-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_12873722-13016476

-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_26148-T1
Valid prediction for snap_scaffold_10-snap.2551-T1
Valid prediction for Augustus_model.g17527.t1
Valid prediction for HiQ_model.g17523.t1
Valid prediction for GeneMark_model.44849_t
Valid prediction for GlimmerHMM_glimmerT_26149-T1
Couldn't classify 36367, 37308
Sorry, prediction pasa_asmbl_4830.p1 fails validation.
(GGT)	 CA	36367-37308	CG	CCC
Valid prediction for HiQ_model.g17539.t1
Valid prediction for GeneMark_model.44829_t
Valid prediction for CodingQuarry_transcript_5602-T1
Valid prediction for GeneMark_model.44859_t
Valid prediction for Augustus_model.g17529.t1
Valid prediction for GlimmerHMM_glimmerT_26136-T1
Valid prediction for GeneMark_model.44834_t
Valid prediction for CodingQuarry_transcript_5595-T1
Valid prediction for HiQ_model.g17538.t1
Valid prediction for snap_scaffold_10-snap.2534-T1
Valid prediction for snap_scaffold_10-snap.2562-T1
Valid prediction for snap_scaffold_10-snap.2550-T1
Valid prediction for GlimmerHMM_glimmerT_26146-T1
Valid prediction for pasa_asmbl_4844.p1
Valid prediction for GeneMark_model.44848_t
Valid prediction for GlimmerHMM_glimmerT_26138-T1
Valid prediction for Augustus_model.g17542.t1
Valid prediction for GeneMark_model.44839_t
Valid prediction for GlimmerHMM_glimmerT_26145-T1
Valid prediction for pasa_asmbl_4842.p1
Valid prediction for GeneMark_model.44850_t
Valid prediction for snap_scaffold_10-snap.2557-T1
Valid prediction for snap_scaffold_10-snap.2548-T1
Valid prediction for pasa_asmbl_4838.p1
Valid prediction for GlimmerHMM_glimmerT_26159-T1
Couldn't classify 85834, 86618
Sorry, prediction pasa_asmbl_5170.p1 fails validation.
(ATG)	 CA	84696-84987	GT	AGG
(GTG)	 AG	85069-85214	GT	AGG
(TCT)	 AG	85393-85512	GT	AGG
(CTG)	 AG	85634-85754	GT	AAG
(CTG)	 AG	85834-86618	GG	GGG
-recovered pasa_asmbl_5170.p1, initial, 84696, 84987
-recovered pasa_asmbl_5170.p1, internal, 85069, 85214
-recovered pasa_asmbl_5170.p1, internal, 85393, 85512
-recovered pasa_asmbl_5170.p1, internal, 85634, 85754
Valid prediction for GlimmerHMM_glimmerT_26135-T1
Valid prediction for GlimmerHMM_glimmerT_26143-T1
Valid prediction for snap_scaffold_10-snap.2549-T1
Valid prediction for GeneMark_model.44860_t
Valid prediction for snap_scaffold_10-snap.2537-T1
Valid prediction for GlimmerHMM_glimmerT_26160-T1
Valid prediction for GeneMark_model.44837_t
Valid prediction for Augustus_model.g17540.t1
Valid prediction for snap_scaffold_10-snap.2552-T1
Valid prediction for GeneMark_model.44835_t
Couldn't classify 11367, 11414
Sorry, prediction pasa_asmbl_4824.p1 fails validation.
(CCA)	 CC	11367-11414	GT	CGG
(CGT)	 AG	12338-12395	GT	GGG
(GCA)	 AG	12500-12565	GT	CAG
(AGT)	 AG	12841-12930	GT	AGG
(GGC)	 AG	13159-13331	GT	AGG
(GCC)	 AG	13566-13694	GT	AGG
(GGC)	 AG	13981-14112	GC	AGG
-recovered pasa_asmbl_4824.p1, terminal, 13981, 14112
-recovered pasa_asmbl_4824.p1, internal, 12338, 12395
-recovered pasa_asmbl_4824.p1, internal, 12500, 12565
-recovered pasa_asmbl_4824.p1, internal, 12841, 12930
-recovered pasa_asmbl_4824.p1, internal, 13159, 13331
-recovered pasa_asmbl_4824.p1, internal, 13566, 13694
-recovered pasa_asmbl_4824.p1, internal, 13981, 14112
Valid prediction for HiQ_model.g17534.t1
Valid prediction for snap_scaffold_10-snap.2547-T1
Valid prediction for CodingQuarry_transcript_5600-T1
Valid prediction for GlimmerHMM_glimmerT_26154-T1
Valid prediction for Augustus_model.g17526.t1
Valid prediction for Augustus_model.g17524.t1
Valid prediction for Augustus_model.g17536.t1
Valid prediction for GlimmerHMM_glimmerT_26134-T1
Valid prediction for GlimmerHMM_glimmerT_26151-T1
Valid prediction for Augustus_model.g17550.t1
Valid prediction for GeneMark_model.44861_t
Valid prediction for GeneMark_model.44836_t
Couldn't classify 91983, 91992
Sorry, prediction pasa_asmbl_4839.p1 fails validation.
(AAA)	 GC	91983-91992	GT	GGG
(GAT)	 AG	92420-93114	GC	GAG
-recovered pasa_asmbl_4839.p1, terminal, 92420, 93114
-recovered pasa_asmbl_4839.p1, internal, 92420, 93114
Valid prediction for Augustus_model.g17533.t1
Valid prediction for CodingQuarry_transcript_5601-T1
Valid prediction for Augustus_model.g17535.t1
Valid prediction for pasa_asmbl_4831.p1
Valid prediction for Augustus_model.g17548.t1
Valid prediction for Augustus_model.g17528.t1
Valid prediction for GeneMark_model.44845_t
Valid prediction for GeneMark_model.44846_t
Valid prediction for GeneMark_model.44863_t
Valid prediction for GlimmerHMM_glimmerT_26152-T1
Valid prediction for GlimmerHMM_glimmerT_26147-T1
Valid prediction for snap_scaffold_10-snap.2539-T1
Valid prediction for GeneMark_model.44847_t
Valid prediction for HiQ_model.g17537.t1
Valid prediction for snap_scaffold_10-snap.2533-T1
Valid prediction for snap_scaffold_10-snap.2546-T1
Valid prediction for snap_scaffold_10-snap.2553-T1
Valid prediction for pasa_asmbl_4832.p1
Valid prediction for snap_scaffold_10-snap.2554-T1
Couldn't classify 73839, 74265
Sorry, prediction pasa_asmbl_4834.p1 fails validation.
(CGT)	 AC	73839-74265	GC	TTG
(CGG)	 AG	74364-74470	GT	AGG
(GGA)	 AG	74560-75375	GT	GGG
(GTT)	 AG	75715-75825	CT	GAC
-recovered pasa_asmbl_4834.p1, terminal, 75715, 75825
-recovered pasa_asmbl_4834.p1, internal, 74364, 74470
-recovered pasa_asmbl_4834.p1, internal, 74560, 75375
Valid prediction for GeneMark_model.44855_t
Valid prediction for snap_scaffold_10-snap.2543-T1
Valid prediction for Augustus_model.g17541.t1
Valid prediction for pasa_asmbl_4836.p1
Valid prediction for GlimmerHMM_glimmerT_26150-T1
Valid prediction for Augustus_model.g17549.t1
Valid prediction for snap_scaffold_10-snap.2536-T1
Valid prediction for GeneMark_model.44862_t
Valid prediction for GeneMark_model.44857_t
Valid prediction for pasa_asmbl_4837.p1
Valid prediction for CodingQuarry_transcript_5606-T1
Valid prediction for CodingQuarry_transcript_5598-T1
Valid prediction for GlimmerHMM_glimmerT_26140-T1
Valid prediction for HiQ_model.g17547.t1
Valid prediction for GlimmerHMM_glimmerT_26142-T1
Valid prediction for GeneMark_model.44830_t
Valid prediction for GeneMark_model.44841_t
Valid prediction for CodingQuarry_transcript_5599-T1
Valid prediction for GlimmerHMM_glimmerT_26153-T1
Valid prediction for GeneMark_model.44854_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.44831_t
Valid prediction for CodingQuarry_transcript_5604-T1
Valid prediction for CodingQuarry_transcript_5605-T1
Valid prediction for GlimmerHMM_glimmerT_26139-T1
Valid prediction for GeneMark_model.44858_t
Valid prediction for snap_scaffold_10-snap.2555-T1
Valid prediction for pasa_asmbl_3748.p1
Valid prediction for snap_scaffold_10-snap.2564-T1
Valid prediction for Augustus_model.g17530.t1
Valid prediction for snap_scaffold_10-snap.2542-T1
Valid prediction for snap_scaffold_10-snap.2563-T1
Valid prediction for GlimmerHMM_glimmerT_26157-T1
Valid prediction for GlimmerHMM_glimmerT_26141-T1
Valid prediction for Augustus_model.g17544.t1
Valid prediction for snap_scaffold_10-snap.2545-T1
Valid prediction for snap_scaffold_10-snap.2556-T1
Valid prediction for snap_scaffold_10-snap.2544-T1
Valid prediction for GeneMark_model.44833_t
Valid prediction for GeneMark_model.44843_t
Valid prediction for Augustus_model.g17531.t1
Valid prediction for HiQ_model.g17532.t1
Valid prediction for Augustus_model.g17543.t1
Valid prediction for GeneMark_model.44828_t
Valid prediction for Augustus_model.g17522.t1
Valid prediction for GeneMark_model.44842_t
Valid prediction for snap_scaffold_10-snap.2535-T1
Valid prediction for snap_scaffold_10-snap.2538-T1
Valid prediction for GeneMark_model.44851_t
Valid prediction for GlimmerHMM_glimmerT_26133-T1
Valid prediction for GeneMark_model.44856_t
Valid prediction for snap_scaffold_10-snap.2532-T1
Valid prediction for HiQ_model.g17525.t1
Valid prediction for pasa_asmbl_3742.p1
Valid prediction for HiQ_model.g17545.t1
Valid prediction for GeneMark_model.44840_t
Valid prediction for HiQ_model.g17546.t1
Valid prediction for pasa_asmbl_3750.p1
Valid prediction for GeneMark_model.44838_t
Valid prediction for snap_scaffold_10-snap.2540-T1
Valid prediction for snap_scaffold_10-snap.2558-T1
Valid prediction for GeneMark_model.44827_t
Valid prediction for Augustus_model.g17521.t1
Valid prediction for snap_scaffold_10-snap.2560-T1
Valid prediction for GlimmerHMM_glimmerT_26155-T1
Valid prediction for GlimmerHMM_glimmerT_26158-T1
Valid prediction for snap_scaffold_10-snap.2541-T1
Couldn't classify 77571, 77629
Sorry, prediction pasa_asmbl_3747.p1 fails validation.
(ATG)	 CC	75369-75432	GT	AGG
(TTC)	 AG	75748-75783	GT	AGG
(TGG)	 AG	75918-76031	GT	TGG
(ACA)	 AG	76350-76379	GT	AGG
(TCC)	 AG	76627-76718	GT	AGG
(GAT)	 AG	76966-77091	GT	AGG
(AAT)	 AG	77292-77391	GT	TCG
(TGG)	 AG	77571-77629	AG	CCA
-recovered pasa_asmbl_3747.p1, initial, 75369, 75432
-recovered pasa_asmbl_3747.p1, internal, 75748, 75783
-recovered pasa_asmbl_3747.p1, internal, 75918, 76031
-recovered pasa_asmbl_3747.p1, internal, 76350, 76379
-recovered pasa_asmbl_3747.p1, internal, 76627, 76718
-recovered pasa_asmbl_3747.p1, internal, 76966, 77091
-recovered pasa_asmbl_3747.p1, internal, 77292, 77391
Valid prediction for CodingQuarry_transcript_5597-T1
Valid prediction for GeneMark_model.44844_t
Valid prediction for snap_scaffold_10-snap.2561-T1
Valid prediction for GlimmerHMM_glimmerT_26156-T1
Valid prediction for GeneMark_model.44852_t
Valid prediction for snap_scaffold_10-snap.2559-T1
Valid prediction for GeneMark_model.44853_t
Valid prediction for GlimmerHMM_glimmerT_26144-T1
Valid prediction for GlimmerHMM_glimmerT_26137-T1
Valid prediction for snap_scaffold_10-snap.2531-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24542, rend_intergenic: 21649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36113, rend_intergenic: 32513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44869, rend_intergenic: 36984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102217, rend_intergenic: 98417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109275, rend_intergenic: 105738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116006, rend_intergenic: 109457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 142755
-exon list size: 482


building trellis

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99.6    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 24542, rend_intergenic: 21649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36113, rend_intergenic: 32513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44869, rend_intergenic: 36984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102217, rend_intergenic: 98417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109275, rend_intergenic: 105738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116006, rend_intergenic: 109457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support