-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_15788283-15959005

-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_2-snap.3071-T1
Valid prediction for GlimmerHMM_glimmerT_5264-T1
Valid prediction for GeneMark_model.8414_t
Valid prediction for snap_scaffold_2-snap.3052-T1
Valid prediction for snap_scaffold_2-snap.3078-T1
Valid prediction for Augustus_model.g3566.t1
Valid prediction for Augustus_model.g3565.t1
Valid prediction for snap_scaffold_2-snap.3067-T1
Valid prediction for snap_scaffold_2-snap.3080-T1
Valid prediction for snap_scaffold_2-snap.3083-T1
Valid prediction for snap_scaffold_2-snap.3051-T1
Valid prediction for GlimmerHMM_glimmerT_5276-T1
Valid prediction for GlimmerHMM_glimmerT_5266-T1
Valid prediction for snap_scaffold_2-snap.3057-T1
Valid prediction for pasa_asmbl_25111.p1
Valid prediction for snap_scaffold_2-snap.3073-T1
Valid prediction for GeneMark_model.8428_t
Valid prediction for GlimmerHMM_glimmerT_5274-T1
Valid prediction for GlimmerHMM_glimmerT_5258-T1
Couldn't classify 48342, 48878
Sorry, prediction pasa_asmbl_25099.p1 fails validation.
(AGT)	 CC	48342-48878	CA	AAC
Valid prediction for GeneMark_model.8407_t
Valid prediction for GeneMark_model.8424_t
Valid prediction for snap_scaffold_2-snap.3081-T1
Valid prediction for GeneMark_model.8411_t
Valid prediction for GlimmerHMM_glimmerT_5275-T1
Valid prediction for snap_scaffold_2-snap.3082-T1
Valid prediction for snap_scaffold_2-snap.3064-T1
Valid prediction for HiQ_model.g3567.t1
Valid prediction for GeneMark_model.8431_t
Valid prediction for Augustus_model.g3564.t1
Valid prediction for GeneMark_model.8425_t
Valid prediction for snap_scaffold_2-snap.3062-T1
Valid prediction for GeneMark_model.8439_t
Valid prediction for snap_scaffold_2-snap.3076-T1
Valid prediction for GlimmerHMM_glimmerT_5267-T1
Valid prediction for snap_scaffold_2-snap.3069-T1
Valid prediction for GlimmerHMM_glimmerT_5269-T1
Valid prediction for Augustus_model.g3560.t1
Valid prediction for GlimmerHMM_glimmerT_5263-T1
Valid prediction for Augustus_model.g3561.t1
Valid prediction for Augustus_model.g3554.t1
Valid prediction for GeneMark_model.8418_t
Valid prediction for GlimmerHMM_glimmerT_5268-T1
Valid prediction for snap_scaffold_2-snap.3070-T1
Valid prediction for GlimmerHMM_glimmerT_5270-T1
Valid prediction for GeneMark_model.8438_t
Valid prediction for Augustus_model.g3563.t1
Valid prediction for GlimmerHMM_glimmerT_5273-T1
Valid prediction for GlimmerHMM_glimmerT_5251-T1
Valid prediction for snap_scaffold_2-snap.3048-T1
Valid prediction for Augustus_model.g3559.t1
Valid prediction for CodingQuarry_transcript_28731-T1
Valid prediction for GlimmerHMM_glimmerT_5257-T1
Valid prediction for Augustus_model.g3553.t1
Valid prediction for GeneMark_model.8412_t
Valid prediction for HiQ_model.g3568.t1
Valid prediction for pasa_asmbl_25101.p1
Valid prediction for GeneMark_model.8421_t
Valid prediction for Augustus_model.g3558.t1
Valid prediction for GeneMark_model.8440_t
Valid prediction for GeneMark_model.8434_t
Valid prediction for snap_scaffold_2-snap.3058-T1
Valid prediction for snap_scaffold_2-snap.3077-T1
Valid prediction for Augustus_model.g3556.t1
Valid prediction for GlimmerHMM_glimmerT_5255-T1
Valid prediction for snap_scaffold_2-snap.3084-T1
Valid prediction for GeneMark_model.8409_t
Valid prediction for GeneMark_model.8433_t
Valid prediction for Augustus_model.g3550.t1
Couldn't classify 32588, 32664
Sorry, prediction pasa_asmbl_25098.p1 fails validation.
(ATG)	 GT	28178-28976	GT	AGG
(AGT)	 AG	31752-31808	GT	GGG
(ATC)	 AG	32588-32664	GG	CAG
-recovered pasa_asmbl_25098.p1, initial, 28178, 28976
-recovered pasa_asmbl_25098.p1, internal, 31752, 31808
Valid prediction for GeneMark_model.8442_t
Couldn't classify 150187, 150215
Sorry, prediction pasa_asmbl_25108.p1 fails validation.
(ATG)	 AA	147172-147424	GT	GGG
(CCT)	 AG	147719-147803	GT	ATG
(GGA)	 AG	147956-148003	GT	AGG
(ATT)	 AG	148160-148250	GT	CAG
(GGC)	 AG	148411-148545	GT	GGG
(AGC)	 AG	148686-148791	GT	CAG
(TCA)	 AG	148888-148961	GT	CGG
(CTT)	 AG	149096-149256	GT	GGG
(ATT)	 AG	149430-149560	GT	CGG
(ATT)	 AG	149658-149835	GT	GGG
(GGT)	 AG	149940-150079	GT	AGG
(ATT)	 AG	150187-150215	GA	GTG
-recovered pasa_asmbl_25108.p1, initial, 147172, 147424
-recovered pasa_asmbl_25108.p1, internal, 147719, 147803
-recovered pasa_asmbl_25108.p1, internal, 147956, 148003
-recovered pasa_asmbl_25108.p1, internal, 148160, 148250
-recovered pasa_asmbl_25108.p1, internal, 148411, 148545
-recovered pasa_asmbl_25108.p1, internal, 148686, 148791
-recovered pasa_asmbl_25108.p1, internal, 148888, 148961
-recovered pasa_asmbl_25108.p1, internal, 149096, 149256
-recovered pasa_asmbl_25108.p1, internal, 149430, 149560
-recovered pasa_asmbl_25108.p1, internal, 149658, 149835
-recovered pasa_asmbl_25108.p1, internal, 149940, 150079
Valid prediction for GeneMark_model.8403_t
Valid prediction for snap_scaffold_2-snap.3075-T1
Valid prediction for snap_scaffold_2-snap.3072-T1
Valid prediction for Augustus_model.g3557.t1
Valid prediction for GeneMark_model.8437_t
Valid prediction for GeneMark_model.8436_t
Valid prediction for GeneMark_model.8430_t
Valid prediction for GeneMark_model.8405_t
Valid prediction for snap_scaffold_2-snap.3054-T1
Valid prediction for GlimmerHMM_glimmerT_5277-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_2-snap.3063-T1
Valid prediction for GeneMark_model.8415_t
Valid prediction for GeneMark_model.8420_t
Valid prediction for GlimmerHMM_glimmerT_5260-T1
Valid prediction for snap_scaffold_2-snap.3074-T1
Valid prediction for snap_scaffold_2-snap.3068-T1
Valid prediction for GlimmerHMM_glimmerT_5272-T1
Valid prediction for snap_scaffold_2-snap.3047-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.8427_t
Valid prediction for GeneMark_model.8423_t
Valid prediction for GeneMark_model.8432_t
Valid prediction for GeneMark_model.8422_t
Valid prediction for snap_scaffold_2-snap.3079-T1
Valid prediction for Augustus_model.g3555.t1
Valid prediction for GlimmerHMM_glimmerT_5256-T1
Valid prediction for GlimmerHMM_glimmerT_5252-T1
Valid prediction for Augustus_model.g3549.t1
Valid prediction for GlimmerHMM_glimmerT_5261-T1
Valid prediction for GlimmerHMM_glimmerT_5253-T1
Valid prediction for GlimmerHMM_glimmerT_5250-T1
Couldn't classify 87548, 87847
Sorry, prediction pasa_asmbl_23675.p2 fails validation.
(ATG)	 AC	87548-87847	AG	CCA
Valid prediction for snap_scaffold_2-snap.3050-T1
Valid prediction for GeneMark_model.8406_t
Valid prediction for snap_scaffold_2-snap.3049-T1
Valid prediction for GlimmerHMM_glimmerT_5259-T1
Valid prediction for GeneMark_model.8410_t
Valid prediction for GlimmerHMM_glimmerT_5262-T1
Valid prediction for GeneMark_model.8402_t
Valid prediction for snap_scaffold_2-snap.3065-T1
Valid prediction for snap_scaffold_2-snap.3061-T1
Valid prediction for snap_scaffold_2-snap.3066-T1
Valid prediction for snap_scaffold_2-snap.3056-T1
Valid prediction for snap_scaffold_2-snap.3060-T1
Valid prediction for HiQ_model.g3562.t1
Valid prediction for GlimmerHMM_glimmerT_5254-T1
Valid prediction for GeneMark_model.8413_t
Valid prediction for CodingQuarry_transcript_28730-T1
Valid prediction for Augustus_model.g3551.t1
Valid prediction for GlimmerHMM_glimmerT_5265-T1
Valid prediction for GlimmerHMM_glimmerT_5271-T1
Valid prediction for GeneMark_model.8416_t
Valid prediction for GeneMark_model.8404_t
Valid prediction for snap_scaffold_2-snap.3055-T1
Valid prediction for GeneMark_model.8441_t
Valid prediction for GeneMark_model.8435_t
Valid prediction for snap_scaffold_2-snap.3053-T1
Valid prediction for GeneMark_model.8429_t
Valid prediction for GeneMark_model.8426_t
Valid prediction for snap_scaffold_2-snap.3059-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.8419_t
Valid prediction for GeneMark_model.8408_t
Valid prediction for Augustus_model.g3552.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8216, rend_intergenic: 6237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21577, rend_intergenic: 12067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45296, rend_intergenic: 40403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67939, rend_intergenic: 65402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79697, rend_intergenic: 74770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92360, rend_intergenic: 89959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93746, rend_intergenic: 92981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 25173, rend_intergenic: 25170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 170723
-exon list size: 585


building trellis

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91.5    
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92.2    
92.3    
92.5    
92.7    
92.8    
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93.9    
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98.0    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 8216, rend_intergenic: 6237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21577, rend_intergenic: 12067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45296, rend_intergenic: 40403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67939, rend_intergenic: 65402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79697, rend_intergenic: 74770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92360, rend_intergenic: 89959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93746, rend_intergenic: 92981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 25173, rend_intergenic: 25170  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