-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_16070462-16294801

-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_10-snap.3269-T1
Couldn't classify 146100, 146255
Sorry, prediction pasa_asmbl_3706.p1 fails validation.
(ATG)	 TC	145664-145822	GT	AGG
(GAT)	 AG	146100-146255	AG	TGA
-recovered pasa_asmbl_3706.p1, initial, 145664, 145822
Valid prediction for snap_scaffold_10-snap.3288-T1
Valid prediction for GlimmerHMM_glimmerT_26108-T1
Valid prediction for snap_scaffold_10-snap.3264-T1
Valid prediction for GlimmerHMM_glimmerT_26095-T1
Valid prediction for snap_scaffold_10-snap.3286-T1
Couldn't classify 187583, 187801
Sorry, prediction pasa_asmbl_3711.p1 fails validation.
(GTG)	 GT	187583-187801	GT	AGG
(GAC)	 AG	188016-188101	GT	TGG
(CAA)	 AG	188989-189058	GT	CGG
(GCT)	 AG	189472-189511	GT	AGG
(TGG)	 AG	189646-189674	TT	GAT
-recovered pasa_asmbl_3711.p1, terminal, 189646, 189674
-recovered pasa_asmbl_3711.p1, internal, 188016, 188101
-recovered pasa_asmbl_3711.p1, internal, 188989, 189058
-recovered pasa_asmbl_3711.p1, internal, 189472, 189511
Couldn't classify 1958, 2027
Sorry, prediction pasa_asmbl_3705.p1 fails validation.
(AAA)	 AG	1958-2027	GT	AGG
(GAA)	 AG	4256-4356	GT	AGG
(TTC)	 AG	5474-5644	GT	TTG
(GTC)	 AG	5960-6139	GC	AGG
-recovered pasa_asmbl_3705.p1, terminal, 5960, 6139
-recovered pasa_asmbl_3705.p1, internal, 1958, 2027
-recovered pasa_asmbl_3705.p1, internal, 4256, 4356
-recovered pasa_asmbl_3705.p1, internal, 5474, 5644
-recovered pasa_asmbl_3705.p1, internal, 5960, 6139
Valid prediction for snap_scaffold_10-snap.3276-T1
Valid prediction for snap_scaffold_10-snap.3302-T1
Valid prediction for Augustus_model.g17355.t1
Valid prediction for snap_scaffold_10-snap.3256-T1
Valid prediction for Augustus_model.g17340.t1
Valid prediction for Augustus_model.g17352.t1
Valid prediction for snap_scaffold_10-snap.3300-T1
Couldn't classify 181883, 181919
Sorry, prediction pasa_asmbl_3709.p1 fails validation.
(CAT)	 TA	181883-181919	GT	AGG
(AGA)	 AG	183429-183493	GT	AGG
(GGA)	 AG	183655-183696	GT	AGG
(GTG)	 AG	183804-183857	GC	AGG
(ATT)	 AG	184460-184579	GT	AGG
(ACG)	 AG	185531-185617	GT	AGG
(GTG)	 AG	186226-186352	GT	CAG
(GTA)	 AG	187129-187256	GT	AGG
(GAC)	 AG	188016-188101	GT	TGG
(CAA)	 AG	188989-189058	GT	CGG
(GCT)	 AG	189472-189511	GT	AGG
(TGG)	 AG	189646-189674	TT	GAT
-recovered pasa_asmbl_3709.p1, terminal, 189646, 189674
-recovered pasa_asmbl_3709.p1, internal, 183429, 183493
-recovered pasa_asmbl_3709.p1, internal, 183655, 183696
-recovered pasa_asmbl_3709.p1, internal, 183804, 183857
-recovered pasa_asmbl_3709.p1, internal, 184460, 184579
-recovered pasa_asmbl_3709.p1, internal, 185531, 185617
-recovered pasa_asmbl_3709.p1, internal, 186226, 186352
-recovered pasa_asmbl_3709.p1, internal, 187129, 187256
-recovered pasa_asmbl_3709.p1, internal, 188016, 188101
-recovered pasa_asmbl_3709.p1, internal, 188989, 189058
-recovered pasa_asmbl_3709.p1, internal, 189472, 189511
Valid prediction for snap_scaffold_10-snap.3267-T1
Valid prediction for snap_scaffold_10-snap.3271-T1
Valid prediction for snap_scaffold_10-snap.3285-T1
Valid prediction for snap_scaffold_10-snap.3274-T1
Valid prediction for snap_scaffold_10-snap.3278-T1
Valid prediction for Augustus_model.g17344.t1
Valid prediction for snap_scaffold_10-snap.3293-T1
Valid prediction for snap_scaffold_10-snap.3258-T1
Valid prediction for snap_scaffold_10-snap.3282-T1
Valid prediction for snap_scaffold_10-snap.3281-T1
Valid prediction for snap_scaffold_10-snap.3292-T1
Valid prediction for GlimmerHMM_glimmerT_26110-T1
Valid prediction for snap_scaffold_10-snap.3266-T1
Valid prediction for GlimmerHMM_glimmerT_26103-T1
Valid prediction for snap_scaffold_10-snap.3257-T1
Valid prediction for snap_scaffold_10-snap.3280-T1
Valid prediction for GlimmerHMM_glimmerT_26106-T1
Valid prediction for Augustus_model.g17345.t1
Valid prediction for CodingQuarry_transcript_5668-T1
Valid prediction for snap_scaffold_10-snap.3273-T1
Valid prediction for Augustus_model.g17349.t1
Valid prediction for GlimmerHMM_glimmerT_26090-T1
Valid prediction for snap_scaffold_10-snap.3279-T1
Valid prediction for snap_scaffold_10-snap.3291-T1
Valid prediction for snap_scaffold_10-snap.3297-T1
Valid prediction for snap_scaffold_10-snap.3262-T1
Valid prediction for GlimmerHMM_glimmerT_26105-T1
Valid prediction for CodingQuarry_transcript_5667-T1
Valid prediction for snap_scaffold_10-snap.3283-T1
Valid prediction for snap_scaffold_10-snap.3268-T1
Valid prediction for snap_scaffold_10-snap.3259-T1
Valid prediction for snap_scaffold_10-snap.3289-T1
Valid prediction for GlimmerHMM_glimmerT_26098-T1
Valid prediction for snap_scaffold_10-snap.3299-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_10-snap.3304-T1
Valid prediction for GlimmerHMM_glimmerT_26112-T1
Valid prediction for snap_scaffold_10-snap.3272-T1
Valid prediction for GlimmerHMM_glimmerT_26096-T1
Couldn't classify 27760, 27900
Sorry, prediction pasa_asmbl_5156.p1 fails validation.
(CAG)	 CT	27760-27900	GT	TGG
(GTG)	 AG	28335-28701	GT	AGG
(GTG)	 AG	29219-30714	AA	GAA
-recovered pasa_asmbl_5156.p1, terminal, 29219, 30714
-recovered pasa_asmbl_5156.p1, internal, 28335, 28701
Valid prediction for Augustus_model.g17351.t1
Valid prediction for snap_scaffold_10-snap.3263-T1
Valid prediction for Augustus_model.g17356.t1
Valid prediction for GlimmerHMM_glimmerT_26091-T1
Valid prediction for GlimmerHMM_glimmerT_26097-T1
Couldn't classify 199525, 199600
Couldn't classify 203847, 203930
Sorry, prediction pasa_asmbl_5224.p1 fails validation.
(GGT)	 AC	199525-199600	GT	GGG
(CGG)	 AG	202409-202507	GT	TGG
(GTG)	 AG	203230-203492	GT	GCG
(GTC)	 AG	203847-203930	TT	CTT
-recovered pasa_asmbl_5224.p1, internal, 202409, 202507
-recovered pasa_asmbl_5224.p1, internal, 203230, 203492
Couldn't classify 22384, 23602
Couldn't classify 25893, 26066
Sorry, prediction pasa_asmbl_4996.p1 fails validation.
(CAA)	 AA	22384-23602	GT	TGG
(ATC)	 AG	24209-24299	GT	AGG
(GTC)	 AG	25268-25361	GT	GGG
(GTG)	 AG	25893-26066	GC	GAG
-recovered pasa_asmbl_4996.p1, internal, 24209, 24299
-recovered pasa_asmbl_4996.p1, internal, 25268, 25361
-recovered pasa_asmbl_4996.p1, internal, 25893, 26066
Valid prediction for GlimmerHMM_glimmerT_26094-T1
Valid prediction for snap_scaffold_10-snap.3305-T1
Valid prediction for snap_scaffold_10-snap.3284-T1
Valid prediction for GlimmerHMM_glimmerT_26114-T1
Valid prediction for GlimmerHMM_glimmerT_26104-T1
Valid prediction for GlimmerHMM_glimmerT_26109-T1
Valid prediction for Augustus_model.g17348.t1
Valid prediction for GlimmerHMM_glimmerT_26093-T1
Valid prediction for Augustus_model.g17347.t1
Valid prediction for snap_scaffold_10-snap.3290-T1
Valid prediction for snap_scaffold_10-snap.3298-T1
Valid prediction for Augustus_model.g17343.t1
Valid prediction for GlimmerHMM_glimmerT_26100-T1
Valid prediction for GlimmerHMM_glimmerT_26107-T1
Valid prediction for GlimmerHMM_glimmerT_26102-T1
Valid prediction for snap_scaffold_10-snap.3277-T1
Valid prediction for GlimmerHMM_glimmerT_26101-T1
Couldn't classify 20536, 21585
Sorry, prediction pasa_asmbl_4997.p1 fails validation.
(GGG)	 AG	20536-21585	TT	GCT
Valid prediction for Augustus_model.g17353.t1
Valid prediction for GlimmerHMM_glimmerT_26099-T1
Valid prediction for Augustus_model.g17346.t1
Valid prediction for snap_scaffold_10-snap.3301-T1
Valid prediction for Augustus_model.g17342.t1
Valid prediction for GlimmerHMM_glimmerT_26092-T1
Valid prediction for snap_scaffold_10-snap.3275-T1
Valid prediction for snap_scaffold_10-snap.3287-T1
Valid prediction for snap_scaffold_10-snap.3296-T1
Valid prediction for Augustus_model.g17357.t1
Valid prediction for Augustus_model.g17354.t1
Valid prediction for snap_scaffold_10-snap.3303-T1
Valid prediction for snap_scaffold_10-snap.3270-T1
Valid prediction for GlimmerHMM_glimmerT_26111-T1
Valid prediction for snap_scaffold_10-snap.3260-T1
Valid prediction for snap_scaffold_10-snap.3261-T1
Valid prediction for Augustus_model.g17350.t1
Valid prediction for Augustus_model.g17341.t1
Valid prediction for GlimmerHMM_glimmerT_26113-T1
Valid prediction for snap_scaffold_10-snap.3295-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.3265-T1
Couldn't classify 189055, 189190
Couldn't classify 193597, 193868
Sorry, prediction pasa_asmbl_4995.p1 fails validation.
(GAC)	 CA	189055-189190	GT	AGG
(ATG)	 AG	190511-190630	GT	ACG
(CCA)	 AG	193597-193868	CC	TGC
-recovered pasa_asmbl_4995.p1, initial, 190511, 190630
-recovered pasa_asmbl_4995.p1, internal, 190511, 190630
Valid prediction for snap_scaffold_10-snap.3294-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28201, rend_intergenic: 19126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35755, rend_intergenic: 30333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38799, rend_intergenic: 38106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41261, rend_intergenic: 39306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43799, rend_intergenic: 41436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58093, rend_intergenic: 44438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65456, rend_intergenic: 58219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70293, rend_intergenic: 65579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83157, rend_intergenic: 73167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92037, rend_intergenic: 90025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92609, rend_intergenic: 92438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126877, rend_intergenic: 92708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130721, rend_intergenic: 127394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144602, rend_intergenic: 131139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150761, rend_intergenic: 147675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154561, rend_intergenic: 151755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169364, rend_intergenic: 157200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172622, rend_intergenic: 169458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189156, rend_intergenic: 186204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200278, rend_intergenic: 195747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201462, rend_intergenic: 200731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207496, rend_intergenic: 202855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209995, rend_intergenic: 207713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 224340
-exon list size: 394


building trellis

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25.5    
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40.9    
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98.0    
98.2    
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98.7    
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99.2    
99.5    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 28201, rend_intergenic: 19126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35755, rend_intergenic: 30333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38799, rend_intergenic: 38106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41261, rend_intergenic: 39306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43799, rend_intergenic: 41436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58093, rend_intergenic: 44438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65456, rend_intergenic: 58219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70293, rend_intergenic: 65579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83157, rend_intergenic: 73167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92037, rend_intergenic: 90025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92609, rend_intergenic: 92438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126877, rend_intergenic: 92708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130721, rend_intergenic: 127394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144602, rend_intergenic: 131139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150761, rend_intergenic: 147675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154561, rend_intergenic: 151755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169364, rend_intergenic: 157200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172622, rend_intergenic: 169458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189156, rend_intergenic: 186204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200278, rend_intergenic: 195747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201462, rend_intergenic: 200731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207496, rend_intergenic: 202855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209995, rend_intergenic: 207713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support