-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_4024828-4240702

-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_19-snap.867-T1
Valid prediction for snap_scaffold_19-snap.873-T1
Valid prediction for GlimmerHMM_glimmerT_43937-T1
Valid prediction for snap_scaffold_19-snap.872-T1
Valid prediction for GlimmerHMM_glimmerT_43952-T1
Valid prediction for pasa_asmbl_21910.p1
Valid prediction for snap_scaffold_19-snap.868-T1
Couldn't classify 196619, 196698
Sorry, prediction pasa_asmbl_21339.p1 fails validation.
(ATG)	 AG	195234-195292	GT	ATG
(CTG)	 AG	195559-195677	GT	AGG
(AGA)	 AG	195824-195960	GT	AGG
(CCC)	 AG	196102-196193	GT	AGG
(GAG)	 AG	196274-196503	GT	AGG
(ACC)	 AG	196619-196698	TA	GCT
-recovered pasa_asmbl_21339.p1, initial, 195234, 195292
-recovered pasa_asmbl_21339.p1, internal, 195234, 195292
-recovered pasa_asmbl_21339.p1, internal, 195559, 195677
-recovered pasa_asmbl_21339.p1, internal, 195824, 195960
-recovered pasa_asmbl_21339.p1, internal, 196102, 196193
-recovered pasa_asmbl_21339.p1, internal, 196274, 196503
Valid prediction for GlimmerHMM_glimmerT_43955-T1
Valid prediction for snap_scaffold_19-snap.890-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.885-T1
Valid prediction for snap_scaffold_19-snap.870-T1
Valid prediction for GlimmerHMM_glimmerT_43958-T1
Valid prediction for GlimmerHMM_glimmerT_43954-T1
Valid prediction for GlimmerHMM_glimmerT_43938-T1
Valid prediction for snap_scaffold_19-snap.879-T1
Valid prediction for snap_scaffold_19-snap.894-T1
Valid prediction for GlimmerHMM_glimmerT_43939-T1
Valid prediction for snap_scaffold_19-snap.887-T1
Valid prediction for snap_scaffold_19-snap.858-T1
Valid prediction for GlimmerHMM_glimmerT_43953-T1
Valid prediction for snap_scaffold_19-snap.851-T1
Valid prediction for snap_scaffold_19-snap.866-T1
Valid prediction for Augustus_model.g29155.t1
Valid prediction for snap_scaffold_19-snap.862-T1
Valid prediction for snap_scaffold_19-snap.881-T1
Valid prediction for snap_scaffold_19-snap.883-T1
Valid prediction for snap_scaffold_19-snap.882-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_43942-T1
Valid prediction for GlimmerHMM_glimmerT_43962-T1
Valid prediction for snap_scaffold_19-snap.853-T1
Valid prediction for snap_scaffold_19-snap.876-T1
Valid prediction for snap_scaffold_19-snap.857-T1
Valid prediction for GlimmerHMM_glimmerT_43964-T1
Valid prediction for snap_scaffold_19-snap.880-T1
Valid prediction for GlimmerHMM_glimmerT_43956-T1
Valid prediction for snap_scaffold_19-snap.865-T1
Valid prediction for GlimmerHMM_glimmerT_43963-T1
Valid prediction for snap_scaffold_19-snap.856-T1
Valid prediction for snap_scaffold_19-snap.892-T1
Valid prediction for snap_scaffold_19-snap.878-T1
Valid prediction for snap_scaffold_19-snap.855-T1
Valid prediction for snap_scaffold_19-snap.861-T1
Valid prediction for snap_scaffold_19-snap.849-T1
Valid prediction for snap_scaffold_19-snap.859-T1
Couldn't classify 199004, 199084
Sorry, prediction pasa_asmbl_21340.p1 fails validation.
(ATG)	 CC	197805-197832	GT	AGG
(ATA)	 AG	198188-198299	GT	AAG
(GCC)	 AG	198526-198682	GT	AGG
(GTG)	 AG	199004-199084	GA	CAG
-recovered pasa_asmbl_21340.p1, initial, 197805, 197832
-recovered pasa_asmbl_21340.p1, internal, 198188, 198299
-recovered pasa_asmbl_21340.p1, internal, 198526, 198682
Valid prediction for GlimmerHMM_glimmerT_43940-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_43950-T1
Valid prediction for snap_scaffold_19-snap.852-T1
Valid prediction for snap_scaffold_19-snap.864-T1
Valid prediction for GlimmerHMM_glimmerT_43936-T1
Valid prediction for GlimmerHMM_glimmerT_43965-T1
Valid prediction for Augustus_model.g29146.t1
Valid prediction for GlimmerHMM_glimmerT_43947-T1
Valid prediction for Augustus_model.g29145.t1
Valid prediction for GlimmerHMM_glimmerT_43944-T1
Valid prediction for GlimmerHMM_glimmerT_43948-T1
Valid prediction for snap_scaffold_19-snap.886-T1
Valid prediction for Augustus_model.g29148.t1
Valid prediction for snap_scaffold_19-snap.884-T1
Valid prediction for snap_scaffold_19-snap.869-T1
Valid prediction for GlimmerHMM_glimmerT_43957-T1
Valid prediction for Augustus_model.g29154.t1
Valid prediction for GlimmerHMM_glimmerT_43943-T1
Valid prediction for Augustus_model.g29149.t1
Valid prediction for snap_scaffold_19-snap.875-T1
Valid prediction for GlimmerHMM_glimmerT_43959-T1
Valid prediction for GlimmerHMM_glimmerT_43951-T1
Valid prediction for Augustus_model.g29152.t1
Valid prediction for GlimmerHMM_glimmerT_43960-T1
Valid prediction for Augustus_model.g29153.t1
Valid prediction for snap_scaffold_19-snap.896-T1
Valid prediction for GlimmerHMM_glimmerT_43945-T1
Valid prediction for snap_scaffold_19-snap.888-T1
Valid prediction for snap_scaffold_19-snap.889-T1
Valid prediction for snap_scaffold_19-snap.895-T1
Valid prediction for snap_scaffold_19-snap.877-T1
Valid prediction for snap_scaffold_19-snap.897-T1
Valid prediction for snap_scaffold_19-snap.860-T1
Valid prediction for GlimmerHMM_glimmerT_43946-T1
Valid prediction for Augustus_model.g29150.t1
Valid prediction for snap_scaffold_19-snap.871-T1
Valid prediction for GlimmerHMM_glimmerT_43941-T1
Valid prediction for Augustus_model.g29143.t1
Couldn't classify 141991, 142251
Couldn't classify 144273, 144452
Sorry, prediction pasa_asmbl_22127.p1 fails validation.
(TTT)	 TG	141991-142251	GT	AGG
(GGT)	 AG	143729-143884	GT	AGG
(GAA)	 AG	144273-144452	GG	TGG
-recovered pasa_asmbl_22127.p1, internal, 143729, 143884
Valid prediction for snap_scaffold_19-snap.863-T1
Valid prediction for GlimmerHMM_glimmerT_43966-T1
Valid prediction for snap_scaffold_19-snap.850-T1
Valid prediction for Augustus_model.g29151.t1
Valid prediction for snap_scaffold_19-snap.854-T1
Valid prediction for snap_scaffold_19-snap.874-T1
Valid prediction for GlimmerHMM_glimmerT_43961-T1
Valid prediction for Augustus_model.g29147.t1
Valid prediction for Augustus_model.g29144.t1
Valid prediction for GlimmerHMM_glimmerT_43949-T1
Valid prediction for snap_scaffold_19-snap.893-T1
Valid prediction for snap_scaffold_19-snap.891-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7876, rend_intergenic: 3792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25147, rend_intergenic: 11498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31285, rend_intergenic: 28360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44796, rend_intergenic: 31581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50724, rend_intergenic: 46992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63046, rend_intergenic: 50852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65163, rend_intergenic: 63071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103666, rend_intergenic: 68460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108252, rend_intergenic: 107052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113662, rend_intergenic: 109667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117546, rend_intergenic: 114414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123568, rend_intergenic: 117974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126914, rend_intergenic: 123893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127457, rend_intergenic: 126949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160254, rend_intergenic: 132626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169143, rend_intergenic: 168840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171944, rend_intergenic: 169388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179975, rend_intergenic: 177656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200294, rend_intergenic: 198998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201687, rend_intergenic: 200348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 215875
-exon list size: 419


building trellis

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91.9    
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93.3    
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96.2    
96.4    
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96.9    
97.1    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 7876, rend_intergenic: 3792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25147, rend_intergenic: 11498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31285, rend_intergenic: 28360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44796, rend_intergenic: 31581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50724, rend_intergenic: 46992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63046, rend_intergenic: 50852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65163, rend_intergenic: 63071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103666, rend_intergenic: 68460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108252, rend_intergenic: 107052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113662, rend_intergenic: 109667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117546, rend_intergenic: 114414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123568, rend_intergenic: 117974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126914, rend_intergenic: 123893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127457, rend_intergenic: 126949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160254, rend_intergenic: 132626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169143, rend_intergenic: 168840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171944, rend_intergenic: 169388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179975, rend_intergenic: 177656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200294, rend_intergenic: 198998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201687, rend_intergenic: 200348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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