-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_15848596-16039357

-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_5-snap.2976-T1
Valid prediction for Augustus_model.g9099.t1
Valid prediction for GlimmerHMM_glimmerT_13597-T1
Valid prediction for snap_scaffold_5-snap.2964-T1
Valid prediction for GeneMark_model.22808_t
Valid prediction for snap_scaffold_5-snap.2947-T1
Valid prediction for GlimmerHMM_glimmerT_13599-T1
Valid prediction for GeneMark_model.22845_t
Valid prediction for GeneMark_model.22801_t
Valid prediction for Augustus_model.g9096.t1
Valid prediction for GlimmerHMM_glimmerT_13603-T1
Valid prediction for GlimmerHMM_glimmerT_13593-T1
Valid prediction for GlimmerHMM_glimmerT_13592-T1
Valid prediction for GlimmerHMM_glimmerT_13598-T1
Valid prediction for snap_scaffold_5-snap.2967-T1
Couldn't classify 174321, 175314
Couldn't classify 175375, 175658
Sorry, prediction CodingQuarry_transcript_52275-T1 fails validation.
(ATG)	 CC	171755-171824	GT	AGG
(CAC)	 AG	174321-175314	CT	GCC
(CCC)	 AC	175375-175658	GT	GGG
(GAT)	 AG	176435-176520	GT	AGG
(CTT)	 AG	176616-176693	GC	AGG
(GCC)	 AG	176806-176952	GT	AGG
(ATT)	 AG	177104-177232	GT	AGG
(GTG)	 AG	177397-177519	GT	TGG
(GAG)	 AG	177625-177639	AC	AGA
-recovered CodingQuarry_transcript_52275-T1, initial, 171755, 171824
-recovered CodingQuarry_transcript_52275-T1, terminal, 177625, 177639
-recovered CodingQuarry_transcript_52275-T1, internal, 176435, 176520
-recovered CodingQuarry_transcript_52275-T1, internal, 176616, 176693
-recovered CodingQuarry_transcript_52275-T1, internal, 176806, 176952
-recovered CodingQuarry_transcript_52275-T1, internal, 177104, 177232
-recovered CodingQuarry_transcript_52275-T1, internal, 177397, 177519
Valid prediction for GeneMark_model.22810_t
Valid prediction for Augustus_model.g9094.t1
Valid prediction for GeneMark_model.22815_t
Valid prediction for Augustus_model.g9085.t1
Valid prediction for pasa_asmbl_44691.p1
Valid prediction for GeneMark_model.22844_t
Valid prediction for Augustus_model.g9097.t1
Valid prediction for Augustus_model.g9101.t1
Valid prediction for snap_scaffold_5-snap.2977-T1
Valid prediction for Augustus_model.g9084.t1
Valid prediction for GeneMark_model.22829_t
Couldn't classify 88050, 88155
Sorry, prediction pasa_asmbl_44693.p3 fails validation.
(ATG)	 AG	86159-86349	GT	AAG
(ACC)	 AG	88050-88155	GT	TGG
-recovered pasa_asmbl_44693.p3, initial, 86159, 86349
-recovered pasa_asmbl_44693.p3, internal, 86159, 86349
-recovered pasa_asmbl_44693.p3, internal, 88050, 88155
Valid prediction for GeneMark_model.22834_t
Valid prediction for Augustus_model.g9098.t1
Valid prediction for GlimmerHMM_glimmerT_13595-T1
Valid prediction for GeneMark_model.22823_t
Valid prediction for GeneMark_model.22847_t
Valid prediction for snap_scaffold_5-snap.2982-T1
Valid prediction for snap_scaffold_5-snap.2971-T1
Valid prediction for GlimmerHMM_glimmerT_13602-T1
Valid prediction for GlimmerHMM_glimmerT_13600-T1
Valid prediction for GlimmerHMM_glimmerT_13583-T1
Valid prediction for snap_scaffold_5-snap.2974-T1
Valid prediction for Augustus_model.g9100.t1
Valid prediction for GlimmerHMM_glimmerT_13594-T1
Valid prediction for GlimmerHMM_glimmerT_13582-T1
Valid prediction for GeneMark_model.22832_t
Valid prediction for GlimmerHMM_glimmerT_13604-T1
Valid prediction for GlimmerHMM_glimmerT_13610-T1
Valid prediction for snap_scaffold_5-snap.2951-T1
Valid prediction for GeneMark_model.22840_t
Valid prediction for snap_scaffold_5-snap.2948-T1
Valid prediction for snap_scaffold_5-snap.2958-T1
Valid prediction for HiQ_model.g9095.t1
Valid prediction for HiQ_model.g9087.t1
Valid prediction for snap_scaffold_5-snap.2963-T1
Valid prediction for snap_scaffold_5-snap.2945-T1
Valid prediction for GeneMark_model.22821_t
Valid prediction for GlimmerHMM_glimmerT_13585-T1
Valid prediction for GlimmerHMM_glimmerT_13596-T1
Valid prediction for snap_scaffold_5-snap.2956-T1
Valid prediction for snap_scaffold_5-snap.2950-T1
Valid prediction for GeneMark_model.22825_t
Valid prediction for HiQ_model.g9093.t1
Valid prediction for Augustus_model.g9104.t1
Couldn't classify 44940, 44984
Sorry, prediction pasa_asmbl_44687.p1 fails validation.
(CCT)	 TT	44940-44984	GT	TGG
(TCT)	 AG	45468-45495	GT	TGG
(AGT)	 AG	47500-47643	GT	GGG
(AGA)	 AG	48495-48668	GT	AGG
(GGG)	 AG	49011-49088	GT	AGG
(AAC)	 AG	50463-50491	AG	GAA
add_exon() Sorry, pasa_asmbl_44687.p1 48495-48668-terminal-1 is invalid.
-recovered pasa_asmbl_44687.p1, terminal, 48495, 48668
-recovered pasa_asmbl_44687.p1, terminal, 50463, 50491
-recovered pasa_asmbl_44687.p1, internal, 45468, 45495
-recovered pasa_asmbl_44687.p1, internal, 47500, 47643
-recovered pasa_asmbl_44687.p1, internal, 48495, 48668
-recovered pasa_asmbl_44687.p1, internal, 49011, 49088
Valid prediction for GeneMark_model.22842_t
Valid prediction for GlimmerHMM_glimmerT_13609-T1
Valid prediction for snap_scaffold_5-snap.2975-T1
Valid prediction for GlimmerHMM_glimmerT_13605-T1
Valid prediction for GlimmerHMM_glimmerT_13606-T1
Valid prediction for GeneMark_model.22798_t
Valid prediction for CodingQuarry_transcript_52274-T1
Valid prediction for GeneMark_model.22819_t
Valid prediction for GeneMark_model.22835_t
Couldn't classify 26807, 26902
Sorry, prediction pasa_asmbl_45055.p1 fails validation.
(ATG)	 AG	26042-26151	GT	CTG
(GTC)	 AG	26584-26701	GT	TAG
(AGG)	 AG	26807-26902	GG	AGG
-recovered pasa_asmbl_45055.p1, initial, 26042, 26151
-recovered pasa_asmbl_45055.p1, internal, 26042, 26151
-recovered pasa_asmbl_45055.p1, internal, 26584, 26701
Valid prediction for GeneMark_model.22803_t
Valid prediction for snap_scaffold_5-snap.2970-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.2953-T1
Valid prediction for Augustus_model.g9089.t1
Valid prediction for snap_scaffold_5-snap.2965-T1
Valid prediction for GlimmerHMM_glimmerT_13586-T1
Valid prediction for pasa_asmbl_44694.p1
Valid prediction for GeneMark_model.22817_t
Valid prediction for GlimmerHMM_glimmerT_13580-T1
Valid prediction for GlimmerHMM_glimmerT_13578-T1
Valid prediction for snap_scaffold_5-snap.2960-T1
Valid prediction for pasa_asmbl_44695.p1
Valid prediction for GeneMark_model.22826_t
Valid prediction for snap_scaffold_5-snap.2979-T1
Valid prediction for GeneMark_model.22839_t

-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.22838_t
Valid prediction for GlimmerHMM_glimmerT_13587-T1
Valid prediction for GeneMark_model.22848_t
Valid prediction for GlimmerHMM_glimmerT_13601-T1
Valid prediction for snap_scaffold_5-snap.2966-T1
Valid prediction for GeneMark_model.22841_t
Valid prediction for GeneMark_model.22796_t
Valid prediction for snap_scaffold_5-snap.2981-T1
Valid prediction for snap_scaffold_5-snap.2955-T1
Valid prediction for GeneMark_model.22818_t
Valid prediction for GlimmerHMM_glimmerT_13591-T1
Valid prediction for snap_scaffold_5-snap.2972-T1
Valid prediction for GeneMark_model.22805_t
Valid prediction for GeneMark_model.22804_t
Valid prediction for GeneMark_model.22824_t
Valid prediction for Augustus_model.g9103.t1
Valid prediction for Augustus_model.g9090.t1
Valid prediction for GeneMark_model.22816_t
Valid prediction for snap_scaffold_5-snap.2978-T1
Valid prediction for GeneMark_model.22797_t
Valid prediction for snap_scaffold_5-snap.2946-T1
Valid prediction for Augustus_model.g9088.t1
Valid prediction for snap_scaffold_5-snap.2983-T1
Valid prediction for GlimmerHMM_glimmerT_13581-T1
Valid prediction for GlimmerHMM_glimmerT_13588-T1
Valid prediction for snap_scaffold_5-snap.2949-T1
Valid prediction for snap_scaffold_5-snap.2973-T1
Valid prediction for GeneMark_model.22820_t
Valid prediction for GeneMark_model.22831_t
Valid prediction for GeneMark_model.22814_t
Valid prediction for Augustus_model.g9102.t1
Valid prediction for Augustus_model.g9092.t1
Couldn't classify 22597, 22959
Couldn't classify 23112, 23225
Sorry, prediction pasa_asmbl_46117.p1 fails validation.
(GAC)	 AG	22597-22959	GT	CGG
(CCG)	 AG	23112-23225	CG	AGC
-recovered pasa_asmbl_46117.p1, internal, 22597, 22959
Valid prediction for snap_scaffold_5-snap.2962-T1
Valid prediction for snap_scaffold_5-snap.2944-T1
Valid prediction for GlimmerHMM_glimmerT_13608-T1
Valid prediction for GeneMark_model.22811_t
Valid prediction for GeneMark_model.22843_t
Valid prediction for Augustus_model.g9086.t1
Valid prediction for GeneMark_model.22833_t
Valid prediction for GeneMark_model.22837_t
Valid prediction for GeneMark_model.22846_t
Valid prediction for GeneMark_model.22822_t
Valid prediction for snap_scaffold_5-snap.2969-T1
Valid prediction for GlimmerHMM_glimmerT_13590-T1
Valid prediction for GeneMark_model.22813_t
Valid prediction for snap_scaffold_5-snap.2980-T1
Valid prediction for GeneMark_model.22802_t
Valid prediction for GeneMark_model.22809_t
Valid prediction for snap_scaffold_5-snap.2957-T1
Valid prediction for snap_scaffold_5-snap.2954-T1
Valid prediction for GeneMark_model.22830_t
Valid prediction for snap_scaffold_5-snap.2952-T1
Valid prediction for GlimmerHMM_glimmerT_13579-T1
Valid prediction for snap_scaffold_5-snap.2942-T1
Valid prediction for GlimmerHMM_glimmerT_13607-T1
Valid prediction for GeneMark_model.22836_t
Valid prediction for GeneMark_model.22812_t
Valid prediction for snap_scaffold_5-snap.2959-T1
Valid prediction for GlimmerHMM_glimmerT_13584-T1
Valid prediction for snap_scaffold_5-snap.2961-T1
Valid prediction for GeneMark_model.22800_t
Valid prediction for GeneMark_model.22807_t
Couldn't classify 20653, 20708
Couldn't classify 22154, 22395
Sorry, prediction pasa_asmbl_46121.p1 fails validation.
(AGC)	 TC	20653-20708	GC	AGG
(GAC)	 AG	21304-21344	GT	AGG
(TTT)	 AG	22154-22395	AG	AGA
-recovered pasa_asmbl_46121.p1, internal, 21304, 21344
Valid prediction for GeneMark_model.22828_t
Valid prediction for GeneMark_model.22827_t
Valid prediction for snap_scaffold_5-snap.2968-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.2943-T1
Valid prediction for Augustus_model.g9091.t1
Valid prediction for GlimmerHMM_glimmerT_13589-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13691, rend_intergenic: 12799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23804, rend_intergenic: 14225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32294, rend_intergenic: 28462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50491, rend_intergenic: 47520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78164, rend_intergenic: 70671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78949, rend_intergenic: 78177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90269, rend_intergenic: 90141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93419, rend_intergenic: 90729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107296, rend_intergenic: 103397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115140, rend_intergenic: 111734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131328, rend_intergenic: 121431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156939, rend_intergenic: 153482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163940, rend_intergenic: 157812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190762
-exon list size: 683


building trellis

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80.9    
81.0    
81.2    
81.3    
81.5    
81.6    
81.8    
81.9    
82.0    
82.2    
82.3    
82.5    
82.6    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.4    
86.6    
86.7    
86.9    
87.0    
87.2    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.3    
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    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.6    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
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    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 13691, rend_intergenic: 12799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23804, rend_intergenic: 14225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32294, rend_intergenic: 28462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50491, rend_intergenic: 47520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78164, rend_intergenic: 70671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78949, rend_intergenic: 78177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90269, rend_intergenic: 90141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93419, rend_intergenic: 90729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107296, rend_intergenic: 103397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115140, rend_intergenic: 111734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131328, rend_intergenic: 121431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156939, rend_intergenic: 153482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163940, rend_intergenic: 157812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 177640 - 190762
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support