-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_5935387-6111948

-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_1-snap.958-T1
Valid prediction for GlimmerHMM_glimmerT_767-T1
Valid prediction for snap_scaffold_1-snap.957-T1
Valid prediction for HiQ_model.g590.t1
Valid prediction for snap_scaffold_1-snap.975-T1
Valid prediction for CodingQuarry_transcript_2640-T1
Valid prediction for snap_scaffold_1-snap.953-T1
Valid prediction for GlimmerHMM_glimmerT_745-T1
Valid prediction for GlimmerHMM_glimmerT_763-T1
Valid prediction for pasa_asmbl_1818.p1
Valid prediction for snap_scaffold_1-snap.970-T1
Valid prediction for GlimmerHMM_glimmerT_744-T1
Valid prediction for HiQ_model.g591.t1
Valid prediction for Augustus_model.g586.t1
Valid prediction for pasa_asmbl_1799.p1
Valid prediction for snap_scaffold_1-snap.978-T1
Couldn't classify 74152, 74328
Sorry, prediction pasa_asmbl_1816.p1 fails validation.
(GCC)	 AC	74152-74328	GT	CTG
(TCG)	 AG	76112-76192	GT	AGG
(ATC)	 AG	76780-76853	GT	GTG
(ATA)	 AG	77032-77125	GT	CTG
(GTG)	 AG	77311-77378	GT	ATG
(GAA)	 AG	77815-77885	GT	AGG
(ACA)	 AG	77972-78021	AG	GAA
-recovered pasa_asmbl_1816.p1, terminal, 77815, 77885
-recovered pasa_asmbl_1816.p1, terminal, 77972, 78021
-recovered pasa_asmbl_1816.p1, internal, 76112, 76192
-recovered pasa_asmbl_1816.p1, internal, 76780, 76853
-recovered pasa_asmbl_1816.p1, internal, 77032, 77125
-recovered pasa_asmbl_1816.p1, internal, 77311, 77378
-recovered pasa_asmbl_1816.p1, internal, 77815, 77885
Valid prediction for CodingQuarry_transcript_2631-T1
Valid prediction for GlimmerHMM_glimmerT_746-T1
Valid prediction for Augustus_model.g605.t1
Valid prediction for snap_scaffold_1-snap.988-T1
Valid prediction for pasa_asmbl_1800.p1
Valid prediction for snap_scaffold_1-snap.959-T1
Valid prediction for GlimmerHMM_glimmerT_741-T1
Valid prediction for snap_scaffold_1-snap.945-T1
Valid prediction for GlimmerHMM_glimmerT_752-T1
Valid prediction for pasa_asmbl_1811.p1
Valid prediction for snap_scaffold_1-snap.980-T1
Valid prediction for Augustus_model.g585.t1
Valid prediction for HiQ_model.g580.t1
Valid prediction for snap_scaffold_1-snap.952-T1
Valid prediction for Augustus_model.g589.t1
Valid prediction for HiQ_model.g579.t1
Valid prediction for snap_scaffold_1-snap.976-T1
Valid prediction for snap_scaffold_1-snap.963-T1
Valid prediction for snap_scaffold_1-snap.951-T1
Valid prediction for GlimmerHMM_glimmerT_762-T1
Valid prediction for snap_scaffold_1-snap.946-T1
Valid prediction for snap_scaffold_1-snap.950-T1
Valid prediction for pasa_asmbl_1812.p1
Valid prediction for GlimmerHMM_glimmerT_754-T1
Valid prediction for GlimmerHMM_glimmerT_740-T1
Valid prediction for HiQ_model.g583.t1
Valid prediction for CodingQuarry_transcript_2630-T1
Valid prediction for Augustus_model.g598.t1
Valid prediction for Augustus_model.g594.t1
Valid prediction for GlimmerHMM_glimmerT_768-T1
Valid prediction for CodingQuarry_transcript_2634-T1
Valid prediction for GlimmerHMM_glimmerT_764-T1
Valid prediction for GlimmerHMM_glimmerT_775-T1
Valid prediction for Augustus_model.g604.t1
Valid prediction for snap_scaffold_1-snap.974-T1
Valid prediction for CodingQuarry_transcript_2635-T1
Valid prediction for snap_scaffold_1-snap.967-T1
Valid prediction for GlimmerHMM_glimmerT_751-T1
Valid prediction for GlimmerHMM_glimmerT_770-T1
Valid prediction for CodingQuarry_transcript_2639-T1
Valid prediction for snap_scaffold_1-snap.971-T1
Valid prediction for GlimmerHMM_glimmerT_776-T1
Valid prediction for Augustus_model.g602.t1
Valid prediction for GlimmerHMM_glimmerT_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: -)Valid prediction for Augustus_model.g578.t1
Valid prediction for GlimmerHMM_glimmerT_758-T1
Valid prediction for snap_scaffold_1-snap.956-T1
Valid prediction for pasa_asmbl_305.p1
Valid prediction for Augustus_model.g595.t1
Valid prediction for snap_scaffold_1-snap.947-T1
Valid prediction for snap_scaffold_1-snap.968-T1
Valid prediction for GlimmerHMM_glimmerT_765-T1
Valid prediction for HiQ_model.g582.t1
Valid prediction for Augustus_model.g599.t1
Valid prediction for snap_scaffold_1-snap.972-T1
Valid prediction for CodingQuarry_transcript_2636-T1
Valid prediction for snap_scaffold_1-snap.983-T1
Valid prediction for snap_scaffold_1-snap.962-T1
Valid prediction for GlimmerHMM_glimmerT_769-T1
Valid prediction for GlimmerHMM_glimmerT_753-T1
Valid prediction for snap_scaffold_1-snap.981-T1
Valid prediction for CodingQuarry_transcript_2637-T1
Valid prediction for GlimmerHMM_glimmerT_743-T1
Valid prediction for GlimmerHMM_glimmerT_772-T1
Valid prediction for Augustus_model.g596.t1
Valid prediction for Augustus_model.g600.t1
Valid prediction for GlimmerHMM_glimmerT_777-T1
Valid prediction for snap_scaffold_1-snap.985-T1
Valid prediction for HiQ_model.g581.t1
Valid prediction for GlimmerHMM_glimmerT_756-T1
Valid prediction for Augustus_model.g587.t1
Valid prediction for CodingQuarry_transcript_2633-T1
Valid prediction for Augustus_model.g601.t1
Valid prediction for GlimmerHMM_glimmerT_774-T1
Valid prediction for Augustus_model.g597.t1
Valid prediction for snap_scaffold_1-snap.943-T1
Couldn't classify 120437, 120526
Sorry, prediction pasa_asmbl_1304.p1 fails validation.
(CTG)	 CT	120437-120526	GT	AGG
(ATT)	 AG	120627-120719	GT	AGG
(TCA)	 AG	120867-121015	GT	AAG
(GGG)	 AG	121116-121277	GT	ATG
(GTC)	 AG	121386-121449	GA	AAG
-recovered pasa_asmbl_1304.p1, terminal, 121386, 121449
-recovered pasa_asmbl_1304.p1, internal, 120627, 120719
-recovered pasa_asmbl_1304.p1, internal, 120867, 121015
-recovered pasa_asmbl_1304.p1, internal, 121116, 121277
Valid prediction for GlimmerHMM_glimmerT_739-T1
Valid prediction for snap_scaffold_1-snap.954-T1
Valid prediction for snap_scaffold_1-snap.960-T1
Valid prediction for Augustus_model.g603.t1
Valid prediction for snap_scaffold_1-snap.948-T1
Valid prediction for GlimmerHMM_glimmerT_749-T1
Valid prediction for snap_scaffold_1-snap.973-T1
Valid prediction for Augustus_model.g593.t1
Valid prediction for GlimmerHMM_glimmerT_761-T1
Valid prediction for snap_scaffold_1-snap.955-T1
Valid prediction for snap_scaffold_1-snap.961-T1
Valid prediction for HiQ_model.g592.t1
Valid prediction for snap_scaffold_1-snap.969-T1
Valid prediction for Augustus_model.g577.t1
Valid prediction for GlimmerHMM_glimmerT_778-T1
Valid prediction for GlimmerHMM_glimmerT_750-T1
Valid prediction for snap_scaffold_1-snap.966-T1
Valid prediction for GlimmerHMM_glimmerT_757-T1
Valid prediction for snap_scaffold_1-snap.944-T1
Valid prediction for GlimmerHMM_glimmerT_748-T1
Valid prediction for snap_scaffold_1-snap.986-T1
Valid prediction for snap_scaffold_1-snap.979-T1
Valid prediction for GlimmerHMM_glimmerT_747-T1
Valid prediction for snap_scaffold_1-snap.965-T1
Valid prediction for GlimmerHMM_glimmerT_773-T1
Valid prediction for GlimmerHMM_glimmerT_779-T1
Valid prediction for GlimmerHMM_glimmerT_766-T1
Valid prediction for Augustus_model.g606.t1
Valid prediction for HiQ_model.g584.t1
Valid prediction for GlimmerHMM_glimmerT_742-T1
Valid prediction for snap_scaffold_1-snap.982-T1
Valid prediction for snap_scaffold_1-snap.984-T1
Valid prediction for snap_scaffold_1-snap.942-T1
Valid prediction for snap_scaffold_1-snap.964-T1
Valid prediction for CodingQuarry_transcript_2638-T1
Valid prediction for GlimmerHMM_glimmerT_755-T1
Valid prediction for GlimmerHMM_glimmerT_759-T1
Valid prediction for Augustus_model.g588.t1
Valid prediction for snap_scaffold_1-snap.949-T1
Valid prediction for snap_scaffold_1-snap.977-T1
Valid prediction for CodingQuarry_transcript_2632-T1
Valid prediction for GlimmerHMM_glimmerT_760-T1
Valid prediction for pasa_asmbl_303.p1
Valid prediction for snap_scaffold_1-snap.987-T1
Couldn't classify 143272, 143946
Sorry, prediction pasa_asmbl_307.p1 fails validation.
(GGA)	 TA	143272-143946	GT	AGG
(GTT)	 AG	144070-144187	GT	AGG
(GGC)	 AG	144418-144687	GT	TGG
(GTG)	 AG	144807-146149	AG	AGA
-recovered pasa_asmbl_307.p1, terminal, 144807, 146149
-recovered pasa_asmbl_307.p1, internal, 144070, 144187
-recovered pasa_asmbl_307.p1, internal, 144418, 144687

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 97623, rend_intergenic: 94194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117581, rend_intergenic: 106096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124725, rend_intergenic: 119569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130728, rend_intergenic: 128455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156864, rend_intergenic: 152646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176562
-exon list size: 448


building trellis

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39.6    
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40.9    
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42.9    
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43.6    
43.8    
44.0    
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44.9    
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45.8    
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46.9    
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91.6    
91.8    
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92.4    
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95.6    
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97.8    
98.0    
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98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 97623, rend_intergenic: 94194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117581, rend_intergenic: 106096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124725, rend_intergenic: 119569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130728, rend_intergenic: 128455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156864, rend_intergenic: 152646  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