-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_10804038-10990145

-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_39003-T1
Couldn't classify 57924, 58089
Couldn't classify 64363, 64433
Sorry, prediction pasa_asmbl_16559.p1 fails validation.
(TTC)	 GC	57924-58089	GT	GGG
(TGA)	 AG	60095-60286	GT	AGG
(ACT)	 AG	62764-62865	GT	AGG
(GGA)	 AG	63965-64105	GT	AGG
(TGC)	 AG	64363-64433	CA	CCC
-recovered pasa_asmbl_16559.p1, internal, 60095, 60286
-recovered pasa_asmbl_16559.p1, internal, 62764, 62865
-recovered pasa_asmbl_16559.p1, internal, 63965, 64105
Valid prediction for CodingQuarry_transcript_20083-T1
Valid prediction for snap_scaffold_16-snap.2000-T1
Valid prediction for GlimmerHMM_glimmerT_38985-T1
Valid prediction for GlimmerHMM_glimmerT_39005-T1
Valid prediction for GlimmerHMM_glimmerT_39002-T1
Valid prediction for Augustus_model.g26048.t1
Valid prediction for Augustus_model.g26043.t1
Valid prediction for HiQ_model.g26034.t1
Valid prediction for GlimmerHMM_glimmerT_38995-T1
Valid prediction for snap_scaffold_16-snap.2003-T1
Valid prediction for Augustus_model.g26042.t1
Valid prediction for snap_scaffold_16-snap.2032-T1
Valid prediction for GlimmerHMM_glimmerT_38987-T1
Valid prediction for GlimmerHMM_glimmerT_38984-T1
Valid prediction for GlimmerHMM_glimmerT_38998-T1
Valid prediction for GlimmerHMM_glimmerT_38991-T1
Valid prediction for Augustus_model.g26037.t1
Valid prediction for GlimmerHMM_glimmerT_38993-T1
Valid prediction for pasa_asmbl_16562.p1
Valid prediction for Augustus_model.g26045.t1
Valid prediction for snap_scaffold_16-snap.2006-T1
Valid prediction for GlimmerHMM_glimmerT_39001-T1
Valid prediction for snap_scaffold_16-snap.2025-T1
Valid prediction for snap_scaffold_16-snap.2028-T1
Valid prediction for GlimmerHMM_glimmerT_38996-T1
Valid prediction for GlimmerHMM_glimmerT_39006-T1
Valid prediction for snap_scaffold_16-snap.2024-T1
Couldn't classify 66133, 66504
Sorry, prediction pasa_asmbl_16561.p2 fails validation.
(GGC)	 CA	66133-66504	GT	AGG
Valid prediction for Augustus_model.g26049.t1
Valid prediction for snap_scaffold_16-snap.2015-T1
Valid prediction for Augustus_model.g26036.t1
Valid prediction for snap_scaffold_16-snap.2016-T1
Valid prediction for Augustus_model.g26035.t1
Valid prediction for Augustus_model.g26047.t1
Valid prediction for snap_scaffold_16-snap.2020-T1
Valid prediction for Augustus_model.g26046.t1
Valid prediction for snap_scaffold_16-snap.2011-T1
Valid prediction for Augustus_model.g26044.t1
Valid prediction for Augustus_model.g26041.t1
Valid prediction for CodingQuarry_transcript_20082-T1
Valid prediction for GlimmerHMM_glimmerT_39000-T1
Valid prediction for snap_scaffold_16-snap.2023-T1
Valid prediction for snap_scaffold_16-snap.2021-T1
Valid prediction for Augustus_model.g26039.t1
Valid prediction for snap_scaffold_16-snap.1998-T1
Valid prediction for GlimmerHMM_glimmerT_39004-T1
Valid prediction for GlimmerHMM_glimmerT_38983-T1
Valid prediction for snap_scaffold_16-snap.1996-T1
Valid prediction for snap_scaffold_16-snap.2001-T1
Valid prediction for snap_scaffold_16-snap.2017-T1
Valid prediction for GlimmerHMM_glimmerT_38988-T1
Valid prediction for snap_scaffold_16-snap.2018-T1
Valid prediction for GlimmerHMM_glimmerT_39009-T1
Valid prediction for pasa_asmbl_16557.p1
Valid prediction for snap_scaffold_16-snap.2005-T1
Valid prediction for GlimmerHMM_glimmerT_38989-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_16-snap.2002-T1
Valid prediction for GlimmerHMM_glimmerT_38994-T1
Valid prediction for snap_scaffold_16-snap.2027-T1
Valid prediction for snap_scaffold_16-snap.2014-T1
Valid prediction for snap_scaffold_16-snap.2019-T1
Valid prediction for GlimmerHMM_glimmerT_38992-T1
Valid prediction for snap_scaffold_16-snap.2004-T1
Valid prediction for snap_scaffold_16-snap.2012-T1
Valid prediction for Augustus_model.g26032.t1
Valid prediction for GlimmerHMM_glimmerT_39011-T1
Valid prediction for GlimmerHMM_glimmerT_39010-T1
Valid prediction for snap_scaffold_16-snap.2029-T1
Valid prediction for snap_scaffold_16-snap.1994-T1
Valid prediction for snap_scaffold_16-snap.1999-T1
Valid prediction for GlimmerHMM_glimmerT_38986-T1
Valid prediction for snap_scaffold_16-snap.2007-T1
Valid prediction for Augustus_model.g26033.t1
Couldn't classify 3817, 3876
Sorry, prediction pasa_asmbl_17320.p1 fails validation.
(AAC)	 CC	3817-3876	GT	AGG
(GTT)	 AG	4297-4472	GT	GTG
(GAA)	 AG	4831-4959	GT	AGG
(ATT)	 AG	5344-5400	GT	GGG
(TAA)	 AG	7787-7916	GT	AGG
(AAG)	 AG	10870-11095	GT	ACG
(GCT)	 AG	11759-12005	GT	AAG
(ATG)	 AG	12224-12320	GT	AAG
(ATC)	 AG	12570-12664	GT	AGG
(CTA)	 AG	12931-13002	GT	AAG
(GGA)	 AG	13899-14065	GT	CCG
(TGG)	 AG	14292-14434	GT	AGG
(CTG)	 AG	14593-14716	GT	AGG
(GAG)	 AG	16473-16506	GT	AGG
(CCC)	 AG	18094-18124	GC	AAG
add_exon() Sorry, pasa_asmbl_17320.p1 12224-12320-initial-1 is invalid.
-recovered pasa_asmbl_17320.p1, initial, 12224, 12320
add_exon() Sorry, pasa_asmbl_17320.p1 12931-13002-terminal-1 is invalid.
-recovered pasa_asmbl_17320.p1, terminal, 12931, 13002
-recovered pasa_asmbl_17320.p1, terminal, 18094, 18124
-recovered pasa_asmbl_17320.p1, internal, 4297, 4472
-recovered pasa_asmbl_17320.p1, internal, 4831, 4959
-recovered pasa_asmbl_17320.p1, internal, 5344, 5400
-recovered pasa_asmbl_17320.p1, internal, 7787, 7916
-recovered pasa_asmbl_17320.p1, internal, 10870, 11095
-recovered pasa_asmbl_17320.p1, internal, 11759, 12005
-recovered pasa_asmbl_17320.p1, internal, 12224, 12320
-recovered pasa_asmbl_17320.p1, internal, 12570, 12664
-recovered pasa_asmbl_17320.p1, internal, 12931, 13002
-recovered pasa_asmbl_17320.p1, internal, 13899, 14065
-recovered pasa_asmbl_17320.p1, internal, 14292, 14434
-recovered pasa_asmbl_17320.p1, internal, 14593, 14716
-recovered pasa_asmbl_17320.p1, internal, 16473, 16506
-recovered pasa_asmbl_17320.p1, internal, 18094, 18124
Valid prediction for snap_scaffold_16-snap.2026-T1
Valid prediction for Augustus_model.g26040.t1
Valid prediction for snap_scaffold_16-snap.2030-T1
Valid prediction for GlimmerHMM_glimmerT_38997-T1
Valid prediction for snap_scaffold_16-snap.2013-T1
Valid prediction for GlimmerHMM_glimmerT_39008-T1
Valid prediction for snap_scaffold_16-snap.2009-T1
Valid prediction for snap_scaffold_16-snap.1995-T1
Valid prediction for GlimmerHMM_glimmerT_38990-T1
Valid prediction for snap_scaffold_16-snap.2031-T1
Valid prediction for snap_scaffold_16-snap.2022-T1
Valid prediction for Augustus_model.g26038.t1
Valid prediction for HiQ_model.g26050.t1
Valid prediction for GlimmerHMM_glimmerT_39007-T1
Valid prediction for snap_scaffold_16-snap.1997-T1
Valid prediction for snap_scaffold_16-snap.2008-T1
Couldn't classify 18360, 19046
Sorry, prediction pasa_asmbl_17319.p1 fails validation.
(GGG)	 CT	18360-19046	GA	GAG
Valid prediction for GlimmerHMM_glimmerT_38999-T1
Valid prediction for snap_scaffold_16-snap.2010-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 71560, rend_intergenic: 71557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17059, rend_intergenic: 15493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43941, rend_intergenic: 38843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46274, rend_intergenic: 44791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58463, rend_intergenic: 52681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67339, rend_intergenic: 58743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68873, rend_intergenic: 67396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84184, rend_intergenic: 70227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120333, rend_intergenic: 106713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129969, rend_intergenic: 125310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141483, rend_intergenic: 134548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146579, rend_intergenic: 143208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163795, rend_intergenic: 146615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181349, rend_intergenic: 174580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 186108
-exon list size: 402


building trellis

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-found 29 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 71560, rend_intergenic: 71557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17059, rend_intergenic: 15493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43941, rend_intergenic: 38843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46274, rend_intergenic: 44791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58463, rend_intergenic: 52681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67339, rend_intergenic: 58743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68873, rend_intergenic: 67396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84184, rend_intergenic: 70227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120333, rend_intergenic: 106713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129969, rend_intergenic: 125310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141483, rend_intergenic: 134548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146579, rend_intergenic: 143208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163795, rend_intergenic: 146615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181349, rend_intergenic: 174580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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