-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_1232772-1445107

-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_28-snap.305-T1
Valid prediction for snap_scaffold_28-snap.312-T1
Valid prediction for snap_scaffold_28-snap.299-T1
Valid prediction for snap_scaffold_28-snap.308-T1
Valid prediction for GlimmerHMM_glimmerT_58114-T1
Valid prediction for snap_scaffold_28-snap.318-T1
Valid prediction for snap_scaffold_28-snap.296-T1
Valid prediction for snap_scaffold_28-snap.321-T1
Valid prediction for snap_scaffold_28-snap.282-T1
Valid prediction for GlimmerHMM_glimmerT_58128-T1
Valid prediction for GlimmerHMM_glimmerT_58124-T1
Valid prediction for snap_scaffold_28-snap.314-T1
Valid prediction for Augustus_model.g38473.t1
Valid prediction for snap_scaffold_28-snap.322-T1
Valid prediction for snap_scaffold_28-snap.290-T1
Valid prediction for GlimmerHMM_glimmerT_58129-T1
Valid prediction for snap_scaffold_28-snap.301-T1
Valid prediction for GlimmerHMM_glimmerT_58139-T1
Valid prediction for snap_scaffold_28-snap.285-T1
Valid prediction for GlimmerHMM_glimmerT_58123-T1
Valid prediction for Augustus_model.g38469.t1
Valid prediction for snap_scaffold_28-snap.277-T1
Valid prediction for GlimmerHMM_glimmerT_58138-T1
Valid prediction for snap_scaffold_28-snap.288-T1
Valid prediction for snap_scaffold_28-snap.307-T1
Couldn't classify 112324, 112476
Couldn't classify 114345, 114403
Sorry, prediction pasa_asmbl_37816.p1 fails validation.
(ATT)	 TC	112324-112476	GT	GGG
(ATC)	 AG	113390-113457	GT	TGG
(GCC)	 AG	113904-114004	GT	AGG
(AGG)	 AG	114345-114403	CA	CTC
-recovered pasa_asmbl_37816.p1, internal, 113390, 113457
-recovered pasa_asmbl_37816.p1, internal, 113904, 114004
Valid prediction for Augustus_model.g38483.t1
Valid prediction for snap_scaffold_28-snap.310-T1
Valid prediction for snap_scaffold_28-snap.292-T1
Valid prediction for GlimmerHMM_glimmerT_58119-T1
Valid prediction for GlimmerHMM_glimmerT_58118-T1
Valid prediction for snap_scaffold_28-snap.303-T1
Valid prediction for snap_scaffold_28-snap.275-T1
Couldn't classify 177479, 177580
Sorry, prediction pasa_asmbl_37306.p1 fails validation.
(TAC)	 GG	177479-177580	GT	AGG
(GAC)	 AG	177855-177974	GT	TGG
(CTG)	 AG	178580-178642	GT	GAG
(GTG)	 AG	179687-179989	AG	AGA
-recovered pasa_asmbl_37306.p1, terminal, 179687, 179989
-recovered pasa_asmbl_37306.p1, internal, 177855, 177974
-recovered pasa_asmbl_37306.p1, internal, 178580, 178642
Valid prediction for Augustus_model.g38488.t1
Valid prediction for GlimmerHMM_glimmerT_58133-T1
Valid prediction for snap_scaffold_28-snap.287-T1
Valid prediction for Augustus_model.g38484.t1
Valid prediction for Augustus_model.g38474.t1
Valid prediction for Augustus_model.g38477.t1
Valid prediction for snap_scaffold_28-snap.280-T1
Valid prediction for snap_scaffold_28-snap.298-T1
Valid prediction for GlimmerHMM_glimmerT_58137-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_28-snap.302-T1
Couldn't classify 6038, 6157
Sorry, prediction pasa_asmbl_37989.p1 fails validation.
(CTG)	 AG	6038-6157	GT	CCG
(TGG)	 AG	7562-7712	GT	CGG
(GAA)	 AG	7872-8064	GT	AGG
(CCA)	 AG	9312-9423	GT	AGG
(CCC)	 AG	9603-9690	GT	AGG
(ATG)	 AG	10887-10978	GT	AGG
(GAT)	 AG	13422-13427	TC	AAT
add_exon() Sorry, pasa_asmbl_37989.p1 10887-10978-initial-1 is invalid.
-recovered pasa_asmbl_37989.p1, initial, 10887, 10978
-recovered pasa_asmbl_37989.p1, terminal, 13422, 13427
-recovered pasa_asmbl_37989.p1, internal, 6038, 6157
-recovered pasa_asmbl_37989.p1, internal, 7562, 7712
-recovered pasa_asmbl_37989.p1, internal, 7872, 8064
-recovered pasa_asmbl_37989.p1, internal, 9312, 9423
-recovered pasa_asmbl_37989.p1, internal, 9603, 9690
-recovered pasa_asmbl_37989.p1, internal, 10887, 10978
Valid prediction for Augustus_model.g38480.t1
Valid prediction for GlimmerHMM_glimmerT_58127-T1
Valid prediction for snap_scaffold_28-snap.323-T1
Valid prediction for snap_scaffold_28-snap.278-T1
Valid prediction for GlimmerHMM_glimmerT_58130-T1
Valid prediction for Augustus_model.g38481.t1
Valid prediction for Augustus_model.g38489.t1
Valid prediction for snap_scaffold_28-snap.279-T1
Valid prediction for snap_scaffold_28-snap.289-T1
Valid prediction for Augustus_model.g38476.t1
Valid prediction for snap_scaffold_28-snap.295-T1
Valid prediction for GlimmerHMM_glimmerT_58116-T1
Valid prediction for GlimmerHMM_glimmerT_58135-T1
Valid prediction for snap_scaffold_28-snap.276-T1
Valid prediction for GlimmerHMM_glimmerT_58111-T1
Valid prediction for snap_scaffold_28-snap.309-T1
Valid prediction for snap_scaffold_28-snap.317-T1
Valid prediction for GlimmerHMM_glimmerT_58117-T1
Valid prediction for Augustus_model.g38479.t1
Valid prediction for Augustus_model.g38471.t1
Valid prediction for Augustus_model.g38478.t1
Valid prediction for GlimmerHMM_glimmerT_58136-T1
Valid prediction for snap_scaffold_28-snap.300-T1
Valid prediction for snap_scaffold_28-snap.320-T1
Valid prediction for GlimmerHMM_glimmerT_58132-T1
Valid prediction for Augustus_model.g38472.t1
Valid prediction for GlimmerHMM_glimmerT_58113-T1
Valid prediction for snap_scaffold_28-snap.306-T1
Valid prediction for snap_scaffold_28-snap.311-T1
Valid prediction for GlimmerHMM_glimmerT_58115-T1
Valid prediction for Augustus_model.g38490.t1
Valid prediction for snap_scaffold_28-snap.325-T1
Valid prediction for snap_scaffold_28-snap.316-T1
Valid prediction for snap_scaffold_28-snap.291-T1
Valid prediction for GlimmerHMM_glimmerT_58141-T1
Valid prediction for GlimmerHMM_glimmerT_58121-T1
Valid prediction for Augustus_model.g38485.t1
Valid prediction for snap_scaffold_28-snap.283-T1
Valid prediction for Augustus_model.g38491.t1
Valid prediction for GlimmerHMM_glimmerT_58120-T1
Valid prediction for GlimmerHMM_glimmerT_58125-T1
Valid prediction for snap_scaffold_28-snap.304-T1
Valid prediction for GlimmerHMM_glimmerT_58134-T1
Valid prediction for snap_scaffold_28-snap.286-T1
Valid prediction for snap_scaffold_28-snap.313-T1
Valid prediction for snap_scaffold_28-snap.293-T1
Valid prediction for Augustus_model.g38475.t1
Valid prediction for snap_scaffold_28-snap.315-T1
Valid prediction for GlimmerHMM_glimmerT_58122-T1
Valid prediction for snap_scaffold_28-snap.281-T1
Valid prediction for GlimmerHMM_glimmerT_58140-T1
Valid prediction for GlimmerHMM_glimmerT_58112-T1
Couldn't classify 17446, 17524
Couldn't classify 19984, 20040
Sorry, prediction pasa_asmbl_37988.p1 fails validation.
(AAC)	 AC	17446-17524	GT	AGG
(GGA)	 AG	17844-17909	GT	AGG
(CTG)	 AG	18072-18128	GT	AGG
(GCA)	 AG	18271-18415	GT	TGG
(GTC)	 AG	19044-19118	GT	AAG
(GAA)	 AG	19730-19808	GT	AGG
(ACG)	 AG	19984-20040	AC	CCA
-recovered pasa_asmbl_37988.p1, internal, 17844, 17909
-recovered pasa_asmbl_37988.p1, internal, 18072, 18128
-recovered pasa_asmbl_37988.p1, internal, 18271, 18415
-recovered pasa_asmbl_37988.p1, internal, 19044, 19118
-recovered pasa_asmbl_37988.p1, internal, 19730, 19808
Valid prediction for snap_scaffold_28-snap.274-T1
Valid prediction for snap_scaffold_28-snap.324-T1
Valid prediction for GlimmerHMM_glimmerT_58126-T1
Valid prediction for GlimmerHMM_glimmerT_58131-T1
Valid prediction for snap_scaffold_28-snap.297-T1
Valid prediction for Augustus_model.g38482.t1
Valid prediction for snap_scaffold_28-snap.284-T1
Valid prediction for snap_scaffold_28-snap.294-T1
Valid prediction for Augustus_model.g38470.t1
Valid prediction for Augustus_model.g38487.t1
Valid prediction for snap_scaffold_28-snap.319-T1
Valid prediction for Augustus_model.g38486.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10893, rend_intergenic: 7819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17374, rend_intergenic: 15529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23494, rend_intergenic: 19388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29368, rend_intergenic: 25148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33561, rend_intergenic: 30085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38657, rend_intergenic: 33929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43521, rend_intergenic: 42282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47092, rend_intergenic: 47008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51800, rend_intergenic: 47689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56765, rend_intergenic: 55388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67547, rend_intergenic: 57897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80595, rend_intergenic: 78726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88651, rend_intergenic: 83948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91662, rend_intergenic: 89630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95785, rend_intergenic: 92884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126300, rend_intergenic: 124669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132843, rend_intergenic: 129336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139455, rend_intergenic: 137228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143874, rend_intergenic: 141384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145084, rend_intergenic: 144365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151175, rend_intergenic: 145189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179989, rend_intergenic: 167088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190652, rend_intergenic: 183932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 212336
-exon list size: 454


building trellis

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-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 10893, rend_intergenic: 7819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17374, rend_intergenic: 15529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23494, rend_intergenic: 19388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29368, rend_intergenic: 25148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33561, rend_intergenic: 30085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38657, rend_intergenic: 33929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43521, rend_intergenic: 42282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47092, rend_intergenic: 47008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51800, rend_intergenic: 47689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56765, rend_intergenic: 55388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67547, rend_intergenic: 57897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80595, rend_intergenic: 78726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88651, rend_intergenic: 83948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91662, rend_intergenic: 89630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95785, rend_intergenic: 92884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126300, rend_intergenic: 124669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132843, rend_intergenic: 129336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139455, rend_intergenic: 137228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143874, rend_intergenic: 141384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145084, rend_intergenic: 144365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151175, rend_intergenic: 145189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179989, rend_intergenic: 167088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190652, rend_intergenic: 183932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11080
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support