-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_3948364-4115779

-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 GlimmerHMM_glimmerT_38177-T1
Valid prediction for Augustus_model.g25477.t1
Valid prediction for snap_scaffold_16-snap.790-T1
Valid prediction for HiQ_model.g25476.t1
Valid prediction for GlimmerHMM_glimmerT_38161-T1
Valid prediction for snap_scaffold_16-snap.764-T1
Couldn't classify 66300, 66345
Couldn't classify 67003, 67163
Sorry, prediction pasa_asmbl_16799.p1 fails validation.
(GTG)	 CT	66300-66345	GT	AGG
(CTC)	 AG	66535-66843	GT	AGG
(CAG)	 AG	67003-67163	TG	ACT
-recovered pasa_asmbl_16799.p1, internal, 66535, 66843
Valid prediction for snap_scaffold_16-snap.778-T1
Valid prediction for pasa_asmbl_16165.p1
Valid prediction for snap_scaffold_16-snap.775-T1
Valid prediction for GlimmerHMM_glimmerT_38164-T1
Valid prediction for Augustus_model.g25461.t1
Valid prediction for GlimmerHMM_glimmerT_38180-T1
Valid prediction for GlimmerHMM_glimmerT_38170-T1
Valid prediction for GlimmerHMM_glimmerT_38176-T1
Valid prediction for pasa_asmbl_16169.p1
Valid prediction for Augustus_model.g25463.t1
Valid prediction for snap_scaffold_16-snap.793-T1
Valid prediction for Augustus_model.g25460.t1
Valid prediction for Augustus_model.g25465.t1
Valid prediction for HiQ_model.g25475.t1
Valid prediction for GlimmerHMM_glimmerT_38169-T1
Valid prediction for snap_scaffold_16-snap.783-T1
Valid prediction for snap_scaffold_16-snap.768-T1
Valid prediction for GlimmerHMM_glimmerT_38175-T1
Couldn't classify 48859, 48911
Sorry, prediction pasa_asmbl_16161.p1 fails validation.
(ATG)	 AC	47637-47706	GT	AGG
(ACG)	 AG	48389-48718	GT	GGG
(CAC)	 AG	48859-48911	NN	NNN
-recovered pasa_asmbl_16161.p1, initial, 47637, 47706
-recovered pasa_asmbl_16161.p1, internal, 48389, 48718
Valid prediction for snap_scaffold_16-snap.789-T1
Valid prediction for Augustus_model.g25469.t1
Valid prediction for CodingQuarry_transcript_19942-T1
Valid prediction for Augustus_model.g25468.t1
Valid prediction for CodingQuarry_transcript_19941-T1
Valid prediction for snap_scaffold_16-snap.782-T1
Valid prediction for snap_scaffold_16-snap.759-T1
Valid prediction for snap_scaffold_16-snap.766-T1
Valid prediction for snap_scaffold_16-snap.760-T1
Valid prediction for snap_scaffold_16-snap.761-T1
Valid prediction for snap_scaffold_16-snap.784-T1
Valid prediction for CodingQuarry_transcript_19939-T1
Valid prediction for GlimmerHMM_glimmerT_38168-T1
Valid prediction for CodingQuarry_transcript_19940-T1
Valid prediction for GlimmerHMM_glimmerT_38178-T1
Valid prediction for snap_scaffold_16-snap.757-T1
Valid prediction for GlimmerHMM_glimmerT_38156-T1
Valid prediction for Augustus_model.g25464.t1
Valid prediction for snap_scaffold_16-snap.774-T1
Valid prediction for snap_scaffold_16-snap.762-T1
Valid prediction for snap_scaffold_16-snap.780-T1
Valid prediction for pasa_asmbl_16174.p1
Valid prediction for snap_scaffold_16-snap.771-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: -)Couldn't classify 134291, 134923
Sorry, prediction pasa_asmbl_17026.p1 fails validation.
(TAC)	 TC	134291-134923	CA	ACC
Valid prediction for HiQ_model.g25470.t1
Valid prediction for GlimmerHMM_glimmerT_38162-T1
Valid prediction for snap_scaffold_16-snap.776-T1
Valid prediction for snap_scaffold_16-snap.769-T1
Valid prediction for Augustus_model.g25479.t1
Valid prediction for GlimmerHMM_glimmerT_38160-T1
Valid prediction for snap_scaffold_16-snap.770-T1
Valid prediction for snap_scaffold_16-snap.785-T1
Valid prediction for GlimmerHMM_glimmerT_38166-T1
Valid prediction for GlimmerHMM_glimmerT_38174-T1
Valid prediction for snap_scaffold_16-snap.773-T1
Couldn't classify 94405, 94474
Sorry, prediction pasa_asmbl_17036.p1 fails validation.
(CTG)	 AG	94405-94474	GT	AGG
(GTC)	 AG	94685-94824	GT	GGG
(GCC)	 AG	94948-95094	CG	GAC
-recovered pasa_asmbl_17036.p1, terminal, 94948, 95094
-recovered pasa_asmbl_17036.p1, internal, 94405, 94474
-recovered pasa_asmbl_17036.p1, internal, 94685, 94824
Valid prediction for GlimmerHMM_glimmerT_38157-T1
Valid prediction for snap_scaffold_16-snap.795-T1
Couldn't classify 135002, 135229
Sorry, prediction pasa_asmbl_17023.p1 fails validation.
(ACC)	 AC	135002-135229	GT	TTG
(GAT)	 AG	135625-135766	GT	GGG
(GGT)	 AG	135966-136064	GT	AGG
(TAG)	 AG	136170-136218	GT	AGG
(GGA)	 AG	136297-136433	GT	GTG
(CTC)	 AG	136549-136652	GC	AGG
(GAG)	 AG	136837-136947	GT	AGG
(GCT)	 AG	137093-137146	GT	GGG
(GCG)	 AG	137359-137562	GT	TGG
(GTG)	 AG	137649-137722	GT	AGG
(TCG)	 AG	137818-138024	GT	AGG
(GCG)	 AG	138166-138211	GT	CTG
(AGA)	 AG	138318-138446	GT	AGG
(CAT)	 AG	138618-138721	GT	ATG
(GAA)	 AG	139010-139097	GT	TGG
(GAA)	 AG	139308-139454	CC	GAC
-recovered pasa_asmbl_17023.p1, terminal, 139308, 139454
-recovered pasa_asmbl_17023.p1, internal, 135625, 135766
-recovered pasa_asmbl_17023.p1, internal, 135966, 136064
-recovered pasa_asmbl_17023.p1, internal, 136170, 136218
-recovered pasa_asmbl_17023.p1, internal, 136297, 136433
-recovered pasa_asmbl_17023.p1, internal, 136549, 136652
-recovered pasa_asmbl_17023.p1, internal, 136837, 136947
-recovered pasa_asmbl_17023.p1, internal, 137093, 137146
-recovered pasa_asmbl_17023.p1, internal, 137359, 137562
-recovered pasa_asmbl_17023.p1, internal, 137649, 137722
-recovered pasa_asmbl_17023.p1, internal, 137818, 138024
-recovered pasa_asmbl_17023.p1, internal, 138166, 138211
-recovered pasa_asmbl_17023.p1, internal, 138318, 138446
-recovered pasa_asmbl_17023.p1, internal, 138618, 138721
-recovered pasa_asmbl_17023.p1, internal, 139010, 139097
Couldn't classify 132440, 133357
Sorry, prediction pasa_asmbl_17028.p1 fails validation.
(TCC)	 TG	132440-133357	CC	GCC
Valid prediction for snap_scaffold_16-snap.786-T1
Valid prediction for Augustus_model.g25459.t1
Valid prediction for snap_scaffold_16-snap.767-T1
Valid prediction for Augustus_model.g25457.t1
Couldn't classify 68669, 68867
Couldn't classify 68925, 69037
Sorry, prediction pasa_asmbl_17043.p2 fails validation.
(GAG)	 AC	68669-68867	GT	AGG
(GTC)	 AG	68925-69037	GG	GAG
Valid prediction for snap_scaffold_16-snap.788-T1
Valid prediction for Augustus_model.g25458.t1
Valid prediction for pasa_asmbl_17045.p1
Valid prediction for snap_scaffold_16-snap.792-T1
Valid prediction for snap_scaffold_16-snap.791-T1
Valid prediction for snap_scaffold_16-snap.779-T1
Valid prediction for Augustus_model.g25471.t1
Valid prediction for Augustus_model.g25478.t1
Couldn't classify 133604, 134080
Sorry, prediction pasa_asmbl_17027.p1 fails validation.
(GGA)	 GT	133604-134080	GC	AAG
Valid prediction for snap_scaffold_16-snap.765-T1
Valid prediction for GlimmerHMM_glimmerT_38171-T1
Couldn't classify 156630, 156756
Couldn't classify 157383, 157557
Sorry, prediction pasa_asmbl_17022.p1 fails validation.
(GGG)	 AC	156630-156756	GT	AGG
(AGA)	 AG	157009-157132	GT	TGG
(CGC)	 AG	157383-157557	GA	GGG
-recovered pasa_asmbl_17022.p1, internal, 157009, 157132
Valid prediction for CodingQuarry_transcript_19938-T1
Valid prediction for GlimmerHMM_glimmerT_38159-T1
Couldn't classify 153792, 153843
Couldn't classify 154547, 154624
Sorry, prediction pasa_asmbl_17582.p1 fails validation.
(GAG)	 TG	153792-153843	GT	AGG
(GTA)	 AG	153928-154049	GT	AGG
(GTC)	 AG	154130-154241	GT	AGG
(ATG)	 AG	154328-154437	GT	AGG
(ATG)	 AG	154547-154624	AT	CCA
-recovered pasa_asmbl_17582.p1, initial, 154328, 154437
-recovered pasa_asmbl_17582.p1, internal, 153928, 154049
-recovered pasa_asmbl_17582.p1, internal, 154130, 154241
-recovered pasa_asmbl_17582.p1, internal, 154328, 154437
Valid prediction for snap_scaffold_16-snap.787-T1
Valid prediction for snap_scaffold_16-snap.794-T1
Valid prediction for GlimmerHMM_glimmerT_38179-T1
Valid prediction for GlimmerHMM_glimmerT_38172-T1
Couldn't classify 98995, 99113
Sorry, prediction pasa_asmbl_17033.p1 fails validation.
(ATG)	 AT	95609-95666	GT	AGG
(AGT)	 AG	95993-96138	GT	TGG
(AAA)	 AG	96608-96652	GT	ACG
(ACC)	 AG	96823-96932	GT	AAG
(TAA)	 AG	97207-97362	GT	ACG
(GTC)	 AG	97534-97652	GT	AGG
(AGA)	 AG	97849-98049	GT	CAG
(GTG)	 AG	98153-98264	GT	AAG
(GTA)	 AG	98393-98507	GT	AGG
(TTC)	 AG	98604-98814	GT	AGG
(TGG)	 AG	98995-99113	GT	AGG
-recovered pasa_asmbl_17033.p1, initial, 95609, 95666
-recovered pasa_asmbl_17033.p1, internal, 95993, 96138
-recovered pasa_asmbl_17033.p1, internal, 96608, 96652
-recovered pasa_asmbl_17033.p1, internal, 96823, 96932
-recovered pasa_asmbl_17033.p1, internal, 97207, 97362
-recovered pasa_asmbl_17033.p1, internal, 97534, 97652
-recovered pasa_asmbl_17033.p1, internal, 97849, 98049
-recovered pasa_asmbl_17033.p1, internal, 98153, 98264
-recovered pasa_asmbl_17033.p1, internal, 98393, 98507
-recovered pasa_asmbl_17033.p1, internal, 98604, 98814
-recovered pasa_asmbl_17033.p1, internal, 98995, 99113
Valid prediction for Augustus_model.g25462.t1
Valid prediction for snap_scaffold_16-snap.758-T1
Valid prediction for GlimmerHMM_glimmerT_38167-T1
Valid prediction for GlimmerHMM_glimmerT_38165-T1
Couldn't classify 69763, 70532
Sorry, prediction pasa_asmbl_17038.p1 fails validation.
(GAT)	 AG	69763-70532	GT	AGG
(CAA)	 AG	73333-73502	GT	AGG
(AAC)	 AG	73651-73768	GT	AGG
(GCG)	 AG	73893-73962	GT	AGG
(CCC)	 AG	74342-74481	GT	AGG
(TGA)	 AG	74657-74771	GT	ATG
(CAT)	 AG	75412-75526	GT	CGG
(GTG)	 AG	75945-75958	TT	GAT
-recovered pasa_asmbl_17038.p1, terminal, 75945, 75958
-recovered pasa_asmbl_17038.p1, internal, 69763, 70532
-recovered pasa_asmbl_17038.p1, internal, 73333, 73502
-recovered pasa_asmbl_17038.p1, internal, 73651, 73768
-recovered pasa_asmbl_17038.p1, internal, 73893, 73962
-recovered pasa_asmbl_17038.p1, internal, 74342, 74481
-recovered pasa_asmbl_17038.p1, internal, 74657, 74771
-recovered pasa_asmbl_17038.p1, internal, 75412, 75526
Valid prediction for CodingQuarry_transcript_19935-T1
Valid prediction for GlimmerHMM_glimmerT_38173-T1
Valid prediction for Augustus_model.g25472.t1
Valid prediction for snap_scaffold_16-snap.777-T1
Valid prediction for pasa_asmbl_17037.p1
Valid prediction for Augustus_model.g25467.t1
Valid prediction for snap_scaffold_16-snap.781-T1
Valid prediction for Augustus_model.g25473.t1
Valid prediction for snap_scaffold_16-snap.772-T1
Valid prediction for HiQ_model.g25474.t1
Valid prediction for snap_scaffold_16-snap.763-T1
Valid prediction for HiQ_model.g25466.t1
Valid prediction for GlimmerHMM_glimmerT_38158-T1
Valid prediction for CodingQuarry_transcript_19937-T1
Valid prediction for GlimmerHMM_glimmerT_38163-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11990, rend_intergenic: 6254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24019, rend_intergenic: 12061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36506, rend_intergenic: 28529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45105, rend_intergenic: 38867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47143, rend_intergenic: 45126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48184, rend_intergenic: 47637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52191, rend_intergenic: 48505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75635, rend_intergenic: 68000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90629, rend_intergenic: 83768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109469, rend_intergenic: 101510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132572, rend_intergenic: 119337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148326, rend_intergenic: 133332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 167416
-exon list size: 496


building trellis

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95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 11990, rend_intergenic: 6254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24019, rend_intergenic: 12061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36506, rend_intergenic: 28529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45105, rend_intergenic: 38867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47143, rend_intergenic: 45126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48184, rend_intergenic: 47637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52191, rend_intergenic: 48505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75635, rend_intergenic: 68000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90629, rend_intergenic: 83768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109469, rend_intergenic: 101510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132572, rend_intergenic: 119337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148326, rend_intergenic: 133332  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