-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_9381792-9559737

-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 GeneMark_model.16477_t
Valid prediction for GlimmerHMM_glimmerT_10133-T1
Valid prediction for snap_scaffold_4-snap.1986-T1
Valid prediction for snap_scaffold_4-snap.1994-T1
Valid prediction for GeneMark_model.16444_t
Valid prediction for snap_scaffold_4-snap.1978-T1
Valid prediction for GeneMark_model.16484_t
Valid prediction for GeneMark_model.16441_t
Valid prediction for GeneMark_model.16490_t
Valid prediction for snap_scaffold_4-snap.2010-T1
Valid prediction for snap_scaffold_4-snap.2019-T1
Valid prediction for snap_scaffold_4-snap.2005-T1
Valid prediction for Augustus_model.g6650.t1
Couldn't classify 163153, 163201
Couldn't classify 169695, 169745
Sorry, prediction pasa_asmbl_42948.p1 fails validation.
(CAA)	 GT	163153-163201	GT	AGG
(AGA)	 AG	164053-164166	GT	CAG
(TCT)	 AG	166241-166305	GT	GGG
(ACC)	 AG	167148-167233	GT	AAG
(GTA)	 AG	168805-168862	GT	CGG
(GTT)	 AG	169695-169745	CC	GCC
-recovered pasa_asmbl_42948.p1, internal, 164053, 164166
-recovered pasa_asmbl_42948.p1, internal, 166241, 166305
-recovered pasa_asmbl_42948.p1, internal, 167148, 167233
-recovered pasa_asmbl_42948.p1, internal, 168805, 168862
Valid prediction for snap_scaffold_4-snap.1993-T1
Valid prediction for GlimmerHMM_glimmerT_10123-T1
Valid prediction for GeneMark_model.16479_t
Valid prediction for snap_scaffold_4-snap.2008-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_10119-T1
Valid prediction for snap_scaffold_4-snap.1980-T1
Valid prediction for GeneMark_model.16476_t
Valid prediction for snap_scaffold_4-snap.2002-T1
Valid prediction for GlimmerHMM_glimmerT_10118-T1
Valid prediction for GlimmerHMM_glimmerT_10112-T1
Valid prediction for GlimmerHMM_glimmerT_10138-T1
Valid prediction for GlimmerHMM_glimmerT_10136-T1
Valid prediction for snap_scaffold_4-snap.2000-T1
Valid prediction for snap_scaffold_4-snap.1985-T1
Valid prediction for snap_scaffold_4-snap.1989-T1
Valid prediction for GlimmerHMM_glimmerT_10129-T1
Valid prediction for snap_scaffold_4-snap.1983-T1
Valid prediction for GeneMark_model.16471_t
Valid prediction for GlimmerHMM_glimmerT_10117-T1
Valid prediction for GlimmerHMM_glimmerT_10110-T1
Valid prediction for GeneMark_model.16464_t
Valid prediction for Augustus_model.g6642.t1
Valid prediction for GeneMark_model.16475_t
Valid prediction for GeneMark_model.16493_t
Valid prediction for GeneMark_model.16456_t
Valid prediction for GeneMark_model.16473_t
Valid prediction for GeneMark_model.16492_t
Valid prediction for snap_scaffold_4-snap.2016-T1
Valid prediction for GeneMark_model.16463_t
Valid prediction for snap_scaffold_4-snap.1992-T1
Valid prediction for snap_scaffold_4-snap.2013-T1
Valid prediction for GeneMark_model.16488_t
Valid prediction for snap_scaffold_4-snap.1973-T1
Valid prediction for snap_scaffold_4-snap.2004-T1
Valid prediction for Augustus_model.g6633.t1
Valid prediction for GeneMark_model.16454_t
Valid prediction for snap_scaffold_4-snap.1997-T1
Valid prediction for Augustus_model.g6644.t1
Valid prediction for GeneMark_model.16481_t
Valid prediction for GeneMark_model.16455_t
Valid prediction for GeneMark_model.16466_t
Valid prediction for Augustus_model.g6634.t1
Valid prediction for GeneMark_model.16459_t
Valid prediction for GeneMark_model.16446_t
Valid prediction for GlimmerHMM_glimmerT_10114-T1
Valid prediction for GlimmerHMM_glimmerT_10131-T1
Valid prediction for GeneMark_model.16452_t
Valid prediction for GlimmerHMM_glimmerT_10134-T1
Valid prediction for GlimmerHMM_glimmerT_10124-T1
Valid prediction for snap_scaffold_4-snap.1984-T1
Valid prediction for Augustus_model.g6648.t1
Valid prediction for snap_scaffold_4-snap.1976-T1
Valid prediction for Augustus_model.g6645.t1
Valid prediction for GeneMark_model.16449_t
Valid prediction for GeneMark_model.16469_t
Valid prediction for snap_scaffold_4-snap.1982-T1
Valid prediction for snap_scaffold_4-snap.1987-T1
Valid prediction for GlimmerHMM_glimmerT_10116-T1
Valid prediction for GlimmerHMM_glimmerT_10140-T1
Valid prediction for snap_scaffold_4-snap.2007-T1
Valid prediction for GlimmerHMM_glimmerT_10126-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 GeneMark_model.16448_t
Valid prediction for GlimmerHMM_glimmerT_10111-T1
Valid prediction for Augustus_model.g6630.t1
Valid prediction for Augustus_model.g6640.t1
Valid prediction for Augustus_model.g6639.t1
Valid prediction for GlimmerHMM_glimmerT_10113-T1
Valid prediction for GeneMark_model.16447_t
Valid prediction for snap_scaffold_4-snap.1990-T1
Valid prediction for GlimmerHMM_glimmerT_10120-T1
Valid prediction for GeneMark_model.16458_t
Valid prediction for Augustus_model.g6635.t1
Valid prediction for GeneMark_model.16467_t
Couldn't classify 21929, 22027
Couldn't classify 25880, 25990
Sorry, prediction pasa_asmbl_41557.p1 fails validation.
(TCA)	 AG	21929-22027	GT	AGG
(ATC)	 AG	23125-23242	GT	CTG
(CAC)	 AG	23602-23719	GT	AGG
(GGA)	 AG	25323-25365	GT	GCG
(TTC)	 AG	25880-25990	AG	GTA
-recovered pasa_asmbl_41557.p1, internal, 21929, 22027
-recovered pasa_asmbl_41557.p1, internal, 23125, 23242
-recovered pasa_asmbl_41557.p1, internal, 23602, 23719
-recovered pasa_asmbl_41557.p1, internal, 25323, 25365
Valid prediction for snap_scaffold_4-snap.1988-T1
Valid prediction for GeneMark_model.16494_t
Valid prediction for snap_scaffold_4-snap.2011-T1
Valid prediction for GlimmerHMM_glimmerT_10121-T1
Valid prediction for GlimmerHMM_glimmerT_10125-T1
Valid prediction for GeneMark_model.16451_t
Valid prediction for GeneMark_model.16462_t
Valid prediction for GeneMark_model.16470_t
Valid prediction for Augustus_model.g6631.t1
Valid prediction for GeneMark_model.16487_t
Valid prediction for GeneMark_model.16461_t
Valid prediction for GeneMark_model.16439_t
Valid prediction for snap_scaffold_4-snap.2012-T1
Valid prediction for GeneMark_model.16442_t
Valid prediction for GeneMark_model.16468_t
Valid prediction for snap_scaffold_4-snap.1974-T1
Valid prediction for snap_scaffold_4-snap.1996-T1
Valid prediction for GeneMark_model.16465_t
Valid prediction for GeneMark_model.16472_t
Valid prediction for snap_scaffold_4-snap.2015-T1
Valid prediction for snap_scaffold_4-snap.1995-T1
Valid prediction for snap_scaffold_4-snap.1981-T1
Valid prediction for GlimmerHMM_glimmerT_10139-T1
Valid prediction for Augustus_model.g6641.t1
Valid prediction for GeneMark_model.16489_t
Couldn't classify 31399, 31524
Couldn't classify 35482, 35571
Sorry, prediction pasa_asmbl_41556.p1 fails validation.
(GTG)	 AG	31399-31524	GT	ACG
(TCC)	 AG	31872-31996	GT	CAG
(GTA)	 AG	34730-34856	GT	AGG
(GAG)	 AG	35482-35571	GA	GGG
-recovered pasa_asmbl_41556.p1, internal, 31399, 31524
-recovered pasa_asmbl_41556.p1, internal, 31872, 31996
-recovered pasa_asmbl_41556.p1, internal, 34730, 34856
Valid prediction for Augustus_model.g6637.t1
Valid prediction for GeneMark_model.16450_t
Valid prediction for GeneMark_model.16480_t
Valid prediction for GeneMark_model.16483_t
Valid prediction for GeneMark_model.16460_t
Valid prediction for GlimmerHMM_glimmerT_10127-T1
Valid prediction for Augustus_model.g6647.t1
Valid prediction for GeneMark_model.16491_t
Valid prediction for Augustus_model.g6643.t1
Valid prediction for snap_scaffold_4-snap.1979-T1
Valid prediction for GlimmerHMM_glimmerT_10137-T1
Valid prediction for snap_scaffold_4-snap.1977-T1
Valid prediction for GeneMark_model.16440_t
Valid prediction for snap_scaffold_4-snap.2006-T1
Valid prediction for GeneMark_model.16457_t
Valid prediction for GeneMark_model.16453_t
Valid prediction for snap_scaffold_4-snap.2014-T1
Valid prediction for GlimmerHMM_glimmerT_10128-T1
Valid prediction for snap_scaffold_4-snap.1991-T1
Valid prediction for GeneMark_model.16478_t
Valid prediction for GeneMark_model.16445_t
Valid prediction for Augustus_model.g6646.t1
Valid prediction for Augustus_model.g6638.t1
Valid prediction for GeneMark_model.16485_t
Valid prediction for GlimmerHMM_glimmerT_10115-T1
Valid prediction for Augustus_model.g6632.t1
Valid prediction for snap_scaffold_4-snap.1975-T1
Valid prediction for snap_scaffold_4-snap.2020-T1
Valid prediction for GeneMark_model.16486_t
Valid prediction for GlimmerHMM_glimmerT_10130-T1
Valid prediction for snap_scaffold_4-snap.2001-T1
Valid prediction for GlimmerHMM_glimmerT_10122-T1
Valid prediction for snap_scaffold_4-snap.2017-T1
Valid prediction for snap_scaffold_4-snap.2018-T1
Valid prediction for GlimmerHMM_glimmerT_10135-T1
Valid prediction for Augustus_model.g6649.t1
Valid prediction for snap_scaffold_4-snap.1999-T1
Valid prediction for Augustus_model.g6636.t1
Valid prediction for GeneMark_model.16474_t
Valid prediction for GlimmerHMM_glimmerT_10132-T1
Valid prediction for GeneMark_model.16482_t
Valid prediction for GeneMark_model.16443_t
Valid prediction for snap_scaffold_4-snap.2003-T1
Valid prediction for snap_scaffold_4-snap.1998-T1
Valid prediction for snap_scaffold_4-snap.2009-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6652, rend_intergenic: 2314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11350, rend_intergenic: 9270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19867, rend_intergenic: 12484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21708, rend_intergenic: 19940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23781, rend_intergenic: 21932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29057, rend_intergenic: 26996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65216, rend_intergenic: 30748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81687, rend_intergenic: 79017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90887, rend_intergenic: 85231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95017, rend_intergenic: 91058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99945, rend_intergenic: 99037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102162, rend_intergenic: 100311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105323, rend_intergenic: 102170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106024, rend_intergenic: 105817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108814, rend_intergenic: 108449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120125, rend_intergenic: 116364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121134, rend_intergenic: 120570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123969, rend_intergenic: 121587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125391, rend_intergenic: 124952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171272, rend_intergenic: 170384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177946
-exon list size: 747


building trellis

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78.6    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.4    
80.5    
80.6    
80.8    
80.9    
81.0    
81.2    
81.3    
81.4    
81.6    
81.7    
81.8    
82.0    
82.1    
82.2    
82.4    
82.5    
82.6    
82.8    
82.9    
83.0    
83.2    
83.3    
83.4    
83.6    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.2    
85.3    
85.4    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.1    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.1    
89.2    
89.3    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.3    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.1    
93.2    
93.3    
93.5    
93.6    
93.7    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.3    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 6652, rend_intergenic: 2314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11350, rend_intergenic: 9270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19867, rend_intergenic: 12484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21708, rend_intergenic: 19940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23781, rend_intergenic: 21932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29057, rend_intergenic: 26996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65216, rend_intergenic: 30748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81687, rend_intergenic: 79017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90887, rend_intergenic: 85231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95017, rend_intergenic: 91058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99945, rend_intergenic: 99037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102162, rend_intergenic: 100311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105323, rend_intergenic: 102170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106024, rend_intergenic: 105817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108814, rend_intergenic: 108449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120125, rend_intergenic: 116364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121134, rend_intergenic: 120570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123969, rend_intergenic: 121587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125391, rend_intergenic: 124952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171272, rend_intergenic: 170384  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