-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_1648925-1835952

-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_19-snap.390-T1
Valid prediction for snap_scaffold_19-snap.386-T1
Valid prediction for GeneMark_model.77806_t
Valid prediction for GeneMark_model.77800_t
Valid prediction for snap_scaffold_19-snap.383-T1
Valid prediction for snap_scaffold_19-snap.362-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.389-T1
Valid prediction for GeneMark_model.77835_t
Valid prediction for snap_scaffold_19-snap.364-T1
Valid prediction for GeneMark_model.77840_t
Valid prediction for snap_scaffold_19-snap.388-T1
Valid prediction for snap_scaffold_19-snap.396-T1
Valid prediction for GlimmerHMM_glimmerT_44663-T1
Valid prediction for GeneMark_model.77795_t
Valid prediction for GeneMark_model.77813_t
Valid prediction for snap_scaffold_19-snap.371-T1
Valid prediction for GlimmerHMM_glimmerT_44673-T1
Valid prediction for GeneMark_model.77826_t
Valid prediction for GlimmerHMM_glimmerT_44669-T1
Valid prediction for GeneMark_model.77802_t
Valid prediction for GeneMark_model.77831_t
Valid prediction for GeneMark_model.77791_t
Valid prediction for GeneMark_model.77836_t
Valid prediction for GeneMark_model.77819_t
Valid prediction for snap_scaffold_19-snap.391-T1
Valid prediction for GlimmerHMM_glimmerT_44667-T1
Valid prediction for snap_scaffold_19-snap.367-T1
Valid prediction for GeneMark_model.77797_t
Valid prediction for GlimmerHMM_glimmerT_44675-T1
Valid prediction for GlimmerHMM_glimmerT_44676-T1
Valid prediction for GeneMark_model.77829_t
Valid prediction for GeneMark_model.77817_t
Valid prediction for snap_scaffold_19-snap.381-T1
Valid prediction for GlimmerHMM_glimmerT_44664-T1
Valid prediction for GeneMark_model.77818_t
Valid prediction for GeneMark_model.77808_t
Valid prediction for Augustus_model.g29820.t1
Valid prediction for snap_scaffold_19-snap.370-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.77789_t
Valid prediction for snap_scaffold_19-snap.365-T1
Valid prediction for GeneMark_model.77834_t
Valid prediction for GeneMark_model.77811_t
Valid prediction for snap_scaffold_19-snap.375-T1
Valid prediction for GeneMark_model.77822_t
Valid prediction for Augustus_model.g29824.t1
Valid prediction for GeneMark_model.77815_t
Valid prediction for GeneMark_model.77804_t
Valid prediction for GlimmerHMM_glimmerT_44671-T1
Valid prediction for snap_scaffold_19-snap.366-T1
Valid prediction for snap_scaffold_19-snap.373-T1
Valid prediction for GeneMark_model.77799_t
Valid prediction for snap_scaffold_19-snap.382-T1
Valid prediction for GeneMark_model.77793_t
Couldn't classify 40912, 41700
Sorry, prediction pasa_asmbl_22054.p1 fails validation.
(ACA)	 AC	40912-41700	AG	AGA
Valid prediction for snap_scaffold_19-snap.385-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_19-snap.384-T1
Valid prediction for GeneMark_model.77823_t
Valid prediction for GeneMark_model.77805_t
Valid prediction for snap_scaffold_19-snap.377-T1
Valid prediction for snap_scaffold_19-snap.378-T1
Valid prediction for GeneMark_model.77788_t
Valid prediction for CodingQuarry_transcript_25545-T1
Valid prediction for snap_scaffold_19-snap.394-T1
Valid prediction for snap_scaffold_19-snap.387-T1
Valid prediction for GeneMark_model.77830_t
Valid prediction for GeneMark_model.77832_t
Valid prediction for CodingQuarry_transcript_25543-T1
Valid prediction for GeneMark_model.77814_t
Valid prediction for GlimmerHMM_glimmerT_44662-T1
Couldn't classify 182137, 182320
Sorry, prediction pasa_asmbl_21939.p2 fails validation.
(TCG)	 TT	182137-182320	GT	AGG
(TGG)	 AG	182642-182787	GT	ATG
(GTG)	 AG	183260-183289	AC	GAA
-recovered pasa_asmbl_21939.p2, terminal, 183260, 183289
-recovered pasa_asmbl_21939.p2, internal, 182642, 182787
Couldn't classify 158171, 158205
Couldn't classify 160954, 161081
Sorry, prediction pasa_asmbl_21246.p2 fails validation.
(CAG)	 AA	158171-158205	GT	AGG
(CCA)	 AG	158320-158333	GT	CGG
(ATG)	 AG	158457-158528	GT	GGG
(GTG)	 AG	159471-159593	GT	AGG
(ACC)	 AG	160190-160283	GT	AAG
(GAA)	 AG	160455-160612	GT	CAG
(AGC)	 AG	160954-161081	TA	GGT
add_exon() Sorry, pasa_asmbl_21246.p2 158457-158528-initial-1 is invalid.
-recovered pasa_asmbl_21246.p2, initial, 158457, 158528
add_exon() Sorry, pasa_asmbl_21246.p2 159471-159593-terminal-1 is invalid.
-recovered pasa_asmbl_21246.p2, terminal, 159471, 159593
-recovered pasa_asmbl_21246.p2, internal, 158320, 158333
-recovered pasa_asmbl_21246.p2, internal, 158457, 158528
-recovered pasa_asmbl_21246.p2, internal, 159471, 159593
-recovered pasa_asmbl_21246.p2, internal, 160190, 160283
-recovered pasa_asmbl_21246.p2, internal, 160455, 160612
Valid prediction for GeneMark_model.77794_t
Valid prediction for GlimmerHMM_glimmerT_44678-T1
Valid prediction for GlimmerHMM_glimmerT_44674-T1
Couldn't classify 95001, 95019
Couldn't classify 100065, 100501
Sorry, prediction pasa_asmbl_21250.p1 fails validation.
(CAG)	 TG	95001-95019	GT	AGG
(TTG)	 AG	97421-97614	GT	AGG
(AGC)	 AG	98844-98969	GT	TAG
(ACG)	 AG	99087-99264	GT	AGG
(ATT)	 AG	99723-99908	GT	GTG
(ATC)	 AG	100065-100501	CC	TCC
-recovered pasa_asmbl_21250.p1, internal, 97421, 97614
-recovered pasa_asmbl_21250.p1, internal, 98844, 98969
-recovered pasa_asmbl_21250.p1, internal, 99087, 99264
-recovered pasa_asmbl_21250.p1, internal, 99723, 99908
Valid prediction for GeneMark_model.77839_t
Valid prediction for snap_scaffold_19-snap.372-T1
Valid prediction for GeneMark_model.77798_t
Valid prediction for GeneMark_model.77838_t
Valid prediction for GeneMark_model.77810_t
Valid prediction for HiQ_model.g29818.t1
Valid prediction for GeneMark_model.77790_t
Valid prediction for CodingQuarry_transcript_25542-T1
Valid prediction for Augustus_model.g29823.t1
Valid prediction for GlimmerHMM_glimmerT_44668-T1
Valid prediction for snap_scaffold_19-snap.380-T1
Valid prediction for GeneMark_model.77807_t
Valid prediction for snap_scaffold_19-snap.369-T1
Valid prediction for GlimmerHMM_glimmerT_44677-T1
Valid prediction for GlimmerHMM_glimmerT_44665-T1
Valid prediction for snap_scaffold_19-snap.376-T1
Valid prediction for GeneMark_model.77821_t
Valid prediction for GlimmerHMM_glimmerT_44666-T1
Valid prediction for GeneMark_model.77812_t
Couldn't classify 174944, 174977
Sorry, prediction pasa_asmbl_21244.p2 fails validation.
(ATG)	 AA	169709-169825	GT	AGG
(TCT)	 AG	172151-172318	GT	AGG
(ACG)	 AG	172570-172746	GT	AGG
(GCC)	 AG	173715-173815	GT	GGG
(GAG)	 AG	174944-174977	CG	TCC
-recovered pasa_asmbl_21244.p2, initial, 169709, 169825
-recovered pasa_asmbl_21244.p2, internal, 172151, 172318
-recovered pasa_asmbl_21244.p2, internal, 172570, 172746
-recovered pasa_asmbl_21244.p2, internal, 173715, 173815
Valid prediction for GeneMark_model.77827_t
Valid prediction for GeneMark_model.77803_t
Valid prediction for GeneMark_model.77841_t
Valid prediction for GeneMark_model.77801_t
Valid prediction for GeneMark_model.77825_t
Valid prediction for GeneMark_model.77796_t
Valid prediction for GeneMark_model.77820_t
Valid prediction for snap_scaffold_19-snap.363-T1
Valid prediction for Augustus_model.g29821.t1
Valid prediction for GeneMark_model.77809_t
Couldn't classify 139581, 139687
Couldn't classify 140233, 140339
Couldn't classify 141303, 141426
Couldn't classify 142407, 142581
Sorry, prediction CodingQuarry_transcript_25544-T1 fails validation.
(ATG)	 AG	133510-133682	GT	AGG
(GAG)	 AG	134175-134238	GT	AGG
(AAG)	 AG	135059-135169	GT	AGG
(AAA)	 AG	137302-137362	GT	TCG
(ACT)	 AG	138195-138319	GT	AGG
(GTC)	 AG	139130-139197	GT	GAG
(CGT)	 AG	139581-139687	GG	GAG
(TCA)	 GA	140233-140339	GT	AGG
(GAC)	 AG	141303-141426	AT	GAA
(CCC)	 AC	142407-142581	GT	AGG
(TGT)	 AG	142813-142921	GT	AGG
(GCG)	 AG	143028-143111	AG	GAA
-recovered CodingQuarry_transcript_25544-T1, initial, 133510, 133682
add_exon() Sorry, CodingQuarry_transcript_25544-T1 139581-139687-terminal-2 is invalid.
-recovered CodingQuarry_transcript_25544-T1, terminal, 139581, 139687
-recovered CodingQuarry_transcript_25544-T1, terminal, 143028, 143111
-recovered CodingQuarry_transcript_25544-T1, internal, 133510, 133682
-recovered CodingQuarry_transcript_25544-T1, internal, 134175, 134238
-recovered CodingQuarry_transcript_25544-T1, internal, 135059, 135169
-recovered CodingQuarry_transcript_25544-T1, internal, 137302, 137362
-recovered CodingQuarry_transcript_25544-T1, internal, 138195, 138319
-recovered CodingQuarry_transcript_25544-T1, internal, 139130, 139197
-recovered CodingQuarry_transcript_25544-T1, internal, 142813, 142921
Valid prediction for snap_scaffold_19-snap.393-T1
Valid prediction for GeneMark_model.77837_t
Valid prediction for Augustus_model.g29822.t1
Valid prediction for GlimmerHMM_glimmerT_44661-T1
Valid prediction for Augustus_model.g29819.t1
Valid prediction for Augustus_model.g29817.t1
Valid prediction for GeneMark_model.77792_t
Valid prediction for snap_scaffold_19-snap.374-T1
Valid prediction for snap_scaffold_19-snap.395-T1
Valid prediction for GlimmerHMM_glimmerT_44670-T1
Valid prediction for GlimmerHMM_glimmerT_44672-T1
Valid prediction for snap_scaffold_19-snap.379-T1
Valid prediction for GeneMark_model.77824_t
Valid prediction for GeneMark_model.77828_t
Valid prediction for snap_scaffold_19-snap.397-T1
Valid prediction for GeneMark_model.77816_t
Valid prediction for snap_scaffold_19-snap.368-T1
Valid prediction for snap_scaffold_19-snap.392-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4926, rend_intergenic: 4212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15306, rend_intergenic: 5204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28875, rend_intergenic: 23213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42390, rend_intergenic: 38834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43891, rend_intergenic: 42720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47682, rend_intergenic: 43918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50383, rend_intergenic: 47807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74694, rend_intergenic: 50390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92031, rend_intergenic: 76852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116610, rend_intergenic: 101520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128743, rend_intergenic: 116785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132454, rend_intergenic: 129907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145550, rend_intergenic: 132508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173625, rend_intergenic: 151376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178820, rend_intergenic: 173813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179760, rend_intergenic: 179186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 187028
-exon list size: 702


building trellis

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80.0    
80.1    
80.3    
80.4    
80.5    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.2    
82.4    
82.5    
82.7    
82.8    
83.0    
83.1    
83.2    
83.4    
83.5    
83.7    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.6    
87.8    
87.9    
88.1    
88.2    
88.4    
88.5    
88.6    
88.8    
88.9    
89.1    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.1    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 4926, rend_intergenic: 4212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15306, rend_intergenic: 5204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28875, rend_intergenic: 23213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42390, rend_intergenic: 38834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43891, rend_intergenic: 42720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47682, rend_intergenic: 43918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50383, rend_intergenic: 47807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74694, rend_intergenic: 50390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92031, rend_intergenic: 76852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116610, rend_intergenic: 101520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128743, rend_intergenic: 116785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132454, rend_intergenic: 129907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145550, rend_intergenic: 132508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173625, rend_intergenic: 151376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178820, rend_intergenic: 173813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179760, rend_intergenic: 179186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support