valid prediction for snap_scaffold_15-snap.732-T1
Valid prediction for snap_scaffold_15-snap.748-T1
Couldn't classify 94764, 95118
Couldn't classify 95945, 96009
Sorry, prediction pasa_asmbl_14042.p1 fails validation.
(GCT)	 AG	94764-95118	GT	AGG
(GCG)	 AG	95945-96009	AC	GTA
-recovered pasa_asmbl_14042.p1, internal, 94764, 95118

-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 GeneMark_model.63046_t
Valid prediction for GlimmerHMM_glimmerT_36628-T1
Valid prediction for snap_scaffold_15-snap.745-T1
Valid prediction for snap_scaffold_15-snap.729-T1
Valid prediction for CodingQuarry_transcript_17911-T1
Valid prediction for GlimmerHMM_glimmerT_36627-T1
Valid prediction for GeneMark_model.63062_t
Valid prediction for GeneMark_model.63054_t
Valid prediction for pasa_asmbl_15105.p1
Valid prediction for snap_scaffold_15-snap.747-T1
Valid prediction for Augustus_model.g24600.t1
Valid prediction for snap_scaffold_15-snap.738-T1
Valid prediction for GeneMark_model.63055_t
Couldn't classify 105404, 105517
Sorry, prediction pasa_asmbl_15094.p1 fails validation.
(ATG)	 GC	102269-102665	GT	AGG
(CTG)	 AG	103014-103381	GT	AAG
(AAC)	 AG	103515-103672	GT	AGG
(GCT)	 AG	104681-104852	GT	AGG
(GAC)	 AG	105050-105298	GT	AGG
(TTC)	 AG	105404-105517	AC	GTA
-recovered pasa_asmbl_15094.p1, initial, 102269, 102665
-recovered pasa_asmbl_15094.p1, internal, 103014, 103381
-recovered pasa_asmbl_15094.p1, internal, 103515, 103672
-recovered pasa_asmbl_15094.p1, internal, 104681, 104852
-recovered pasa_asmbl_15094.p1, internal, 105050, 105298
Valid prediction for GlimmerHMM_glimmerT_36641-T1
Valid prediction for snap_scaffold_15-snap.740-T1
Valid prediction for GeneMark_model.63065_t
Valid prediction for GlimmerHMM_glimmerT_36631-T1
Couldn't classify 84254, 84364
Sorry, prediction pasa_asmbl_15103.p2 fails validation.
(ATG)	 AG	82299-82440	GT	TGG
(ACC)	 AG	82964-83085	GT	AGG
(TTG)	 AG	83589-83672	GT	TGG
(GTG)	 AG	83769-83852	GT	CTG
(TGG)	 AG	84254-84364	TG	GGT
-recovered pasa_asmbl_15103.p2, initial, 82299, 82440
-recovered pasa_asmbl_15103.p2, internal, 82299, 82440
-recovered pasa_asmbl_15103.p2, internal, 82964, 83085
-recovered pasa_asmbl_15103.p2, internal, 83589, 83672
-recovered pasa_asmbl_15103.p2, internal, 83769, 83852
Valid prediction for GlimmerHMM_glimmerT_36634-T1
Valid prediction for GeneMark_model.63074_t
Valid prediction for GeneMark_model.63068_t
Couldn't classify 100226, 100260
Couldn't classify 100318, 100354
Sorry, prediction CodingQuarry_transcript_17912-T1 fails validation.
(ATG)	 GG	100012-100122	GT	AGG
(ATG)	 AG	100226-100260	AC	ACA
(GCT)	 AC	100318-100354	TG	GAT
-recovered CodingQuarry_transcript_17912-T1, initial, 100012, 100122
Valid prediction for snap_scaffold_15-snap.749-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.63056_t
Valid prediction for snap_scaffold_15-snap.736-T1
Valid prediction for GlimmerHMM_glimmerT_36643-T1
Valid prediction for GlimmerHMM_glimmerT_36640-T1
Valid prediction for GlimmerHMM_glimmerT_36647-T1
Valid prediction for snap_scaffold_15-snap.737-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.63072_t
Valid prediction for GeneMark_model.63049_t
Valid prediction for GeneMark_model.63070_t
Valid prediction for GeneMark_model.63069_t
Valid prediction for GeneMark_model.63043_t
Valid prediction for GlimmerHMM_glimmerT_36632-T1
Valid prediction for snap_scaffold_15-snap.723-T1
Valid prediction for GlimmerHMM_glimmerT_36633-T1
Valid prediction for snap_scaffold_15-snap.752-T1
Valid prediction for snap_scaffold_15-snap.725-T1
Valid prediction for GlimmerHMM_glimmerT_36649-T1
Valid prediction for Augustus_model.g24598.t1
Valid prediction for HiQ_model.g24596.t1
Valid prediction for GeneMark_model.63045_t
Valid prediction for GlimmerHMM_glimmerT_36642-T1
Valid prediction for Augustus_model.g24599.t1
Valid prediction for Augustus_model.g24605.t1
Valid prediction for GlimmerHMM_glimmerT_36644-T1
Valid prediction for GlimmerHMM_glimmerT_36626-T1
Valid prediction for GeneMark_model.63060_t
Valid prediction for Augustus_model.g24609.t1
Valid prediction for snap_scaffold_15-snap.724-T1
Valid prediction for snap_scaffold_15-snap.728-T1
Valid prediction for snap_scaffold_15-snap.726-T1
Valid prediction for Augustus_model.g24606.t1
Valid prediction for snap_scaffold_15-snap.722-T1
Valid prediction for GlimmerHMM_glimmerT_36646-T1
Valid prediction for GeneMark_model.63041_t
Valid prediction for CodingQuarry_transcript_17914-T1
Valid prediction for snap_scaffold_15-snap.731-T1
Valid prediction for Augustus_model.g24603.t1
Valid prediction for GeneMark_model.63066_t
Valid prediction for CodingQuarry_transcript_17913-T1
Valid prediction for GeneMark_model.63051_t
Valid prediction for Augustus_model.g24608.t1
Valid prediction for GeneMark_model.63052_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 38173, rend_intergenic: 33125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67607, rend_intergenic: 55958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70595, rend_intergenic: 70065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77609, rend_intergenic: 70852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93205, rend_intergenic: 91348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98595, rend_intergenic: 93221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102056, rend_intergenic: 99667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111057, rend_intergenic: 105121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 113689
-exon list size: 515


building trellis

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29.6    
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31.1    
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31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.7    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.4    
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38.3    
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46.4    
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76.2    
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76.6    
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79.3    
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80.3    
80.5    
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80.9    
81.0    
81.2    
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81.6    
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82.2    
82.4    
82.6    
82.8    
83.0    
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84.3    
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85.3    
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85.9    
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87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.7    
89.9    
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90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
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95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 38173, rend_intergenic: 33125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67607, rend_intergenic: 55958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70595, rend_intergenic: 70065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77609, rend_intergenic: 70852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93205, rend_intergenic: 91348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98595, rend_intergenic: 93221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102056, rend_intergenic: 99667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111057, rend_intergenic: 105121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support