-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_15047096-15242023

-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.69554_t
Valid prediction for snap_scaffold_16-snap.2948-T1
Valid prediction for GeneMark_model.69566_t
Valid prediction for GeneMark_model.69588_t
Valid prediction for GeneMark_model.69593_t
Couldn't classify 170947, 171123
Sorry, prediction pasa_asmbl_17524.p1 fails validation.
(GAG)	 TG	170947-171123	GT	AGG
(GCG)	 AG	171319-171483	GT	AGG
(GTG)	 AG	171728-171865	GT	AGG
(GCC)	 AG	173618-173773	GT	AGG
(GAG)	 AG	173854-173964	GT	GGG
(GAG)	 AG	174158-174247	GT	AGG
(CAC)	 AG	176451-176594	GT	AGG
(TCC)	 AG	176767-176866	GT	AGG
(GTC)	 AG	177517-177676	GT	TGG
(TTC)	 AG	177964-178054	GT	AGG
(GAG)	 AG	178221-178364	GT	AGG
(TCT)	 AG	178444-178663	GT	AGG
(ACA)	 AG	178996-179081	GT	AAG
(AGC)	 AG	180722-180862	AG	AAA
-recovered pasa_asmbl_17524.p1, terminal, 180722, 180862
-recovered pasa_asmbl_17524.p1, internal, 171319, 171483
-recovered pasa_asmbl_17524.p1, internal, 171728, 171865
-recovered pasa_asmbl_17524.p1, internal, 173618, 173773
-recovered pasa_asmbl_17524.p1, internal, 173854, 173964
-recovered pasa_asmbl_17524.p1, internal, 174158, 174247
-recovered pasa_asmbl_17524.p1, internal, 176451, 176594
-recovered pasa_asmbl_17524.p1, internal, 176767, 176866
-recovered pasa_asmbl_17524.p1, internal, 177517, 177676
-recovered pasa_asmbl_17524.p1, internal, 177964, 178054
-recovered pasa_asmbl_17524.p1, internal, 178221, 178364
-recovered pasa_asmbl_17524.p1, internal, 178444, 178663
-recovered pasa_asmbl_17524.p1, internal, 178996, 179081
Valid prediction for snap_scaffold_16-snap.2968-T1
Valid prediction for GlimmerHMM_glimmerT_40408-T1
Valid prediction for GeneMark_model.69556_t
Valid prediction for GeneMark_model.69568_t
Valid prediction for snap_scaffold_16-snap.2928-T1
Valid prediction for CodingQuarry_transcript_20102-T1
Valid prediction for GlimmerHMM_glimmerT_40410-T1
Valid prediction for GeneMark_model.69558_t
Valid prediction for snap_scaffold_16-snap.2930-T1
Valid prediction for snap_scaffold_16-snap.2956-T1
Valid prediction for GlimmerHMM_glimmerT_40424-T1
Valid prediction for GlimmerHMM_glimmerT_40402-T1
Valid prediction for snap_scaffold_16-snap.2946-T1
Valid prediction for snap_scaffold_16-snap.2938-T1
Valid prediction for snap_scaffold_16-snap.2964-T1
Valid prediction for GeneMark_model.69563_t
Valid prediction for snap_scaffold_16-snap.2945-T1
Valid prediction for snap_scaffold_16-snap.2957-T1
Valid prediction for snap_scaffold_16-snap.2927-T1
Valid prediction for GeneMark_model.69591_t
Valid prediction for GeneMark_model.69569_t
Valid prediction for snap_scaffold_16-snap.2949-T1
Valid prediction for GeneMark_model.69595_t
Valid prediction for CodingQuarry_transcript_20103-T1
Valid prediction for GeneMark_model.69572_t
Valid prediction for GlimmerHMM_glimmerT_40413-T1
Valid prediction for snap_scaffold_16-snap.2933-T1
Valid prediction for GeneMark_model.69545_t
Valid prediction for GlimmerHMM_glimmerT_40417-T1
Valid prediction for GlimmerHMM_glimmerT_40414-T1
Valid prediction for GeneMark_model.69571_t
Valid prediction for GlimmerHMM_glimmerT_40419-T1
Valid prediction for GlimmerHMM_glimmerT_40412-T1
Valid prediction for GeneMark_model.69551_t
Valid prediction for CodingQuarry_transcript_20104-T1
Valid prediction for GlimmerHMM_glimmerT_40404-T1
Valid prediction for GeneMark_model.69583_t
Valid prediction for snap_scaffold_16-snap.2959-T1
Valid prediction for GeneMark_model.69574_t
Valid prediction for GeneMark_model.69547_t
Valid prediction for snap_scaffold_16-snap.2936-T1
Valid prediction for snap_scaffold_16-snap.2952-T1
Valid prediction for snap_scaffold_16-snap.2941-T1
Valid prediction for GeneMark_model.69549_t
Valid prediction for snap_scaffold_16-snap.2943-T1
Valid prediction for GlimmerHMM_glimmerT_40426-T1
Couldn't classify 127219, 127257
Sorry, prediction pasa_asmbl_17520.p1 fails validation.
(AGC)	 TG	127219-127257	GT	TGG
(GTG)	 AG	127683-127767	GT	AGG
(GAA)	 AG	128373-128474	GT	AGG
(CTA)	 AG	128804-128891	GT	AGG
(TCT)	 AG	129026-129086	TG	GAT
-recovered pasa_asmbl_17520.p1, terminal, 128373, 128474
-recovered pasa_asmbl_17520.p1, terminal, 129026, 129086
-recovered pasa_asmbl_17520.p1, internal, 127683, 127767
-recovered pasa_asmbl_17520.p1, internal, 128373, 128474
-recovered pasa_asmbl_17520.p1, internal, 128804, 128891
Valid prediction for snap_scaffold_16-snap.2953-T1
Valid prediction for GeneMark_model.69587_t
Valid prediction for GlimmerHMM_glimmerT_40425-T1
Valid prediction for GeneMark_model.69561_t
Valid prediction for GeneMark_model.69585_t
Valid prediction for GlimmerHMM_glimmerT_40415-T1
Couldn't classify 175713, 175790
Sorry, prediction pasa_asmbl_17525.p1 fails validation.
(GTT)	 CA	175713-175790	GT	AGG
(CAC)	 AG	176451-176594	GT	AGG
(TCC)	 AG	176767-176866	GT	AGG
(GTC)	 AG	177517-177676	GT	TGG
(TTC)	 AG	177964-178054	GT	AGG
(GAG)	 AG	178221-178364	GT	AGG
(TCT)	 AG	178444-178663	GT	AGG
(ACA)	 AG	178996-179081	GT	AAG
(AGC)	 AG	180722-180862	AG	AAA
-recovered pasa_asmbl_17525.p1, terminal, 180722, 180862
-recovered pasa_asmbl_17525.p1, internal, 176451, 176594
-recovered pasa_asmbl_17525.p1, internal, 176767, 176866
-recovered pasa_asmbl_17525.p1, internal, 177517, 177676
-recovered pasa_asmbl_17525.p1, internal, 177964, 178054
-recovered pasa_asmbl_17525.p1, internal, 178221, 178364
-recovered pasa_asmbl_17525.p1, internal, 178444, 178663
-recovered pasa_asmbl_17525.p1, internal, 178996, 179081
Valid prediction for snap_scaffold_16-snap.2934-T1
Valid prediction for GlimmerHMM_glimmerT_40427-T1
Valid prediction for GeneMark_model.69559_t
Valid prediction for GeneMark_model.69576_t
Valid prediction for GeneMark_model.69553_t
Valid prediction for GlimmerHMM_glimmerT_40406-T1
Valid prediction for snap_scaffold_16-snap.2961-T1
Valid prediction for snap_scaffold_16-snap.2966-T1
Valid prediction for snap_scaffold_16-snap.2950-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_16-snap.2931-T1
Valid prediction for GeneMark_model.69555_t
Valid prediction for GeneMark_model.69557_t
Valid prediction for snap_scaffold_16-snap.2942-T1
Valid prediction for GeneMark_model.69567_t
Valid prediction for snap_scaffold_16-snap.2965-T1
Valid prediction for GeneMark_model.69581_t
Valid prediction for GlimmerHMM_glimmerT_40423-T1
Valid prediction for snap_scaffold_16-snap.2951-T1
Valid prediction for GeneMark_model.69573_t
Valid prediction for GeneMark_model.69560_t
Valid prediction for GeneMark_model.69577_t
Valid prediction for snap_scaffold_16-snap.2939-T1
Valid prediction for snap_scaffold_16-snap.2962-T1
Valid prediction for snap_scaffold_16-snap.2954-T1
Valid prediction for snap_scaffold_16-snap.2958-T1
Valid prediction for GeneMark_model.69596_t
Valid prediction for GeneMark_model.69575_t
Valid prediction for snap_scaffold_16-snap.2947-T1
Valid prediction for snap_scaffold_16-snap.2963-T1
Valid prediction for GlimmerHMM_glimmerT_40418-T1
Valid prediction for snap_scaffold_16-snap.2944-T1
Valid prediction for GeneMark_model.69590_t
Valid prediction for GlimmerHMM_glimmerT_40407-T1
Valid prediction for snap_scaffold_16-snap.2969-T1
Valid prediction for GeneMark_model.69564_t
Valid prediction for GlimmerHMM_glimmerT_40422-T1
Valid prediction for snap_scaffold_16-snap.2967-T1
Valid prediction for GeneMark_model.69584_t
Valid prediction for snap_scaffold_16-snap.2926-T1
Valid prediction for snap_scaffold_16-snap.2960-T1
Valid prediction for GeneMark_model.69548_t
Valid prediction for GeneMark_model.69565_t
Valid prediction for GeneMark_model.69586_t
Valid prediction for snap_scaffold_16-snap.2935-T1
Valid prediction for snap_scaffold_16-snap.2932-T1
Valid prediction for GeneMark_model.69592_t
Valid prediction for snap_scaffold_16-snap.2955-T1
Valid prediction for snap_scaffold_16-snap.2929-T1
Valid prediction for snap_scaffold_16-snap.2940-T1
Valid prediction for GeneMark_model.69550_t
Valid prediction for GeneMark_model.69582_t
Valid prediction for GeneMark_model.69570_t
Valid prediction for GeneMark_model.69552_t
Valid prediction for snap_scaffold_16-snap.2937-T1
Valid prediction for GeneMark_model.69589_t
Valid prediction for GeneMark_model.69546_t
Valid prediction for GeneMark_model.69594_t
Valid prediction for GlimmerHMM_glimmerT_40411-T1
Valid prediction for GlimmerHMM_glimmerT_40416-T1
Valid prediction for GlimmerHMM_glimmerT_40421-T1
Valid prediction for GlimmerHMM_glimmerT_40403-T1
Valid prediction for GeneMark_model.69578_t
Valid prediction for GlimmerHMM_glimmerT_40409-T1
Valid prediction for GlimmerHMM_glimmerT_40420-T1
Valid prediction for GeneMark_model.69562_t
Valid prediction for GlimmerHMM_glimmerT_40405-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8096, rend_intergenic: 2114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13499, rend_intergenic: 9568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19340, rend_intergenic: 14644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25961, rend_intergenic: 21098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36055, rend_intergenic: 28790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45632, rend_intergenic: 44878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69616, rend_intergenic: 47831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71681, rend_intergenic: 69914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73671, rend_intergenic: 73201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74555, rend_intergenic: 73925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78952, rend_intergenic: 74574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84104, rend_intergenic: 80831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102065, rend_intergenic: 84513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107255, rend_intergenic: 102288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132064, rend_intergenic: 130240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138897, rend_intergenic: 134575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141002, rend_intergenic: 139104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151700, rend_intergenic: 144623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163953, rend_intergenic: 155345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166020, rend_intergenic: 164155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167964, rend_intergenic: 167415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180862, rend_intergenic: 168138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193219, rend_intergenic: 186927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 194928
-exon list size: 814


building trellis

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66.5    
66.7    
66.8    
66.9    
67.0    
67.2    
67.3    
67.4    
67.5    
67.6    
67.8    
67.9    
68.0    
68.1    
68.3    
68.4    
68.5    
68.6    
68.8    
68.9    
69.0    
69.1    
69.2    
69.4    
69.5    
69.6    
69.7    
69.9    
70.0    
70.1    
70.2    
70.3    
70.5    
70.6    
70.7    
70.8    
71.0    
71.1    
71.2    
71.3    
71.4    
71.6    
71.7    
71.8    
71.9    
72.1    
72.2    
72.3    
72.4    
72.5    
72.7    
72.8    
72.9    
73.0    
73.2    
73.3    
73.4    
73.5    
73.7    
73.8    
73.9    
74.0    
74.1    
74.3    
74.4    
74.5    
74.6    
74.8    
74.9    
75.0    
75.1    
75.2    
75.4    
75.5    
75.6    
75.7    
75.9    
76.0    
76.1    
76.2    
76.3    
76.5    
76.6    
76.7    
76.8    
77.0    
77.1    
77.2    
77.3    
77.5    
77.6    
77.7    
77.8    
77.9    
78.1    
78.2    
78.3    
78.4    
78.6    
78.7    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.5    
79.7    
79.8    
79.9    
80.0    
80.1    
80.3    
80.4    
80.5    
80.6    
80.8    
80.9    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.7    
81.9    
82.0    
82.1    
82.2    
82.4    
82.5    
82.6    
82.7    
82.8    
83.0    
83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
84.9    
85.0    
85.2    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.1    
87.3    
87.4    
87.5    
87.6    
87.7    
87.9    
88.0    
88.1    
88.2    
88.4    
88.5    
88.6    
88.7    
88.8    
89.0    
89.1    
89.2    
89.3    
89.5    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.0    
92.2    
92.3    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.7    
94.9    
95.0    
95.1    
95.2    
95.3    
95.5    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.4    
97.5    
97.7    
97.8    
97.9    
98.0    
98.2    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.0    
99.1    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 8096, rend_intergenic: 2114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13499, rend_intergenic: 9568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19340, rend_intergenic: 14644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25961, rend_intergenic: 21098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36055, rend_intergenic: 28790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45632, rend_intergenic: 44878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69616, rend_intergenic: 47831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71681, rend_intergenic: 69914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73671, rend_intergenic: 73201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74555, rend_intergenic: 73925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78952, rend_intergenic: 74574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84104, rend_intergenic: 80831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102065, rend_intergenic: 84513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107255, rend_intergenic: 102288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132064, rend_intergenic: 130240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138897, rend_intergenic: 134575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141002, rend_intergenic: 139104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151700, rend_intergenic: 144623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163953, rend_intergenic: 155345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166020, rend_intergenic: 164155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167964, rend_intergenic: 167415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180862, rend_intergenic: 168138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193219, rend_intergenic: 186927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support