-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_7011296-7160411

-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 57221, 57420
Sorry, prediction pasa_asmbl_8671.p1 fails validation.
(TTC)	 CA	57221-57420	GT	TGG
(GTA)	 AG	57625-58033	GG	AAG
-recovered pasa_asmbl_8671.p1, terminal, 57625, 58033
Valid prediction for GeneMark_model.52031_t
Valid prediction for snap_scaffold_12-snap.1313-T1
Valid prediction for GeneMark_model.52023_t
Valid prediction for snap_scaffold_12-snap.1288-T1
Couldn't classify 137011, 138726
Sorry, prediction pasa_asmbl_8681.p1 fails validation.
(CGG)	 AC	137011-138726	CA	AGC
Valid prediction for CodingQuarry_transcript_10236-T1
Valid prediction for GlimmerHMM_glimmerT_30126-T1
Valid prediction for CodingQuarry_transcript_10235-T1
Couldn't classify 93291, 93423
Couldn't classify 94978, 95034
Sorry, prediction pasa_asmbl_8674.p1 fails validation.
(TTC)	 TC	93291-93423	GT	AGG
(GGC)	 AG	93643-93746	GT	AGG
(GTA)	 AG	93838-93958	GT	CGG
(AGG)	 AG	94159-94450	GT	AAG
(GTT)	 AG	94654-94819	GT	AGG
(ATT)	 AG	94978-95034	AA	CCA
-recovered pasa_asmbl_8674.p1, internal, 93643, 93746
-recovered pasa_asmbl_8674.p1, internal, 93838, 93958
-recovered pasa_asmbl_8674.p1, internal, 94159, 94450
-recovered pasa_asmbl_8674.p1, internal, 94654, 94819
Valid prediction for GeneMark_model.52026_t
Valid prediction for GlimmerHMM_glimmerT_30123-T1
Valid prediction for snap_scaffold_12-snap.1292-T1
Valid prediction for GeneMark_model.52032_t
Valid prediction for Augustus_model.g20046.t1
Valid prediction for GlimmerHMM_glimmerT_30128-T1
Valid prediction for snap_scaffold_12-snap.1307-T1
Valid prediction for Augustus_model.g20041.t1
Valid prediction for Augustus_model.g20033.t1
Valid prediction for GeneMark_model.52012_t
Valid prediction for snap_scaffold_12-snap.1298-T1
Valid prediction for GlimmerHMM_glimmerT_30114-T1
Valid prediction for GlimmerHMM_glimmerT_30117-T1
Valid prediction for GeneMark_model.52011_t
Valid prediction for GeneMark_model.52016_t
Valid prediction for GeneMark_model.52040_t
Valid prediction for GeneMark_model.52034_t
Valid prediction for GeneMark_model.52036_t
Valid prediction for snap_scaffold_12-snap.1310-T1
Valid prediction for snap_scaffold_12-snap.1285-T1
Valid prediction for GlimmerHMM_glimmerT_30113-T1
Couldn't classify 84837, 84915
Couldn't classify 85482, 85629
Sorry, prediction pasa_asmbl_8672.p1 fails validation.
(ATG)	 GC	84837-84915	AT	CAA
(AGT)	 AC	85482-85629	GT	AAG
(GAA)	 AG	85764-85920	GT	GAG
(GCT)	 AG	86546-86674	GT	AAG
(AAC)	 AG	86845-86964	GT	AGG
(TTG)	 AG	87172-87275	GT	AGG
(ACT)	 AG	87405-87551	GT	GAG
(CAG)	 AG	87677-87796	GT	AGG
(GAG)	 AG	87977-88054	GT	TTG
(GGT)	 AG	88836-88875	GT	AGG
(ACG)	 AG	89064-89230	GT	AGG
(CAG)	 AG	89453-90073	GT	AGG
(TGC)	 AG	90235-90391	AG	GAA
-recovered pasa_asmbl_8672.p1, terminal, 90235, 90391
-recovered pasa_asmbl_8672.p1, internal, 85764, 85920
-recovered pasa_asmbl_8672.p1, internal, 86546, 86674
-recovered pasa_asmbl_8672.p1, internal, 86845, 86964
-recovered pasa_asmbl_8672.p1, internal, 87172, 87275
-recovered pasa_asmbl_8672.p1, internal, 87405, 87551
-recovered pasa_asmbl_8672.p1, internal, 87677, 87796
-recovered pasa_asmbl_8672.p1, internal, 87977, 88054
-recovered pasa_asmbl_8672.p1, internal, 88836, 88875
-recovered pasa_asmbl_8672.p1, internal, 89064, 89230
-recovered pasa_asmbl_8672.p1, internal, 89453, 90073
Valid prediction for Augustus_model.g20048.t1
Valid prediction for Augustus_model.g20039.t1
Valid prediction for snap_scaffold_12-snap.1299-T1
Valid prediction for snap_scaffold_12-snap.1308-T1
Valid prediction for Augustus_model.g20038.t1
Couldn't classify 97347, 97630
Sorry, prediction pasa_asmbl_8675.p1 fails validation.
(GAA)	 TG	97347-97630	GT	GAG
(AGA)	 AG	97980-98145	GT	CCG
(GTG)	 AG	98436-98639	GC	AGG
(GAG)	 AG	98777-99005	GT	AGG
(CGA)	 AG	99232-99414	GT	TGG
(GTG)	 AG	99542-99658	GT	ACG
(AAT)	 AG	99773-99844	GT	AGG
(ATA)	 AG	99943-100028	GT	AAG
(GTG)	 AG	100173-100334	GT	ATG
(ATC)	 AG	100468-100612	GT	TAG
(GCT)	 AG	100771-100922	GT	AGG
(AAC)	 AG	101865-102047	GT	AGG
(GTC)	 AG	102312-102467	GA	GAG
add_exon() Sorry, pasa_asmbl_8675.p1 99773-99844-terminal-1 is invalid.
-recovered pasa_asmbl_8675.p1, terminal, 99773, 99844
-recovered pasa_asmbl_8675.p1, terminal, 102312, 102467
-recovered pasa_asmbl_8675.p1, internal, 97980, 98145
-recovered pasa_asmbl_8675.p1, internal, 98436, 98639
-recovered pasa_asmbl_8675.p1, internal, 98777, 99005
-recovered pasa_asmbl_8675.p1, internal, 99232, 99414
-recovered pasa_asmbl_8675.p1, internal, 99542, 99658
-recovered pasa_asmbl_8675.p1, internal, 99773, 99844
-recovered pasa_asmbl_8675.p1, internal, 99943, 100028
-recovered pasa_asmbl_8675.p1, internal, 100173, 100334
-recovered pasa_asmbl_8675.p1, internal, 100468, 100612
-recovered pasa_asmbl_8675.p1, internal, 100771, 100922
-recovered pasa_asmbl_8675.p1, internal, 101865, 102047
Valid prediction for GlimmerHMM_glimmerT_30119-T1
Valid prediction for GlimmerHMM_glimmerT_30132-T1
Valid prediction for GlimmerHMM_glimmerT_30112-T1
Valid prediction for snap_scaffold_12-snap.1302-T1
Valid prediction for Augustus_model.g20037.t1
Valid prediction for snap_scaffold_12-snap.1306-T1
Valid prediction for GeneMark_model.52018_t
Valid prediction for snap_scaffold_12-snap.1296-T1
Valid prediction for GlimmerHMM_glimmerT_30127-T1
Valid prediction for snap_scaffold_12-snap.1287-T1
Couldn't classify 101784, 102047
Sorry, prediction pasa_asmbl_8677.p1 fails validation.
(CTC)	 CT	101784-102047	GT	AGG
(GTC)	 AG	102312-102467	GA	GAG
-recovered pasa_asmbl_8677.p1, terminal, 102312, 102467
Valid prediction for snap_scaffold_12-snap.1295-T1
Valid prediction for snap_scaffold_12-snap.1314-T1
Valid prediction for Augustus_model.g20042.t1
Valid prediction for Augustus_model.g20044.t1
Valid prediction for snap_scaffold_12-snap.1300-T1
Couldn't classify 124220, 124687
Sorry, prediction pasa_asmbl_8678.p1 fails validation.
(CCT)	 GC	124220-124687	TC	GAT
Valid prediction for GlimmerHMM_glimmerT_30120-T1
Valid prediction for GeneMark_model.52035_t
Valid prediction for GlimmerHMM_glimmerT_30124-T1
Valid prediction for HiQ_model.g20051.t1
Valid prediction for pasa_asmbl_8679.p1
Valid prediction for snap_scaffold_12-snap.1286-T1
Valid prediction for Augustus_model.g20036.t1
Valid prediction for snap_scaffold_12-snap.1305-T1
Valid prediction for snap_scaffold_12-snap.1301-T1
Valid prediction for GeneMark_model.52028_t
Couldn't classify 42243, 42331
Couldn't classify 43780, 43925
Sorry, prediction pasa_asmbl_9183.p2 fails validation.
(TCC)	 GC	42243-42331	GT	AGG
(GGT)	 AG	43338-43465	GT	AGG
(CCC)	 AG	43780-43925	GA	GTG
-recovered pasa_asmbl_9183.p2, internal, 43338, 43465
Valid prediction for GlimmerHMM_glimmerT_30115-T1
Valid prediction for Augustus_model.g20040.t1
Valid prediction for GlimmerHMM_glimmerT_30121-T1
Valid prediction for GeneMark_model.52030_t
Valid prediction for HiQ_model.g20045.t1
Valid prediction for CodingQuarry_transcript_10237-T1
Couldn't classify 135286, 135293
Sorry, prediction pasa_asmbl_8680.p1 fails validation.
(ATC)	 AG	135286-135293	GT	TGG
(TGC)	 AG	135410-135466	GT	AGG
(CTA)	 AG	135620-135746	GT	AGG
(GAT)	 AG	135829-135981	TG	GAT
-recovered pasa_asmbl_8680.p1, terminal, 135829, 135981
-recovered pasa_asmbl_8680.p1, internal, 135286, 135293
-recovered pasa_asmbl_8680.p1, internal, 135410, 135466
-recovered pasa_asmbl_8680.p1, internal, 135620, 135746
Valid prediction for Augustus_model.g20035.t1
Valid prediction for Augustus_model.g20047.t1
Valid prediction for GlimmerHMM_glimmerT_30116-T1
Valid prediction for GlimmerHMM_glimmerT_30108-T1
Valid prediction for GeneMark_model.52020_t
Valid prediction for snap_scaffold_12-snap.1289-T1
Valid prediction for GlimmerHMM_glimmerT_30125-T1
Valid prediction for GlimmerHMM_glimmerT_30118-T1
Valid prediction for GlimmerHMM_glimmerT_30111-T1
Valid prediction for GlimmerHMM_glimmerT_30109-T1
Couldn't classify 18796, 19161
Sorry, prediction pasa_asmbl_8670.p2 fails validation.
(ATG)	 AG	18796-19161	AC	ACA

-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 pasa_asmbl_7685.p1
Valid prediction for GeneMark_model.52022_t
Valid prediction for snap_scaffold_12-snap.1290-T1
Valid prediction for GlimmerHMM_glimmerT_30129-T1
Valid prediction for GeneMark_model.52009_t
Valid prediction for snap_scaffold_12-snap.1283-T1
Valid prediction for snap_scaffold_12-snap.1304-T1
Valid prediction for GeneMark_model.52038_t
Valid prediction for GlimmerHMM_glimmerT_30122-T1
Valid prediction for Augustus_model.g20034.t1
Valid prediction for GlimmerHMM_glimmerT_30107-T1
Valid prediction for snap_scaffold_12-snap.1294-T1
Valid prediction for Augustus_model.g20050.t1
Valid prediction for snap_scaffold_12-snap.1309-T1
Valid prediction for GeneMark_model.52010_t
Valid prediction for GeneMark_model.52039_t
Valid prediction for GlimmerHMM_glimmerT_30131-T1
Valid prediction for GeneMark_model.52017_t
Valid prediction for snap_scaffold_12-snap.1311-T1
Valid prediction for Augustus_model.g20043.t1
Valid prediction for Augustus_model.g20032.t1
Valid prediction for GeneMark_model.52015_t
Valid prediction for snap_scaffold_12-snap.1293-T1
Valid prediction for GeneMark_model.52014_t
Valid prediction for CodingQuarry_transcript_10238-T1
Valid prediction for snap_scaffold_12-snap.1291-T1
Valid prediction for GeneMark_model.52025_t
Valid prediction for GeneMark_model.52027_t
Valid prediction for GeneMark_model.52008_t
Valid prediction for GlimmerHMM_glimmerT_30130-T1
Valid prediction for GeneMark_model.52024_t
Valid prediction for GeneMark_model.52029_t
Valid prediction for GeneMark_model.52021_t
Valid prediction for GeneMark_model.52013_t
Valid prediction for snap_scaffold_12-snap.1312-T1
Valid prediction for snap_scaffold_12-snap.1303-T1
Valid prediction for GlimmerHMM_glimmerT_30110-T1
Valid prediction for HiQ_model.g20049.t1
Valid prediction for GeneMark_model.52019_t
Valid prediction for snap_scaffold_12-snap.1297-T1
Valid prediction for snap_scaffold_12-snap.1284-T1
Valid prediction for GeneMark_model.52033_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 51897, rend_intergenic: 38492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58033, rend_intergenic: 54347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90391, rend_intergenic: 84609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135981, rend_intergenic: 132885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145330, rend_intergenic: 141821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 149116
-exon list size: 463


building trellis

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-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 51897, rend_intergenic: 38492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58033, rend_intergenic: 54347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90391, rend_intergenic: 84609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135981, rend_intergenic: 132885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145330, rend_intergenic: 141821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support