-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_17334717-17524823

-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 HiQ_model.g18958.t1
Valid prediction for snap_scaffold_11-snap.3578-T1
Valid prediction for Augustus_model.g18977.t1
Valid prediction for GlimmerHMM_glimmerT_28623-T1
Valid prediction for GlimmerHMM_glimmerT_28636-T1
Valid prediction for snap_scaffold_11-snap.3579-T1
Valid prediction for HiQ_model.g18956.t1
Valid prediction for GlimmerHMM_glimmerT_28632-T1
Valid prediction for CodingQuarry_transcript_8365-T1
Valid prediction for pasa_asmbl_6220.p1
Valid prediction for snap_scaffold_11-snap.3574-T1
Valid prediction for pasa_asmbl_6218.p1
Valid prediction for snap_scaffold_11-snap.3577-T1
Valid prediction for snap_scaffold_11-snap.3557-T1
Valid prediction for snap_scaffold_11-snap.3553-T1
Valid prediction for Augustus_model.g18969.t1
Valid prediction for HiQ_model.g18952.t1
Valid prediction for snap_scaffold_11-snap.3550-T1
Valid prediction for GlimmerHMM_glimmerT_28645-T1
Valid prediction for snap_scaffold_11-snap.3535-T1
Valid prediction for GlimmerHMM_glimmerT_28639-T1
Valid prediction for pasa_asmbl_6228.p1
Valid prediction for snap_scaffold_11-snap.3576-T1
Valid prediction for snap_scaffold_11-snap.3564-T1
Valid prediction for HiQ_model.g18954.t1
Valid prediction for snap_scaffold_11-snap.3543-T1
Valid prediction for Augustus_model.g18968.t1
Valid prediction for GlimmerHMM_glimmerT_28624-T1
Valid prediction for snap_scaffold_11-snap.3538-T1
Valid prediction for pasa_asmbl_6217.p1
Valid prediction for snap_scaffold_11-snap.3536-T1
Valid prediction for HiQ_model.g18961.t1
Valid prediction for snap_scaffold_11-snap.3571-T1
Valid prediction for snap_scaffold_11-snap.3559-T1
Valid prediction for CodingQuarry_transcript_8368-T1
Valid prediction for GlimmerHMM_glimmerT_28633-T1
Valid prediction for HiQ_model.g18975.t1
Valid prediction for GlimmerHMM_glimmerT_28642-T1
Valid prediction for GlimmerHMM_glimmerT_28628-T1
Valid prediction for Augustus_model.g18967.t1
Valid prediction for snap_scaffold_11-snap.3544-T1
Valid prediction for snap_scaffold_11-snap.3561-T1
Valid prediction for Augustus_model.g18962.t1
Valid prediction for Augustus_model.g18965.t1
Valid prediction for GlimmerHMM_glimmerT_28640-T1
Valid prediction for snap_scaffold_11-snap.3570-T1
Valid prediction for Augustus_model.g18970.t1
Valid prediction for Augustus_model.g18964.t1
Valid prediction for snap_scaffold_11-snap.3552-T1
Valid prediction for Augustus_model.g18974.t1
Valid prediction for GlimmerHMM_glimmerT_28647-T1
Valid prediction for snap_scaffold_11-snap.3556-T1
Valid prediction for snap_scaffold_11-snap.3540-T1
Valid prediction for pasa_asmbl_6214.p1
Valid prediction for Augustus_model.g18971.t1
Valid prediction for snap_scaffold_11-snap.3563-T1
Valid prediction for CodingQuarry_transcript_8363-T1
Valid prediction for snap_scaffold_11-snap.3551-T1
Valid prediction for GlimmerHMM_glimmerT_28626-T1
Valid prediction for Augustus_model.g18972.t1
Valid prediction for snap_scaffold_11-snap.3549-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 snap_scaffold_11-snap.3575-T1
Valid prediction for Augustus_model.g18953.t1
Valid prediction for Augustus_model.g18978.t1
Valid prediction for snap_scaffold_11-snap.3537-T1
Valid prediction for GlimmerHMM_glimmerT_28629-T1
Valid prediction for snap_scaffold_11-snap.3573-T1
Valid prediction for snap_scaffold_11-snap.3534-T1
Valid prediction for GlimmerHMM_glimmerT_28646-T1
Valid prediction for snap_scaffold_11-snap.3554-T1
Valid prediction for snap_scaffold_11-snap.3547-T1
Valid prediction for Augustus_model.g18957.t1
Valid prediction for GlimmerHMM_glimmerT_28625-T1
Valid prediction for HiQ_model.g18959.t1
Valid prediction for snap_scaffold_11-snap.3560-T1
Valid prediction for snap_scaffold_11-snap.3568-T1
Valid prediction for snap_scaffold_11-snap.3541-T1
Valid prediction for snap_scaffold_11-snap.3569-T1
Valid prediction for HiQ_model.g18976.t1
Valid prediction for Augustus_model.g18966.t1
Valid prediction for snap_scaffold_11-snap.3562-T1
Valid prediction for snap_scaffold_11-snap.3558-T1
Valid prediction for snap_scaffold_11-snap.3542-T1
Valid prediction for pasa_asmbl_7267.p1
Valid prediction for GlimmerHMM_glimmerT_28638-T1
Valid prediction for CodingQuarry_transcript_8369-T1
Valid prediction for pasa_asmbl_7273.p1
Valid prediction for GlimmerHMM_glimmerT_28634-T1
Valid prediction for snap_scaffold_11-snap.3539-T1
Valid prediction for snap_scaffold_11-snap.3546-T1
Valid prediction for Augustus_model.g18973.t1
Valid prediction for GlimmerHMM_glimmerT_28637-T1
Valid prediction for GlimmerHMM_glimmerT_28643-T1
Couldn't classify 49585, 49744
Sorry, prediction pasa_asmbl_7271.p1 fails validation.
(TAT)	 AC	49585-49744	GT	CGG
(ATG)	 AG	49966-50185	GT	CGG
(ATA)	 AG	50516-50747	AG	GAA
add_exon() Sorry, pasa_asmbl_7271.p1 49966-50185-initial-1 is invalid.
-recovered pasa_asmbl_7271.p1, initial, 49966, 50185
-recovered pasa_asmbl_7271.p1, terminal, 50516, 50747
-recovered pasa_asmbl_7271.p1, internal, 49966, 50185
Valid prediction for snap_scaffold_11-snap.3555-T1
Valid prediction for snap_scaffold_11-snap.3580-T1
Valid prediction for snap_scaffold_11-snap.3567-T1
Valid prediction for pasa_asmbl_7274.p1
Valid prediction for snap_scaffold_11-snap.3566-T1
Valid prediction for GlimmerHMM_glimmerT_28631-T1
Valid prediction for GlimmerHMM_glimmerT_28635-T1
Valid prediction for GlimmerHMM_glimmerT_28627-T1
Valid prediction for CodingQuarry_transcript_8364-T1
Valid prediction for CodingQuarry_transcript_8367-T1
Valid prediction for Augustus_model.g18960.t1
Valid prediction for Augustus_model.g18955.t1
Valid prediction for GlimmerHMM_glimmerT_28630-T1
Valid prediction for CodingQuarry_transcript_8366-T1
Valid prediction for GlimmerHMM_glimmerT_28648-T1
Valid prediction for GlimmerHMM_glimmerT_28644-T1
Valid prediction for snap_scaffold_11-snap.3565-T1
Valid prediction for snap_scaffold_11-snap.3545-T1
Valid prediction for GlimmerHMM_glimmerT_28622-T1
Valid prediction for GlimmerHMM_glimmerT_28641-T1
Valid prediction for pasa_asmbl_7265.p1
Valid prediction for snap_scaffold_11-snap.3548-T1
Valid prediction for HiQ_model.g18963.t1
Valid prediction for snap_scaffold_11-snap.3572-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11422, rend_intergenic: 11054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24724, rend_intergenic: 18500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66237, rend_intergenic: 61948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82544, rend_intergenic: 75955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89969, rend_intergenic: 86827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91708, rend_intergenic: 89985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95072, rend_intergenic: 91737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96810, rend_intergenic: 95446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97358, rend_intergenic: 96928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104484, rend_intergenic: 100371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132398, rend_intergenic: 108810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178084, rend_intergenic: 166834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190107
-exon list size: 454


building trellis

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31.8    
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34.9    
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86.0    
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88.8    
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89.9    
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90.4    
90.6    
90.8    
91.0    
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91.4    
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92.5    
92.8    
93.0    
93.2    
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93.6    
93.9    
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97.6    
97.8    
98.0    
98.2    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 11422, rend_intergenic: 11054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24724, rend_intergenic: 18500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66237, rend_intergenic: 61948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82544, rend_intergenic: 75955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89969, rend_intergenic: 86827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91708, rend_intergenic: 89985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95072, rend_intergenic: 91737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96810, rend_intergenic: 95446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97358, rend_intergenic: 96928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104484, rend_intergenic: 100371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132398, rend_intergenic: 108810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178084, rend_intergenic: 166834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support