-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_3888078-4053789

-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_12-snap.828-T1
Valid prediction for GlimmerHMM_glimmerT_29752-T1
Valid prediction for GeneMark_model.51427_t
Valid prediction for GeneMark_model.51436_t
Valid prediction for GlimmerHMM_glimmerT_29769-T1
Valid prediction for GlimmerHMM_glimmerT_29753-T1
Valid prediction for snap_scaffold_12-snap.820-T1
Valid prediction for snap_scaffold_12-snap.800-T1
Valid prediction for GeneMark_model.51419_t
Valid prediction for GlimmerHMM_glimmerT_29768-T1
Valid prediction for Augustus_model.g19813.t1
Valid prediction for GeneMark_model.51430_t
Valid prediction for Augustus_model.g19815.t1
Valid prediction for GeneMark_model.51429_t
Valid prediction for Augustus_model.g19811.t1
Valid prediction for CodingQuarry_transcript_10142-T1
Valid prediction for snap_scaffold_12-snap.822-T1
Valid prediction for GlimmerHMM_glimmerT_29763-T1
Valid prediction for snap_scaffold_12-snap.821-T1
Valid prediction for snap_scaffold_12-snap.816-T1
Valid prediction for CodingQuarry_transcript_10141-T1
Valid prediction for Augustus_model.g19805.t1
Valid prediction for GeneMark_model.51406_t
Valid prediction for Augustus_model.g19816.t1
Valid prediction for GeneMark_model.51431_t
Valid prediction for GlimmerHMM_glimmerT_29749-T1
Valid prediction for GeneMark_model.51426_t
Valid prediction for GlimmerHMM_glimmerT_29758-T1
Valid prediction for GlimmerHMM_glimmerT_29771-T1
Valid prediction for snap_scaffold_12-snap.815-T1
Valid prediction for HiQ_model.g19804.t1
Valid prediction for GeneMark_model.51439_t
Valid prediction for GeneMark_model.51435_t
Valid prediction for snap_scaffold_12-snap.818-T1
Valid prediction for Augustus_model.g19814.t1
Couldn't classify 75014, 75097
Sorry, prediction pasa_asmbl_8537.p1 fails validation.
(GCG)	 TG	75014-75097	GC	AGG
(GAG)	 AG	75927-76032	GT	TTG
(TCT)	 AG	76375-76527	GT	GAG
(GTG)	 AG	76655-76726	GT	AGG
(ACT)	 AG	76926-77031	GT	AGG
(TTC)	 AG	77224-77266	GT	AGG
(CAG)	 AG	77817-77903	GT	AGG
(GTC)	 AG	78466-78546	GT	AGG
(GCT)	 AG	78906-78956	AA	AAA
-recovered pasa_asmbl_8537.p1, terminal, 78906, 78956
-recovered pasa_asmbl_8537.p1, internal, 75927, 76032
-recovered pasa_asmbl_8537.p1, internal, 76375, 76527
-recovered pasa_asmbl_8537.p1, internal, 76655, 76726
-recovered pasa_asmbl_8537.p1, internal, 76926, 77031
-recovered pasa_asmbl_8537.p1, internal, 77224, 77266
-recovered pasa_asmbl_8537.p1, internal, 77817, 77903
-recovered pasa_asmbl_8537.p1, internal, 78466, 78546
Valid prediction for snap_scaffold_12-snap.830-T1
Valid prediction for GeneMark_model.51421_t
Valid prediction for snap_scaffold_12-snap.802-T1
Valid prediction for GeneMark_model.51438_t
Valid prediction for GlimmerHMM_glimmerT_29751-T1
Valid prediction for GeneMark_model.51413_t
Valid prediction for snap_scaffold_12-snap.799-T1
Valid prediction for GlimmerHMM_glimmerT_29755-T1
Valid prediction for GeneMark_model.51416_t
Valid prediction for Augustus_model.g19807.t1
Valid prediction for Augustus_model.g19810.t1
Valid prediction for snap_scaffold_12-snap.812-T1
Valid prediction for GeneMark_model.51410_t
Valid prediction for snap_scaffold_12-snap.826-T1
Valid prediction for snap_scaffold_12-snap.809-T1
Valid prediction for GlimmerHMM_glimmerT_29762-T1
Valid prediction for snap_scaffold_12-snap.804-T1
Valid prediction for GeneMark_model.51405_t
Valid prediction for Augustus_model.g19809.t1
Valid prediction for snap_scaffold_12-snap.808-T1
Valid prediction for GeneMark_model.51415_t
Valid prediction for CodingQuarry_transcript_10140-T1
Valid prediction for GlimmerHMM_glimmerT_29764-T1
Valid prediction for GlimmerHMM_glimmerT_29754-T1
Valid prediction for GlimmerHMM_glimmerT_29765-T1
Valid prediction for snap_scaffold_12-snap.806-T1
Couldn't classify 7079, 7151
Couldn't classify 11113, 11205
Sorry, prediction pasa_asmbl_8535.p1 fails validation.
(TAC)	 AA	7079-7151	GT	TGG
(GTT)	 AG	7445-7527	GT	CAG
(GTG)	 AG	7899-8018	GT	GTG
(TTG)	 AG	8448-8541	GT	CAG
(GTG)	 AG	8722-8819	GT	CGG
(AAA)	 AG	9089-9162	GT	GAG
(TGA)	 AG	9265-9340	GT	AGG
(AGC)	 AG	11113-11205	GT	AGG
add_exon() Sorry, pasa_asmbl_8535.p1 9089-9162-terminal-2 is invalid.
-recovered pasa_asmbl_8535.p1, terminal, 9089, 9162
-recovered pasa_asmbl_8535.p1, internal, 7445, 7527
-recovered pasa_asmbl_8535.p1, internal, 7899, 8018
-recovered pasa_asmbl_8535.p1, internal, 8448, 8541
-recovered pasa_asmbl_8535.p1, internal, 8722, 8819
-recovered pasa_asmbl_8535.p1, internal, 9089, 9162
-recovered pasa_asmbl_8535.p1, internal, 9265, 9340
-recovered pasa_asmbl_8535.p1, internal, 11113, 11205
Valid prediction for snap_scaffold_12-snap.823-T1
Valid prediction for snap_scaffold_12-snap.827-T1
Valid prediction for GlimmerHMM_glimmerT_29750-T1
Valid prediction for GeneMark_model.51417_t

-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.51412_t
Valid prediction for GeneMark_model.51425_t
Valid prediction for snap_scaffold_12-snap.805-T1
Valid prediction for GeneMark_model.51407_t
Valid prediction for GeneMark_model.51437_t
Valid prediction for GlimmerHMM_glimmerT_29759-T1
Valid prediction for GeneMark_model.51414_t
Valid prediction for Augustus_model.g19817.t1
Valid prediction for GeneMark_model.51418_t
Valid prediction for GlimmerHMM_glimmerT_29760-T1
Valid prediction for snap_scaffold_12-snap.824-T1
Valid prediction for GlimmerHMM_glimmerT_29767-T1
Valid prediction for GeneMark_model.51408_t
Valid prediction for snap_scaffold_12-snap.803-T1
Couldn't classify 82672, 82837
Sorry, prediction pasa_asmbl_7511.p1 fails validation.
(AAA)	 AG	82672-82837	GT	AGG
(GTC)	 AG	83469-83929	CT	GAC
-recovered pasa_asmbl_7511.p1, terminal, 83469, 83929
-recovered pasa_asmbl_7511.p1, internal, 82672, 82837
Valid prediction for GeneMark_model.51411_t
Valid prediction for GeneMark_model.51432_t
Valid prediction for GlimmerHMM_glimmerT_29766-T1
Valid prediction for GeneMark_model.51420_t
Valid prediction for GeneMark_model.51423_t
Valid prediction for snap_scaffold_12-snap.811-T1
Valid prediction for GeneMark_model.51440_t
Valid prediction for HiQ_model.g19812.t1
Valid prediction for snap_scaffold_12-snap.831-T1
Valid prediction for snap_scaffold_12-snap.829-T1
Valid prediction for GlimmerHMM_glimmerT_29770-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.51424_t
Valid prediction for GeneMark_model.51433_t
Valid prediction for Augustus_model.g19806.t1
Valid prediction for snap_scaffold_12-snap.825-T1
Valid prediction for Augustus_model.g19808.t1
Valid prediction for GeneMark_model.51409_t
Valid prediction for GlimmerHMM_glimmerT_29756-T1
Valid prediction for snap_scaffold_12-snap.817-T1
Valid prediction for GeneMark_model.51428_t
Valid prediction for GeneMark_model.51434_t
Valid prediction for GlimmerHMM_glimmerT_29772-T1
Valid prediction for GlimmerHMM_glimmerT_29757-T1
Valid prediction for snap_scaffold_12-snap.810-T1
Valid prediction for snap_scaffold_12-snap.801-T1
Valid prediction for snap_scaffold_12-snap.813-T1
Valid prediction for snap_scaffold_12-snap.807-T1
Valid prediction for snap_scaffold_12-snap.814-T1
Valid prediction for GlimmerHMM_glimmerT_29773-T1
Valid prediction for GlimmerHMM_glimmerT_29774-T1
Valid prediction for Augustus_model.g19818.t1
Valid prediction for GlimmerHMM_glimmerT_29761-T1
Valid prediction for snap_scaffold_12-snap.819-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11259, rend_intergenic: 7827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24285, rend_intergenic: 20778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27396, rend_intergenic: 25650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31377, rend_intergenic: 28338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56193, rend_intergenic: 53614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72340, rend_intergenic: 64144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96161, rend_intergenic: 92628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113041, rend_intergenic: 111639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156701, rend_intergenic: 152936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 165712
-exon list size: 441


building trellis

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89.6    
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91.9    
92.1    
92.3    
92.6    
92.8    
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96.6    
96.8    
97.1    
97.3    
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97.7    
98.0    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 11259, rend_intergenic: 7827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24285, rend_intergenic: 20778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27396, rend_intergenic: 25650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31377, rend_intergenic: 28338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56193, rend_intergenic: 53614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72340, rend_intergenic: 64144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96161, rend_intergenic: 92628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113041, rend_intergenic: 111639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156701, rend_intergenic: 152936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support