-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_14617865-14795110

-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.73459_t
Valid prediction for GeneMark_model.73485_t
Valid prediction for pasa_asmbl_18539.p1
Valid prediction for GeneMark_model.73453_t
Valid prediction for GlimmerHMM_glimmerT_42482-T1
Valid prediction for GeneMark_model.73457_t
Valid prediction for snap_scaffold_17-snap.3097-T1
Valid prediction for snap_scaffold_17-snap.3057-T1
Valid prediction for snap_scaffold_17-snap.3074-T1
Valid prediction for snap_scaffold_17-snap.3079-T1
Valid prediction for GeneMark_model.73477_t
Couldn't classify 111611, 112747
Sorry, prediction pasa_asmbl_18540.p1 fails validation.
(ATG)	 AG	110783-111031	GT	AGG
(GTC)	 AG	111611-112747	GG	GAG
-recovered pasa_asmbl_18540.p1, initial, 110783, 111031
-recovered pasa_asmbl_18540.p1, internal, 110783, 111031
Valid prediction for snap_scaffold_17-snap.3075-T1
Valid prediction for GeneMark_model.73468_t
Valid prediction for snap_scaffold_17-snap.3058-T1
Valid prediction for GlimmerHMM_glimmerT_42507-T1
Valid prediction for snap_scaffold_17-snap.3078-T1
Valid prediction for snap_scaffold_17-snap.3059-T1
Valid prediction for CodingQuarry_transcript_22225-T1
Valid prediction for GeneMark_model.73473_t
Valid prediction for snap_scaffold_17-snap.3086-T1
Valid prediction for GlimmerHMM_glimmerT_42486-T1
Valid prediction for pasa_asmbl_18534.p1
Valid prediction for GlimmerHMM_glimmerT_42502-T1
Valid prediction for GlimmerHMM_glimmerT_42483-T1
Valid prediction for snap_scaffold_17-snap.3072-T1
Valid prediction for GeneMark_model.73462_t
Valid prediction for GlimmerHMM_glimmerT_42487-T1
Valid prediction for snap_scaffold_17-snap.3068-T1
Valid prediction for snap_scaffold_17-snap.3063-T1
Valid prediction for GlimmerHMM_glimmerT_42505-T1
Valid prediction for GeneMark_model.73464_t
Valid prediction for GeneMark_model.73470_t
Valid prediction for snap_scaffold_17-snap.3062-T1
Valid prediction for GeneMark_model.73483_t
Valid prediction for snap_scaffold_17-snap.3090-T1
Valid prediction for GlimmerHMM_glimmerT_42496-T1
Valid prediction for GlimmerHMM_glimmerT_42497-T1
Valid prediction for GeneMark_model.73496_t
Valid prediction for GeneMark_model.73498_t
Valid prediction for snap_scaffold_17-snap.3066-T1
Valid prediction for snap_scaffold_17-snap.3088-T1
Valid prediction for snap_scaffold_17-snap.3096-T1
Valid prediction for GlimmerHMM_glimmerT_42490-T1
Valid prediction for GeneMark_model.73481_t
Valid prediction for snap_scaffold_17-snap.3093-T1
Valid prediction for GlimmerHMM_glimmerT_42499-T1
Valid prediction for GeneMark_model.73452_t
Valid prediction for snap_scaffold_17-snap.3077-T1
Valid prediction for snap_scaffold_17-snap.3081-T1
Valid prediction for GeneMark_model.73461_t
Valid prediction for GeneMark_model.73479_t
Valid prediction for GeneMark_model.73465_t
Valid prediction for GeneMark_model.73449_t
Valid prediction for snap_scaffold_17-snap.3084-T1
Valid prediction for GeneMark_model.73475_t
Valid prediction for GlimmerHMM_glimmerT_42504-T1
Valid prediction for GeneMark_model.73458_t
Valid prediction for GeneMark_model.73487_t
Valid prediction for GeneMark_model.73495_t
Valid prediction for GlimmerHMM_glimmerT_42494-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 GlimmerHMM_glimmerT_42485-T1
Valid prediction for snap_scaffold_17-snap.3073-T1
Couldn't classify 169599, 169697
Sorry, prediction pasa_asmbl_19484.p2 fails validation.
(ATG)	 CC	169043-169220	GT	AGG
(TGG)	 AG	169406-169494	GT	AGG
(GTG)	 AG	169599-169697	AA	AGA
-recovered pasa_asmbl_19484.p2, initial, 169043, 169220
-recovered pasa_asmbl_19484.p2, internal, 169406, 169494
Valid prediction for GlimmerHMM_glimmerT_42481-T1
Valid prediction for GeneMark_model.73484_t
Valid prediction for GeneMark_model.73454_t
Valid prediction for snap_scaffold_17-snap.3061-T1
Valid prediction for GeneMark_model.73456_t
Valid prediction for GeneMark_model.73474_t
Valid prediction for pasa_asmbl_19493.p1
Valid prediction for GeneMark_model.73491_t
Valid prediction for snap_scaffold_17-snap.3082-T1
Couldn't classify 150519, 150546
Couldn't classify 151744, 151817
Sorry, prediction pasa_asmbl_19523.p1 fails validation.
(AAG)	 CA	150519-150546	GT	TGG
(GCG)	 AG	151088-151200	GT	ACG
(AGG)	 AG	151442-151559	GT	ATG
(TCA)	 AG	151744-151817	GG	TTG
-recovered pasa_asmbl_19523.p1, internal, 151088, 151200
-recovered pasa_asmbl_19523.p1, internal, 151442, 151559
Valid prediction for CodingQuarry_transcript_22226-T1
Valid prediction for GeneMark_model.73450_t
Valid prediction for GlimmerHMM_glimmerT_42484-T1
Couldn't classify 78604, 79128
Sorry, prediction pasa_asmbl_19495.p1 fails validation.
(TCC)	 CT	78604-79128	AC	GAA
Valid prediction for GeneMark_model.73492_t
Valid prediction for snap_scaffold_17-snap.3067-T1
Valid prediction for GeneMark_model.73482_t
Valid prediction for GlimmerHMM_glimmerT_42495-T1
Valid prediction for GeneMark_model.73466_t
Valid prediction for GlimmerHMM_glimmerT_42488-T1
Valid prediction for GeneMark_model.73497_t
Valid prediction for GlimmerHMM_glimmerT_42501-T1
Valid prediction for snap_scaffold_17-snap.3070-T1
Valid prediction for GlimmerHMM_glimmerT_42489-T1
Valid prediction for snap_scaffold_17-snap.3060-T1
Valid prediction for GeneMark_model.73494_t
Valid prediction for GeneMark_model.73488_t
Valid prediction for GlimmerHMM_glimmerT_42498-T1
Valid prediction for GeneMark_model.73448_t
Couldn't classify 169857, 170861
Sorry, prediction pasa_asmbl_19483.p1 fails validation.
(CAT)	 GG	169857-170861	TT	AAT
Valid prediction for snap_scaffold_17-snap.3080-T1
Valid prediction for snap_scaffold_17-snap.3087-T1
Valid prediction for GeneMark_model.73490_t
Valid prediction for GeneMark_model.73478_t
Valid prediction for snap_scaffold_17-snap.3091-T1
Valid prediction for GeneMark_model.73451_t
Valid prediction for GlimmerHMM_glimmerT_42503-T1
Valid prediction for GeneMark_model.73489_t
Valid prediction for GlimmerHMM_glimmerT_42500-T1
Valid prediction for GeneMark_model.73463_t
Valid prediction for GeneMark_model.73460_t
Valid prediction for snap_scaffold_17-snap.3069-T1
Valid prediction for GeneMark_model.73486_t
Valid prediction for GlimmerHMM_glimmerT_42493-T1
Valid prediction for snap_scaffold_17-snap.3094-T1
Valid prediction for snap_scaffold_17-snap.3089-T1
Valid prediction for snap_scaffold_17-snap.3092-T1
Valid prediction for GlimmerHMM_glimmerT_42506-T1
Valid prediction for GeneMark_model.73480_t
Valid prediction for snap_scaffold_17-snap.3071-T1
Valid prediction for GeneMark_model.73455_t
Valid prediction for GlimmerHMM_glimmerT_42492-T1
Valid prediction for snap_scaffold_17-snap.3076-T1
Valid prediction for GeneMark_model.73469_t
Valid prediction for pasa_asmbl_19540.p1
Valid prediction for GeneMark_model.73467_t
Couldn't classify 73758, 73867
Couldn't classify 74661, 74763
Sorry, prediction pasa_asmbl_19498.p3 fails validation.
(CAG)	 GG	73758-73867	GT	AAG
(GCT)	 AG	74245-74427	GT	AGG
(GGG)	 AG	74661-74763	CT	ACC
-recovered pasa_asmbl_19498.p3, internal, 74245, 74427
Valid prediction for snap_scaffold_17-snap.3064-T1
Valid prediction for GeneMark_model.73499_t
Valid prediction for GeneMark_model.73493_t
Valid prediction for GeneMark_model.73472_t
Valid prediction for snap_scaffold_17-snap.3085-T1
Valid prediction for CodingQuarry_transcript_22227-T1
Valid prediction for GlimmerHMM_glimmerT_42491-T1
Valid prediction for snap_scaffold_17-snap.3065-T1
Valid prediction for snap_scaffold_17-snap.3083-T1
Valid prediction for GeneMark_model.73476_t
Valid prediction for snap_scaffold_17-snap.3095-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17144, rend_intergenic: 11639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27005, rend_intergenic: 18042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35509, rend_intergenic: 31234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42422, rend_intergenic: 38154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52923, rend_intergenic: 42489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71725, rend_intergenic: 68439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72487, rend_intergenic: 71740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87084, rend_intergenic: 73048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87546, rend_intergenic: 87433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94274, rend_intergenic: 87806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100635, rend_intergenic: 100467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105926, rend_intergenic: 100662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112927, rend_intergenic: 110783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118008, rend_intergenic: 117342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121452, rend_intergenic: 118040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125444, rend_intergenic: 123126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134911, rend_intergenic: 125444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140611, rend_intergenic: 136528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171016, rend_intergenic: 143338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175103, rend_intergenic: 171461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177246
-exon list size: 832


building trellis

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79.4    
79.5    
79.6    
79.7    
79.9    
80.0    
80.1    
80.2    
80.3    
80.5    
80.6    
80.7    
80.8    
80.9    
81.1    
81.2    
81.3    
81.4    
81.5    
81.7    
81.8    
81.9    
82.0    
82.1    
82.3    
82.4    
82.5    
82.6    
82.7    
82.9    
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    
84.5    
84.7    
84.8    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.6    
85.7    
85.9    
86.0    
86.1    
86.2    
86.3    
86.5    
86.6    
86.7    
86.8    
86.9    
87.1    
87.2    
87.3    
87.4    
87.5    
87.6    
87.8    
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    
89.4    
89.6    
89.7    
89.8    
89.9    
90.0    
90.2    
90.3    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.1    
91.2    
91.4    
91.5    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
92.9    
93.0    
93.2    
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    
94.8    
95.0    
95.1    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 17144, rend_intergenic: 11639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27005, rend_intergenic: 18042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35509, rend_intergenic: 31234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42422, rend_intergenic: 38154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52923, rend_intergenic: 42489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71725, rend_intergenic: 68439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72487, rend_intergenic: 71740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87084, rend_intergenic: 73048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87546, rend_intergenic: 87433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94274, rend_intergenic: 87806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100635, rend_intergenic: 100467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105926, rend_intergenic: 100662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112927, rend_intergenic: 110783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118008, rend_intergenic: 117342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121452, rend_intergenic: 118040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125444, rend_intergenic: 123126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134911, rend_intergenic: 125444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140611, rend_intergenic: 136528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171016, rend_intergenic: 143338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175103, rend_intergenic: 171461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support