-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_14484564-14681037

-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.40915_t
Valid prediction for GeneMark_model.40964_t
Valid prediction for GlimmerHMM_glimmerT_23870-T1
Valid prediction for snap_scaffold_9-snap.2955-T1
Valid prediction for snap_scaffold_9-snap.2982-T1
Valid prediction for snap_scaffold_9-snap.2966-T1
Valid prediction for snap_scaffold_9-snap.2968-T1
Valid prediction for snap_scaffold_9-snap.2940-T1
Valid prediction for snap_scaffold_9-snap.2957-T1
Valid prediction for GeneMark_model.40947_t
Valid prediction for Augustus_model.g15978.t1
Valid prediction for Augustus_model.g15992.t1
Valid prediction for GeneMark_model.40966_t
Valid prediction for GeneMark_model.40950_t
Valid prediction for GlimmerHMM_glimmerT_23871-T1
Valid prediction for snap_scaffold_9-snap.2977-T1
Valid prediction for snap_scaffold_9-snap.2985-T1
Valid prediction for snap_scaffold_9-snap.2944-T1
Valid prediction for GlimmerHMM_glimmerT_23855-T1
Valid prediction for Augustus_model.g15985.t1
Valid prediction for snap_scaffold_9-snap.2971-T1
Valid prediction for Augustus_model.g15979.t1
Valid prediction for snap_scaffold_9-snap.2979-T1
Valid prediction for GeneMark_model.40962_t
Valid prediction for snap_scaffold_9-snap.2946-T1
Valid prediction for GlimmerHMM_glimmerT_23867-T1
Valid prediction for snap_scaffold_9-snap.2950-T1
Valid prediction for GeneMark_model.40907_t
Valid prediction for snap_scaffold_9-snap.2974-T1
Valid prediction for GlimmerHMM_glimmerT_23857-T1
Valid prediction for GeneMark_model.40929_t
Valid prediction for GeneMark_model.40943_t
Valid prediction for GeneMark_model.40913_t
Valid prediction for GeneMark_model.40956_t
Valid prediction for GeneMark_model.40935_t
Valid prediction for snap_scaffold_9-snap.2963-T1
Valid prediction for snap_scaffold_9-snap.2961-T1
Valid prediction for snap_scaffold_9-snap.2970-T1
Valid prediction for GeneMark_model.40921_t
Valid prediction for GeneMark_model.40949_t
Couldn't classify 97601, 98443
Sorry, prediction pasa_asmbl_54512.p1 fails validation.
(TGC)	 TG	97601-98443	GG	GAG
Valid prediction for snap_scaffold_9-snap.2941-T1
Valid prediction for Augustus_model.g15990.t1
Valid prediction for snap_scaffold_9-snap.2983-T1
Valid prediction for GlimmerHMM_glimmerT_23863-T1
Valid prediction for GlimmerHMM_glimmerT_23846-T1
Valid prediction for GeneMark_model.40945_t
Valid prediction for GeneMark_model.40959_t
Valid prediction for GeneMark_model.40908_t
Valid prediction for GeneMark_model.40916_t
Valid prediction for GlimmerHMM_glimmerT_23852-T1
Valid prediction for snap_scaffold_9-snap.2954-T1
Valid prediction for snap_scaffold_9-snap.2959-T1
Valid prediction for GeneMark_model.40920_t
Valid prediction for snap_scaffold_9-snap.2952-T1
Valid prediction for GlimmerHMM_glimmerT_23853-T1
Valid prediction for GeneMark_model.40954_t
Valid prediction for snap_scaffold_9-snap.2953-T1
Valid prediction for Augustus_model.g15980.t1
Valid prediction for Augustus_model.g15991.t1
Valid prediction for GeneMark_model.40937_t
Valid prediction for GeneMark_model.40933_t
Valid prediction for Augustus_model.g15976.t1
Valid prediction for GeneMark_model.40931_t
Valid prediction for GlimmerHMM_glimmerT_23849-T1
Valid prediction for GeneMark_model.40940_t
Valid prediction for GeneMark_model.40923_t
Valid prediction for GeneMark_model.40911_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.40944_t
Valid prediction for GeneMark_model.40930_t
Valid prediction for snap_scaffold_9-snap.2962-T1
Valid prediction for snap_scaffold_9-snap.2939-T1
Valid prediction for GeneMark_model.40932_t
Valid prediction for GeneMark_model.40910_t
Valid prediction for GeneMark_model.40942_t
Valid prediction for snap_scaffold_9-snap.2978-T1
Valid prediction for GeneMark_model.40927_t
Valid prediction for GlimmerHMM_glimmerT_23865-T1
Valid prediction for Augustus_model.g15982.t1
Valid prediction for GeneMark_model.40958_t
Valid prediction for snap_scaffold_9-snap.2967-T1
Valid prediction for GeneMark_model.40928_t
Valid prediction for GeneMark_model.40968_t
Valid prediction for snap_scaffold_9-snap.2964-T1
Valid prediction for snap_scaffold_9-snap.2972-T1
Valid prediction for snap_scaffold_9-snap.2973-T1
Valid prediction for Augustus_model.g15981.t1
Valid prediction for GeneMark_model.40918_t
Valid prediction for GeneMark_model.40905_t
Valid prediction for GeneMark_model.40912_t
Valid prediction for GlimmerHMM_glimmerT_23864-T1
Valid prediction for GlimmerHMM_glimmerT_23850-T1
Valid prediction for GeneMark_model.40939_t
Valid prediction for GeneMark_model.40952_t
Valid prediction for Augustus_model.g15989.t1
Valid prediction for Augustus_model.g15987.t1
Valid prediction for GlimmerHMM_glimmerT_23856-T1
Valid prediction for snap_scaffold_9-snap.2975-T1
Valid prediction for snap_scaffold_9-snap.2965-T1
Valid prediction for Augustus_model.g15988.t1
Valid prediction for GlimmerHMM_glimmerT_23859-T1
Valid prediction for snap_scaffold_9-snap.2960-T1
Valid prediction for GlimmerHMM_glimmerT_23858-T1
Valid prediction for snap_scaffold_9-snap.2958-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.40938_t
Valid prediction for snap_scaffold_9-snap.2984-T1
Valid prediction for GeneMark_model.40961_t
Valid prediction for Augustus_model.g15984.t1
Valid prediction for GlimmerHMM_glimmerT_23862-T1
Valid prediction for snap_scaffold_9-snap.2949-T1
Valid prediction for snap_scaffold_9-snap.2948-T1
Couldn't classify 87317, 87727
Sorry, prediction pasa_asmbl_55447.p1 fails validation.
(AAA)	 CC	87317-87727	GC	GAG
Valid prediction for GeneMark_model.40917_t
Valid prediction for GeneMark_model.40960_t
Valid prediction for GeneMark_model.40909_t
Valid prediction for GeneMark_model.40941_t
Valid prediction for Augustus_model.g15977.t1
Valid prediction for snap_scaffold_9-snap.2942-T1
Valid prediction for GlimmerHMM_glimmerT_23860-T1
Valid prediction for snap_scaffold_9-snap.2976-T1
Valid prediction for GeneMark_model.40967_t
Valid prediction for GlimmerHMM_glimmerT_23868-T1
Valid prediction for GeneMark_model.40955_t
Valid prediction for snap_scaffold_9-snap.2980-T1
Valid prediction for GeneMark_model.40936_t
Valid prediction for GlimmerHMM_glimmerT_23851-T1
Valid prediction for GeneMark_model.40951_t
Valid prediction for snap_scaffold_9-snap.2951-T1
Valid prediction for snap_scaffold_9-snap.2947-T1
Valid prediction for GeneMark_model.40919_t
Valid prediction for GeneMark_model.40925_t
Valid prediction for snap_scaffold_9-snap.2981-T1
Valid prediction for GeneMark_model.40963_t
Valid prediction for GeneMark_model.40953_t
Valid prediction for GlimmerHMM_glimmerT_23866-T1
Valid prediction for GeneMark_model.40948_t
Valid prediction for GlimmerHMM_glimmerT_23861-T1
Valid prediction for Augustus_model.g15986.t1
Valid prediction for snap_scaffold_9-snap.2945-T1
Valid prediction for GeneMark_model.40946_t
Valid prediction for GlimmerHMM_glimmerT_23847-T1
Valid prediction for GeneMark_model.40965_t
Valid prediction for GlimmerHMM_glimmerT_23854-T1
Valid prediction for snap_scaffold_9-snap.2986-T1
Valid prediction for snap_scaffold_9-snap.2969-T1
Valid prediction for GlimmerHMM_glimmerT_23848-T1
Valid prediction for Augustus_model.g15983.t1
Valid prediction for GeneMark_model.40906_t
Valid prediction for GeneMark_model.40904_t
Valid prediction for GeneMark_model.40924_t
Valid prediction for snap_scaffold_9-snap.2943-T1
Valid prediction for GeneMark_model.40922_t
Valid prediction for GlimmerHMM_glimmerT_23869-T1
Valid prediction for snap_scaffold_9-snap.2956-T1
Valid prediction for snap_scaffold_9-snap.2987-T1
Valid prediction for GeneMark_model.40914_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13086, rend_intergenic: 4475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25077, rend_intergenic: 21173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33558, rend_intergenic: 30856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69985, rend_intergenic: 37251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72819, rend_intergenic: 69992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91382, rend_intergenic: 74514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95481, rend_intergenic: 92397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107561, rend_intergenic: 102635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116544, rend_intergenic: 114167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123978, rend_intergenic: 120348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126249, rend_intergenic: 125938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133526, rend_intergenic: 128079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134561, rend_intergenic: 133750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140904, rend_intergenic: 136196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154769, rend_intergenic: 151341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159742, rend_intergenic: 158228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160646, rend_intergenic: 159882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166605, rend_intergenic: 163030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169417, rend_intergenic: 167968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174848, rend_intergenic: 173289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176629, rend_intergenic: 175208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194482, rend_intergenic: 177034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 196474
-exon list size: 758


building trellis

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88.0    
88.2    
88.3    
88.4    
88.6    
88.7    
88.8    
88.9    
89.1    
89.2    
89.3    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.3    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.6    
93.7    
93.8    
93.9    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 50 predictions from path traversal
Error with prediction: snap lend_intergenic: 13086, rend_intergenic: 4475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25077, rend_intergenic: 21173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33558, rend_intergenic: 30856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69985, rend_intergenic: 37251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72819, rend_intergenic: 69992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91382, rend_intergenic: 74514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95481, rend_intergenic: 92397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107561, rend_intergenic: 102635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116544, rend_intergenic: 114167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123978, rend_intergenic: 120348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126249, rend_intergenic: 125938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133526, rend_intergenic: 128079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134561, rend_intergenic: 133750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140904, rend_intergenic: 136196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154769, rend_intergenic: 151341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159742, rend_intergenic: 158228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160646, rend_intergenic: 159882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166605, rend_intergenic: 163030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169417, rend_intergenic: 167968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174848, rend_intergenic: 173289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176629, rend_intergenic: 175208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194482, rend_intergenic: 177034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support