-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_8055213-8472007

-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_9-snap.1741-T1
Valid prediction for snap_scaffold_9-snap.1704-T1
Valid prediction for HiQ_model.g15002.t1
Valid prediction for CodingQuarry_transcript_62240-T1
Valid prediction for pasa_asmbl_54159.p1
Valid prediction for GlimmerHMM_glimmerT_22576-T1
Valid prediction for Augustus_model.g14998.t1
Couldn't classify 116510, 116992
Sorry, prediction pasa_asmbl_54154.p1 fails validation.
(GAC)	 CT	116510-116992	AC	AAA
Valid prediction for Augustus_model.g14989.t1
Valid prediction for snap_scaffold_9-snap.1739-T1
Valid prediction for CodingQuarry_transcript_62239-T1
Valid prediction for snap_scaffold_9-snap.1742-T1
Valid prediction for snap_scaffold_9-snap.1723-T1
Valid prediction for pasa_asmbl_54158.p1
Valid prediction for snap_scaffold_9-snap.1696-T1
Valid prediction for GlimmerHMM_glimmerT_22572-T1
Valid prediction for Augustus_model.g15003.t1
Valid prediction for snap_scaffold_9-snap.1691-T1
Valid prediction for snap_scaffold_9-snap.1714-T1
Valid prediction for GlimmerHMM_glimmerT_22554-T1
Couldn't classify 93001, 93126
Sorry, prediction pasa_asmbl_54150.p1 fails validation.
(GTG)	 CT	93001-93126	GT	AGG
(GCA)	 AG	93443-93795	GT	AGG
(GAT)	 AG	93959-94171	GT	AGG
(ATT)	 AG	94420-94586	GT	AGG
(CCC)	 AG	94732-94856	GT	AGG
(GTG)	 AG	95226-95549	GC	GAG
-recovered pasa_asmbl_54150.p1, terminal, 95226, 95549
-recovered pasa_asmbl_54150.p1, internal, 93443, 93795
-recovered pasa_asmbl_54150.p1, internal, 93959, 94171
-recovered pasa_asmbl_54150.p1, internal, 94420, 94586
-recovered pasa_asmbl_54150.p1, internal, 94732, 94856
-recovered pasa_asmbl_54150.p1, internal, 95226, 95549
Valid prediction for snap_scaffold_9-snap.1705-T1
Valid prediction for Augustus_model.g15008.t1
Valid prediction for Augustus_model.g15026.t1
Valid prediction for Augustus_model.g14987.t1
Valid prediction for pasa_asmbl_54173.p1
Valid prediction for Augustus_model.g15010.t1
Valid prediction for Augustus_model.g15012.t1
Valid prediction for GlimmerHMM_glimmerT_22573-T1
Valid prediction for Augustus_model.g15004.t1
Valid prediction for Augustus_model.g14997.t1
Valid prediction for snap_scaffold_9-snap.1706-T1
Valid prediction for snap_scaffold_9-snap.1716-T1
Valid prediction for snap_scaffold_9-snap.1722-T1
Valid prediction for snap_scaffold_9-snap.1730-T1
Valid prediction for CodingQuarry_transcript_62242-T1
Valid prediction for snap_scaffold_9-snap.1692-T1
Valid prediction for Augustus_model.g14990.t1
Valid prediction for snap_scaffold_9-snap.1699-T1
Valid prediction for snap_scaffold_9-snap.1684-T1
Valid prediction for snap_scaffold_9-snap.1715-T1
Valid prediction for GlimmerHMM_glimmerT_22566-T1
Valid prediction for snap_scaffold_9-snap.1727-T1
Valid prediction for pasa_asmbl_54714.p1
Valid prediction for snap_scaffold_9-snap.1701-T1
Valid prediction for snap_scaffold_9-snap.1697-T1
Valid prediction for snap_scaffold_9-snap.1707-T1
Valid prediction for snap_scaffold_9-snap.1718-T1
Valid prediction for Augustus_model.g15011.t1
Valid prediction for GlimmerHMM_glimmerT_22568-T1
Valid prediction for Augustus_model.g15014.t1
Valid prediction for snap_scaffold_9-snap.1744-T1
Valid prediction for GlimmerHMM_glimmerT_22562-T1
Valid prediction for snap_scaffold_9-snap.1721-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.1694-T1
Valid prediction for HiQ_model.g15019.t1
Valid prediction for Augustus_model.g15006.t1
Valid prediction for GlimmerHMM_glimmerT_22571-T1
Valid prediction for snap_scaffold_9-snap.1734-T1
Valid prediction for GlimmerHMM_glimmerT_22564-T1
Valid prediction for Augustus_model.g15001.t1
Valid prediction for Augustus_model.g15016.t1
Valid prediction for Augustus_model.g15007.t1
Valid prediction for snap_scaffold_9-snap.1700-T1
Valid prediction for Augustus_model.g15015.t1
Valid prediction for HiQ_model.g15018.t1
Valid prediction for GlimmerHMM_glimmerT_22565-T1
Couldn't classify 378341, 378534
Couldn't classify 379248, 379451
Sorry, prediction pasa_asmbl_54174.p1 fails validation.
(AGT)	 TA	378341-378534	GT	ACG
(GGT)	 AG	378633-378828	GT	AGG
(GAT)	 AG	379248-379451	GT	AGG
-recovered pasa_asmbl_54174.p1, internal, 378633, 378828
-recovered pasa_asmbl_54174.p1, internal, 379248, 379451
Valid prediction for GlimmerHMM_glimmerT_22577-T1
Valid prediction for GlimmerHMM_glimmerT_22550-T1
Valid prediction for snap_scaffold_9-snap.1698-T1
Valid prediction for pasa_asmbl_54155.p1
Valid prediction for snap_scaffold_9-snap.1717-T1
Valid prediction for Augustus_model.g15017.t1
Couldn't classify 16553, 16744
Sorry, prediction pasa_asmbl_54148.p1 fails validation.
(AAC)	 AG	16553-16744	GT	AGG
(GTT)	 AG	16873-18072	AG	AGA
-recovered pasa_asmbl_54148.p1, terminal, 16873, 18072
-recovered pasa_asmbl_54148.p1, internal, 16553, 16744
Valid prediction for snap_scaffold_9-snap.1719-T1
Valid prediction for snap_scaffold_9-snap.1702-T1
Valid prediction for CodingQuarry_transcript_62241-T1
Valid prediction for snap_scaffold_9-snap.1695-T1
Valid prediction for GlimmerHMM_glimmerT_22570-T1
Valid prediction for snap_scaffold_9-snap.1731-T1
Valid prediction for CodingQuarry_transcript_62238-T1
Valid prediction for GlimmerHMM_glimmerT_22557-T1
Valid prediction for GlimmerHMM_glimmerT_22551-T1
Valid prediction for snap_scaffold_9-snap.1682-T1
Valid prediction for snap_scaffold_9-snap.1693-T1
Valid prediction for snap_scaffold_9-snap.1688-T1
Valid prediction for Augustus_model.g15024.t1
Valid prediction for Augustus_model.g14999.t1
Valid prediction for GlimmerHMM_glimmerT_22558-T1
Valid prediction for snap_scaffold_9-snap.1728-T1
Valid prediction for snap_scaffold_9-snap.1709-T1
Valid prediction for Augustus_model.g14994.t1
Valid prediction for GlimmerHMM_glimmerT_22560-T1
Valid prediction for snap_scaffold_9-snap.1711-T1
Valid prediction for Augustus_model.g15005.t1
Valid prediction for GlimmerHMM_glimmerT_22561-T1
Valid prediction for Augustus_model.g15025.t1
Valid prediction for Augustus_model.g15009.t1
Valid prediction for GlimmerHMM_glimmerT_22581-T1
Valid prediction for snap_scaffold_9-snap.1743-T1
Valid prediction for HiQ_model.g15013.t1
Valid prediction for pasa_asmbl_54147.p1
Valid prediction for pasa_asmbl_54153.p1
Valid prediction for snap_scaffold_9-snap.1729-T1
Valid prediction for Augustus_model.g14995.t1
Valid prediction for snap_scaffold_9-snap.1710-T1
Valid prediction for snap_scaffold_9-snap.1712-T1
Valid prediction for GlimmerHMM_glimmerT_22563-T1
Valid prediction for snap_scaffold_9-snap.1740-T1
Valid prediction for GlimmerHMM_glimmerT_22578-T1
Valid prediction for pasa_asmbl_54164.p1
Valid prediction for snap_scaffold_9-snap.1703-T1
Valid prediction for snap_scaffold_9-snap.1726-T1
Valid prediction for snap_scaffold_9-snap.1713-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.g14991.t1
Valid prediction for snap_scaffold_9-snap.1683-T1
Valid prediction for snap_scaffold_9-snap.1725-T1
Valid prediction for snap_scaffold_9-snap.1733-T1
Valid prediction for GlimmerHMM_glimmerT_22580-T1
Valid prediction for snap_scaffold_9-snap.1746-T1
Couldn't classify 381360, 381415
Sorry, prediction pasa_asmbl_55121.p1 fails validation.
(ATG)	 TT	377307-377426	GT	AGG
(GAA)	 AG	377737-377880	GT	AGG
(GAA)	 AG	378079-378150	GT	AGG
(GCT)	 AG	378241-378299	GT	AAG
(TCA)	 AG	379530-379641	GT	AGG
(GAC)	 AG	379781-379863	GT	GGG
(GCT)	 AG	380116-380186	GT	GAG
(ATG)	 AG	380453-380546	GT	AAG
(GTA)	 AG	380717-380845	GT	AGG
(GTA)	 AG	380997-381088	GT	AGG
(GAC)	 AG	381360-381415	CC	GAC
-recovered pasa_asmbl_55121.p1, initial, 377307, 377426
add_exon() Sorry, pasa_asmbl_55121.p1 380453-380546-initial-1 is invalid.
-recovered pasa_asmbl_55121.p1, initial, 380453, 380546
-recovered pasa_asmbl_55121.p1, internal, 377737, 377880
-recovered pasa_asmbl_55121.p1, internal, 378079, 378150
-recovered pasa_asmbl_55121.p1, internal, 378241, 378299
-recovered pasa_asmbl_55121.p1, internal, 379530, 379641
-recovered pasa_asmbl_55121.p1, internal, 379781, 379863
-recovered pasa_asmbl_55121.p1, internal, 380116, 380186
-recovered pasa_asmbl_55121.p1, internal, 380453, 380546
-recovered pasa_asmbl_55121.p1, internal, 380717, 380845
-recovered pasa_asmbl_55121.p1, internal, 380997, 381088
Valid prediction for snap_scaffold_9-snap.1681-T1
Valid prediction for snap_scaffold_9-snap.1720-T1
Valid prediction for CodingQuarry_transcript_62237-T1
Valid prediction for snap_scaffold_9-snap.1738-T1
Couldn't classify 68803, 68970
Sorry, prediction pasa_asmbl_55127.p1 fails validation.
(GCT)	 CA	68803-68970	GT	AGG
(GAG)	 AG	70863-70996	GT	AGG
(CGG)	 AG	72087-72199	GT	AGG
(GAG)	 AG	72283-72518	AG	AGA
add_exon() Sorry, pasa_asmbl_55127.p1 70863-70996-terminal-2 is invalid.
-recovered pasa_asmbl_55127.p1, terminal, 70863, 70996
-recovered pasa_asmbl_55127.p1, terminal, 72283, 72518
-recovered pasa_asmbl_55127.p1, internal, 70863, 70996
-recovered pasa_asmbl_55127.p1, internal, 72087, 72199
Valid prediction for HiQ_model.g14988.t1
Valid prediction for Augustus_model.g14993.t1
Valid prediction for snap_scaffold_9-snap.1747-T1
Valid prediction for Augustus_model.g15021.t1
Valid prediction for GlimmerHMM_glimmerT_22555-T1
Valid prediction for Augustus_model.g15027.t1
Valid prediction for snap_scaffold_9-snap.1689-T1
Valid prediction for Augustus_model.g15023.t1
Valid prediction for GlimmerHMM_glimmerT_22567-T1
Valid prediction for GlimmerHMM_glimmerT_22575-T1
Valid prediction for GlimmerHMM_glimmerT_22574-T1
Valid prediction for CodingQuarry_transcript_62235-T1
Valid prediction for GlimmerHMM_glimmerT_22556-T1
Valid prediction for GlimmerHMM_glimmerT_22553-T1
Couldn't classify 359322, 360302
Sorry, prediction pasa_asmbl_55123.p1 fails validation.
(AGC)	 AC	359322-360302	TC	GAT
Valid prediction for snap_scaffold_9-snap.1687-T1
Valid prediction for GlimmerHMM_glimmerT_22569-T1
Valid prediction for pasa_asmbl_55126.p1
Valid prediction for GlimmerHMM_glimmerT_22559-T1
Valid prediction for HiQ_model.g15022.t1
Valid prediction for snap_scaffold_9-snap.1690-T1
Valid prediction for Augustus_model.g14996.t1
Valid prediction for snap_scaffold_9-snap.1732-T1
Valid prediction for Augustus_model.g14992.t1
Valid prediction for GlimmerHMM_glimmerT_22552-T1
Valid prediction for snap_scaffold_9-snap.1736-T1
Valid prediction for HiQ_model.g15020.t1
Valid prediction for snap_scaffold_9-snap.1724-T1
Valid prediction for HiQ_model.g15000.t1
Valid prediction for snap_scaffold_9-snap.1735-T1
Valid prediction for snap_scaffold_9-snap.1708-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.1737-T1
Valid prediction for pasa_asmbl_55125.p1
Valid prediction for pasa_asmbl_55120.p1
Valid prediction for snap_scaffold_9-snap.1745-T1
Valid prediction for CodingQuarry_transcript_62243-T1
Valid prediction for GlimmerHMM_glimmerT_22579-T1
Couldn't classify 56071, 56283
Sorry, prediction pasa_asmbl_55130.p1 fails validation.
(ATG)	 TA	54935-55135	GT	AAG
(GCC)	 AG	56071-56283	TC	CTT
-recovered pasa_asmbl_55130.p1, initial, 54935, 55135
Valid prediction for snap_scaffold_9-snap.1686-T1
Valid prediction for snap_scaffold_9-snap.1685-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 301560, rend_intergenic: 297507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 416795
-exon list size: 520


building trellis

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99.8    
-found 56 predictions from path traversal
Error with prediction: snap lend_intergenic: 301560, rend_intergenic: 297507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 54 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 403901 - 416795
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
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-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 406393 - 416795
-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