-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_14552816-14757905

-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_5-snap.2687-T1
Valid prediction for GlimmerHMM_glimmerT_13113-T1
Valid prediction for snap_scaffold_5-snap.2671-T1
Valid prediction for HiQ_model.g8719.t1
Couldn't classify 128366, 129331
Sorry, prediction pasa_asmbl_45957.p1 fails validation.
(GGC)	 CA	128366-129331	AA	GAA
Valid prediction for snap_scaffold_5-snap.2695-T1
Valid prediction for snap_scaffold_5-snap.2686-T1
Valid prediction for snap_scaffold_5-snap.2673-T1
Valid prediction for GlimmerHMM_glimmerT_13112-T1
Couldn't classify 143705, 143746
Sorry, prediction pasa_asmbl_45958.p1 fails validation.
(CAA)	 AA	143705-143746	GT	AGG
(CTT)	 AG	144610-144712	GT	AGG
(ATG)	 AG	144968-145017	GT	AGG
(GAC)	 AG	145101-145168	GT	GAG
(GGC)	 AG	145350-145401	GT	AGG
(AAA)	 AG	145631-145704	GT	AGG
(GTT)	 AG	145790-145827	GT	AGG
(GTG)	 AG	145935-145957	GT	CAG
(CCT)	 AG	146052-146129	GT	AGG
(GTT)	 AG	146250-146333	GT	AGG
(GCA)	 AG	146419-146460	AC	AAA
add_exon() Sorry, pasa_asmbl_45958.p1 144968-145017-initial-1 is invalid.
-recovered pasa_asmbl_45958.p1, initial, 144968, 145017
-recovered pasa_asmbl_45958.p1, terminal, 146419, 146460
-recovered pasa_asmbl_45958.p1, internal, 144610, 144712
-recovered pasa_asmbl_45958.p1, internal, 144968, 145017
-recovered pasa_asmbl_45958.p1, internal, 145101, 145168
-recovered pasa_asmbl_45958.p1, internal, 145350, 145401
-recovered pasa_asmbl_45958.p1, internal, 145631, 145704
-recovered pasa_asmbl_45958.p1, internal, 145790, 145827
-recovered pasa_asmbl_45958.p1, internal, 145935, 145957
-recovered pasa_asmbl_45958.p1, internal, 146052, 146129
-recovered pasa_asmbl_45958.p1, internal, 146250, 146333
Valid prediction for GlimmerHMM_glimmerT_13088-T1
Valid prediction for snap_scaffold_5-snap.2694-T1
Valid prediction for GlimmerHMM_glimmerT_13108-T1
Valid prediction for Augustus_model.g8705.t1
Couldn't classify 128107, 128240
Sorry, prediction pasa_asmbl_45955.p1 fails validation.
(ATG)	 AC	126644-126646	GT	TGG
(CGT)	 AG	127774-127996	GT	TGG
(ATG)	 AG	128107-128240	AG	ACA
-recovered pasa_asmbl_45955.p1, initial, 126644, 126646
-recovered pasa_asmbl_45955.p1, internal, 127774, 127996
Valid prediction for Augustus_model.g8725.t1
Valid prediction for GlimmerHMM_glimmerT_13091-T1
Valid prediction for snap_scaffold_5-snap.2682-T1
Couldn't classify 108421, 108541
Sorry, prediction pasa_asmbl_45952.p1 fails validation.
(AGG)	 CC	108421-108541	GT	AGG
(GGC)	 AG	109651-110552	GT	AGG
(GGG)	 AG	110700-110780	GA	GAG
-recovered pasa_asmbl_45952.p1, terminal, 110700, 110780
-recovered pasa_asmbl_45952.p1, internal, 109651, 110552
Valid prediction for pasa_asmbl_45950.p1
Valid prediction for HiQ_model.g8722.t1
Valid prediction for GlimmerHMM_glimmerT_13099-T1
Valid prediction for snap_scaffold_5-snap.2667-T1
Valid prediction for Augustus_model.g8723.t1
Valid prediction for Augustus_model.g8715.t1
Couldn't classify 102157, 102974
Sorry, prediction pasa_asmbl_45951.p1 fails validation.
(ATG)	 GT	100458-100836	GT	AGG
(GCA)	 AG	102157-102974	TA	GGT
-recovered pasa_asmbl_45951.p1, initial, 100458, 100836
Valid prediction for GlimmerHMM_glimmerT_13101-T1
Valid prediction for snap_scaffold_5-snap.2698-T1
Valid prediction for GlimmerHMM_glimmerT_13097-T1
Valid prediction for snap_scaffold_5-snap.2684-T1
Valid prediction for HiQ_model.g8714.t1
Valid prediction for snap_scaffold_5-snap.2674-T1
Valid prediction for HiQ_model.g8707.t1
Valid prediction for snap_scaffold_5-snap.2676-T1
Valid prediction for GlimmerHMM_glimmerT_13110-T1
Valid prediction for CodingQuarry_transcript_52356-T1
Valid prediction for snap_scaffold_5-snap.2691-T1
Valid prediction for snap_scaffold_5-snap.2685-T1
Couldn't classify 149824, 150043
Sorry, prediction pasa_asmbl_46408.p1 fails validation.
(CTT)	 TC	149824-150043	GT	TGG
(AGC)	 AG	150256-150326	GT	AGG
(GCG)	 AG	150426-151712	AC	GAA
-recovered pasa_asmbl_46408.p1, terminal, 150426, 151712
-recovered pasa_asmbl_46408.p1, internal, 150256, 150326
Valid prediction for GlimmerHMM_glimmerT_13093-T1
Valid prediction for GlimmerHMM_glimmerT_13109-T1
Valid prediction for GlimmerHMM_glimmerT_13105-T1
Valid prediction for GlimmerHMM_glimmerT_13090-T1
Valid prediction for pasa_asmbl_45949.p1
Valid prediction for pasa_asmbl_45963.p1
Valid prediction for snap_scaffold_5-snap.2696-T1
Valid prediction for snap_scaffold_5-snap.2699-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 pasa_asmbl_44602.p1
Valid prediction for HiQ_model.g8706.t1
Valid prediction for snap_scaffold_5-snap.2679-T1
Couldn't classify 90544, 91059
Sorry, prediction pasa_asmbl_44611.p1 fails validation.
(GCT)	 CA	90544-91059	TA	AGT
Valid prediction for GlimmerHMM_glimmerT_13106-T1
Valid prediction for snap_scaffold_5-snap.2697-T1
Valid prediction for snap_scaffold_5-snap.2675-T1
Valid prediction for Augustus_model.g8713.t1
Valid prediction for snap_scaffold_5-snap.2669-T1
Valid prediction for HiQ_model.g8709.t1
Valid prediction for GlimmerHMM_glimmerT_13107-T1
Valid prediction for snap_scaffold_5-snap.2681-T1
Valid prediction for HiQ_model.g8703.t1
Valid prediction for snap_scaffold_5-snap.2693-T1
Valid prediction for GlimmerHMM_glimmerT_13094-T1
Valid prediction for GlimmerHMM_glimmerT_13100-T1
Valid prediction for snap_scaffold_5-snap.2670-T1
Valid prediction for snap_scaffold_5-snap.2692-T1
Valid prediction for GlimmerHMM_glimmerT_13111-T1
Valid prediction for GlimmerHMM_glimmerT_13095-T1
Couldn't classify 198377, 198973
Sorry, prediction pasa_asmbl_44598.p1 fails validation.
(TCC)	 TG	198377-198973	CC	ACC
Valid prediction for snap_scaffold_5-snap.2678-T1
Valid prediction for GlimmerHMM_glimmerT_13096-T1
Couldn't classify 83156, 83587
Sorry, prediction pasa_asmbl_44613.p1 fails validation.
(ATG)	 AA	81869-81871	GT	TGG
(CGT)	 AG	82579-82801	GT	TGG
(ATG)	 AG	82912-83060	GT	TGG
(GCT)	 AG	83156-83587	GC	TGG
-recovered pasa_asmbl_44613.p1, initial, 81869, 81871
-recovered pasa_asmbl_44613.p1, initial, 82912, 83060
-recovered pasa_asmbl_44613.p1, internal, 82579, 82801
-recovered pasa_asmbl_44613.p1, internal, 82912, 83060
-recovered pasa_asmbl_44613.p1, internal, 83156, 83587
Valid prediction for Augustus_model.g8716.t1
Valid prediction for GlimmerHMM_glimmerT_13087-T1
Valid prediction for snap_scaffold_5-snap.2703-T1
Valid prediction for GlimmerHMM_glimmerT_13118-T1
Valid prediction for CodingQuarry_transcript_52357-T1
Valid prediction for pasa_asmbl_44609.p1
Valid prediction for Augustus_model.g8708.t1
Valid prediction for GlimmerHMM_glimmerT_13098-T1
Valid prediction for HiQ_model.g8727.t1
Valid prediction for CodingQuarry_transcript_52353-T1
Valid prediction for Augustus_model.g8729.t1
Valid prediction for snap_scaffold_5-snap.2690-T1
Valid prediction for pasa_asmbl_44618.p1
Valid prediction for snap_scaffold_5-snap.2680-T1
Valid prediction for Augustus_model.g8717.t1
Valid prediction for pasa_asmbl_44597.p1
Valid prediction for snap_scaffold_5-snap.2672-T1
Valid prediction for Augustus_model.g8712.t1
Valid prediction for Augustus_model.g8711.t1
Valid prediction for Augustus_model.g8710.t1
Valid prediction for GlimmerHMM_glimmerT_13086-T1
Valid prediction for GlimmerHMM_glimmerT_13089-T1
Valid prediction for CodingQuarry_transcript_52354-T1
Valid prediction for snap_scaffold_5-snap.2689-T1
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 87465, 87770
Sorry, prediction pasa_asmbl_44612.p1 fails validation.
(ATC)	 CA	87465-87770	GA	GTG
Valid prediction for GlimmerHMM_glimmerT_13114-T1
Valid prediction for pasa_asmbl_44614.p1
Valid prediction for CodingQuarry_transcript_52350-T1
Valid prediction for GlimmerHMM_glimmerT_13116-T1
Valid prediction for GlimmerHMM_glimmerT_13092-T1
Valid prediction for CodingQuarry_transcript_52351-T1
Valid prediction for Augustus_model.g8728.t1
Valid prediction for Augustus_model.g8702.t1
Valid prediction for GlimmerHMM_glimmerT_13104-T1
Valid prediction for snap_scaffold_5-snap.2668-T1
Valid prediction for Augustus_model.g8724.t1
Valid prediction for GlimmerHMM_glimmerT_13103-T1
Valid prediction for snap_scaffold_5-snap.2702-T1
Valid prediction for GlimmerHMM_glimmerT_13102-T1
Valid prediction for GlimmerHMM_glimmerT_13085-T1
Valid prediction for Augustus_model.g8720.t1
Valid prediction for Augustus_model.g8721.t1
Valid prediction for snap_scaffold_5-snap.2677-T1
Valid prediction for snap_scaffold_5-snap.2683-T1
Valid prediction for CodingQuarry_transcript_52358-T1
Valid prediction for HiQ_model.g8718.t1
Couldn't classify 173418, 173573
Sorry, prediction pasa_asmbl_44603.p1 fails validation.
(AGC)	 GC	173418-173573	GT	AGG
(GTG)	 AG	174296-174512	GT	CAG
(GTC)	 AG	175130-175378	GT	AGG
(CCT)	 AG	176337-176563	GT	TGG
(TGG)	 AG	176723-177019	AG	AGA
-recovered pasa_asmbl_44603.p1, terminal, 176723, 177019
-recovered pasa_asmbl_44603.p1, internal, 174296, 174512
-recovered pasa_asmbl_44603.p1, internal, 175130, 175378
-recovered pasa_asmbl_44603.p1, internal, 176337, 176563
Valid prediction for snap_scaffold_5-snap.2688-T1
Valid prediction for snap_scaffold_5-snap.2701-T1
Valid prediction for snap_scaffold_5-snap.2700-T1
Valid prediction for GlimmerHMM_glimmerT_13117-T1
Valid prediction for GlimmerHMM_glimmerT_13115-T1
Valid prediction for CodingQuarry_transcript_52352-T1
Valid prediction for snap_scaffold_5-snap.2704-T1
Valid prediction for HiQ_model.g8726.t1
Valid prediction for snap_scaffold_5-snap.2666-T1
Valid prediction for Augustus_model.g8704.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10937, rend_intergenic: 7587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205090
-exon list size: 388


building trellis

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32.3    
32.6    
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33.6    
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38.7    
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39.5    
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40.0    
40.3    
40.5    
40.8    
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41.3    
41.5    
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42.1    
42.3    
42.6    
42.8    
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43.6    
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44.6    
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45.4    
45.6    
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47.9    
48.2    
48.5    
48.7    
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50.3    
50.5    
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60.3    
60.5    
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61.0    
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64.1    
64.4    
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68.5    
68.7    
69.0    
69.2    
69.5    
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70.3    
70.5    
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71.0    
71.3    
71.5    
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72.3    
72.6    
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73.1    
73.3    
73.6    
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74.6    
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79.0    
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80.0    
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80.8    
81.0    
81.3    
81.5    
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82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.6    
83.8    
84.1    
84.4    
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88.7    
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89.5    
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90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.5    
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92.3    
92.6    
92.8    
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93.3    
93.6    
93.8    
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97.4    
97.7    
97.9    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 10937, rend_intergenic: 7587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 37 predictions persist after filtering for low support