-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_3054308-3231977

-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_11907-T1
Valid prediction for Augustus_model.g7829.t1
Valid prediction for snap_scaffold_5-snap.620-T1
Couldn't classify 45377, 45503
Sorry, prediction pasa_asmbl_43876.p2 fails validation.
(CTT)	 CT	45377-45503	GT	TCG
(GTG)	 AG	45836-45997	GT	AGG
(GTT)	 AG	46560-46691	GT	AGG
(TGA)	 AG	48149-48218	GT	AGG
(GAT)	 AG	48648-48672	AA	AGA
-recovered pasa_asmbl_43876.p2, terminal, 48648, 48672
-recovered pasa_asmbl_43876.p2, internal, 45836, 45997
-recovered pasa_asmbl_43876.p2, internal, 46560, 46691
-recovered pasa_asmbl_43876.p2, internal, 48149, 48218
Valid prediction for GlimmerHMM_glimmerT_11902-T1
Valid prediction for snap_scaffold_5-snap.615-T1
Valid prediction for Augustus_model.g7823.t1
Valid prediction for GeneMark_model.20059_t
Valid prediction for snap_scaffold_5-snap.609-T1
Valid prediction for GeneMark_model.20048_t
Valid prediction for GlimmerHMM_glimmerT_11904-T1
Valid prediction for Augustus_model.g7828.t1
Valid prediction for snap_scaffold_5-snap.611-T1
Valid prediction for GeneMark_model.20066_t
Valid prediction for GeneMark_model.20044_t
Valid prediction for GeneMark_model.20046_t
Valid prediction for snap_scaffold_5-snap.610-T1
Valid prediction for GlimmerHMM_glimmerT_11909-T1
Valid prediction for GlimmerHMM_glimmerT_11908-T1
Valid prediction for GlimmerHMM_glimmerT_11903-T1
Valid prediction for snap_scaffold_5-snap.625-T1
Valid prediction for GeneMark_model.20036_t
Valid prediction for snap_scaffold_5-snap.621-T1
Valid prediction for snap_scaffold_5-snap.628-T1
Valid prediction for GeneMark_model.20063_t
Valid prediction for GeneMark_model.20071_t
Valid prediction for GeneMark_model.20057_t
Valid prediction for GeneMark_model.20039_t
Valid prediction for GlimmerHMM_glimmerT_11905-T1
Valid prediction for Augustus_model.g7825.t1
Valid prediction for GeneMark_model.20061_t
Couldn't classify 34386, 34434
Couldn't classify 39044, 39165
Sorry, prediction pasa_asmbl_43874.p1 fails validation.
(AAG)	 GC	34386-34434	GT	AGG
(CGC)	 AG	34705-34775	GT	AGG
(CCC)	 AG	35973-36195	GT	TGG
(TGC)	 AG	37387-37502	GT	ACG
(GTT)	 AG	38545-38749	GT	AGG
(CTC)	 AG	39044-39165	GG	CCG
-recovered pasa_asmbl_43874.p1, internal, 34705, 34775
-recovered pasa_asmbl_43874.p1, internal, 35973, 36195
-recovered pasa_asmbl_43874.p1, internal, 37387, 37502
-recovered pasa_asmbl_43874.p1, internal, 38545, 38749
Valid prediction for snap_scaffold_5-snap.630-T1
Valid prediction for GeneMark_model.20052_t
Valid prediction for Augustus_model.g7824.t1
Valid prediction for GeneMark_model.20055_t
Valid prediction for GeneMark_model.20070_t
Valid prediction for GeneMark_model.20068_t
Valid prediction for GeneMark_model.20065_t
Valid prediction for GeneMark_model.20038_t
Couldn't classify 30021, 30096
Couldn't classify 31574, 31706
Sorry, prediction pasa_asmbl_43873.p1 fails validation.
(GTC)	 AC	30021-30096	GT	TGG
(ATG)	 AG	30456-30596	GT	GAG
(ACA)	 AG	31080-31191	GT	TGG
(GAG)	 AG	31574-31706	GG	AGG
add_exon() Sorry, pasa_asmbl_43873.p1 30456-30596-initial-1 is invalid.
-recovered pasa_asmbl_43873.p1, initial, 30456, 30596
add_exon() Sorry, pasa_asmbl_43873.p1 30456-30596-terminal-1 is invalid.
-recovered pasa_asmbl_43873.p1, terminal, 30456, 30596
-recovered pasa_asmbl_43873.p1, internal, 30456, 30596
-recovered pasa_asmbl_43873.p1, internal, 31080, 31191
Valid prediction for GeneMark_model.20041_t
Valid prediction for Augustus_model.g7826.t1
Valid prediction for snap_scaffold_5-snap.633-T1
Valid prediction for snap_scaffold_5-snap.617-T1
Valid prediction for snap_scaffold_5-snap.624-T1
Valid prediction for snap_scaffold_5-snap.623-T1
Valid prediction for snap_scaffold_5-snap.634-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 GeneMark_model.20053_t
Valid prediction for GeneMark_model.20050_t
Valid prediction for GeneMark_model.20051_t
Valid prediction for GeneMark_model.20072_t
Valid prediction for GeneMark_model.20033_t
Valid prediction for GeneMark_model.20043_t
Valid prediction for Augustus_model.g7832.t1
Valid prediction for snap_scaffold_5-snap.616-T1
Valid prediction for GeneMark_model.20054_t
Valid prediction for GeneMark_model.20040_t
Valid prediction for snap_scaffold_5-snap.619-T1
Valid prediction for GeneMark_model.20035_t
Valid prediction for snap_scaffold_5-snap.629-T1
Valid prediction for GeneMark_model.20031_t
Valid prediction for GeneMark_model.20032_t
Valid prediction for snap_scaffold_5-snap.631-T1
Valid prediction for GeneMark_model.20062_t
Valid prediction for GeneMark_model.20037_t
Valid prediction for GlimmerHMM_glimmerT_11906-T1
Valid prediction for GlimmerHMM_glimmerT_11910-T1
Valid prediction for GeneMark_model.20034_t
Valid prediction for Augustus_model.g7833.t1
Valid prediction for GeneMark_model.20049_t
Valid prediction for snap_scaffold_5-snap.635-T1
Valid prediction for GeneMark_model.20064_t
Valid prediction for Augustus_model.g7827.t1
Valid prediction for GeneMark_model.20069_t
Valid prediction for GeneMark_model.20056_t
Valid prediction for GeneMark_model.20045_t
Valid prediction for snap_scaffold_5-snap.618-T1
Valid prediction for snap_scaffold_5-snap.627-T1
Valid prediction for snap_scaffold_5-snap.622-T1
Valid prediction for Augustus_model.g7831.t1
Valid prediction for snap_scaffold_5-snap.612-T1
Valid prediction for GeneMark_model.20058_t
Valid prediction for snap_scaffold_5-snap.614-T1
Valid prediction for GeneMark_model.20067_t
Valid prediction for snap_scaffold_5-snap.613-T1
Valid prediction for snap_scaffold_5-snap.632-T1
Valid prediction for Augustus_model.g7830.t1
Valid prediction for GeneMark_model.20073_t
Valid prediction for GeneMark_model.20060_t
Valid prediction for GlimmerHMM_glimmerT_11901-T1
Valid prediction for GeneMark_model.20047_t
Valid prediction for snap_scaffold_5-snap.626-T1
Valid prediction for GlimmerHMM_glimmerT_11911-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 41210, rend_intergenic: 36443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51474, rend_intergenic: 48932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128295, rend_intergenic: 126566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130117, rend_intergenic: 128729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148059, rend_intergenic: 141952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161733, rend_intergenic: 153852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170274, rend_intergenic: 165592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174482, rend_intergenic: 171035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177670
-exon list size: 485


building trellis

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-found 17 predictions from path traversal
Error with prediction: snap lend_intergenic: 41210, rend_intergenic: 36443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51474, rend_intergenic: 48932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128295, rend_intergenic: 126566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130117, rend_intergenic: 128729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148059, rend_intergenic: 141952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161733, rend_intergenic: 153852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170274, rend_intergenic: 165592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174482, rend_intergenic: 171035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 9 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12530
-exon list size: 8


building trellis

10.0    
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30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support