-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_13954716-14117318

-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 GeneMark_model.61396_t
Valid prediction for snap_scaffold_14-snap.2904-T1
Valid prediction for snap_scaffold_14-snap.2890-T1
Valid prediction for GeneMark_model.61423_t
Valid prediction for GeneMark_model.61411_t
Valid prediction for GeneMark_model.61417_t
Valid prediction for snap_scaffold_14-snap.2885-T1
Valid prediction for GeneMark_model.61414_t
Valid prediction for Augustus_model.g24130.t1
Valid prediction for GlimmerHMM_glimmerT_35837-T1
Valid prediction for GlimmerHMM_glimmerT_35831-T1
Valid prediction for GlimmerHMM_glimmerT_35825-T1
Valid prediction for snap_scaffold_14-snap.2893-T1
Valid prediction for GeneMark_model.61427_t
Valid prediction for snap_scaffold_14-snap.2884-T1
Valid prediction for GlimmerHMM_glimmerT_35832-T1
Valid prediction for GeneMark_model.61403_t
Valid prediction for GeneMark_model.61419_t
Valid prediction for GeneMark_model.61413_t
Valid prediction for GlimmerHMM_glimmerT_35826-T1
Valid prediction for snap_scaffold_14-snap.2897-T1
Valid prediction for GlimmerHMM_glimmerT_35840-T1
Valid prediction for GeneMark_model.61434_t
Valid prediction for snap_scaffold_14-snap.2909-T1
Valid prediction for snap_scaffold_14-snap.2887-T1
Valid prediction for GeneMark_model.61401_t
Valid prediction for GeneMark_model.61425_t
Valid prediction for snap_scaffold_14-snap.2899-T1
Valid prediction for snap_scaffold_14-snap.2896-T1
Valid prediction for Augustus_model.g24128.t1
Valid prediction for GlimmerHMM_glimmerT_35828-T1
Valid prediction for GeneMark_model.61432_t
Valid prediction for snap_scaffold_14-snap.2905-T1
Valid prediction for snap_scaffold_14-snap.2903-T1
Valid prediction for GeneMark_model.61407_t
Valid prediction for GlimmerHMM_glimmerT_35830-T1
Valid prediction for Augustus_model.g24132.t1
Valid prediction for GlimmerHMM_glimmerT_35843-T1
Valid prediction for GeneMark_model.61436_t
Valid prediction for GeneMark_model.61394_t
Valid prediction for GeneMark_model.61431_t
Valid prediction for GeneMark_model.61408_t
Valid prediction for GeneMark_model.61416_t
Valid prediction for snap_scaffold_14-snap.2910-T1
Valid prediction for GeneMark_model.61397_t
Valid prediction for snap_scaffold_14-snap.2915-T1
Valid prediction for GlimmerHMM_glimmerT_35841-T1
Valid prediction for Augustus_model.g24127.t1
Valid prediction for snap_scaffold_14-snap.2895-T1
Valid prediction for GlimmerHMM_glimmerT_35846-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_14-snap.2911-T1
Valid prediction for GeneMark_model.61409_t
Valid prediction for pasa_asmbl_13654.p1
Valid prediction for snap_scaffold_14-snap.2907-T1
Valid prediction for GeneMark_model.61420_t
Couldn't classify 10039, 10098
Couldn't classify 11469, 11878
Sorry, prediction pasa_asmbl_13661.p1 fails validation.
(TGT)	 GC	10039-10098	GT	AGG
(ACT)	 AG	10812-10870	GT	AGG
(GTC)	 AG	10995-11143	GT	AGG
(GTG)	 AG	11469-11878	AG	AGA
-recovered pasa_asmbl_13661.p1, internal, 10812, 10870
-recovered pasa_asmbl_13661.p1, internal, 10995, 11143
Valid prediction for GeneMark_model.61400_t
Valid prediction for GeneMark_model.61422_t
Valid prediction for GlimmerHMM_glimmerT_35829-T1
Valid prediction for GeneMark_model.61430_t
Valid prediction for snap_scaffold_14-snap.2892-T1
Sorry, intron length (7) is less than minimum required (10)
Sorry, intron length (7) is less than minimum required (10)
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.61404_t
Valid prediction for CodingQuarry_transcript_15875-T1
Valid prediction for GeneMark_model.61415_t
Valid prediction for GlimmerHMM_glimmerT_35845-T1
Valid prediction for snap_scaffold_14-snap.2906-T1
Valid prediction for GeneMark_model.61406_t
Valid prediction for snap_scaffold_14-snap.2913-T1
Valid prediction for GlimmerHMM_glimmerT_35844-T1
Valid prediction for GlimmerHMM_glimmerT_35839-T1
Valid prediction for GeneMark_model.61435_t
Valid prediction for GeneMark_model.61410_t
Couldn't classify 9405, 9743
Sorry, prediction pasa_asmbl_13663.p2 fails validation.
(GAA)	 CA	9405-9743	GG	CAG
Valid prediction for Augustus_model.g24120.t1
Valid prediction for snap_scaffold_14-snap.2902-T1
Valid prediction for snap_scaffold_14-snap.2891-T1
Valid prediction for GlimmerHMM_glimmerT_35836-T1
Valid prediction for GlimmerHMM_glimmerT_35835-T1
Valid prediction for GlimmerHMM_glimmerT_35833-T1
Valid prediction for GeneMark_model.61433_t
Valid prediction for snap_scaffold_14-snap.2883-T1
Valid prediction for HiQ_model.g24124.t1
Valid prediction for GlimmerHMM_glimmerT_35827-T1
Valid prediction for CodingQuarry_transcript_15876-T1
Valid prediction for GeneMark_model.61393_t
Valid prediction for snap_scaffold_14-snap.2886-T1
Valid prediction for snap_scaffold_14-snap.2914-T1
Valid prediction for GlimmerHMM_glimmerT_35823-T1
Valid prediction for Augustus_model.g24125.t1
Valid prediction for GeneMark_model.61418_t
Valid prediction for GeneMark_model.61412_t
Valid prediction for GlimmerHMM_glimmerT_35834-T1
Valid prediction for snap_scaffold_14-snap.2908-T1
Valid prediction for snap_scaffold_14-snap.2912-T1
Valid prediction for GeneMark_model.61399_t
Valid prediction for GlimmerHMM_glimmerT_35838-T1
Valid prediction for GeneMark_model.61395_t
Valid prediction for GlimmerHMM_glimmerT_35822-T1
Valid prediction for HiQ_model.g24121.t1
Valid prediction for pasa_asmbl_13658.p1
Valid prediction for Augustus_model.g24122.t1
Valid prediction for HiQ_model.g24126.t1
Valid prediction for GeneMark_model.61424_t
Valid prediction for Augustus_model.g24131.t1
Valid prediction for snap_scaffold_14-snap.2889-T1
Valid prediction for snap_scaffold_14-snap.2888-T1
Valid prediction for GeneMark_model.61426_t
Valid prediction for Augustus_model.g24123.t1
Valid prediction for GeneMark_model.61402_t
Valid prediction for snap_scaffold_14-snap.2901-T1
Valid prediction for GeneMark_model.61421_t
Valid prediction for GeneMark_model.61428_t
Valid prediction for snap_scaffold_14-snap.2894-T1
Valid prediction for snap_scaffold_14-snap.2898-T1
Valid prediction for GlimmerHMM_glimmerT_35824-T1
Couldn't classify 50627, 50697
Couldn't classify 54313, 54518
Sorry, prediction pasa_asmbl_13655.p1 fails validation.
(GTG)	 AG	50627-50697	GT	AAG
(GGT)	 AG	52297-52447	GT	AGG
(GTC)	 AG	53341-53449	GT	AGG
(GGA)	 AG	53828-53950	GT	AGG
(GAA)	 AG	54313-54518	CT	CCC
-recovered pasa_asmbl_13655.p1, internal, 50627, 50697
-recovered pasa_asmbl_13655.p1, internal, 52297, 52447
-recovered pasa_asmbl_13655.p1, internal, 53341, 53449
-recovered pasa_asmbl_13655.p1, internal, 53828, 53950
Valid prediction for GlimmerHMM_glimmerT_35842-T1
Valid prediction for Augustus_model.g24129.t1
Valid prediction for snap_scaffold_14-snap.2900-T1
Valid prediction for GlimmerHMM_glimmerT_35821-T1
Valid prediction for GeneMark_model.61429_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11225, rend_intergenic: 3922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15557, rend_intergenic: 12150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18791, rend_intergenic: 17473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21780, rend_intergenic: 19787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38454, rend_intergenic: 32637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48917, rend_intergenic: 42041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63914, rend_intergenic: 51207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113313, rend_intergenic: 108059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135138, rend_intergenic: 132726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147781, rend_intergenic: 145147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158138, rend_intergenic: 157766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 162603
-exon list size: 567


building trellis

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87.3    
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88.4    
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89.5    
89.6    
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90.9    
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91.2    
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91.6    
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92.6    
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96.8    
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97.4    
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98.1    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 11225, rend_intergenic: 3922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15557, rend_intergenic: 12150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18791, rend_intergenic: 17473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21780, rend_intergenic: 19787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38454, rend_intergenic: 32637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48917, rend_intergenic: 42041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63914, rend_intergenic: 51207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113313, rend_intergenic: 108059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135138, rend_intergenic: 132726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147781, rend_intergenic: 145147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158138, rend_intergenic: 157766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support