-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_8/scaffold_8_7425127-7565477

-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: +)Couldn't classify 75444, 75656
Couldn't classify 77550, 77591
Sorry, prediction pasa_asmbl_51975.p1 fails validation.
(GTG)	 AG	75444-75656	GT	AGG
(GCG)	 AG	76337-76477	GT	AGG
(GCG)	 AG	76594-76689	GT	AGG
(GGC)	 AG	76861-77022	GT	CAG
(CAC)	 AG	77550-77591	GG	ACG
-recovered pasa_asmbl_51975.p1, internal, 75444, 75656
-recovered pasa_asmbl_51975.p1, internal, 76337, 76477
-recovered pasa_asmbl_51975.p1, internal, 76594, 76689
-recovered pasa_asmbl_51975.p1, internal, 76861, 77022
Valid prediction for GlimmerHMM_glimmerT_20447-T1
Valid prediction for GlimmerHMM_glimmerT_20452-T1
Valid prediction for CodingQuarry_transcript_59546-T1
Valid prediction for snap_scaffold_8-snap.1448-T1
Valid prediction for snap_scaffold_8-snap.1475-T1
Valid prediction for snap_scaffold_8-snap.1452-T1
Valid prediction for Augustus_model.g13686.t1
Valid prediction for GlimmerHMM_glimmerT_20466-T1
Couldn't classify 32304, 32648
Sorry, prediction pasa_asmbl_51972.p1 fails validation.
(GTC)	 CT	32304-32648	TA	AAT
Valid prediction for Augustus_model.g13677.t1
Valid prediction for GeneMark_model.34972_t
Valid prediction for GeneMark_model.34969_t
Valid prediction for snap_scaffold_8-snap.1449-T1
Valid prediction for GeneMark_model.34964_t
Valid prediction for GeneMark_model.34977_t
Valid prediction for GeneMark_model.34968_t
Valid prediction for snap_scaffold_8-snap.1465-T1
Valid prediction for GeneMark_model.34957_t
Valid prediction for GlimmerHMM_glimmerT_20453-T1
Valid prediction for Augustus_model.g13681.t1
Valid prediction for GlimmerHMM_glimmerT_20462-T1
Valid prediction for snap_scaffold_8-snap.1467-T1
Valid prediction for snap_scaffold_8-snap.1461-T1
Valid prediction for snap_scaffold_8-snap.1454-T1
Valid prediction for snap_scaffold_8-snap.1463-T1
Valid prediction for snap_scaffold_8-snap.1470-T1
Valid prediction for Augustus_model.g13680.t1
Valid prediction for GlimmerHMM_glimmerT_20463-T1
Valid prediction for Augustus_model.g13675.t1
Valid prediction for GlimmerHMM_glimmerT_20458-T1
Valid prediction for GeneMark_model.34966_t
Valid prediction for GeneMark_model.34962_t
Valid prediction for snap_scaffold_8-snap.1474-T1
Couldn't classify 80939, 81308
Sorry, prediction pasa_asmbl_51976.p1 fails validation.
(CAG)	 TC	80939-81308	GT	AGG
(TCG)	 AG	82256-82421	GT	GGG
(GGA)	 AG	82724-82861	GT	AGG
(AAA)	 AG	83114-83240	AG	GAA
-recovered pasa_asmbl_51976.p1, terminal, 83114, 83240
-recovered pasa_asmbl_51976.p1, internal, 82256, 82421
-recovered pasa_asmbl_51976.p1, internal, 82724, 82861
Couldn't classify 80344, 80781
Sorry, prediction pasa_asmbl_52664.p2 fails validation.
(GGC)	 CC	80344-80781	CG	TCC
Valid prediction for snap_scaffold_8-snap.1450-T1
Valid prediction for Augustus_model.g13684.t1
Valid prediction for Augustus_model.g13674.t1
Valid prediction for GeneMark_model.34960_t
Valid prediction for GlimmerHMM_glimmerT_20459-T1
Valid prediction for snap_scaffold_8-snap.1457-T1
Valid prediction for GlimmerHMM_glimmerT_20461-T1
Couldn't classify 18773, 19135
Sorry, prediction pasa_asmbl_52895.p2 fails validation.
(CCC)	 TA	18773-19135	GT	GAG
Valid prediction for GeneMark_model.34974_t
Valid prediction for GeneMark_model.34981_t
Valid prediction for GeneMark_model.34982_t
Valid prediction for snap_scaffold_8-snap.1444-T1
Valid prediction for GlimmerHMM_glimmerT_20455-T1
Valid prediction for GlimmerHMM_glimmerT_20454-T1
Valid prediction for snap_scaffold_8-snap.1462-T1
Valid prediction for Augustus_model.g13676.t1
Couldn't classify 70488, 70964
Sorry, prediction pasa_asmbl_51974.p1 fails validation.
(ATG)	 TT	70488-70964	GA	ACG
Valid prediction for GeneMark_model.34954_t
Valid prediction for Augustus_model.g13685.t1
Valid prediction for GlimmerHMM_glimmerT_20465-T1
Valid prediction for snap_scaffold_8-snap.1451-T1
Valid prediction for GeneMark_model.34976_t
Valid prediction for Augustus_model.g13683.t1
Valid prediction for snap_scaffold_8-snap.1469-T1
Valid prediction for GeneMark_model.34971_t
Valid prediction for snap_scaffold_8-snap.1458-T1
Valid prediction for snap_scaffold_8-snap.1468-T1
Valid prediction for GeneMark_model.34979_t
Valid prediction for GeneMark_model.34950_t
Valid prediction for snap_scaffold_8-snap.1471-T1
Valid prediction for GeneMark_model.34956_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 HiQ_model.g13679.t1
Valid prediction for GeneMark_model.34955_t
Valid prediction for GlimmerHMM_glimmerT_20449-T1
Valid prediction for GlimmerHMM_glimmerT_20457-T1
Valid prediction for snap_scaffold_8-snap.1472-T1
Valid prediction for GlimmerHMM_glimmerT_20446-T1
Valid prediction for GeneMark_model.34948_t
Valid prediction for CodingQuarry_transcript_59544-T1
Valid prediction for snap_scaffold_8-snap.1460-T1
Valid prediction for GlimmerHMM_glimmerT_20451-T1
Valid prediction for GeneMark_model.34952_t
Valid prediction for HiQ_model.g13682.t1
Couldn't classify 118068, 118259
Sorry, prediction pasa_asmbl_52897.p1 fails validation.
(CTC)	 CC	118068-118259	GC	AGG
(ATT)	 AG	118384-118466	GT	AAG
(AAT)	 AG	118609-118745	GT	AGG
(CGA)	 AG	118827-118915	GT	AGG
(TGT)	 AG	119068-119211	GT	AGG
(ATG)	 AG	119300-119476	GT	AGG
(ATC)	 AG	119574-119687	TA	AGT
-recovered pasa_asmbl_52897.p1, initial, 119300, 119476
-recovered pasa_asmbl_52897.p1, terminal, 119574, 119687
-recovered pasa_asmbl_52897.p1, internal, 118384, 118466
-recovered pasa_asmbl_52897.p1, internal, 118609, 118745
-recovered pasa_asmbl_52897.p1, internal, 118827, 118915
-recovered pasa_asmbl_52897.p1, internal, 119068, 119211
-recovered pasa_asmbl_52897.p1, internal, 119300, 119476
Valid prediction for snap_scaffold_8-snap.1476-T1
Valid prediction for GlimmerHMM_glimmerT_20445-T1
Valid prediction for CodingQuarry_transcript_59548-T1
Valid prediction for snap_scaffold_8-snap.1447-T1
Valid prediction for pasa_asmbl_52903.p1
Valid prediction for HiQ_model.g13671.t1
Valid prediction for CodingQuarry_transcript_59545-T1
Valid prediction for GeneMark_model.34978_t
Valid prediction for GeneMark_model.34961_t
Valid prediction for GeneMark_model.34973_t
Valid prediction for HiQ_model.g13672.t1
Valid prediction for snap_scaffold_8-snap.1453-T1
Valid prediction for GeneMark_model.34980_t
Valid prediction for snap_scaffold_8-snap.1473-T1
Valid prediction for GeneMark_model.34958_t
Valid prediction for GlimmerHMM_glimmerT_20456-T1
Valid prediction for pasa_asmbl_52909.p1
Valid prediction for snap_scaffold_8-snap.1464-T1
Valid prediction for GlimmerHMM_glimmerT_20450-T1
Valid prediction for Augustus_model.g13678.t1
Valid prediction for snap_scaffold_8-snap.1445-T1
Valid prediction for snap_scaffold_8-snap.1442-T1
Valid prediction for GlimmerHMM_glimmerT_20448-T1
Valid prediction for GeneMark_model.34983_t
Valid prediction for snap_scaffold_8-snap.1443-T1
Valid prediction for HiQ_model.g13673.t1
Valid prediction for GlimmerHMM_glimmerT_20460-T1
Valid prediction for pasa_asmbl_52896.p1
Couldn't classify 131233, 131355
Couldn't classify 135416, 135424
Sorry, prediction pasa_asmbl_52894.p1 fails validation.
(CTG)	 GG	131233-131355	GT	AGG
(GTC)	 AG	132648-132694	GT	AGG
(CGA)	 AG	133182-133302	GT	CGG
(GTG)	 AG	133406-133513	GT	AGG
(AAG)	 AG	133692-133820	GT	AGG
(CTC)	 AG	134029-134242	GT	AGG
(AGA)	 AG	134535-134661	GT	AGG
(TAT)	 AG	134766-134869	GT	TGG
(GAA)	 AG	135033-135235	GT	CTG
(GAC)	 AG	135416-135424	GG	ATG
-recovered pasa_asmbl_52894.p1, internal, 132648, 132694
-recovered pasa_asmbl_52894.p1, internal, 133182, 133302
-recovered pasa_asmbl_52894.p1, internal, 133406, 133513
-recovered pasa_asmbl_52894.p1, internal, 133692, 133820
-recovered pasa_asmbl_52894.p1, internal, 134029, 134242
-recovered pasa_asmbl_52894.p1, internal, 134535, 134661
-recovered pasa_asmbl_52894.p1, internal, 134766, 134869
-recovered pasa_asmbl_52894.p1, internal, 135033, 135235
Valid prediction for snap_scaffold_8-snap.1441-T1
Valid prediction for GeneMark_model.34970_t
Valid prediction for snap_scaffold_8-snap.1456-T1
Valid prediction for GeneMark_model.34959_t
Valid prediction for CodingQuarry_transcript_59547-T1
Valid prediction for snap_scaffold_8-snap.1477-T1
Valid prediction for GeneMark_model.34975_t
Valid prediction for GlimmerHMM_glimmerT_20464-T1
Valid prediction for snap_scaffold_8-snap.1455-T1
Valid prediction for GeneMark_model.34949_t
Valid prediction for snap_scaffold_8-snap.1459-T1
Valid prediction for GeneMark_model.34967_t
Valid prediction for snap_scaffold_8-snap.1466-T1
Couldn't classify 135416, 135562
Sorry, prediction pasa_asmbl_52893.p1 fails validation.
(GAC)	 AG	135416-135562	GT	AGG
(GGC)	 AG	135785-135940	GC	AGG
-recovered pasa_asmbl_52893.p1, terminal, 135785, 135940
-recovered pasa_asmbl_52893.p1, internal, 135416, 135562
-recovered pasa_asmbl_52893.p1, internal, 135785, 135940
Valid prediction for GeneMark_model.34965_t
Valid prediction for GeneMark_model.34963_t
Valid prediction for snap_scaffold_8-snap.1446-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17259, rend_intergenic: 10284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46697, rend_intergenic: 42948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49456, rend_intergenic: 46989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83660, rend_intergenic: 77559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108647, rend_intergenic: 102345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111540, rend_intergenic: 110584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 140351
-exon list size: 460


building trellis

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-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 17259, rend_intergenic: 10284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46697, rend_intergenic: 42948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49456, rend_intergenic: 46989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83660, rend_intergenic: 77559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108647, rend_intergenic: 102345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111540, rend_intergenic: 110584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support