-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_1100051-1347651

-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_53589-T1
Valid prediction for GlimmerHMM_glimmerT_53591-T1
Valid prediction for GlimmerHMM_glimmerT_53586-T1
Valid prediction for snap_scaffold_25-snap.244-T1
Valid prediction for snap_scaffold_25-snap.221-T1
Valid prediction for snap_scaffold_25-snap.263-T1
Valid prediction for snap_scaffold_25-snap.253-T1
Valid prediction for snap_scaffold_25-snap.266-T1
Valid prediction for snap_scaffold_25-snap.262-T1
Valid prediction for snap_scaffold_25-snap.249-T1
Valid prediction for GlimmerHMM_glimmerT_53587-T1
Valid prediction for snap_scaffold_25-snap.258-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_53597-T1
Valid prediction for snap_scaffold_25-snap.229-T1
Valid prediction for Augustus_model.g35625.t1
Valid prediction for GlimmerHMM_glimmerT_53593-T1
Valid prediction for snap_scaffold_25-snap.250-T1
Valid prediction for Augustus_model.g35623.t1
Valid prediction for snap_scaffold_25-snap.232-T1
Valid prediction for snap_scaffold_25-snap.260-T1
Valid prediction for GlimmerHMM_glimmerT_53579-T1
Valid prediction for GlimmerHMM_glimmerT_53600-T1
Valid prediction for GlimmerHMM_glimmerT_53590-T1
Valid prediction for GlimmerHMM_glimmerT_53592-T1
Valid prediction for snap_scaffold_25-snap.234-T1
Valid prediction for snap_scaffold_25-snap.228-T1
Valid prediction for snap_scaffold_25-snap.255-T1
Valid prediction for snap_scaffold_25-snap.226-T1
Valid prediction for GlimmerHMM_glimmerT_53580-T1
Valid prediction for snap_scaffold_25-snap.245-T1
Valid prediction for snap_scaffold_25-snap.238-T1
Valid prediction for GlimmerHMM_glimmerT_53577-T1
Valid prediction for snap_scaffold_25-snap.236-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.230-T1
Valid prediction for snap_scaffold_25-snap.240-T1
Valid prediction for GlimmerHMM_glimmerT_53599-T1
Valid prediction for snap_scaffold_25-snap.224-T1
Valid prediction for snap_scaffold_25-snap.247-T1
Valid prediction for snap_scaffold_25-snap.227-T1
Valid prediction for snap_scaffold_25-snap.233-T1
Valid prediction for snap_scaffold_25-snap.256-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 133170, 133562
Sorry, prediction pasa_asmbl_33369.p1 fails validation.
(ATG)	 CC	132571-132702	GT	AGG
(GTG)	 AG	133170-133562	GT	GGG
-recovered pasa_asmbl_33369.p1, initial, 132571, 132702
-recovered pasa_asmbl_33369.p1, internal, 133170, 133562
Valid prediction for snap_scaffold_25-snap.241-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_25-snap.242-T1
Valid prediction for GlimmerHMM_glimmerT_53575-T1
Couldn't classify 117312, 117734
Sorry, prediction pasa_asmbl_34028.p2 fails validation.
(CTG)	 AC	117312-117734	GG	GGG
Valid prediction for snap_scaffold_25-snap.261-T1
Valid prediction for snap_scaffold_25-snap.264-T1
Valid prediction for GlimmerHMM_glimmerT_53598-T1
Valid prediction for GlimmerHMM_glimmerT_53594-T1
Valid prediction for snap_scaffold_25-snap.252-T1
Valid prediction for Augustus_model.g35624.t1
Valid prediction for Augustus_model.g35622.t1
Valid prediction for GlimmerHMM_glimmerT_53582-T1
Valid prediction for GlimmerHMM_glimmerT_53573-T1
Valid prediction for snap_scaffold_25-snap.243-T1
Valid prediction for GlimmerHMM_glimmerT_53585-T1
Valid prediction for GlimmerHMM_glimmerT_53581-T1
Valid prediction for snap_scaffold_25-snap.237-T1
Valid prediction for CodingQuarry_transcript_38641-T1
Valid prediction for snap_scaffold_25-snap.239-T1
Valid prediction for snap_scaffold_25-snap.222-T1
Valid prediction for Augustus_model.g35626.t1
Valid prediction for GlimmerHMM_glimmerT_53588-T1
Valid prediction for snap_scaffold_25-snap.225-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_53578-T1
Valid prediction for snap_scaffold_25-snap.254-T1
Valid prediction for GlimmerHMM_glimmerT_53583-T1
Valid prediction for snap_scaffold_25-snap.248-T1
Valid prediction for GlimmerHMM_glimmerT_53574-T1
Valid prediction for GlimmerHMM_glimmerT_53601-T1
Valid prediction for GlimmerHMM_glimmerT_53584-T1
Valid prediction for snap_scaffold_25-snap.265-T1
Valid prediction for snap_scaffold_25-snap.223-T1
Valid prediction for Augustus_model.g35619.t1
Valid prediction for snap_scaffold_25-snap.246-T1
Valid prediction for snap_scaffold_25-snap.251-T1
Valid prediction for GlimmerHMM_glimmerT_53595-T1
Couldn't classify 49177, 49683
Sorry, prediction pasa_asmbl_34029.p1 fails validation.
(ATG)	 TC	42133-42349	GT	TGG
(TGA)	 AG	43780-43931	GT	AGG
(GAA)	 AG	44828-44981	GT	TGG
(CTC)	 AG	46195-46277	GT	AGG
(CAT)	 AG	46808-47018	GT	ACG
(GTC)	 AG	47504-47716	GT	CGG
(GAG)	 AG	47841-47924	GT	AGG
(CCA)	 AG	48034-48127	GT	CAG
(CAT)	 AG	48508-48583	GT	AGG
(GCA)	 AG	49177-49683	GA	GGG
-recovered pasa_asmbl_34029.p1, initial, 42133, 42349
-recovered pasa_asmbl_34029.p1, internal, 43780, 43931
-recovered pasa_asmbl_34029.p1, internal, 44828, 44981
-recovered pasa_asmbl_34029.p1, internal, 46195, 46277
-recovered pasa_asmbl_34029.p1, internal, 46808, 47018
-recovered pasa_asmbl_34029.p1, internal, 47504, 47716
-recovered pasa_asmbl_34029.p1, internal, 47841, 47924
-recovered pasa_asmbl_34029.p1, internal, 48034, 48127
-recovered pasa_asmbl_34029.p1, internal, 48508, 48583
Valid prediction for snap_scaffold_25-snap.259-T1
Valid prediction for GlimmerHMM_glimmerT_53596-T1
Valid prediction for Augustus_model.g35621.t1
Valid prediction for GlimmerHMM_glimmerT_53576-T1
Valid prediction for HiQ_model.g35620.t1
Valid prediction for snap_scaffold_25-snap.257-T1
Valid prediction for snap_scaffold_25-snap.231-T1
Valid prediction for snap_scaffold_25-snap.235-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15484, rend_intergenic: 11780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19841, rend_intergenic: 15488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26113, rend_intergenic: 20469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74940, rend_intergenic: 26132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84419, rend_intergenic: 75550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102402, rend_intergenic: 84531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116571, rend_intergenic: 105773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117406, rend_intergenic: 117022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123922, rend_intergenic: 117437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127491, rend_intergenic: 123942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130482, rend_intergenic: 128759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136712, rend_intergenic: 132868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156151, rend_intergenic: 138953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170742, rend_intergenic: 157581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194188, rend_intergenic: 180824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206415, rend_intergenic: 197583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213228, rend_intergenic: 206780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215169, rend_intergenic: 214005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225786, rend_intergenic: 223365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228613, rend_intergenic: 226716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231287, rend_intergenic: 229923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 241019, rend_intergenic: 233668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 246403, rend_intergenic: 243808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 247601
-exon list size: 383


building trellis

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88.3    
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88.8    
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90.1    
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97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 15484, rend_intergenic: 11780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19841, rend_intergenic: 15488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26113, rend_intergenic: 20469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74940, rend_intergenic: 26132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84419, rend_intergenic: 75550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102402, rend_intergenic: 84531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116571, rend_intergenic: 105773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117406, rend_intergenic: 117022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123922, rend_intergenic: 117437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127491, rend_intergenic: 123942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130482, rend_intergenic: 128759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136712, rend_intergenic: 132868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156151, rend_intergenic: 138953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170742, rend_intergenic: 157581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194188, rend_intergenic: 180824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206415, rend_intergenic: 197583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213228, rend_intergenic: 206780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215169, rend_intergenic: 214005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225786, rend_intergenic: 223365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228613, rend_intergenic: 226716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231287, rend_intergenic: 229923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 241019, rend_intergenic: 233668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 246403, rend_intergenic: 243808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11995
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11471
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support