-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_8166174-8408853

-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 GlimmerHMM_glimmerT_36547-T1
Valid prediction for GlimmerHMM_glimmerT_36574-T1
Valid prediction for GlimmerHMM_glimmerT_36567-T1
Valid prediction for snap_scaffold_15-snap.1730-T1
Valid prediction for GlimmerHMM_glimmerT_36565-T1
Valid prediction for GlimmerHMM_glimmerT_36579-T1
Valid prediction for GlimmerHMM_glimmerT_36578-T1
Valid prediction for snap_scaffold_15-snap.1740-T1
Valid prediction for snap_scaffold_15-snap.1736-T1
Valid prediction for snap_scaffold_15-snap.1737-T1
Valid prediction for GlimmerHMM_glimmerT_36550-T1
Valid prediction for snap_scaffold_15-snap.1756-T1
Valid prediction for Augustus_model.g24340.t1
Couldn't classify 198166, 198573
Sorry, prediction pasa_asmbl_14841.p1 fails validation.
(CCA)	 GG	198166-198573	CG	AGC
Valid prediction for GlimmerHMM_glimmerT_36571-T1
Valid prediction for GlimmerHMM_glimmerT_36556-T1
Valid prediction for GlimmerHMM_glimmerT_36561-T1
Valid prediction for snap_scaffold_15-snap.1748-T1
Valid prediction for snap_scaffold_15-snap.1746-T1
Valid prediction for snap_scaffold_15-snap.1745-T1
Valid prediction for Augustus_model.g24346.t1
Valid prediction for snap_scaffold_15-snap.1741-T1
Valid prediction for snap_scaffold_15-snap.1755-T1
Valid prediction for GlimmerHMM_glimmerT_36549-T1
Valid prediction for snap_scaffold_15-snap.1743-T1
Couldn't classify 133, 423
Sorry, prediction pasa_asmbl_15323.p1 fails validation.
(AAA)	 CC	133-423	GT	AGG
(GTG)	 AG	617-721	AG	AGA
-recovered pasa_asmbl_15323.p1, terminal, 617, 721
Valid prediction for snap_scaffold_15-snap.1722-T1
Valid prediction for snap_scaffold_15-snap.1731-T1
Valid prediction for snap_scaffold_15-snap.1733-T1
Valid prediction for GlimmerHMM_glimmerT_36569-T1
Couldn't classify 183989, 184010
Couldn't classify 185006, 185376
Sorry, prediction pasa_asmbl_15936.p1 fails validation.
(GAC)	 CT	183989-184010	GT	AGG
(CTC)	 AG	184198-184334	GC	AGG
(GAA)	 AG	184643-184802	GT	AGG
(TCA)	 AG	185006-185376	GG	GAG
-recovered pasa_asmbl_15936.p1, internal, 184198, 184334
-recovered pasa_asmbl_15936.p1, internal, 184643, 184802
Valid prediction for snap_scaffold_15-snap.1753-T1
Valid prediction for snap_scaffold_15-snap.1758-T1
Valid prediction for Augustus_model.g24350.t1
Valid prediction for Augustus_model.g24349.t1
Valid prediction for snap_scaffold_15-snap.1751-T1
Valid prediction for snap_scaffold_15-snap.1744-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_15-snap.1716-T1
Valid prediction for GlimmerHMM_glimmerT_36577-T1
Valid prediction for snap_scaffold_15-snap.1750-T1
Valid prediction for Augustus_model.g24348.t1
Valid prediction for Augustus_model.g24341.t1
Valid prediction for snap_scaffold_15-snap.1718-T1
Valid prediction for snap_scaffold_15-snap.1738-T1
Valid prediction for snap_scaffold_15-snap.1726-T1
Valid prediction for Augustus_model.g24351.t1
Valid prediction for snap_scaffold_15-snap.1717-T1
Valid prediction for snap_scaffold_15-snap.1759-T1
Valid prediction for Augustus_model.g24342.t1
Valid prediction for snap_scaffold_15-snap.1728-T1
Valid prediction for snap_scaffold_15-snap.1714-T1
Valid prediction for GlimmerHMM_glimmerT_36570-T1
Valid prediction for snap_scaffold_15-snap.1723-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_36548-T1
Valid prediction for snap_scaffold_15-snap.1739-T1
Valid prediction for snap_scaffold_15-snap.1757-T1
Valid prediction for GlimmerHMM_glimmerT_36560-T1
Valid prediction for Augustus_model.g24347.t1
Valid prediction for snap_scaffold_15-snap.1747-T1
Valid prediction for GlimmerHMM_glimmerT_36553-T1
Valid prediction for Augustus_model.g24344.t1
Valid prediction for GlimmerHMM_glimmerT_36564-T1
Valid prediction for snap_scaffold_15-snap.1724-T1
Valid prediction for Augustus_model.g24353.t1
Valid prediction for snap_scaffold_15-snap.1729-T1
Valid prediction for snap_scaffold_15-snap.1742-T1
Valid prediction for GlimmerHMM_glimmerT_36563-T1
Valid prediction for snap_scaffold_15-snap.1721-T1
Valid prediction for GlimmerHMM_glimmerT_36572-T1
Valid prediction for Augustus_model.g24352.t1
Valid prediction for snap_scaffold_15-snap.1715-T1
Valid prediction for GlimmerHMM_glimmerT_36558-T1
Valid prediction for GlimmerHMM_glimmerT_36576-T1
Valid prediction for GlimmerHMM_glimmerT_36575-T1
Valid prediction for GlimmerHMM_glimmerT_36562-T1
Valid prediction for GlimmerHMM_glimmerT_36568-T1
Valid prediction for snap_scaffold_15-snap.1725-T1
Valid prediction for snap_scaffold_15-snap.1752-T1
Valid prediction for GlimmerHMM_glimmerT_36557-T1
Valid prediction for snap_scaffold_15-snap.1754-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_36559-T1
Valid prediction for HiQ_model.g24345.t1
Valid prediction for Augustus_model.g24354.t1
Valid prediction for GlimmerHMM_glimmerT_36552-T1
Valid prediction for snap_scaffold_15-snap.1735-T1
Valid prediction for snap_scaffold_15-snap.1760-T1
Valid prediction for Augustus_model.g24343.t1
Valid prediction for snap_scaffold_15-snap.1720-T1
Valid prediction for snap_scaffold_15-snap.1734-T1
Valid prediction for GlimmerHMM_glimmerT_36555-T1
Valid prediction for GlimmerHMM_glimmerT_36573-T1
Valid prediction for snap_scaffold_15-snap.1727-T1
Valid prediction for CodingQuarry_transcript_18067-T1
Valid prediction for snap_scaffold_15-snap.1749-T1
Couldn't classify 117087, 117174
Sorry, prediction pasa_asmbl_14335.p1 fails validation.
(TAT)	 GC	117087-117174	GT	ACG
(GAT)	 AG	117425-117551	GT	AAG
(GTT)	 AG	117646-117764	GT	TGG
(GTA)	 AG	117881-118015	GT	AGG
(GGG)	 AG	118151-118332	GT	CAG
(ATC)	 AG	118491-118712	TG	GAT
-recovered pasa_asmbl_14335.p1, terminal, 118491, 118712
-recovered pasa_asmbl_14335.p1, internal, 117425, 117551
-recovered pasa_asmbl_14335.p1, internal, 117646, 117764
-recovered pasa_asmbl_14335.p1, internal, 117881, 118015
-recovered pasa_asmbl_14335.p1, internal, 118151, 118332
Valid prediction for snap_scaffold_15-snap.1719-T1
Valid prediction for GlimmerHMM_glimmerT_36551-T1
Valid prediction for GlimmerHMM_glimmerT_36554-T1
Valid prediction for GlimmerHMM_glimmerT_36566-T1
Valid prediction for snap_scaffold_15-snap.1732-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17793, rend_intergenic: 4425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29785, rend_intergenic: 19169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45137, rend_intergenic: 30574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46909, rend_intergenic: 45195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53000, rend_intergenic: 48460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59388, rend_intergenic: 53208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63964, rend_intergenic: 60148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67991, rend_intergenic: 64100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74420, rend_intergenic: 68041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77008, rend_intergenic: 74869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105447, rend_intergenic: 80380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115888, rend_intergenic: 107285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121109, rend_intergenic: 117392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122658, rend_intergenic: 121379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131060, rend_intergenic: 130065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161166, rend_intergenic: 132416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177525, rend_intergenic: 166414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185904, rend_intergenic: 182346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235920, rend_intergenic: 230604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 242680
-exon list size: 395


building trellis

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35.3    
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40.1    
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92.4    
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92.9    
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97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 17793, rend_intergenic: 4425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29785, rend_intergenic: 19169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45137, rend_intergenic: 30574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46909, rend_intergenic: 45195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53000, rend_intergenic: 48460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59388, rend_intergenic: 53208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63964, rend_intergenic: 60148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67991, rend_intergenic: 64100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74420, rend_intergenic: 68041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77008, rend_intergenic: 74869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105447, rend_intergenic: 80380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115888, rend_intergenic: 107285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121109, rend_intergenic: 117392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122658, rend_intergenic: 121379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131060, rend_intergenic: 130065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161166, rend_intergenic: 132416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177525, rend_intergenic: 166414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185904, rend_intergenic: 182346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235920, rend_intergenic: 230604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support