-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_6333681-6562291

-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_11-snap.1507-T1
Valid prediction for Augustus_model.g18049.t1
Valid prediction for snap_scaffold_11-snap.1520-T1
Valid prediction for snap_scaffold_11-snap.1518-T1
Valid prediction for snap_scaffold_11-snap.1502-T1
Valid prediction for snap_scaffold_11-snap.1528-T1
Valid prediction for GlimmerHMM_glimmerT_27250-T1
Valid prediction for GlimmerHMM_glimmerT_27257-T1
Valid prediction for GlimmerHMM_glimmerT_27261-T1
Valid prediction for pasa_asmbl_5627.p1
Valid prediction for Augustus_model.g18046.t1
Valid prediction for GlimmerHMM_glimmerT_27258-T1
Valid prediction for GlimmerHMM_glimmerT_27268-T1
Valid prediction for GlimmerHMM_glimmerT_27263-T1
Valid prediction for Augustus_model.g18047.t1
Valid prediction for snap_scaffold_11-snap.1509-T1
Valid prediction for snap_scaffold_11-snap.1499-T1
Valid prediction for snap_scaffold_11-snap.1529-T1
Valid prediction for GlimmerHMM_glimmerT_27267-T1
Valid prediction for snap_scaffold_11-snap.1505-T1
Valid prediction for GlimmerHMM_glimmerT_27272-T1
Valid prediction for snap_scaffold_11-snap.1506-T1
Valid prediction for snap_scaffold_11-snap.1497-T1
Valid prediction for snap_scaffold_11-snap.1503-T1
Valid prediction for GlimmerHMM_glimmerT_27273-T1
Valid prediction for GlimmerHMM_glimmerT_27260-T1
Valid prediction for GlimmerHMM_glimmerT_27256-T1
Valid prediction for snap_scaffold_11-snap.1512-T1
Valid prediction for snap_scaffold_11-snap.1515-T1
Valid prediction for snap_scaffold_11-snap.1519-T1
Valid prediction for snap_scaffold_11-snap.1532-T1
Valid prediction for snap_scaffold_11-snap.1530-T1
Valid prediction for snap_scaffold_11-snap.1533-T1
Valid prediction for Augustus_model.g18041.t1
Valid prediction for GlimmerHMM_glimmerT_27266-T1
Valid prediction for HiQ_model.g18044.t1
Valid prediction for snap_scaffold_11-snap.1522-T1
Valid prediction for snap_scaffold_11-snap.1498-T1
Valid prediction for Augustus_model.g18052.t1
Valid prediction for Augustus_model.g18045.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_11-snap.1526-T1
Valid prediction for GlimmerHMM_glimmerT_27254-T1
Valid prediction for snap_scaffold_11-snap.1504-T1
Couldn't classify 116470, 117324
Sorry, prediction pasa_asmbl_6263.p1 fails validation.
(TCT)	 TG	116470-117324	AA	TCA
Valid prediction for Augustus_model.g18037.t1
Valid prediction for snap_scaffold_11-snap.1510-T1
Couldn't classify 50990, 51171
Sorry, prediction pasa_asmbl_6715.p1 fails validation.
(GCT)	 CT	50990-51171	GT	AGG
(AAC)	 AG	51273-51438	AC	AGA
-recovered pasa_asmbl_6715.p1, terminal, 51273, 51438
Valid prediction for snap_scaffold_11-snap.1525-T1
Valid prediction for CodingQuarry_transcript_8098-T1
Valid prediction for snap_scaffold_11-snap.1514-T1
Valid prediction for pasa_asmbl_6707.p1
Valid prediction for GlimmerHMM_glimmerT_27271-T1
Valid prediction for snap_scaffold_11-snap.1524-T1
Couldn't classify 46552, 46606
Couldn't classify 48616, 48645
Sorry, prediction pasa_asmbl_6716.p1 fails validation.
(CAG)	 TC	46552-46606	GT	AGG
(GAA)	 AG	46803-46909	GT	AGG
(GAG)	 AG	47000-47118	GT	GTG
(GCT)	 AG	47552-47682	GT	CGG
(GTG)	 AG	47800-47940	GT	AGG
(TGG)	 AG	48213-48397	GT	TCG
(GAG)	 AG	48616-48645	TA	GAT
-recovered pasa_asmbl_6716.p1, internal, 46803, 46909
-recovered pasa_asmbl_6716.p1, internal, 47000, 47118
-recovered pasa_asmbl_6716.p1, internal, 47552, 47682
-recovered pasa_asmbl_6716.p1, internal, 47800, 47940
-recovered pasa_asmbl_6716.p1, internal, 48213, 48397
Valid prediction for GlimmerHMM_glimmerT_27251-T1
Valid prediction for GlimmerHMM_glimmerT_27269-T1
Valid prediction for snap_scaffold_11-snap.1508-T1
Valid prediction for snap_scaffold_11-snap.1513-T1
Valid prediction for HiQ_model.g18042.t1
Valid prediction for GlimmerHMM_glimmerT_27265-T1
Valid prediction for Augustus_model.g18038.t1
Valid prediction for snap_scaffold_11-snap.1523-T1
Valid prediction for snap_scaffold_11-snap.1521-T1
Couldn't classify 190203, 190751
Sorry, prediction pasa_asmbl_6705.p1 fails validation.
(TTA)	 AT	190203-190751	GC	AGG
Valid prediction for Augustus_model.g18040.t1
Valid prediction for GlimmerHMM_glimmerT_27259-T1
Couldn't classify 42549, 43069
Couldn't classify 46377, 46416
Sorry, prediction pasa_asmbl_6717.p1 fails validation.
(ATC)	 CA	42549-43069	GT	AGG
(TGT)	 AG	43666-43802	GT	AGG
(GGG)	 AG	43885-44071	GT	AGG
(TCA)	 AG	44168-44360	GT	AGG
(ATC)	 AG	44464-44559	GT	AGG
(CTA)	 AG	44697-44882	GT	ACG
(GTG)	 AG	45141-45293	GT	AGG
(GCC)	 AG	45676-45808	GT	CGG
(TGT)	 AG	45908-46031	GT	AGG
(AAT)	 AG	46377-46416	GT	AGG
add_exon() Sorry, pasa_asmbl_6717.p1 45908-46031-terminal-3 is invalid.
-recovered pasa_asmbl_6717.p1, terminal, 45908, 46031
-recovered pasa_asmbl_6717.p1, internal, 43666, 43802
-recovered pasa_asmbl_6717.p1, internal, 43885, 44071
-recovered pasa_asmbl_6717.p1, internal, 44168, 44360
-recovered pasa_asmbl_6717.p1, internal, 44464, 44559
-recovered pasa_asmbl_6717.p1, internal, 44697, 44882
-recovered pasa_asmbl_6717.p1, internal, 45141, 45293
-recovered pasa_asmbl_6717.p1, internal, 45676, 45808
-recovered pasa_asmbl_6717.p1, internal, 45908, 46031
-recovered pasa_asmbl_6717.p1, internal, 46377, 46416
Valid prediction for snap_scaffold_11-snap.1527-T1
Valid prediction for GlimmerHMM_glimmerT_27253-T1
Valid prediction for snap_scaffold_11-snap.1516-T1
Valid prediction for Augustus_model.g18050.t1
Valid prediction for snap_scaffold_11-snap.1517-T1
Valid prediction for pasa_asmbl_6719.p1
Valid prediction for snap_scaffold_11-snap.1501-T1
Valid prediction for snap_scaffold_11-snap.1511-T1
Valid prediction for Augustus_model.g18039.t1
Valid prediction for Augustus_model.g18043.t1
Valid prediction for GlimmerHMM_glimmerT_27264-T1
Valid prediction for GlimmerHMM_glimmerT_27262-T1
Valid prediction for GlimmerHMM_glimmerT_27270-T1
Valid prediction for CodingQuarry_transcript_8095-T1
Valid prediction for Augustus_model.g18051.t1
Valid prediction for snap_scaffold_11-snap.1531-T1
Valid prediction for Augustus_model.g18048.t1
Valid prediction for GlimmerHMM_glimmerT_27255-T1
Couldn't classify 34054, 34120
Sorry, prediction pasa_asmbl_6718.p1 fails validation.
(CTG)	 AC	34054-34120	GT	AAG
(ATC)	 AG	34445-34592	GT	AGG
(GAA)	 AG	34800-34971	GT	AGG
(AGA)	 AG	35234-35338	GT	AGG
(CGA)	 AG	35449-35499	GT	GGG
(AAA)	 AG	35620-35809	GT	AGG
(AGA)	 AG	35917-35927	CC	GAC
-recovered pasa_asmbl_6718.p1, terminal, 35917, 35927
-recovered pasa_asmbl_6718.p1, internal, 34445, 34592
-recovered pasa_asmbl_6718.p1, internal, 34800, 34971
-recovered pasa_asmbl_6718.p1, internal, 35234, 35338
-recovered pasa_asmbl_6718.p1, internal, 35449, 35499
-recovered pasa_asmbl_6718.p1, internal, 35620, 35809
Couldn't classify 150396, 150452
Couldn't classify 151658, 151840
Sorry, prediction pasa_asmbl_6713.p1 fails validation.
(CTG)	 CC	150396-150452	GT	AGG
(GAG)	 AG	150761-150948	GT	AGG
(GAT)	 AG	151308-151458	GT	AGG
(GCT)	 AG	151658-151840	GT	AGG
add_exon() Sorry, pasa_asmbl_6713.p1 150761-150948-terminal-2 is invalid.
-recovered pasa_asmbl_6713.p1, terminal, 150761, 150948
-recovered pasa_asmbl_6713.p1, internal, 150761, 150948
-recovered pasa_asmbl_6713.p1, internal, 151308, 151458
-recovered pasa_asmbl_6713.p1, internal, 151658, 151840
Valid prediction for snap_scaffold_11-snap.1500-T1
Valid prediction for GlimmerHMM_glimmerT_27252-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 38714, rend_intergenic: 36877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112574, rend_intergenic: 103344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143868, rend_intergenic: 118878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169230, rend_intergenic: 165742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214685, rend_intergenic: 212153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216119, rend_intergenic: 214890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 228611
-exon list size: 542


building trellis

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99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 38714, rend_intergenic: 36877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112574, rend_intergenic: 103344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143868, rend_intergenic: 118878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169230, rend_intergenic: 165742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214685, rend_intergenic: 212153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216119, rend_intergenic: 214890  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

-building DP trellis

-building trellis in range 1 - 10915
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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

-building DP trellis

-building trellis in range 1 - 10134
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

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