-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_3391726-3598665

-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_20-snap.728-T1
Valid prediction for GlimmerHMM_glimmerT_45746-T1
Valid prediction for Augustus_model.g30379.t1
Valid prediction for pasa_asmbl_26533.p1
Valid prediction for Augustus_model.g30381.t1
Valid prediction for snap_scaffold_20-snap.735-T1
Valid prediction for Augustus_model.g30369.t1
Valid prediction for snap_scaffold_20-snap.746-T1
Valid prediction for GlimmerHMM_glimmerT_45749-T1
Valid prediction for GlimmerHMM_glimmerT_45727-T1
Valid prediction for snap_scaffold_20-snap.736-T1
Valid prediction for HiQ_model.g30371.t1
Valid prediction for GlimmerHMM_glimmerT_45740-T1
Valid prediction for snap_scaffold_20-snap.719-T1
Valid prediction for snap_scaffold_20-snap.745-T1
Couldn't classify 63011, 63130
Couldn't classify 68680, 68739
Sorry, prediction pasa_asmbl_27147.p1 fails validation.
(CTT)	 CA	63011-63130	GT	AAG
(TCA)	 AG	63503-63605	GT	AGG
(ACC)	 AG	63996-64169	GT	GGG
(GTC)	 AG	64349-64542	GT	AGG
(ATG)	 AG	64873-65005	GT	AGG
(GTA)	 AG	65701-65846	GT	AGG
(TCA)	 AG	66165-66364	GT	TGG
(GGC)	 AG	66564-66684	GT	AGG
(ACC)	 AG	67016-67094	GT	GAG
(AGA)	 AG	67189-67298	GT	AGG
(GTG)	 AG	67569-67676	GT	AGG
(TTC)	 AG	67928-68044	GT	AGG
(GTG)	 AG	68209-68391	GT	AGG
(TAC)	 AG	68680-68739	AC	AGA
-recovered pasa_asmbl_27147.p1, initial, 64873, 65005
-recovered pasa_asmbl_27147.p1, terminal, 67016, 67094
-recovered pasa_asmbl_27147.p1, internal, 63503, 63605
-recovered pasa_asmbl_27147.p1, internal, 63996, 64169
-recovered pasa_asmbl_27147.p1, internal, 64349, 64542
-recovered pasa_asmbl_27147.p1, internal, 64873, 65005
-recovered pasa_asmbl_27147.p1, internal, 65701, 65846
-recovered pasa_asmbl_27147.p1, internal, 66165, 66364
-recovered pasa_asmbl_27147.p1, internal, 66564, 66684
-recovered pasa_asmbl_27147.p1, internal, 67016, 67094
-recovered pasa_asmbl_27147.p1, internal, 67189, 67298
-recovered pasa_asmbl_27147.p1, internal, 67569, 67676
-recovered pasa_asmbl_27147.p1, internal, 67928, 68044
-recovered pasa_asmbl_27147.p1, internal, 68209, 68391
Valid prediction for snap_scaffold_20-snap.727-T1
Valid prediction for Augustus_model.g30370.t1
Valid prediction for GlimmerHMM_glimmerT_45732-T1
Valid prediction for GlimmerHMM_glimmerT_45747-T1
Valid prediction for snap_scaffold_20-snap.713-T1
Valid prediction for GlimmerHMM_glimmerT_45735-T1
Valid prediction for snap_scaffold_20-snap.715-T1
Valid prediction for snap_scaffold_20-snap.733-T1
Valid prediction for snap_scaffold_20-snap.743-T1
Valid prediction for GlimmerHMM_glimmerT_45736-T1
Valid prediction for GlimmerHMM_glimmerT_45734-T1
Valid prediction for snap_scaffold_20-snap.710-T1
Valid prediction for Augustus_model.g30384.t1
Valid prediction for GlimmerHMM_glimmerT_45745-T1
Valid prediction for GlimmerHMM_glimmerT_45733-T1
Valid prediction for snap_scaffold_20-snap.729-T1
Valid prediction for snap_scaffold_20-snap.718-T1
Valid prediction for GlimmerHMM_glimmerT_45750-T1
Valid prediction for snap_scaffold_20-snap.714-T1
Valid prediction for GlimmerHMM_glimmerT_45742-T1
Valid prediction for snap_scaffold_20-snap.716-T1
Couldn't classify 56089, 56181
Sorry, prediction pasa_asmbl_26531.p1 fails validation.
(GTT)	 TG	56089-56181	GT	AGG
(GAC)	 AG	56763-56943	GT	GGG
(GTA)	 AG	57144-57271	AC	AGA
-recovered pasa_asmbl_26531.p1, terminal, 57144, 57271
-recovered pasa_asmbl_26531.p1, internal, 56763, 56943
Couldn't classify 58249, 58392
Couldn't classify 59725, 59748
Sorry, prediction pasa_asmbl_26532.p1 fails validation.
(GAG)	 TG	58249-58392	GT	AGG
(ACT)	 AG	59068-59163	GT	AGG
(GAG)	 AG	59353-59433	GT	AGG
(GTG)	 AG	59725-59748	GG	GGG
-recovered pasa_asmbl_26532.p1, internal, 59068, 59163
-recovered pasa_asmbl_26532.p1, internal, 59353, 59433
Valid prediction for snap_scaffold_20-snap.744-T1
Valid prediction for snap_scaffold_20-snap.709-T1
Valid prediction for snap_scaffold_20-snap.741-T1
Valid prediction for snap_scaffold_20-snap.725-T1
Valid prediction for Augustus_model.g30367.t1
Valid prediction for snap_scaffold_20-snap.723-T1
Valid prediction for snap_scaffold_20-snap.721-T1
Valid prediction for Augustus_model.g30376.t1
Valid prediction for snap_scaffold_20-snap.738-T1
Valid prediction for GlimmerHMM_glimmerT_45730-T1
Valid prediction for GlimmerHMM_glimmerT_45728-T1
Valid prediction for CodingQuarry_transcript_30475-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 GlimmerHMM_glimmerT_45741-T1
Valid prediction for Augustus_model.g30372.t1
Valid prediction for snap_scaffold_20-snap.734-T1
Valid prediction for GlimmerHMM_glimmerT_45731-T1
Valid prediction for GlimmerHMM_glimmerT_45753-T1
Valid prediction for GlimmerHMM_glimmerT_45752-T1
Valid prediction for Augustus_model.g30377.t1
Valid prediction for pasa_asmbl_25702.p1
Valid prediction for Augustus_model.g30386.t1
Valid prediction for Augustus_model.g30378.t1
Valid prediction for Augustus_model.g30374.t1
Valid prediction for snap_scaffold_20-snap.724-T1
Valid prediction for snap_scaffold_20-snap.740-T1
Valid prediction for GlimmerHMM_glimmerT_45748-T1
Couldn't classify 124829, 124879
Couldn't classify 125401, 125805
Sorry, prediction pasa_asmbl_25697.p1 fails validation.
(AAG)	 AC	124829-124879	GT	AGG
(GAC)	 AG	125401-125805	AC	TGA
Valid prediction for Augustus_model.g30387.t1
Valid prediction for Augustus_model.g30373.t1
Valid prediction for GlimmerHMM_glimmerT_45743-T1
Valid prediction for snap_scaffold_20-snap.708-T1
Valid prediction for snap_scaffold_20-snap.717-T1
Valid prediction for snap_scaffold_20-snap.731-T1
Valid prediction for GlimmerHMM_glimmerT_45751-T1
Valid prediction for snap_scaffold_20-snap.711-T1
Valid prediction for snap_scaffold_20-snap.730-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_30474-T1
Valid prediction for snap_scaffold_20-snap.732-T1
Valid prediction for snap_scaffold_20-snap.712-T1
Valid prediction for snap_scaffold_20-snap.739-T1
Valid prediction for Augustus_model.g30385.t1
Valid prediction for GlimmerHMM_glimmerT_45737-T1
Valid prediction for pasa_asmbl_25691.p1
Valid prediction for snap_scaffold_20-snap.742-T1
Couldn't classify 127391, 127590
Couldn't classify 129508, 129594
Sorry, prediction pasa_asmbl_25695.p1 fails validation.
(TCC)	 CC	127391-127590	GT	AGG
(CAT)	 AG	127918-128146	GT	TGG
(GCT)	 AG	128349-128497	GT	AGG
(TAA)	 AG	128778-128861	GT	CAG
(CAT)	 AG	129134-129203	GT	AGG
(CTG)	 AG	129275-129409	GT	AGG
(GAG)	 AG	129508-129594	TA	GGT
-recovered pasa_asmbl_25695.p1, internal, 127918, 128146
-recovered pasa_asmbl_25695.p1, internal, 128349, 128497
-recovered pasa_asmbl_25695.p1, internal, 128778, 128861
-recovered pasa_asmbl_25695.p1, internal, 129134, 129203
-recovered pasa_asmbl_25695.p1, internal, 129275, 129409
Couldn't classify 106151, 106309
Sorry, prediction CodingQuarry_transcript_30478-T1 fails validation.
(ATG)	 GA	106151-106309	AG	AGA
(TGC)	 AG	106334-106372	GA	GAG
-recovered CodingQuarry_transcript_30478-T1, terminal, 106334, 106372
Valid prediction for GlimmerHMM_glimmerT_45738-T1
Valid prediction for snap_scaffold_20-snap.720-T1
Valid prediction for GlimmerHMM_glimmerT_45739-T1
Valid prediction for Augustus_model.g30388.t1
Valid prediction for Augustus_model.g30383.t1
Valid prediction for GlimmerHMM_glimmerT_45744-T1
Valid prediction for Augustus_model.g30368.t1
Couldn't classify 106151, 106307
Sorry, prediction CodingQuarry_transcript_30477-T1 fails validation.
(ATG)	 GA	106151-106307	AG	AGA
(TGC)	 AG	106334-106386	TT	AGT
-recovered CodingQuarry_transcript_30477-T1, terminal, 106334, 106386
Valid prediction for Augustus_model.g30382.t1
Valid prediction for snap_scaffold_20-snap.737-T1
Valid prediction for snap_scaffold_20-snap.722-T1
Valid prediction for GlimmerHMM_glimmerT_45729-T1
Valid prediction for Augustus_model.g30375.t1
Valid prediction for HiQ_model.g30380.t1
Valid prediction for snap_scaffold_20-snap.726-T1
Couldn't classify 106151, 106253
Sorry, prediction CodingQuarry_transcript_30476-T1 fails validation.
(ATG)	 GA	106151-106253	TG	AGT
(AGT)	 AG	106282-106352	GA	GAG
-recovered CodingQuarry_transcript_30476-T1, terminal, 106282, 106352

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10487, rend_intergenic: 3519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32070, rend_intergenic: 11433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48825, rend_intergenic: 34293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52047, rend_intergenic: 50376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57271, rend_intergenic: 53783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62492, rend_intergenic: 57933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81399, rend_intergenic: 63020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92238, rend_intergenic: 88026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93856, rend_intergenic: 92825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100790, rend_intergenic: 94004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116886, rend_intergenic: 102221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123763, rend_intergenic: 117279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138096, rend_intergenic: 127197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151189, rend_intergenic: 144323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165203, rend_intergenic: 163473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205018, rend_intergenic: 168933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 206940
-exon list size: 443


building trellis

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31.5    
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31.9    
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32.6    
32.8    
33.0    
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33.5    
33.7    
33.9    
34.2    
34.4    
34.6    
34.8    
35.1    
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35.5    
35.7    
36.0    
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36.9    
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37.8    
38.0    
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38.9    
39.1    
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39.6    
39.8    
40.0    
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40.7    
40.9    
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92.4    
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96.9    
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97.3    
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97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 10487, rend_intergenic: 3519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32070, rend_intergenic: 11433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48825, rend_intergenic: 34293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52047, rend_intergenic: 50376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57271, rend_intergenic: 53783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62492, rend_intergenic: 57933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81399, rend_intergenic: 63020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92238, rend_intergenic: 88026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93856, rend_intergenic: 92825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100790, rend_intergenic: 94004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116886, rend_intergenic: 102221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123763, rend_intergenic: 117279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138096, rend_intergenic: 127197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151189, rend_intergenic: 144323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165203, rend_intergenic: 163473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205018, rend_intergenic: 168933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support