-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_8563215-8728465

-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_6-snap.1924-T1
Valid prediction for snap_scaffold_6-snap.1900-T1
Valid prediction for GlimmerHMM_glimmerT_15159-T1
Valid prediction for snap_scaffold_6-snap.1910-T1
Valid prediction for Augustus_model.g10056.t1
Valid prediction for HiQ_model.g10051.t1
Valid prediction for GlimmerHMM_glimmerT_15163-T1
Valid prediction for pasa_asmbl_47168.p1
Valid prediction for GlimmerHMM_glimmerT_15143-T1
Valid prediction for CodingQuarry_transcript_55143-T1
Valid prediction for Augustus_model.g10059.t1
Valid prediction for snap_scaffold_6-snap.1898-T1
Valid prediction for Augustus_model.g10046.t1
Valid prediction for snap_scaffold_6-snap.1903-T1
Valid prediction for snap_scaffold_6-snap.1904-T1
Valid prediction for Augustus_model.g10044.t1
Valid prediction for snap_scaffold_6-snap.1928-T1
Valid prediction for Augustus_model.g10054.t1
Valid prediction for GlimmerHMM_glimmerT_15157-T1
Valid prediction for snap_scaffold_6-snap.1918-T1
Valid prediction for pasa_asmbl_47152.p1
Valid prediction for snap_scaffold_6-snap.1920-T1
Valid prediction for CodingQuarry_transcript_55142-T1
Valid prediction for GlimmerHMM_glimmerT_15172-T1
Valid prediction for GlimmerHMM_glimmerT_15140-T1
Valid prediction for CodingQuarry_transcript_55139-T1
Valid prediction for snap_scaffold_6-snap.1921-T1
Valid prediction for pasa_asmbl_47165.p1
Valid prediction for snap_scaffold_6-snap.1919-T1
Valid prediction for snap_scaffold_6-snap.1916-T1
Valid prediction for GlimmerHMM_glimmerT_15150-T1
Valid prediction for snap_scaffold_6-snap.1905-T1
Valid prediction for snap_scaffold_6-snap.1927-T1
Valid prediction for Augustus_model.g10061.t1
Valid prediction for Augustus_model.g10058.t1
Valid prediction for pasa_asmbl_47159.p1
Valid prediction for GlimmerHMM_glimmerT_15137-T1
Valid prediction for GlimmerHMM_glimmerT_15138-T1
Valid prediction for HiQ_model.g10045.t1
Valid prediction for snap_scaffold_6-snap.1933-T1
Valid prediction for snap_scaffold_6-snap.1901-T1
Valid prediction for snap_scaffold_6-snap.1925-T1
Valid prediction for GlimmerHMM_glimmerT_15141-T1
Valid prediction for GlimmerHMM_glimmerT_15139-T1
Valid prediction for Augustus_model.g10057.t1
Valid prediction for GlimmerHMM_glimmerT_15158-T1
Valid prediction for HiQ_model.g10043.t1
Valid prediction for snap_scaffold_6-snap.1922-T1
Valid prediction for GlimmerHMM_glimmerT_15162-T1
Valid prediction for GlimmerHMM_glimmerT_15167-T1
Valid prediction for GlimmerHMM_glimmerT_15144-T1
Valid prediction for snap_scaffold_6-snap.1897-T1
Valid prediction for GlimmerHMM_glimmerT_15151-T1
Valid prediction for GlimmerHMM_glimmerT_15168-T1
Valid prediction for snap_scaffold_6-snap.1902-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 Augustus_model.g10060.t1
Valid prediction for snap_scaffold_6-snap.1912-T1
Valid prediction for GlimmerHMM_glimmerT_15142-T1
Couldn't classify 96756, 96808
Sorry, prediction pasa_asmbl_48574.p1 fails validation.
(TTC)	 CC	96756-96808	GT	ACG
(GGT)	 AG	97162-97221	GT	GGG
(GAA)	 AG	97681-97765	GT	AGG
(GTG)	 AG	97893-98013	GT	TGG
(GTG)	 AG	98171-98310	GT	CGG
(GTG)	 AG	98415-98578	GT	AGG
(CCC)	 AG	98680-98773	AC	GAA
-recovered pasa_asmbl_48574.p1, terminal, 98680, 98773
-recovered pasa_asmbl_48574.p1, internal, 97162, 97221
-recovered pasa_asmbl_48574.p1, internal, 97681, 97765
-recovered pasa_asmbl_48574.p1, internal, 97893, 98013
-recovered pasa_asmbl_48574.p1, internal, 98171, 98310
-recovered pasa_asmbl_48574.p1, internal, 98415, 98578
Valid prediction for Augustus_model.g10049.t1
Valid prediction for GlimmerHMM_glimmerT_15154-T1
Valid prediction for GlimmerHMM_glimmerT_15166-T1
Valid prediction for snap_scaffold_6-snap.1932-T1
Couldn't classify 74683, 74809
Couldn't classify 76357, 76430
Sorry, prediction pasa_asmbl_48585.p1 fails validation.
(GAC)	 TA	74683-74809	GT	CGG
(GCG)	 AG	74935-75160	GT	AAG
(ACA)	 AG	75347-75437	GT	AGG
(GTT)	 AG	75567-75735	GT	AGG
(ACG)	 AG	76357-76430	TC	AGT
-recovered pasa_asmbl_48585.p1, internal, 74935, 75160
-recovered pasa_asmbl_48585.p1, internal, 75347, 75437
-recovered pasa_asmbl_48585.p1, internal, 75567, 75735
Valid prediction for GlimmerHMM_glimmerT_15171-T1
Valid prediction for GlimmerHMM_glimmerT_15147-T1
Valid prediction for CodingQuarry_transcript_55144-T1
Valid prediction for Augustus_model.g10064.t1
Valid prediction for Augustus_model.g10062.t1
Valid prediction for snap_scaffold_6-snap.1906-T1
Valid prediction for pasa_asmbl_48579.p1
Valid prediction for Augustus_model.g10050.t1
Valid prediction for snap_scaffold_6-snap.1899-T1
Couldn't classify 89460, 89559
Sorry, prediction pasa_asmbl_48576.p3 fails validation.
(CCG)	 TC	89460-89559	GT	AGG
(AAC)	 AG	89892-90127	AG	AAA
-recovered pasa_asmbl_48576.p3, terminal, 89892, 90127
Valid prediction for GlimmerHMM_glimmerT_15161-T1
Valid prediction for GlimmerHMM_glimmerT_15152-T1
Valid prediction for CodingQuarry_transcript_55145-T1
Valid prediction for snap_scaffold_6-snap.1926-T1
Valid prediction for GlimmerHMM_glimmerT_15148-T1
Valid prediction for snap_scaffold_6-snap.1913-T1
Valid prediction for GlimmerHMM_glimmerT_15170-T1
Valid prediction for CodingQuarry_transcript_55146-T1
Valid prediction for GlimmerHMM_glimmerT_15164-T1
Couldn't classify 77520, 78488
Sorry, prediction pasa_asmbl_48584.p1 fails validation.
(ATG)	 GT	77046-77100	GT	GGG
(GTA)	 AG	77235-77332	GT	AGG
(GAA)	 AG	77520-78488	GC	TGG
-recovered pasa_asmbl_48584.p1, initial, 77046, 77100
-recovered pasa_asmbl_48584.p1, internal, 77235, 77332
-recovered pasa_asmbl_48584.p1, internal, 77520, 78488
Valid prediction for snap_scaffold_6-snap.1909-T1
Valid prediction for HiQ_model.g10048.t1
Valid prediction for GlimmerHMM_glimmerT_15173-T1
Valid prediction for GlimmerHMM_glimmerT_15169-T1
Valid prediction for GlimmerHMM_glimmerT_15165-T1
Valid prediction for GlimmerHMM_glimmerT_15153-T1
Valid prediction for GlimmerHMM_glimmerT_15145-T1
Valid prediction for snap_scaffold_6-snap.1930-T1
Valid prediction for GlimmerHMM_glimmerT_15146-T1
Couldn't classify 91998, 91999
Sorry, prediction CodingQuarry_transcript_55141-T1 fails validation.
(ATG)	 AA	91998-91999	GT	ATG
(GGT)	 AG	92255-92314	GT	GGG
(GGA)	 AG	92635-92716	GT	AGG
(GTG)	 AG	92869-92989	GT	TGG
(GTG)	 AG	93155-93294	GT	TGG
(GTG)	 AG	93677-93840	GT	AGG
(CCC)	 AG	93999-94092	GC	GAG
-recovered CodingQuarry_transcript_55141-T1, terminal, 93999, 94092
-recovered CodingQuarry_transcript_55141-T1, internal, 92255, 92314
-recovered CodingQuarry_transcript_55141-T1, internal, 92635, 92716
-recovered CodingQuarry_transcript_55141-T1, internal, 92869, 92989
-recovered CodingQuarry_transcript_55141-T1, internal, 93155, 93294
-recovered CodingQuarry_transcript_55141-T1, internal, 93677, 93840
-recovered CodingQuarry_transcript_55141-T1, internal, 93999, 94092
Valid prediction for GlimmerHMM_glimmerT_15160-T1
Valid prediction for snap_scaffold_6-snap.1915-T1
Couldn't classify 89213, 89311
Sorry, prediction pasa_asmbl_48578.p1 fails validation.
(ATG)	 AA	87532-87549	GT	AGG
(CTG)	 AG	87916-88051	GT	AGG
(ACC)	 AG	88190-88239	GT	AGG
(AAT)	 AG	88336-88401	GT	AGG
(GCC)	 AG	88689-88730	GT	AGG
(GAA)	 AG	88874-89029	GT	GGG
(GTA)	 AG	89213-89311	TT	TCT
-recovered pasa_asmbl_48578.p1, initial, 87532, 87549
-recovered pasa_asmbl_48578.p1, internal, 87916, 88051
-recovered pasa_asmbl_48578.p1, internal, 88190, 88239
-recovered pasa_asmbl_48578.p1, internal, 88336, 88401
-recovered pasa_asmbl_48578.p1, internal, 88689, 88730
-recovered pasa_asmbl_48578.p1, internal, 88874, 89029
Valid prediction for snap_scaffold_6-snap.1923-T1
Valid prediction for GlimmerHMM_glimmerT_15156-T1
Valid prediction for snap_scaffold_6-snap.1931-T1
Valid prediction for GlimmerHMM_glimmerT_15155-T1
Valid prediction for snap_scaffold_6-snap.1907-T1
Valid prediction for snap_scaffold_6-snap.1929-T1
Valid prediction for Augustus_model.g10053.t1
Valid prediction for HiQ_model.g10052.t1
Valid prediction for snap_scaffold_6-snap.1917-T1
Valid prediction for pasa_asmbl_48587.p1
Couldn't classify 73938, 74086
Couldn't classify 74212, 74461
Sorry, prediction pasa_asmbl_49425.p1 fails validation.
(GAC)	 GC	73938-74086	GT	AAG
(CCC)	 AG	74212-74461	CA	GCC
Valid prediction for Augustus_model.g10047.t1
Valid prediction for snap_scaffold_6-snap.1911-T1
Valid prediction for snap_scaffold_6-snap.1914-T1
Valid prediction for Augustus_model.g10055.t1
Couldn't classify 78588, 79016
Sorry, prediction pasa_asmbl_48583.p1 fails validation.
(CCG)	 CC	78588-79016	AG	AAA
Valid prediction for GlimmerHMM_glimmerT_15149-T1
Valid prediction for HiQ_model.g10063.t1
Valid prediction for snap_scaffold_6-snap.1908-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10057, rend_intergenic: 8958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103216, rend_intergenic: 99123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106248, rend_intergenic: 103468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131873, rend_intergenic: 127612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140138, rend_intergenic: 135716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146438, rend_intergenic: 142717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 132021, rend_intergenic: 132018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 145496, rend_intergenic: 145493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 165251
-exon list size: 442


building trellis

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-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 10057, rend_intergenic: 8958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103216, rend_intergenic: 99123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106248, rend_intergenic: 103468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131873, rend_intergenic: 127612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140138, rend_intergenic: 135716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146438, rend_intergenic: 142717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 132021, rend_intergenic: 132018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 145496, rend_intergenic: 145493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support