-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_8396473-8569049

-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 Augustus_model.g10027.t1
Valid prediction for GlimmerHMM_glimmerT_15112-T1
Couldn't classify 128837, 128862
Couldn't classify 129870, 129887
Sorry, prediction pasa_asmbl_47143.p1 fails validation.
(GCG)	 TG	128837-128862	GT	ACG
(TGG)	 AG	129158-129191	GT	AGG
(GAA)	 AG	129294-129564	GT	GGG
(CTC)	 AG	129685-129758	GT	GAG
(CTA)	 AG	129870-129887	AA	CCA
-recovered pasa_asmbl_47143.p1, internal, 129158, 129191
-recovered pasa_asmbl_47143.p1, internal, 129294, 129564
-recovered pasa_asmbl_47143.p1, internal, 129685, 129758
Valid prediction for snap_scaffold_6-snap.1895-T1
Valid prediction for snap_scaffold_6-snap.1877-T1
Valid prediction for snap_scaffold_6-snap.1866-T1
Valid prediction for pasa_asmbl_47141.p1
Valid prediction for HiQ_model.g10026.t1
Valid prediction for GlimmerHMM_glimmerT_15129-T1
Valid prediction for Augustus_model.g10033.t1
Valid prediction for snap_scaffold_6-snap.1874-T1
Valid prediction for snap_scaffold_6-snap.1880-T1
Valid prediction for GlimmerHMM_glimmerT_15125-T1
Valid prediction for GlimmerHMM_glimmerT_15122-T1
Valid prediction for GlimmerHMM_glimmerT_15124-T1
Valid prediction for CodingQuarry_transcript_55134-T1
Valid prediction for snap_scaffold_6-snap.1881-T1
Valid prediction for snap_scaffold_6-snap.1868-T1
Valid prediction for Augustus_model.g10022.t1
Valid prediction for snap_scaffold_6-snap.1882-T1
Valid prediction for Augustus_model.g10020.t1
Valid prediction for pasa_asmbl_47131.p1
Valid prediction for snap_scaffold_6-snap.1873-T1
Valid prediction for GlimmerHMM_glimmerT_15107-T1
Valid prediction for snap_scaffold_6-snap.1883-T1
Valid prediction for GlimmerHMM_glimmerT_15115-T1
Valid prediction for GlimmerHMM_glimmerT_15113-T1
Valid prediction for Augustus_model.g10031.t1
Valid prediction for GlimmerHMM_glimmerT_15133-T1
Valid prediction for CodingQuarry_transcript_55138-T1
Valid prediction for snap_scaffold_6-snap.1889-T1
Valid prediction for CodingQuarry_transcript_55133-T1
Valid prediction for Augustus_model.g10032.t1
Valid prediction for Augustus_model.g10035.t1
Valid prediction for Augustus_model.g10023.t1
Valid prediction for snap_scaffold_6-snap.1871-T1
Valid prediction for snap_scaffold_6-snap.1885-T1
Valid prediction for GlimmerHMM_glimmerT_15119-T1
Valid prediction for Augustus_model.g10039.t1
Valid prediction for snap_scaffold_6-snap.1862-T1
Couldn't classify 130069, 130145
Sorry, prediction pasa_asmbl_47144.p1 fails validation.
(CTA)	 TA	130069-130145	GT	AGG
(GGA)	 AG	130254-130304	GT	AGG
(GTT)	 AG	130399-130470	GT	AGG
(ACG)	 AG	130608-130755	GT	TGG
(ATG)	 AG	130845-130932	GT	GGG
(CGT)	 AG	131021-131103	TC	AAT
-recovered pasa_asmbl_47144.p1, initial, 130845, 130932
-recovered pasa_asmbl_47144.p1, terminal, 131021, 131103
-recovered pasa_asmbl_47144.p1, internal, 130254, 130304
-recovered pasa_asmbl_47144.p1, internal, 130399, 130470
-recovered pasa_asmbl_47144.p1, internal, 130608, 130755
-recovered pasa_asmbl_47144.p1, internal, 130845, 130932
Valid prediction for pasa_asmbl_47124.p1
Couldn't classify 99650, 99734
Sorry, prediction pasa_asmbl_47136.p1 fails validation.
(ATG)	 GG	98402-98404	GT	TGG
(AAC)	 AG	98497-98658	GT	AGG
(TTG)	 AG	98793-98930	GT	AGG
(GCC)	 AG	99222-99412	GT	AGG
(GTC)	 AG	99650-99734	AA	CCA
-recovered pasa_asmbl_47136.p1, initial, 98402, 98404
-recovered pasa_asmbl_47136.p1, internal, 98497, 98658
-recovered pasa_asmbl_47136.p1, internal, 98793, 98930
-recovered pasa_asmbl_47136.p1, internal, 99222, 99412
Valid prediction for GlimmerHMM_glimmerT_15127-T1
Valid prediction for HiQ_model.g10028.t1
Valid prediction for Augustus_model.g10038.t1
Valid prediction for GlimmerHMM_glimmerT_15114-T1
Valid prediction for snap_scaffold_6-snap.1865-T1
Couldn't classify 100267, 100416
Couldn't classify 100749, 100925
Sorry, prediction pasa_asmbl_47137.p2 fails validation.
(TCC)	 AC	100267-100416	GT	AGG
(TGT)	 AG	100749-100925	GT	AGG
-recovered pasa_asmbl_47137.p2, internal, 100749, 100925
Valid prediction for GlimmerHMM_glimmerT_15128-T1
Valid prediction for snap_scaffold_6-snap.1861-T1
Valid prediction for GlimmerHMM_glimmerT_15111-T1
Valid prediction for Augustus_model.g10021.t1
Valid prediction for snap_scaffold_6-snap.1887-T1
Valid prediction for HiQ_model.g10037.t1
Valid prediction for GlimmerHMM_glimmerT_15121-T1
Valid prediction for snap_scaffold_6-snap.1875-T1
Valid prediction for GlimmerHMM_glimmerT_15106-T1
Valid prediction for snap_scaffold_6-snap.1863-T1
Valid prediction for GlimmerHMM_glimmerT_15120-T1
Valid prediction for pasa_asmbl_47135.p1
Valid prediction for snap_scaffold_6-snap.1888-T1
Valid prediction for Augustus_model.g10040.t1
Valid prediction for snap_scaffold_6-snap.1891-T1
Valid prediction for CodingQuarry_transcript_55137-T1
Valid prediction for CodingQuarry_transcript_55130-T1
Valid prediction for GlimmerHMM_glimmerT_15105-T1
Valid prediction for CodingQuarry_transcript_55129-T1
Couldn't classify 79641, 79681
Sorry, prediction pasa_asmbl_47134.p1 fails validation.
(ACT)	 AA	79641-79681	GT	AGG
(AGA)	 AG	80091-80358	GT	AGG
(AAT)	 AG	80457-80564	GT	AGG
(ACC)	 AG	80737-80838	GT	AGG
(GAA)	 AG	81449-81589	GT	AGG
(CAA)	 AG	81769-81915	CA	AAC
-recovered pasa_asmbl_47134.p1, terminal, 81769, 81915
-recovered pasa_asmbl_47134.p1, internal, 80091, 80358
-recovered pasa_asmbl_47134.p1, internal, 80457, 80564
-recovered pasa_asmbl_47134.p1, internal, 80737, 80838
-recovered pasa_asmbl_47134.p1, internal, 81449, 81589
Valid prediction for Augustus_model.g10024.t1
Valid prediction for snap_scaffold_6-snap.1870-T1
Couldn't classify 101124, 101159
Couldn't classify 101614, 101944
Sorry, prediction pasa_asmbl_47138.p1 fails validation.
(GAC)	 AC	101124-101159	GT	AGG
(CTT)	 AG	101321-101523	GT	CGG
(GGT)	 AG	101614-101944	GA	TGG
-recovered pasa_asmbl_47138.p1, internal, 101321, 101523

-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: -)Couldn't classify 52285, 52286
Sorry, prediction pasa_asmbl_48562.p1 fails validation.
(ATG)	 AC	52285-52286	GT	ATG
(GCA)	 AG	52468-52608	GT	CAG
(CCC)	 AG	52756-52907	GT	CGG
(CAG)	 AG	53056-53084	GA	AGG
-recovered pasa_asmbl_48562.p1, terminal, 53056, 53084
-recovered pasa_asmbl_48562.p1, internal, 52468, 52608
-recovered pasa_asmbl_48562.p1, internal, 52756, 52907
Valid prediction for snap_scaffold_6-snap.1896-T1
Valid prediction for snap_scaffold_6-snap.1878-T1
Valid prediction for GlimmerHMM_glimmerT_15132-T1
Valid prediction for Augustus_model.g10030.t1
Couldn't classify 6337, 7165
Sorry, prediction pasa_asmbl_48567.p1 fails validation.
(TTC)	 CT	6337-7165	GT	AGG
(GCC)	 AG	7270-7379	GT	AGG
(CGA)	 AG	7561-7708	GT	AAG
(ATG)	 AG	7832-7956	GT	AGG
(GAT)	 AG	8121-8326	GT	CGG
(GGG)	 AG	8414-8705	GT	CGG
(ATG)	 AG	8837-8905	GG	GAG
add_exon() Sorry, pasa_asmbl_48567.p1 7832-7956-initial-1 is invalid.
-recovered pasa_asmbl_48567.p1, initial, 7832, 7956
-recovered pasa_asmbl_48567.p1, terminal, 8837, 8905
-recovered pasa_asmbl_48567.p1, internal, 7270, 7379
-recovered pasa_asmbl_48567.p1, internal, 7561, 7708
-recovered pasa_asmbl_48567.p1, internal, 7832, 7956
-recovered pasa_asmbl_48567.p1, internal, 8121, 8326
-recovered pasa_asmbl_48567.p1, internal, 8414, 8705
Valid prediction for snap_scaffold_6-snap.1894-T1
Valid prediction for snap_scaffold_6-snap.1890-T1
Valid prediction for GlimmerHMM_glimmerT_15130-T1
Valid prediction for GlimmerHMM_glimmerT_15135-T1
Valid prediction for snap_scaffold_6-snap.1892-T1
Couldn't classify 52285, 52286
Sorry, prediction CodingQuarry_transcript_55136-T1 fails validation.
(ATG)	 AC	52285-52286	GT	ATG
(GCA)	 AG	52468-52608	GT	CAG
(CCC)	 AG	52756-52907	GT	CGG
(CAG)	 AG	53056-53084	GA	AGG
-recovered CodingQuarry_transcript_55136-T1, terminal, 53056, 53084
-recovered CodingQuarry_transcript_55136-T1, internal, 52468, 52608
-recovered CodingQuarry_transcript_55136-T1, internal, 52756, 52907
Valid prediction for pasa_asmbl_48560.p1
Valid prediction for snap_scaffold_6-snap.1867-T1
Valid prediction for GlimmerHMM_glimmerT_15116-T1
Valid prediction for snap_scaffold_6-snap.1864-T1
Valid prediction for GlimmerHMM_glimmerT_15118-T1
Valid prediction for Augustus_model.g10029.t1
Valid prediction for HiQ_model.g10041.t1
Valid prediction for HiQ_model.g10036.t1
Valid prediction for snap_scaffold_6-snap.1869-T1
Valid prediction for GlimmerHMM_glimmerT_15126-T1
Valid prediction for GlimmerHMM_glimmerT_15131-T1
Valid prediction for Augustus_model.g10034.t1
Valid prediction for GlimmerHMM_glimmerT_15123-T1
Valid prediction for GlimmerHMM_glimmerT_15134-T1
Valid prediction for GlimmerHMM_glimmerT_15110-T1
Valid prediction for GlimmerHMM_glimmerT_15117-T1
Valid prediction for snap_scaffold_6-snap.1893-T1
Valid prediction for snap_scaffold_6-snap.1884-T1
Valid prediction for CodingQuarry_transcript_55131-T1
Valid prediction for GlimmerHMM_glimmerT_15136-T1
Valid prediction for snap_scaffold_6-snap.1879-T1
Couldn't classify 14326, 14416
Sorry, prediction pasa_asmbl_48564.p1 fails validation.
(CGC)	 GG	14326-14416	GT	GGG
(GAG)	 AG	15008-15267	GT	AGG
(GAT)	 AG	15449-15541	TG	GAT
-recovered pasa_asmbl_48564.p1, terminal, 15449, 15541
-recovered pasa_asmbl_48564.p1, internal, 15008, 15267
Couldn't classify 96486, 96844
Sorry, prediction pasa_asmbl_48559.p1 fails validation.
(ATG)	 AA	95742-96018	GT	GGG
(ACG)	 AG	96096-96214	GT	AGG
(GCA)	 AG	96295-96403	GT	AGG
(GGT)	 AG	96486-96844	GA	GAG
-recovered pasa_asmbl_48559.p1, initial, 95742, 96018
-recovered pasa_asmbl_48559.p1, internal, 96096, 96214
-recovered pasa_asmbl_48559.p1, internal, 96295, 96403
Valid prediction for pasa_asmbl_48554.p1
Valid prediction for snap_scaffold_6-snap.1886-T1
Valid prediction for GlimmerHMM_glimmerT_15109-T1
Valid prediction for CodingQuarry_transcript_55132-T1
Valid prediction for GlimmerHMM_glimmerT_15108-T1
Valid prediction for snap_scaffold_6-snap.1872-T1
Valid prediction for Augustus_model.g10025.t1
Valid prediction for snap_scaffold_6-snap.1876-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18152, rend_intergenic: 17697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23564, rend_intergenic: 22393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27918, rend_intergenic: 25350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40701, rend_intergenic: 32134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149237, rend_intergenic: 142799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154532, rend_intergenic: 149245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166742, rend_intergenic: 163673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 172577
-exon list size: 411


building trellis

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99.3    
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-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 18152, rend_intergenic: 17697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23564, rend_intergenic: 22393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27918, rend_intergenic: 25350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40701, rend_intergenic: 32134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149237, rend_intergenic: 142799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154532, rend_intergenic: 149245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166742, rend_intergenic: 163673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support