-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_12326186-12449753

-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.49405_t
Valid prediction for GeneMark_model.49396_t
Valid prediction for GeneMark_model.49413_t
Valid prediction for GeneMark_model.49423_t
Valid prediction for snap_scaffold_11-snap.2661-T1
Valid prediction for GeneMark_model.49428_t
Valid prediction for GlimmerHMM_glimmerT_28620-T1
Valid prediction for snap_scaffold_11-snap.2640-T1
Valid prediction for GeneMark_model.49425_t
Valid prediction for GeneMark_model.49410_t
Valid prediction for GeneMark_model.49421_t
Valid prediction for snap_scaffold_11-snap.2657-T1
Valid prediction for snap_scaffold_11-snap.2648-T1
Valid prediction for GeneMark_model.49416_t
Valid prediction for GeneMark_model.49419_t
Valid prediction for GeneMark_model.49402_t
Valid prediction for snap_scaffold_11-snap.2654-T1
Valid prediction for snap_scaffold_11-snap.2665-T1
Valid prediction for snap_scaffold_11-snap.2644-T1
Valid prediction for GeneMark_model.49431_t
Valid prediction for snap_scaffold_11-snap.2666-T1
Valid prediction for GlimmerHMM_glimmerT_28618-T1
Valid prediction for snap_scaffold_11-snap.2670-T1
Valid prediction for snap_scaffold_11-snap.2647-T1
Valid prediction for GeneMark_model.49412_t
Valid prediction for snap_scaffold_11-snap.2645-T1
Valid prediction for GeneMark_model.49394_t
Valid prediction for snap_scaffold_11-snap.2652-T1
Valid prediction for GlimmerHMM_glimmerT_28616-T1
Valid prediction for GeneMark_model.49414_t
Valid prediction for GeneMark_model.49417_t
Valid prediction for GlimmerHMM_glimmerT_28630-T1
Valid prediction for GlimmerHMM_glimmerT_28627-T1
Valid prediction for snap_scaffold_11-snap.2638-T1
Valid prediction for GeneMark_model.49398_t
Valid prediction for snap_scaffold_11-snap.2663-T1
Valid prediction for GeneMark_model.49401_t
Valid prediction for GlimmerHMM_glimmerT_28625-T1
Valid prediction for snap_scaffold_11-snap.2650-T1
Valid prediction for snap_scaffold_11-snap.2664-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 GlimmerHMM_glimmerT_28617-T1
Valid prediction for GlimmerHMM_glimmerT_28622-T1
Valid prediction for GeneMark_model.49411_t
Valid prediction for GeneMark_model.49422_t
Valid prediction for CodingQuarry_transcript_8236-T1
Couldn't classify 13713, 14111
Sorry, prediction pasa_asmbl_7071.p1 fails validation.
(ACC)	 CC	13713-14111	AC	GAA
Valid prediction for snap_scaffold_11-snap.2641-T1
Valid prediction for GlimmerHMM_glimmerT_28621-T1
Valid prediction for GeneMark_model.49432_t
Couldn't classify 12534, 13478
Sorry, prediction pasa_asmbl_7072.p1 fails validation.
(AGC)	 CA	12534-13478	GA	GGG
Valid prediction for GeneMark_model.49393_t
Valid prediction for snap_scaffold_11-snap.2649-T1
Valid prediction for GeneMark_model.49418_t
Valid prediction for Augustus_model.g19111.t1
Valid prediction for GlimmerHMM_glimmerT_28628-T1
Valid prediction for GlimmerHMM_glimmerT_28615-T1
Valid prediction for snap_scaffold_11-snap.2639-T1
Valid prediction for GeneMark_model.49409_t
Valid prediction for GeneMark_model.49399_t
Valid prediction for GlimmerHMM_glimmerT_28623-T1
Valid prediction for GlimmerHMM_glimmerT_28626-T1
Couldn't classify 52125, 52295
Sorry, prediction pasa_asmbl_7067.p1 fails validation.
(ATG)	 TC	39455-39487	GT	GTG
(GCT)	 AG	39621-39730	GT	AGG
(GTA)	 AG	42513-42648	GT	AGG
(GTG)	 AG	43593-43802	GT	AGG
(GAG)	 AG	46014-46151	GT	AGG
(TAT)	 AG	46337-46408	GT	AGG
(AAC)	 AG	47782-47969	GT	AGG
(TCT)	 AG	49064-49235	GT	AGG
(AAC)	 AG	52125-52295	GT	AGG
-recovered pasa_asmbl_7067.p1, initial, 39455, 39487
-recovered pasa_asmbl_7067.p1, internal, 39621, 39730
-recovered pasa_asmbl_7067.p1, internal, 42513, 42648
-recovered pasa_asmbl_7067.p1, internal, 43593, 43802
-recovered pasa_asmbl_7067.p1, internal, 46014, 46151
-recovered pasa_asmbl_7067.p1, internal, 46337, 46408
-recovered pasa_asmbl_7067.p1, internal, 47782, 47969
-recovered pasa_asmbl_7067.p1, internal, 49064, 49235
-recovered pasa_asmbl_7067.p1, internal, 52125, 52295
Valid prediction for snap_scaffold_11-snap.2671-T1
Valid prediction for GeneMark_model.49427_t
Valid prediction for snap_scaffold_11-snap.2643-T1
Valid prediction for GlimmerHMM_glimmerT_28631-T1
Valid prediction for snap_scaffold_11-snap.2669-T1
Valid prediction for GeneMark_model.49403_t
Valid prediction for GeneMark_model.49406_t
Valid prediction for Augustus_model.g19105.t1
Valid prediction for snap_scaffold_11-snap.2658-T1
Valid prediction for snap_scaffold_11-snap.2659-T1
Valid prediction for Augustus_model.g19107.t1
Valid prediction for Augustus_model.g19106.t1
Valid prediction for GeneMark_model.49415_t
Valid prediction for GeneMark_model.49426_t
Valid prediction for snap_scaffold_11-snap.2642-T1
Valid prediction for Augustus_model.g19108.t1
Valid prediction for GeneMark_model.49400_t
Valid prediction for GeneMark_model.49430_t
Valid prediction for snap_scaffold_11-snap.2651-T1
Valid prediction for snap_scaffold_11-snap.2667-T1
Valid prediction for snap_scaffold_11-snap.2668-T1
Valid prediction for HiQ_model.g19104.t1
Valid prediction for Augustus_model.g19109.t1
Valid prediction for snap_scaffold_11-snap.2653-T1
Couldn't classify 59302, 59478
Sorry, prediction pasa_asmbl_7066.p1 fails validation.
(AGG)	 TC	59302-59478	GT	CCG
(AGA)	 AG	60396-60512	GT	AGG
(CAA)	 AG	61440-61697	AG	AGA
-recovered pasa_asmbl_7066.p1, terminal, 61440, 61697
-recovered pasa_asmbl_7066.p1, internal, 60396, 60512
Valid prediction for GeneMark_model.49397_t
Valid prediction for snap_scaffold_11-snap.2662-T1
Valid prediction for GeneMark_model.49408_t
Valid prediction for snap_scaffold_11-snap.2655-T1
Valid prediction for GeneMark_model.49429_t
Valid prediction for HiQ_model.g19103.t1
Valid prediction for snap_scaffold_11-snap.2646-T1
Valid prediction for snap_scaffold_11-snap.2656-T1
Valid prediction for GlimmerHMM_glimmerT_28614-T1
Valid prediction for GeneMark_model.49407_t
Valid prediction for GeneMark_model.49404_t
Couldn't classify 18756, 18817
Sorry, prediction pasa_asmbl_7070.p1 fails validation.
(ATG)	 TC	15123-15197	GT	AGG
(TTG)	 AG	15294-15350	GT	AGG
(GTC)	 AG	15434-15474	GT	AAG
(GTT)	 AG	15582-15617	GT	AGG
(TCA)	 AG	15706-15826	GT	AGG
(GTG)	 AG	16358-16498	GT	TGG
(GAG)	 AG	16994-17062	GT	CGG
(TCG)	 AG	17427-17527	GT	TTG
(AGC)	 AG	17673-17749	GT	AGG
(GTG)	 AG	18756-18817	GA	TGG
-recovered pasa_asmbl_7070.p1, initial, 15123, 15197
-recovered pasa_asmbl_7070.p1, internal, 15294, 15350
-recovered pasa_asmbl_7070.p1, internal, 15434, 15474
-recovered pasa_asmbl_7070.p1, internal, 15582, 15617
-recovered pasa_asmbl_7070.p1, internal, 15706, 15826
-recovered pasa_asmbl_7070.p1, internal, 16358, 16498
-recovered pasa_asmbl_7070.p1, internal, 16994, 17062
-recovered pasa_asmbl_7070.p1, internal, 17427, 17527
-recovered pasa_asmbl_7070.p1, internal, 17673, 17749
Valid prediction for Augustus_model.g19110.t1
Valid prediction for snap_scaffold_11-snap.2660-T1
Valid prediction for GeneMark_model.49420_t
Valid prediction for GlimmerHMM_glimmerT_28619-T1
Valid prediction for GeneMark_model.49424_t
Valid prediction for GlimmerHMM_glimmerT_28624-T1
Valid prediction for GlimmerHMM_glimmerT_28629-T1
Couldn't classify 62578, 62814
Sorry, prediction pasa_asmbl_7065.p1 fails validation.
(CAG)	 TT	62578-62814	GT	AGG
(ACC)	 AG	64596-64820	GT	GAG
-recovered pasa_asmbl_7065.p1, terminal, 64596, 64820
-recovered pasa_asmbl_7065.p1, internal, 64596, 64820
Valid prediction for GeneMark_model.49395_t
Valid prediction for pasa_asmbl_7063.p2

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 69902, rend_intergenic: 69899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12621, rend_intergenic: 5785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12641, rend_intergenic: 12640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15913, rend_intergenic: 12979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21898, rend_intergenic: 19862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32714, rend_intergenic: 25934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43075, rend_intergenic: 36382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61275, rend_intergenic: 61227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66135, rend_intergenic: 61872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69557, rend_intergenic: 67186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72769, rend_intergenic: 69752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80310, rend_intergenic: 78320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99265, rend_intergenic: 82719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106172, rend_intergenic: 104263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120778, rend_intergenic: 116584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 123568
-exon list size: 486


building trellis

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98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 22 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 69902, rend_intergenic: 69899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12621, rend_intergenic: 5785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12641, rend_intergenic: 12640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15913, rend_intergenic: 12979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21898, rend_intergenic: 19862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32714, rend_intergenic: 25934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43075, rend_intergenic: 36382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61275, rend_intergenic: 61227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66135, rend_intergenic: 61872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69557, rend_intergenic: 67186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72769, rend_intergenic: 69752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80310, rend_intergenic: 78320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99265, rend_intergenic: 82719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106172, rend_intergenic: 104263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120778, rend_intergenic: 116584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support