-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_3460686-3700639

-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_15-snap.785-T1
Valid prediction for GlimmerHMM_glimmerT_36662-T1
Valid prediction for snap_scaffold_15-snap.762-T1
Valid prediction for GeneMark_model.63084_t
Valid prediction for snap_scaffold_15-snap.772-T1
Valid prediction for GlimmerHMM_glimmerT_36659-T1
Valid prediction for GeneMark_model.63104_t
Valid prediction for GeneMark_model.63092_t
Valid prediction for snap_scaffold_15-snap.760-T1
Valid prediction for GlimmerHMM_glimmerT_36673-T1
Valid prediction for GeneMark_model.63117_t
Valid prediction for GeneMark_model.63107_t
Valid prediction for snap_scaffold_15-snap.767-T1
Valid prediction for GeneMark_model.63114_t
Valid prediction for snap_scaffold_15-snap.774-T1
Valid prediction for GeneMark_model.63077_t
Valid prediction for GeneMark_model.63102_t
Valid prediction for snap_scaffold_15-snap.788-T1
Valid prediction for GlimmerHMM_glimmerT_36669-T1
Valid prediction for GeneMark_model.63089_t
Valid prediction for GeneMark_model.63103_t
Valid prediction for snap_scaffold_15-snap.754-T1
Valid prediction for GlimmerHMM_glimmerT_36678-T1
Couldn't classify 214439, 214756
Sorry, prediction pasa_asmbl_14046.p1 fails validation.
(TCC)	 CG	214439-214756	AC	AGA
Valid prediction for GeneMark_model.63124_t
Valid prediction for GeneMark_model.63079_t
Valid prediction for GeneMark_model.63129_t
Valid prediction for GeneMark_model.63126_t
Valid prediction for GlimmerHMM_glimmerT_36661-T1
Valid prediction for snap_scaffold_15-snap.768-T1
Valid prediction for snap_scaffold_15-snap.756-T1
Valid prediction for GlimmerHMM_glimmerT_36656-T1
Valid prediction for GeneMark_model.63090_t
Valid prediction for Augustus_model.g24622.t1
Valid prediction for GeneMark_model.63096_t
Valid prediction for snap_scaffold_15-snap.771-T1
Valid prediction for GeneMark_model.63082_t
Valid prediction for GlimmerHMM_glimmerT_36658-T1
Valid prediction for GlimmerHMM_glimmerT_36652-T1
Valid prediction for GeneMark_model.63087_t
Valid prediction for snap_scaffold_15-snap.759-T1
Valid prediction for GeneMark_model.63080_t
Valid prediction for snap_scaffold_15-snap.783-T1
Valid prediction for snap_scaffold_15-snap.773-T1
Valid prediction for GlimmerHMM_glimmerT_36657-T1
Valid prediction for GeneMark_model.63112_t
Valid prediction for snap_scaffold_15-snap.779-T1
Valid prediction for GlimmerHMM_glimmerT_36670-T1
Valid prediction for Augustus_model.g24616.t1
Valid prediction for GeneMark_model.63110_t
Valid prediction for GeneMark_model.63076_t
Valid prediction for snap_scaffold_15-snap.790-T1
Couldn't classify 212522, 212589
Couldn't classify 214046, 214192
Sorry, prediction pasa_asmbl_14045.p1 fails validation.
(ACG)	 AC	212522-212589	GT	AGG
(TGT)	 AG	212690-212873	GT	AGG
(GTC)	 AG	213005-213180	GT	AGG
(GAT)	 AG	213275-213369	GT	AGG
(GAG)	 AG	213486-213653	GT	AGG
(GCG)	 AG	213757-213914	GT	TGG
(ACT)	 AG	214046-214192	AG	TGA
-recovered pasa_asmbl_14045.p1, internal, 212690, 212873
-recovered pasa_asmbl_14045.p1, internal, 213005, 213180
-recovered pasa_asmbl_14045.p1, internal, 213275, 213369
-recovered pasa_asmbl_14045.p1, internal, 213486, 213653
-recovered pasa_asmbl_14045.p1, internal, 213757, 213914
Valid prediction for GeneMark_model.63101_t
Valid prediction for GeneMark_model.63105_t
Valid prediction for GlimmerHMM_glimmerT_36664-T1
Valid prediction for GeneMark_model.63086_t
Valid prediction for snap_scaffold_15-snap.792-T1
Valid prediction for snap_scaffold_15-snap.777-T1
Valid prediction for GeneMark_model.63123_t
Valid prediction for GeneMark_model.63094_t
Valid prediction for GeneMark_model.63131_t
Valid prediction for snap_scaffold_15-snap.780-T1
Valid prediction for snap_scaffold_15-snap.757-T1
Valid prediction for snap_scaffold_15-snap.787-T1
Valid prediction for GeneMark_model.63108_t
Valid prediction for Augustus_model.g24621.t1
Valid prediction for GeneMark_model.63100_t
Valid prediction for GeneMark_model.63132_t
Valid prediction for snap_scaffold_15-snap.764-T1
Valid prediction for Augustus_model.g24623.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_36651-T1
Valid prediction for snap_scaffold_15-snap.791-T1
Valid prediction for snap_scaffold_15-snap.763-T1
Valid prediction for GeneMark_model.63081_t
Valid prediction for GeneMark_model.63085_t
Valid prediction for snap_scaffold_15-snap.770-T1
Valid prediction for snap_scaffold_15-snap.761-T1
Valid prediction for GeneMark_model.63111_t
Valid prediction for GeneMark_model.63122_t
Valid prediction for GlimmerHMM_glimmerT_36675-T1
Valid prediction for snap_scaffold_15-snap.789-T1
Valid prediction for GeneMark_model.63098_t
Valid prediction for snap_scaffold_15-snap.775-T1
Valid prediction for GeneMark_model.63106_t
Valid prediction for GeneMark_model.63115_t
Valid prediction for Augustus_model.g24619.t1
Valid prediction for GlimmerHMM_glimmerT_36667-T1
Valid prediction for snap_scaffold_15-snap.758-T1
Valid prediction for GlimmerHMM_glimmerT_36660-T1
Valid prediction for snap_scaffold_15-snap.786-T1
Valid prediction for GeneMark_model.63120_t
Valid prediction for snap_scaffold_15-snap.765-T1
Valid prediction for snap_scaffold_15-snap.793-T1
Valid prediction for Augustus_model.g24618.t1
Valid prediction for snap_scaffold_15-snap.755-T1
Valid prediction for GeneMark_model.63127_t
Valid prediction for GeneMark_model.63075_t
Valid prediction for pasa_asmbl_15118.p1
Valid prediction for GeneMark_model.63097_t
Valid prediction for GeneMark_model.63121_t
Valid prediction for snap_scaffold_15-snap.782-T1
Valid prediction for snap_scaffold_15-snap.766-T1
Valid prediction for GeneMark_model.63113_t
Valid prediction for Augustus_model.g24615.t1
Valid prediction for GeneMark_model.63118_t
Valid prediction for snap_scaffold_15-snap.794-T1
Valid prediction for snap_scaffold_15-snap.778-T1
Valid prediction for GlimmerHMM_glimmerT_36655-T1
Valid prediction for GlimmerHMM_glimmerT_36668-T1
Valid prediction for GlimmerHMM_glimmerT_36666-T1
Valid prediction for GlimmerHMM_glimmerT_36653-T1
Valid prediction for Augustus_model.g24624.t1
Valid prediction for snap_scaffold_15-snap.795-T1
Valid prediction for GeneMark_model.63093_t
Valid prediction for snap_scaffold_15-snap.776-T1
Valid prediction for GeneMark_model.63091_t
Valid prediction for GeneMark_model.63099_t
Valid prediction for CodingQuarry_transcript_17919-T1
Valid prediction for GeneMark_model.63134_t
Valid prediction for Augustus_model.g24612.t1
Valid prediction for GeneMark_model.63130_t
Valid prediction for snap_scaffold_15-snap.781-T1
Valid prediction for GeneMark_model.63133_t
Valid prediction for GlimmerHMM_glimmerT_36676-T1
Valid prediction for GeneMark_model.63116_t
Couldn't classify 66403, 66676
Sorry, prediction pasa_asmbl_15112.p1 fails validation.
(ATG)	 TC	61508-61777	GT	AGG
(GTT)	 AG	63486-63778	GT	AGG
(GAG)	 AG	66403-66676	AA	CCA
-recovered pasa_asmbl_15112.p1, initial, 61508, 61777
-recovered pasa_asmbl_15112.p1, internal, 63486, 63778
Valid prediction for snap_scaffold_15-snap.796-T1
Valid prediction for HiQ_model.g24620.t1
Valid prediction for GlimmerHMM_glimmerT_36672-T1
Valid prediction for pasa_asmbl_15121.p1
Valid prediction for GlimmerHMM_glimmerT_36665-T1
Valid prediction for GeneMark_model.63095_t
Valid prediction for GlimmerHMM_glimmerT_36677-T1
Valid prediction for Augustus_model.g24613.t1
Valid prediction for Augustus_model.g24617.t1
Valid prediction for GlimmerHMM_glimmerT_36674-T1
Valid prediction for GlimmerHMM_glimmerT_36663-T1
Valid prediction for GeneMark_model.63083_t
Valid prediction for snap_scaffold_15-snap.769-T1
Valid prediction for Augustus_model.g24614.t1
Valid prediction for snap_scaffold_15-snap.753-T1
Valid prediction for GlimmerHMM_glimmerT_36654-T1
Valid prediction for HiQ_model.g24625.t1
Valid prediction for GeneMark_model.63078_t
Valid prediction for GlimmerHMM_glimmerT_36671-T1
Valid prediction for GeneMark_model.63128_t
Valid prediction for Augustus_model.g24611.t1
Valid prediction for GeneMark_model.63088_t
Valid prediction for GeneMark_model.63109_t
Couldn't classify 216553, 216670
Couldn't classify 218022, 218203
Sorry, prediction pasa_asmbl_15865.p1 fails validation.
(ACG)	 TG	216553-216670	GT	AGG
(GAG)	 AG	218022-218203	TA	GGT
Valid prediction for snap_scaffold_15-snap.784-T1
Valid prediction for GeneMark_model.63125_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5668, rend_intergenic: 5460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23507, rend_intergenic: 6963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40568, rend_intergenic: 23924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43014, rend_intergenic: 42177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58979, rend_intergenic: 56228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68068, rend_intergenic: 65405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84091, rend_intergenic: 80548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91676, rend_intergenic: 88410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97698, rend_intergenic: 96770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125075, rend_intergenic: 104412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129000, rend_intergenic: 125821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133982, rend_intergenic: 132624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140620, rend_intergenic: 134327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153845, rend_intergenic: 150721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187198, rend_intergenic: 184465  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207316, rend_intergenic: 189074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 239954
-exon list size: 761


building trellis

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87.0    
87.2    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.6    
89.8    
89.9    
90.0    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.1    
93.2    
93.3    
93.4    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
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    
99.0    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 5668, rend_intergenic: 5460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23507, rend_intergenic: 6963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40568, rend_intergenic: 23924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43014, rend_intergenic: 42177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58979, rend_intergenic: 56228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68068, rend_intergenic: 65405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84091, rend_intergenic: 80548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91676, rend_intergenic: 88410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97698, rend_intergenic: 96770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125075, rend_intergenic: 104412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129000, rend_intergenic: 125821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133982, rend_intergenic: 132624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140620, rend_intergenic: 134327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153845, rend_intergenic: 150721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187198, rend_intergenic: 184465  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207316, rend_intergenic: 189074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support