-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_8775919-8950200

-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_11-snap.1998-T1
Valid prediction for snap_scaffold_11-snap.2017-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_27592-T1
Valid prediction for snap_scaffold_11-snap.1989-T1
Valid prediction for snap_scaffold_11-snap.2001-T1
Valid prediction for Augustus_model.g18281.t1
Valid prediction for GlimmerHMM_glimmerT_27596-T1
Valid prediction for GlimmerHMM_glimmerT_27612-T1
Valid prediction for GlimmerHMM_glimmerT_27609-T1
Couldn't classify 879, 1072
Couldn't classify 5681, 5733
Sorry, prediction pasa_asmbl_6251.p1 fails validation.
(GAG)	 TA	879-1072	GT	AGG
(GTA)	 AG	2320-2402	GT	AGG
(GTT)	 AG	4077-4182	GT	AGG
(GTT)	 AG	4565-4809	GT	GGG
(GTG)	 AG	5681-5733	AG	TCA
-recovered pasa_asmbl_6251.p1, internal, 2320, 2402
-recovered pasa_asmbl_6251.p1, internal, 4077, 4182
-recovered pasa_asmbl_6251.p1, internal, 4565, 4809
Valid prediction for snap_scaffold_11-snap.1996-T1
Valid prediction for Augustus_model.g18265.t1
Valid prediction for CodingQuarry_transcript_8192-T1
Valid prediction for snap_scaffold_11-snap.2019-T1
Valid prediction for GlimmerHMM_glimmerT_27606-T1
Valid prediction for snap_scaffold_11-snap.1995-T1
Valid prediction for HiQ_model.g18276.t1
Valid prediction for snap_scaffold_11-snap.1986-T1
Valid prediction for Augustus_model.g18268.t1
Valid prediction for snap_scaffold_11-snap.2004-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 57964, 58113
Couldn't classify 59607, 59628
Sorry, prediction pasa_asmbl_5845.p1 fails validation.
(GGC)	 CG	57964-58113	GT	GGG
(GGT)	 AG	58278-58528	GT	AGG
(GGC)	 AG	58733-58828	GT	AGG
(TGC)	 AG	58976-59078	GT	TGG
(GTG)	 AG	59233-59312	GT	AGG
(TTT)	 AG	59607-59628	CC	AGC
-recovered pasa_asmbl_5845.p1, internal, 58278, 58528
-recovered pasa_asmbl_5845.p1, internal, 58733, 58828
-recovered pasa_asmbl_5845.p1, internal, 58976, 59078
-recovered pasa_asmbl_5845.p1, internal, 59233, 59312
Valid prediction for pasa_asmbl_5847.p1
Valid prediction for snap_scaffold_11-snap.2007-T1
Valid prediction for snap_scaffold_11-snap.2013-T1
Valid prediction for Augustus_model.g18261.t1
Valid prediction for GlimmerHMM_glimmerT_27593-T1
Valid prediction for GlimmerHMM_glimmerT_27589-T1
Valid prediction for snap_scaffold_11-snap.2000-T1
Valid prediction for Augustus_model.g18267.t1
Valid prediction for Augustus_model.g18277.t1
Valid prediction for Augustus_model.g18269.t1
Valid prediction for GlimmerHMM_glimmerT_27597-T1
Valid prediction for snap_scaffold_11-snap.1999-T1
Valid prediction for snap_scaffold_11-snap.1997-T1
Valid prediction for GlimmerHMM_glimmerT_27600-T1
Valid prediction for GlimmerHMM_glimmerT_27614-T1
Valid prediction for Augustus_model.g18266.t1
Valid prediction for snap_scaffold_11-snap.2003-T1
Valid prediction for snap_scaffold_11-snap.2012-T1
Valid prediction for GlimmerHMM_glimmerT_27615-T1
Valid prediction for snap_scaffold_11-snap.1987-T1
Valid prediction for GlimmerHMM_glimmerT_27608-T1
Valid prediction for Augustus_model.g18263.t1
Valid prediction for snap_scaffold_11-snap.1985-T1
Valid prediction for GlimmerHMM_glimmerT_27602-T1
Valid prediction for snap_scaffold_11-snap.1983-T1
Valid prediction for GlimmerHMM_glimmerT_27594-T1
Valid prediction for snap_scaffold_11-snap.1991-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_11-snap.2002-T1
Valid prediction for snap_scaffold_11-snap.2011-T1
Valid prediction for GlimmerHMM_glimmerT_27599-T1
Couldn't classify 70400, 70519
Couldn't classify 72843, 72892
Sorry, prediction pasa_asmbl_7341.p1 fails validation.
(GGG)	 CA	70400-70519	GT	TGG
(TGC)	 AG	70672-70822	GT	GGG
(TCC)	 AG	72843-72892	CA	CCC
-recovered pasa_asmbl_7341.p1, internal, 70672, 70822
Valid prediction for snap_scaffold_11-snap.1992-T1
Couldn't classify 51220, 51364
Sorry, prediction pasa_asmbl_6884.p1 fails validation.
(GAG)	 CC	51220-51364	GT	GAG
(GGG)	 AG	53648-53760	GT	TCG
(GGC)	 AG	53967-54122	CC	AGC
-recovered pasa_asmbl_6884.p1, terminal, 53967, 54122
-recovered pasa_asmbl_6884.p1, internal, 53648, 53760
Couldn't classify 25217, 25621
Sorry, prediction pasa_asmbl_6891.p1 fails validation.
(GTG)	 CT	25217-25621	CC	CCC
Valid prediction for GlimmerHMM_glimmerT_27601-T1
Valid prediction for GlimmerHMM_glimmerT_27607-T1
Valid prediction for snap_scaffold_11-snap.2014-T1
Valid prediction for GlimmerHMM_glimmerT_27605-T1
Valid prediction for snap_scaffold_11-snap.1984-T1
Valid prediction for GlimmerHMM_glimmerT_27588-T1
Valid prediction for GlimmerHMM_glimmerT_27587-T1
Valid prediction for Augustus_model.g18271.t1
Valid prediction for snap_scaffold_11-snap.2020-T1
Valid prediction for GlimmerHMM_glimmerT_27613-T1
Valid prediction for snap_scaffold_11-snap.1993-T1
Valid prediction for snap_scaffold_11-snap.1982-T1
Valid prediction for GlimmerHMM_glimmerT_27598-T1
Valid prediction for snap_scaffold_11-snap.2006-T1
Valid prediction for GlimmerHMM_glimmerT_27591-T1
Valid prediction for snap_scaffold_11-snap.2009-T1
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 131087, 131177
Couldn't classify 134425, 134541
Sorry, prediction pasa_asmbl_6880.p1 fails validation.
(CAG)	 CC	131087-131177	GT	AGG
(GAT)	 AG	131402-131486	GT	AGG
(GAC)	 AG	131634-131737	GT	TGG
(AGC)	 AG	131978-132104	GT	AAG
(GAA)	 AG	132351-132443	GT	AGG
(CAT)	 AG	133471-133554	GT	CGG
(GAT)	 AG	133931-134057	GT	AGG
(AGA)	 AG	134425-134541	GT	AGG
-recovered pasa_asmbl_6880.p1, internal, 131402, 131486
-recovered pasa_asmbl_6880.p1, internal, 131634, 131737
-recovered pasa_asmbl_6880.p1, internal, 131978, 132104
-recovered pasa_asmbl_6880.p1, internal, 132351, 132443
-recovered pasa_asmbl_6880.p1, internal, 133471, 133554
-recovered pasa_asmbl_6880.p1, internal, 133931, 134057
-recovered pasa_asmbl_6880.p1, internal, 134425, 134541
Valid prediction for snap_scaffold_11-snap.1988-T1
Couldn't classify 28960, 29021
Sorry, prediction pasa_asmbl_6889.p1 fails validation.
(CGA)	 CC	28960-29021	GT	AAG
(GCA)	 AG	29181-29307	GT	AGG
(ATG)	 AG	29703-30010	GT	AGG
(GAA)	 AG	30169-30275	GT	AGG
(AGC)	 AG	30360-30495	GT	AGG
(GAA)	 AG	30646-31011	GT	AGG
(GAT)	 AG	31103-31319	GG	GAG
-recovered pasa_asmbl_6889.p1, initial, 29703, 30010
-recovered pasa_asmbl_6889.p1, terminal, 31103, 31319
-recovered pasa_asmbl_6889.p1, internal, 29181, 29307
-recovered pasa_asmbl_6889.p1, internal, 29703, 30010
-recovered pasa_asmbl_6889.p1, internal, 30169, 30275
-recovered pasa_asmbl_6889.p1, internal, 30360, 30495
-recovered pasa_asmbl_6889.p1, internal, 30646, 31011
Valid prediction for Augustus_model.g18275.t1
Valid prediction for Augustus_model.g18270.t1
Valid prediction for Augustus_model.g18272.t1
Valid prediction for GlimmerHMM_glimmerT_27595-T1
Valid prediction for Augustus_model.g18264.t1
Valid prediction for Augustus_model.g18273.t1
Valid prediction for Augustus_model.g18282.t1
Valid prediction for snap_scaffold_11-snap.1994-T1
Couldn't classify 23763, 23877
Couldn't classify 24984, 25048
Sorry, prediction pasa_asmbl_6892.p1 fails validation.
(GGC)	 GG	23763-23877	GT	AGG
(TGG)	 AG	24245-24388	GT	AGG
(CTG)	 AG	24984-25048	CC	TGC
-recovered pasa_asmbl_6892.p1, internal, 24245, 24388
Couldn't classify 20126, 20158
Couldn't classify 23575, 23627
Sorry, prediction pasa_asmbl_6893.p1 fails validation.
(GAC)	 AG	20126-20158	GT	AAG
(GCA)	 AG	21196-21270	GT	AGG
(GAC)	 AG	22356-22496	GT	CAG
(GGC)	 AG	22997-23198	GT	AGG
(CCG)	 AG	23575-23627	CC	CCC
-recovered pasa_asmbl_6893.p1, internal, 20126, 20158
-recovered pasa_asmbl_6893.p1, internal, 21196, 21270
-recovered pasa_asmbl_6893.p1, internal, 22356, 22496
-recovered pasa_asmbl_6893.p1, internal, 22997, 23198
Valid prediction for snap_scaffold_11-snap.2015-T1
Valid prediction for snap_scaffold_11-snap.2016-T1
Valid prediction for GlimmerHMM_glimmerT_27611-T1
Valid prediction for snap_scaffold_11-snap.1990-T1
Valid prediction for snap_scaffold_11-snap.2010-T1
Valid prediction for Augustus_model.g18274.t1
Valid prediction for GlimmerHMM_glimmerT_27590-T1
Valid prediction for snap_scaffold_11-snap.2008-T1
Valid prediction for GlimmerHMM_glimmerT_27610-T1
Valid prediction for CodingQuarry_transcript_8191-T1
Valid prediction for Augustus_model.g18262.t1
Valid prediction for Augustus_model.g18278.t1
Valid prediction for Augustus_model.g18280.t1
Valid prediction for snap_scaffold_11-snap.2005-T1
Valid prediction for Augustus_model.g18279.t1
Valid prediction for snap_scaffold_11-snap.2018-T1
Valid prediction for GlimmerHMM_glimmerT_27603-T1
Valid prediction for GlimmerHMM_glimmerT_27604-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8993, rend_intergenic: 7047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10534, rend_intergenic: 9027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13257, rend_intergenic: 12273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27388, rend_intergenic: 23376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38414, rend_intergenic: 37286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38669, rend_intergenic: 38522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51342, rend_intergenic: 41651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63477, rend_intergenic: 51583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99167, rend_intergenic: 97236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104442, rend_intergenic: 100381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113475, rend_intergenic: 107095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152074, rend_intergenic: 149035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168061, rend_intergenic: 155851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168601, rend_intergenic: 168344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 174282
-exon list size: 472


building trellis

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97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 8993, rend_intergenic: 7047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10534, rend_intergenic: 9027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13257, rend_intergenic: 12273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27388, rend_intergenic: 23376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38414, rend_intergenic: 37286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38669, rend_intergenic: 38522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51342, rend_intergenic: 41651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63477, rend_intergenic: 51583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99167, rend_intergenic: 97236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104442, rend_intergenic: 100381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113475, rend_intergenic: 107095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152074, rend_intergenic: 149035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168061, rend_intergenic: 155851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168601, rend_intergenic: 168344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support