-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_17457956-17565610

-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_3-snap.3405-T1
Valid prediction for snap_scaffold_3-snap.3423-T1
Valid prediction for Augustus_model.g5565.t1
Valid prediction for GlimmerHMM_glimmerT_8379-T1
Valid prediction for GeneMark_model.13633_t
Valid prediction for HiQ_model.g5569.t1
Valid prediction for snap_scaffold_3-snap.3414-T1
Valid prediction for GlimmerHMM_glimmerT_8383-T1
Valid prediction for GeneMark_model.13630_t
Valid prediction for snap_scaffold_3-snap.3400-T1
Valid prediction for CodingQuarry_transcript_46341-T1
Valid prediction for GlimmerHMM_glimmerT_8377-T1
Valid prediction for GeneMark_model.13652_t
Valid prediction for Augustus_model.g5566.t1
Valid prediction for GeneMark_model.13634_t
Valid prediction for GeneMark_model.13654_t
Valid prediction for GlimmerHMM_glimmerT_8380-T1
Valid prediction for GlimmerHMM_glimmerT_8390-T1
Valid prediction for GlimmerHMM_glimmerT_8381-T1
Valid prediction for GeneMark_model.13636_t
Valid prediction for snap_scaffold_3-snap.3421-T1
Valid prediction for snap_scaffold_3-snap.3424-T1
Valid prediction for GlimmerHMM_glimmerT_8389-T1
Valid prediction for Augustus_model.g5562.t1
Valid prediction for GeneMark_model.13631_t
Valid prediction for GlimmerHMM_glimmerT_8374-T1
Valid prediction for snap_scaffold_3-snap.3417-T1
Valid prediction for CodingQuarry_transcript_46342-T1
Valid prediction for GeneMark_model.13646_t
Valid prediction for snap_scaffold_3-snap.3418-T1
Valid prediction for GeneMark_model.13648_t
Valid prediction for Augustus_model.g5564.t1
Valid prediction for GeneMark_model.13639_t
Valid prediction for GlimmerHMM_glimmerT_8393-T1
Valid prediction for GeneMark_model.13662_t
Valid prediction for snap_scaffold_3-snap.3416-T1
Valid prediction for snap_scaffold_3-snap.3408-T1
Valid prediction for GlimmerHMM_glimmerT_8391-T1
Valid prediction for GeneMark_model.13660_t
Valid prediction for snap_scaffold_3-snap.3403-T1
Valid prediction for GlimmerHMM_glimmerT_8378-T1
Valid prediction for GeneMark_model.13643_t
Valid prediction for Augustus_model.g5560.t1
Valid prediction for GeneMark_model.13650_t
Valid prediction for pasa_asmbl_40646.p1
Valid prediction for GlimmerHMM_glimmerT_8387-T1
Valid prediction for snap_scaffold_3-snap.3413-T1
Valid prediction for Augustus_model.g5572.t1
Valid prediction for GeneMark_model.13641_t
Valid prediction for snap_scaffold_3-snap.3410-T1
Valid prediction for GeneMark_model.13664_t
Valid prediction for GeneMark_model.13656_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 snap_scaffold_3-snap.3406-T1
Valid prediction for GlimmerHMM_glimmerT_8385-T1
Valid prediction for GeneMark_model.13632_t
Valid prediction for GeneMark_model.13657_t
Valid prediction for GeneMark_model.13665_t
Valid prediction for HiQ_model.g5570.t1
Valid prediction for GlimmerHMM_glimmerT_8394-T1
Valid prediction for GeneMark_model.13640_t
Valid prediction for GeneMark_model.13658_t
Valid prediction for GeneMark_model.13635_t
Valid prediction for GlimmerHMM_glimmerT_8392-T1
Valid prediction for snap_scaffold_3-snap.3426-T1
Valid prediction for GlimmerHMM_glimmerT_8376-T1
Valid prediction for snap_scaffold_3-snap.3422-T1
Valid prediction for Augustus_model.g5561.t1
Valid prediction for Augustus_model.g5567.t1
Valid prediction for GeneMark_model.13647_t
Valid prediction for GeneMark_model.13663_t
Valid prediction for GlimmerHMM_glimmerT_8384-T1
Couldn't classify 63132, 63149
Sorry, prediction pasa_asmbl_39512.p2 fails validation.
(ATG)	 AC	60156-60185	GT	GGG
(GAT)	 AG	60528-60589	GT	AGG
(GGT)	 AG	61729-61818	GT	AGG
(GGT)	 AG	62918-63017	GT	AGG
(CAT)	 AG	63132-63149	AT	AGA
-recovered pasa_asmbl_39512.p2, initial, 60156, 60185
-recovered pasa_asmbl_39512.p2, internal, 60528, 60589
-recovered pasa_asmbl_39512.p2, internal, 61729, 61818
-recovered pasa_asmbl_39512.p2, internal, 62918, 63017
Valid prediction for snap_scaffold_3-snap.3415-T1
Valid prediction for GeneMark_model.13649_t
Valid prediction for GeneMark_model.13653_t
Valid prediction for GeneMark_model.13651_t
Valid prediction for snap_scaffold_3-snap.3407-T1
Valid prediction for Augustus_model.g5571.t1
Valid prediction for snap_scaffold_3-snap.3409-T1
Valid prediction for GlimmerHMM_glimmerT_8388-T1
Valid prediction for GeneMark_model.13655_t
Valid prediction for snap_scaffold_3-snap.3402-T1
Valid prediction for Augustus_model.g5568.t1
Valid prediction for CodingQuarry_transcript_46344-T1
Valid prediction for GeneMark_model.13659_t
Valid prediction for GlimmerHMM_glimmerT_8382-T1
Valid prediction for snap_scaffold_3-snap.3401-T1
Valid prediction for snap_scaffold_3-snap.3412-T1
Valid prediction for GlimmerHMM_glimmerT_8386-T1
Valid prediction for GeneMark_model.13637_t
Valid prediction for GlimmerHMM_glimmerT_8375-T1
Valid prediction for Augustus_model.g5563.t1
Valid prediction for pasa_asmbl_39518.p1
Valid prediction for snap_scaffold_3-snap.3404-T1
Valid prediction for GeneMark_model.13644_t
Valid prediction for GeneMark_model.13645_t
Couldn't classify 47724, 47832
Couldn't classify 50503, 50580
Sorry, prediction pasa_asmbl_39513.p1 fails validation.
(GCC)	 AT	47724-47832	GT	CGG
(GTC)	 AG	47949-48023	GT	AAG
(GCA)	 AG	49270-49341	GT	TGG
(GTG)	 AG	49567-49646	GT	TGG
(AAC)	 AG	50503-50580	CT	GAC
-recovered pasa_asmbl_39513.p1, internal, 47949, 48023
-recovered pasa_asmbl_39513.p1, internal, 49270, 49341
-recovered pasa_asmbl_39513.p1, internal, 49567, 49646
Valid prediction for snap_scaffold_3-snap.3420-T1
Valid prediction for snap_scaffold_3-snap.3411-T1
Valid prediction for snap_scaffold_3-snap.3425-T1
Valid prediction for CodingQuarry_transcript_46343-T1
Valid prediction for GeneMark_model.13638_t
Valid prediction for snap_scaffold_3-snap.3419-T1
Valid prediction for Augustus_model.g5573.t1
Valid prediction for GeneMark_model.13661_t
Valid prediction for GeneMark_model.13642_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11450, rend_intergenic: 11010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13037, rend_intergenic: 11607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18131, rend_intergenic: 16095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26246, rend_intergenic: 21663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49624, rend_intergenic: 41585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56647, rend_intergenic: 51986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62496, rend_intergenic: 57896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 107655
-exon list size: 450


building trellis

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99.1    
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-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 11450, rend_intergenic: 11010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13037, rend_intergenic: 11607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18131, rend_intergenic: 16095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26246, rend_intergenic: 21663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49624, rend_intergenic: 41585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56647, rend_intergenic: 51986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62496, rend_intergenic: 57896  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