-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_9929270-10126357

-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 CodingQuarry_transcript_22146-T1
Valid prediction for snap_scaffold_17-snap.1973-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_17-snap.2000-T1
Valid prediction for GlimmerHMM_glimmerT_40899-T1
Valid prediction for snap_scaffold_17-snap.2002-T1
Valid prediction for GlimmerHMM_glimmerT_40893-T1
Valid prediction for GlimmerHMM_glimmerT_40912-T1
Valid prediction for GlimmerHMM_glimmerT_40900-T1
Valid prediction for Augustus_model.g27312.t1
Valid prediction for CodingQuarry_transcript_22155-T1
Valid prediction for CodingQuarry_transcript_22147-T1
Valid prediction for Augustus_model.g27308.t1
Valid prediction for pasa_asmbl_19161.p2
Valid prediction for GlimmerHMM_glimmerT_40908-T1
Valid prediction for CodingQuarry_transcript_22153-T1
Valid prediction for snap_scaffold_17-snap.2005-T1
Valid prediction for HiQ_model.g27307.t1
Valid prediction for HiQ_model.g27300.t1
Valid prediction for HiQ_model.g27301.t1
Valid prediction for CodingQuarry_transcript_22148-T1
Valid prediction for CodingQuarry_transcript_22154-T1
Valid prediction for snap_scaffold_17-snap.2008-T1
Valid prediction for CodingQuarry_transcript_22149-T1
Valid prediction for GlimmerHMM_glimmerT_40907-T1
Valid prediction for GlimmerHMM_glimmerT_40910-T1
Valid prediction for Augustus_model.g27310.t1
Valid prediction for pasa_asmbl_19166.p1
Valid prediction for pasa_asmbl_19148.p1
Valid prediction for snap_scaffold_17-snap.1999-T1
Valid prediction for snap_scaffold_17-snap.1979-T1
Valid prediction for snap_scaffold_17-snap.1970-T1
Valid prediction for snap_scaffold_17-snap.1986-T1
Valid prediction for HiQ_model.g27296.t1
Valid prediction for Augustus_model.g27311.t1
Valid prediction for snap_scaffold_17-snap.2013-T1
Couldn't classify 163776, 164537
Sorry, prediction pasa_asmbl_19175.p1 fails validation.
(CCT)	 GA	163776-164537	GT	CGG
(GCA)	 AG	165295-165517	GT	TGG
(CGG)	 AG	167020-167186	CC	AAC
-recovered pasa_asmbl_19175.p1, terminal, 167020, 167186
-recovered pasa_asmbl_19175.p1, internal, 165295, 165517
Valid prediction for Augustus_model.g27302.t1
Valid prediction for Augustus_model.g27297.t1
Valid prediction for snap_scaffold_17-snap.2006-T1
Valid prediction for GlimmerHMM_glimmerT_40911-T1
Valid prediction for snap_scaffold_17-snap.1982-T1
Valid prediction for pasa_asmbl_19156.p1
Valid prediction for HiQ_model.g27309.t1
Valid prediction for snap_scaffold_17-snap.1987-T1
Valid prediction for CodingQuarry_transcript_22156-T1
Valid prediction for pasa_asmbl_19144.p1
Valid prediction for HiQ_model.g27305.t1
Valid prediction for Augustus_model.g27299.t1
Couldn't classify 76119, 76405
Sorry, prediction pasa_asmbl_19152.p1 fails validation.
(CAG)	 TA	76119-76405	GT	AGG
(GTA)	 AG	78109-78163	GT	AGG
(CTT)	 AG	78318-78387	GT	GGG
(CTT)	 AG	78802-78929	GT	AGG
(CTG)	 AG	79058-79211	GT	AGG
(ATA)	 AG	79409-79509	GT	AGG
(GAG)	 AG	81051-81167	GT	AGG
(CAC)	 AG	81552-81774	GT	CGG
(ATC)	 AG	81950-82073	GT	GGG
(TGT)	 AG	82264-82441	GT	AGG
(TCT)	 AG	82541-82652	GT	AGG
(AGG)	 AG	82896-83065	GT	AGG
(GTG)	 AG	83242-83490	GT	AGG
(ACA)	 AG	83876-84010	GT	AGG
(TTC)	 AG	84486-84580	GT	AAG
(GGA)	 AG	84705-84834	GT	TCG
(GCT)	 AG	85583-85698	GT	GGG
(GTA)	 AG	85823-86006	GC	AAG
-recovered pasa_asmbl_19152.p1, terminal, 85823, 86006
-recovered pasa_asmbl_19152.p1, internal, 78109, 78163
-recovered pasa_asmbl_19152.p1, internal, 78318, 78387
-recovered pasa_asmbl_19152.p1, internal, 78802, 78929
-recovered pasa_asmbl_19152.p1, internal, 79058, 79211
-recovered pasa_asmbl_19152.p1, internal, 79409, 79509
-recovered pasa_asmbl_19152.p1, internal, 81051, 81167
-recovered pasa_asmbl_19152.p1, internal, 81552, 81774
-recovered pasa_asmbl_19152.p1, internal, 81950, 82073
-recovered pasa_asmbl_19152.p1, internal, 82264, 82441
-recovered pasa_asmbl_19152.p1, internal, 82541, 82652
-recovered pasa_asmbl_19152.p1, internal, 82896, 83065
-recovered pasa_asmbl_19152.p1, internal, 83242, 83490
-recovered pasa_asmbl_19152.p1, internal, 83876, 84010
-recovered pasa_asmbl_19152.p1, internal, 84486, 84580
-recovered pasa_asmbl_19152.p1, internal, 84705, 84834
-recovered pasa_asmbl_19152.p1, internal, 85583, 85698
-recovered pasa_asmbl_19152.p1, internal, 85823, 86006
Valid prediction for Augustus_model.g27313.t1
Valid prediction for snap_scaffold_17-snap.2003-T1
Valid prediction for pasa_asmbl_19168.p1
Valid prediction for snap_scaffold_17-snap.1997-T1
Couldn't classify 191173, 191337
Sorry, prediction pasa_asmbl_19180.p1 fails validation.
(TGT)	 AG	191173-191337	GT	AGG
(GAG)	 AG	192478-192699	GT	AGG
(GTA)	 AG	192859-192991	GT	AGG
(CGG)	 AG	193191-193306	GT	AGG
(GAC)	 AG	193413-193496	GT	AGG
(GTG)	 AG	193677-193783	GT	CGG
(TTA)	 AG	193996-194140	GT	AGG
(GTG)	 AG	194286-194372	CA	GAC
-recovered pasa_asmbl_19180.p1, terminal, 194286, 194372
-recovered pasa_asmbl_19180.p1, internal, 191173, 191337
-recovered pasa_asmbl_19180.p1, internal, 192478, 192699
-recovered pasa_asmbl_19180.p1, internal, 192859, 192991
-recovered pasa_asmbl_19180.p1, internal, 193191, 193306
-recovered pasa_asmbl_19180.p1, internal, 193413, 193496
-recovered pasa_asmbl_19180.p1, internal, 193677, 193783
-recovered pasa_asmbl_19180.p1, internal, 193996, 194140
Valid prediction for pasa_asmbl_19128.p1
Valid prediction for GlimmerHMM_glimmerT_40905-T1
Valid prediction for snap_scaffold_17-snap.1976-T1
Valid prediction for GlimmerHMM_glimmerT_40898-T1
Valid prediction for snap_scaffold_17-snap.1995-T1
Valid prediction for GlimmerHMM_glimmerT_40902-T1
Valid prediction for GlimmerHMM_glimmerT_40909-T1
Valid prediction for GlimmerHMM_glimmerT_40894-T1
Valid prediction for snap_scaffold_17-snap.2011-T1
Valid prediction for pasa_asmbl_19169.p1
Valid prediction for snap_scaffold_17-snap.1993-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_17-snap.1996-T1
Valid prediction for GlimmerHMM_glimmerT_40903-T1
Valid prediction for snap_scaffold_17-snap.2001-T1
Valid prediction for snap_scaffold_17-snap.2007-T1
Valid prediction for snap_scaffold_17-snap.2014-T1
Valid prediction for Augustus_model.g27304.t1
Valid prediction for snap_scaffold_17-snap.2012-T1
Valid prediction for GlimmerHMM_glimmerT_40897-T1
Valid prediction for pasa_asmbl_18228.p1
Valid prediction for snap_scaffold_17-snap.1969-T1
Valid prediction for snap_scaffold_17-snap.1975-T1
Couldn't classify 72849, 72999
Couldn't classify 73267, 73315
Sorry, prediction CodingQuarry_transcript_22152-T1 fails validation.
(ATG)	 AA	72207-72287	GT	AGG
(ATC)	 AG	72378-72469	GT	GAG
(GCA)	 AG	72560-72660	GT	AGG
(GCC)	 AG	72849-72999	GG	AAG
(AGG)	 CC	73267-73315	GA	GAG
-recovered CodingQuarry_transcript_22152-T1, initial, 72207, 72287
add_exon() Sorry, CodingQuarry_transcript_22152-T1 72378-72469-terminal-2 is invalid.
-recovered CodingQuarry_transcript_22152-T1, terminal, 72378, 72469
-recovered CodingQuarry_transcript_22152-T1, internal, 72378, 72469
-recovered CodingQuarry_transcript_22152-T1, internal, 72560, 72660
Valid prediction for snap_scaffold_17-snap.1990-T1
Valid prediction for snap_scaffold_17-snap.1984-T1
Valid prediction for snap_scaffold_17-snap.1971-T1
Valid prediction for GlimmerHMM_glimmerT_40895-T1
Valid prediction for snap_scaffold_17-snap.1983-T1
Valid prediction for snap_scaffold_17-snap.1992-T1
Valid prediction for snap_scaffold_17-snap.1980-T1
Valid prediction for snap_scaffold_17-snap.2004-T1
Valid prediction for CodingQuarry_transcript_22150-T1
Valid prediction for snap_scaffold_17-snap.1974-T1
Valid prediction for snap_scaffold_17-snap.2010-T1
Valid prediction for pasa_asmbl_18223.p1
Valid prediction for pasa_asmbl_18226.p1
Valid prediction for snap_scaffold_17-snap.2009-T1
Valid prediction for GlimmerHMM_glimmerT_40904-T1
Valid prediction for snap_scaffold_17-snap.1994-T1
Valid prediction for snap_scaffold_17-snap.1991-T1
Valid prediction for snap_scaffold_17-snap.1985-T1
Valid prediction for snap_scaffold_17-snap.1972-T1
Valid prediction for GlimmerHMM_glimmerT_40906-T1
Valid prediction for snap_scaffold_17-snap.1998-T1
Valid prediction for snap_scaffold_17-snap.1988-T1
Valid prediction for snap_scaffold_17-snap.1978-T1
Valid prediction for snap_scaffold_17-snap.1977-T1
Valid prediction for snap_scaffold_17-snap.1981-T1
Valid prediction for CodingQuarry_transcript_22151-T1
Valid prediction for HiQ_model.g27303.t1
Valid prediction for HiQ_model.g27306.t1
Valid prediction for GlimmerHMM_glimmerT_40896-T1
Valid prediction for Augustus_model.g27298.t1
Valid prediction for snap_scaffold_17-snap.1989-T1
Valid prediction for GlimmerHMM_glimmerT_40901-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14017, rend_intergenic: 4736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25761, rend_intergenic: 18161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29062, rend_intergenic: 26649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31327, rend_intergenic: 29629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34173, rend_intergenic: 31330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42012, rend_intergenic: 34835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49590, rend_intergenic: 43995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51332, rend_intergenic: 50575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62501, rend_intergenic: 51611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70277, rend_intergenic: 67435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100744, rend_intergenic: 77690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114287, rend_intergenic: 111783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125282, rend_intergenic: 117273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132776, rend_intergenic: 129405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145509, rend_intergenic: 140120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154728, rend_intergenic: 149078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164659, rend_intergenic: 156322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169949, rend_intergenic: 167016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175709, rend_intergenic: 172646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181283, rend_intergenic: 176250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187374, rend_intergenic: 181291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194372, rend_intergenic: 192078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 197088
-exon list size: 532


building trellis

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99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 14017, rend_intergenic: 4736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25761, rend_intergenic: 18161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29062, rend_intergenic: 26649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31327, rend_intergenic: 29629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34173, rend_intergenic: 31330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42012, rend_intergenic: 34835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49590, rend_intergenic: 43995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51332, rend_intergenic: 50575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62501, rend_intergenic: 51611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70277, rend_intergenic: 67435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100744, rend_intergenic: 77690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114287, rend_intergenic: 111783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125282, rend_intergenic: 117273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132776, rend_intergenic: 129405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145509, rend_intergenic: 140120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154728, rend_intergenic: 149078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164659, rend_intergenic: 156322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169949, rend_intergenic: 167016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175709, rend_intergenic: 172646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181283, rend_intergenic: 176250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187374, rend_intergenic: 181291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194372, rend_intergenic: 192078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support