-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_8854568-9041728

-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.26208_t
Valid prediction for snap_scaffold_6-snap.1970-T1
Valid prediction for pasa_asmbl_47122.p1
Valid prediction for GlimmerHMM_glimmerT_15543-T1
Valid prediction for pasa_asmbl_47121.p1
Valid prediction for HiQ_model.g10368.t1
Valid prediction for CodingQuarry_transcript_55008-T1
Valid prediction for GeneMark_model.26217_t
Valid prediction for Augustus_model.g10388.t1
Valid prediction for GeneMark_model.26207_t
Valid prediction for snap_scaffold_6-snap.1990-T1
Valid prediction for snap_scaffold_6-snap.1982-T1
Valid prediction for Augustus_model.g10387.t1
Valid prediction for GeneMark_model.26212_t
Valid prediction for snap_scaffold_6-snap.1985-T1
Valid prediction for Augustus_model.g10391.t1
Valid prediction for GeneMark_model.26193_t
Valid prediction for Augustus_model.g10384.t1
Valid prediction for snap_scaffold_6-snap.1999-T1
Valid prediction for GeneMark_model.26196_t
Valid prediction for GlimmerHMM_glimmerT_15562-T1
Valid prediction for snap_scaffold_6-snap.1983-T1
Valid prediction for snap_scaffold_6-snap.2005-T1
Valid prediction for Augustus_model.g10386.t1
Valid prediction for pasa_asmbl_47950.p1
Valid prediction for HiQ_model.g10389.t1
Valid prediction for GlimmerHMM_glimmerT_15546-T1
Valid prediction for Augustus_model.g10381.t1
Valid prediction for HiQ_model.g10369.t1
Valid prediction for GeneMark_model.26192_t
Valid prediction for GlimmerHMM_glimmerT_15542-T1
Valid prediction for GlimmerHMM_glimmerT_15570-T1
Valid prediction for snap_scaffold_6-snap.1984-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_55004-T1
Valid prediction for snap_scaffold_6-snap.1989-T1
Valid prediction for GlimmerHMM_glimmerT_15571-T1
Valid prediction for GeneMark_model.26200_t
Valid prediction for GeneMark_model.26214_t
Valid prediction for GeneMark_model.26224_t
Valid prediction for snap_scaffold_6-snap.1981-T1
Valid prediction for GlimmerHMM_glimmerT_15550-T1
Valid prediction for GlimmerHMM_glimmerT_15555-T1
Valid prediction for snap_scaffold_6-snap.2002-T1
Valid prediction for snap_scaffold_6-snap.1986-T1
Valid prediction for Augustus_model.g10385.t1
Valid prediction for snap_scaffold_6-snap.2000-T1
Valid prediction for CodingQuarry_transcript_55009-T1
Valid prediction for Augustus_model.g10382.t1
Valid prediction for Augustus_model.g10378.t1
Valid prediction for GlimmerHMM_glimmerT_15554-T1
Valid prediction for GlimmerHMM_glimmerT_15551-T1
Valid prediction for GeneMark_model.26186_t
Couldn't classify 19957, 20015
Sorry, prediction pasa_asmbl_47113.p1 fails validation.
(TTC)	 CT	19957-20015	GT	GAG
(TTC)	 AG	20104-20150	GT	AGG
(GTA)	 AG	20693-20781	GT	AGG
(ATT)	 AG	20948-21007	GT	AGG
(AAC)	 AG	21136-21240	GT	AGG
(GAC)	 AG	21377-21578	GT	CGG
(CGG)	 AG	21690-21800	GT	AGG
(CTG)	 AG	22033-22169	GT	AAG
(GGT)	 AG	22256-22362	GT	AAG
(ACC)	 AG	22454-22469	GA	GAG
-recovered pasa_asmbl_47113.p1, terminal, 22454, 22469
-recovered pasa_asmbl_47113.p1, internal, 20104, 20150
-recovered pasa_asmbl_47113.p1, internal, 20693, 20781
-recovered pasa_asmbl_47113.p1, internal, 20948, 21007
-recovered pasa_asmbl_47113.p1, internal, 21136, 21240
-recovered pasa_asmbl_47113.p1, internal, 21377, 21578
-recovered pasa_asmbl_47113.p1, internal, 21690, 21800
-recovered pasa_asmbl_47113.p1, internal, 22033, 22169
-recovered pasa_asmbl_47113.p1, internal, 22256, 22362
Valid prediction for HiQ_model.g10380.t1
Valid prediction for pasa_asmbl_47117.p2
Valid prediction for GeneMark_model.26203_t
Valid prediction for GeneMark_model.26201_t
Valid prediction for GeneMark_model.26210_t
Valid prediction for snap_scaffold_6-snap.1973-T1
Valid prediction for GlimmerHMM_glimmerT_15569-T1
Valid prediction for snap_scaffold_6-snap.1995-T1
Valid prediction for GlimmerHMM_glimmerT_15566-T1
Valid prediction for CodingQuarry_transcript_55007-T1
Valid prediction for GlimmerHMM_glimmerT_15559-T1
Valid prediction for pasa_asmbl_47123.p1
Couldn't classify 89343, 89391
Sorry, prediction pasa_asmbl_47120.p1 fails validation.
(CAA)	 CG	89343-89391	GT	TTG
(ACA)	 AG	89480-89731	GT	TGG
(GTA)	 AG	89817-89824	TG	AAT
-recovered pasa_asmbl_47120.p1, terminal, 89817, 89824
-recovered pasa_asmbl_47120.p1, internal, 89480, 89731
Valid prediction for snap_scaffold_6-snap.1968-T1
Valid prediction for snap_scaffold_6-snap.1969-T1
Valid prediction for HiQ_model.g10379.t1
Valid prediction for GlimmerHMM_glimmerT_15563-T1
Valid prediction for GeneMark_model.26202_t
Valid prediction for pasa_asmbl_47119.p1
Valid prediction for snap_scaffold_6-snap.1988-T1
Valid prediction for GeneMark_model.26216_t
Valid prediction for GlimmerHMM_glimmerT_15560-T1
Valid prediction for GlimmerHMM_glimmerT_15561-T1
Valid prediction for GlimmerHMM_glimmerT_15541-T1
Valid prediction for GlimmerHMM_glimmerT_15558-T1
Valid prediction for snap_scaffold_6-snap.1997-T1
Valid prediction for CodingQuarry_transcript_55006-T1
Valid prediction for GlimmerHMM_glimmerT_15556-T1
Valid prediction for GeneMark_model.26220_t
Valid prediction for GlimmerHMM_glimmerT_15565-T1
Valid prediction for GlimmerHMM_glimmerT_15547-T1
Valid prediction for GeneMark_model.26205_t
Valid prediction for GlimmerHMM_glimmerT_15564-T1
Valid prediction for Augustus_model.g10372.t1
Valid prediction for HiQ_model.g10377.t1
Valid prediction for GeneMark_model.26218_t
Valid prediction for pasa_asmbl_47128.p1
Valid prediction for snap_scaffold_6-snap.1993-T1
Valid prediction for GlimmerHMM_glimmerT_15567-T1
Valid prediction for Augustus_model.g10375.t1
Valid prediction for GlimmerHMM_glimmerT_15573-T1
Valid prediction for GlimmerHMM_glimmerT_15557-T1
Valid prediction for GeneMark_model.26198_t
Valid prediction for snap_scaffold_6-snap.1987-T1
Valid prediction for Augustus_model.g10376.t1
Valid prediction for GeneMark_model.26187_t
Valid prediction for snap_scaffold_6-snap.1996-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.26184_t
Valid prediction for GeneMark_model.26211_t
Valid prediction for GeneMark_model.26222_t
Valid prediction for GeneMark_model.26197_t
Valid prediction for snap_scaffold_6-snap.1991-T1
Valid prediction for Augustus_model.g10367.t1
Valid prediction for GlimmerHMM_glimmerT_15544-T1
Valid prediction for GeneMark_model.26190_t
Couldn't classify 120163, 120477
Sorry, prediction pasa_asmbl_48535.p1 fails validation.
(ATG)	 AG	120163-120477	GA	AGG
Valid prediction for GeneMark_model.26195_t
Valid prediction for GeneMark_model.26209_t
Valid prediction for snap_scaffold_6-snap.1977-T1
Valid prediction for GeneMark_model.26199_t
Valid prediction for GeneMark_model.26191_t
Valid prediction for snap_scaffold_6-snap.1994-T1
Valid prediction for Augustus_model.g10371.t1
Valid prediction for Augustus_model.g10373.t1
Valid prediction for snap_scaffold_6-snap.1974-T1
Valid prediction for GeneMark_model.26223_t
Valid prediction for snap_scaffold_6-snap.1992-T1
Valid prediction for Augustus_model.g10374.t1
Valid prediction for snap_scaffold_6-snap.1975-T1
Valid prediction for GeneMark_model.26221_t
Valid prediction for GlimmerHMM_glimmerT_15553-T1
Valid prediction for GeneMark_model.26215_t
Valid prediction for GlimmerHMM_glimmerT_15540-T1
Valid prediction for GlimmerHMM_glimmerT_15572-T1
Valid prediction for snap_scaffold_6-snap.1966-T1
Couldn't classify 157015, 157029
Sorry, prediction pasa_asmbl_48529.p1 fails validation.
(CTC)	 TC	157015-157029	GT	AGG
(ACG)	 AG	157135-157322	GT	AGG
(GAG)	 AG	158104-158287	GT	AGG
(GTT)	 AG	158437-158534	GT	AGG
(ATG)	 AG	158759-158912	GT	AGG
(GCT)	 AG	159037-159149	GT	AGG
(GAT)	 AG	159237-159438	GT	AGG
(GGT)	 AG	159521-159654	GT	AGG
(GTT)	 AG	159753-159932	GT	GGG
(GGT)	 AG	160072-160296	GT	AGG
(ACC)	 AG	160417-160609	GT	AGG
(GCG)	 AG	160709-160799	GT	AGG
(GTA)	 AG	160914-161048	GT	TGG
(GGA)	 AG	161193-161475	GT	AGG
(TTA)	 AG	161583-161724	GT	AGG
(GCT)	 AG	161829-161995	GT	CGG
(GGG)	 AG	162085-162262	GT	AGG
(GAC)	 AG	162348-162543	GT	AGG
(GTA)	 AG	162633-162796	GT	AGG
(GGG)	 AG	163012-163128	GT	AGG
(GTT)	 AG	163227-163320	GT	AGG
(AAA)	 AG	163400-163452	CA	AGC
add_exon() Sorry, pasa_asmbl_48529.p1 158759-158912-initial-1 is invalid.
-recovered pasa_asmbl_48529.p1, initial, 158759, 158912
-recovered pasa_asmbl_48529.p1, terminal, 163400, 163452
-recovered pasa_asmbl_48529.p1, internal, 157135, 157322
-recovered pasa_asmbl_48529.p1, internal, 158104, 158287
-recovered pasa_asmbl_48529.p1, internal, 158437, 158534
-recovered pasa_asmbl_48529.p1, internal, 158759, 158912
-recovered pasa_asmbl_48529.p1, internal, 159037, 159149
-recovered pasa_asmbl_48529.p1, internal, 159237, 159438
-recovered pasa_asmbl_48529.p1, internal, 159521, 159654
-recovered pasa_asmbl_48529.p1, internal, 159753, 159932
-recovered pasa_asmbl_48529.p1, internal, 160072, 160296
-recovered pasa_asmbl_48529.p1, internal, 160417, 160609
-recovered pasa_asmbl_48529.p1, internal, 160709, 160799
-recovered pasa_asmbl_48529.p1, internal, 160914, 161048
-recovered pasa_asmbl_48529.p1, internal, 161193, 161475
-recovered pasa_asmbl_48529.p1, internal, 161583, 161724
-recovered pasa_asmbl_48529.p1, internal, 161829, 161995
-recovered pasa_asmbl_48529.p1, internal, 162085, 162262
-recovered pasa_asmbl_48529.p1, internal, 162348, 162543
-recovered pasa_asmbl_48529.p1, internal, 162633, 162796
-recovered pasa_asmbl_48529.p1, internal, 163012, 163128
-recovered pasa_asmbl_48529.p1, internal, 163227, 163320
Valid prediction for snap_scaffold_6-snap.1978-T1
Valid prediction for Augustus_model.g10370.t1
Valid prediction for snap_scaffold_6-snap.1976-T1
Valid prediction for Augustus_model.g10390.t1
Valid prediction for snap_scaffold_6-snap.1998-T1
Valid prediction for snap_scaffold_6-snap.1972-T1
Valid prediction for GlimmerHMM_glimmerT_15548-T1
Valid prediction for Augustus_model.g10383.t1
Valid prediction for snap_scaffold_6-snap.2003-T1
Valid prediction for GeneMark_model.26204_t
Valid prediction for Augustus_model.g10366.t1
Valid prediction for snap_scaffold_6-snap.2001-T1
Valid prediction for GeneMark_model.26185_t
Valid prediction for GeneMark_model.26188_t
Valid prediction for snap_scaffold_6-snap.2004-T1
Valid prediction for GeneMark_model.26219_t
Valid prediction for GeneMark_model.26194_t
Couldn't classify 180445, 180640
Couldn't classify 181427, 181644
Sorry, prediction pasa_asmbl_48528.p1 fails validation.
(AAC)	 GG	180445-180640	GT	ATG
(ACG)	 AG	181015-181242	GT	GCG
(ACG)	 AG	181427-181644	AC	CCA
-recovered pasa_asmbl_48528.p1, internal, 181015, 181242
Valid prediction for snap_scaffold_6-snap.1967-T1
Couldn't classify 162662, 162796
Sorry, prediction pasa_asmbl_48530.p1 fails validation.
(TTC)	 AG	162662-162796	GT	AGG
(GGG)	 AG	163012-163128	GT	AGG
(GTT)	 AG	163227-163331	CG	GAC
-recovered pasa_asmbl_48530.p1, terminal, 163227, 163331
-recovered pasa_asmbl_48530.p1, internal, 162662, 162796
-recovered pasa_asmbl_48530.p1, internal, 163012, 163128
Valid prediction for snap_scaffold_6-snap.1980-T1
Valid prediction for GlimmerHMM_glimmerT_15568-T1
Valid prediction for snap_scaffold_6-snap.1979-T1
Valid prediction for GlimmerHMM_glimmerT_15545-T1
Couldn't classify 154834, 155062
Couldn't classify 155369, 155441
Sorry, prediction pasa_asmbl_48532.p1 fails validation.
(AAA)	 CT	154834-155062	GT	GAG
(AAT)	 AG	155173-155248	GT	GTG
(TCA)	 AG	155369-155441	GA	AGG
-recovered pasa_asmbl_48532.p1, internal, 155173, 155248
Valid prediction for snap_scaffold_6-snap.1971-T1
Valid prediction for GeneMark_model.26213_t
Valid prediction for GlimmerHMM_glimmerT_15552-T1
Valid prediction for GlimmerHMM_glimmerT_15549-T1
Valid prediction for GeneMark_model.26206_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 42248, rend_intergenic: 38135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132185, rend_intergenic: 130541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136606, rend_intergenic: 135834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148647, rend_intergenic: 146160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167541, rend_intergenic: 165248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170496, rend_intergenic: 168425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 187161
-exon list size: 655


building trellis

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72.3    
72.5    
72.6    
72.8    
72.9    
73.1    
73.2    
73.4    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.2    
75.3    
75.5    
75.6    
75.8    
76.0    
76.1    
76.3    
76.4    
76.6    
76.7    
76.9    
77.0    
77.2    
77.3    
77.5    
77.6    
77.8    
77.9    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
79.0    
79.1    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
80.7    
80.8    
81.0    
81.1    
81.3    
81.4    
81.6    
81.7    
81.9    
82.0    
82.2    
82.3    
82.5    
82.6    
82.8    
83.0    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 42248, rend_intergenic: 38135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132185, rend_intergenic: 130541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136606, rend_intergenic: 135834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148647, rend_intergenic: 146160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167541, rend_intergenic: 165248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170496, rend_intergenic: 168425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support