-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_9473283-9749997

-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.g28628.t1
Valid prediction for snap_scaffold_18-snap.2063-T1
Valid prediction for GlimmerHMM_glimmerT_42932-T1
Valid prediction for GlimmerHMM_glimmerT_42916-T1
Valid prediction for GlimmerHMM_glimmerT_42941-T1
Valid prediction for GlimmerHMM_glimmerT_42930-T1
Valid prediction for snap_scaffold_18-snap.2046-T1
Valid prediction for snap_scaffold_18-snap.2059-T1
Valid prediction for snap_scaffold_18-snap.2012-T1
Valid prediction for GlimmerHMM_glimmerT_42921-T1
Valid prediction for snap_scaffold_18-snap.2055-T1
Valid prediction for snap_scaffold_18-snap.2071-T1
Valid prediction for snap_scaffold_18-snap.2048-T1
Valid prediction for Augustus_model.g28626.t1
Valid prediction for snap_scaffold_18-snap.2066-T1
Valid prediction for snap_scaffold_18-snap.2010-T1
Valid prediction for snap_scaffold_18-snap.2043-T1
Valid prediction for GlimmerHMM_glimmerT_42918-T1
Valid prediction for CodingQuarry_transcript_23878-T1
Valid prediction for pasa_asmbl_20887.p1
Valid prediction for snap_scaffold_18-snap.2050-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_18-snap.2041-T1
Valid prediction for GlimmerHMM_glimmerT_42934-T1
Valid prediction for Augustus_model.g28622.t1
Valid prediction for GlimmerHMM_glimmerT_42945-T1
Valid prediction for snap_scaffold_18-snap.2054-T1
Valid prediction for snap_scaffold_18-snap.2057-T1
Valid prediction for Augustus_model.g28627.t1
Valid prediction for snap_scaffold_18-snap.2074-T1
Valid prediction for snap_scaffold_18-snap.2027-T1
Valid prediction for snap_scaffold_18-snap.2014-T1
Valid prediction for Augustus_model.g28617.t1
Valid prediction for GlimmerHMM_glimmerT_42944-T1
Valid prediction for GlimmerHMM_glimmerT_42927-T1
Valid prediction for snap_scaffold_18-snap.2021-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_23877-T1
Valid prediction for GlimmerHMM_glimmerT_42915-T1
Valid prediction for snap_scaffold_18-snap.2009-T1
Valid prediction for GlimmerHMM_glimmerT_42917-T1
Valid prediction for snap_scaffold_18-snap.2023-T1
Valid prediction for snap_scaffold_18-snap.2076-T1
Valid prediction for snap_scaffold_18-snap.2051-T1
Valid prediction for snap_scaffold_18-snap.2062-T1
Valid prediction for GlimmerHMM_glimmerT_42924-T1
Valid prediction for snap_scaffold_18-snap.2052-T1
Valid prediction for snap_scaffold_18-snap.2015-T1
Valid prediction for GlimmerHMM_glimmerT_42919-T1
Valid prediction for GlimmerHMM_glimmerT_42940-T1
Valid prediction for snap_scaffold_18-snap.2039-T1
Valid prediction for snap_scaffold_18-snap.2049-T1
Valid prediction for snap_scaffold_18-snap.2069-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_18-snap.2037-T1
Valid prediction for snap_scaffold_18-snap.2035-T1
Valid prediction for snap_scaffold_18-snap.2064-T1
Valid prediction for snap_scaffold_18-snap.2031-T1
Valid prediction for Augustus_model.g28630.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_18-snap.2040-T1
Valid prediction for GlimmerHMM_glimmerT_42929-T1
Valid prediction for CodingQuarry_transcript_23874-T1
Couldn't classify 85704, 85841
Couldn't classify 89430, 89544
Sorry, prediction pasa_asmbl_20076.p1 fails validation.
(GTG)	 AG	85704-85841	GT	AGG
(CGC)	 AG	86301-86443	GT	AGG
(GTC)	 AG	89430-89544	AG	AGA
-recovered pasa_asmbl_20076.p1, internal, 85704, 85841
-recovered pasa_asmbl_20076.p1, internal, 86301, 86443
Valid prediction for snap_scaffold_18-snap.2033-T1
Valid prediction for snap_scaffold_18-snap.2068-T1
Valid prediction for snap_scaffold_18-snap.2042-T1
Valid prediction for HiQ_model.g28621.t1
Valid prediction for GlimmerHMM_glimmerT_42923-T1
Valid prediction for snap_scaffold_18-snap.2028-T1
Valid prediction for snap_scaffold_18-snap.2020-T1
Valid prediction for GlimmerHMM_glimmerT_42935-T1
Valid prediction for snap_scaffold_18-snap.2026-T1
Valid prediction for GlimmerHMM_glimmerT_42933-T1
Valid prediction for snap_scaffold_18-snap.2056-T1
Valid prediction for GlimmerHMM_glimmerT_42939-T1
Valid prediction for snap_scaffold_18-snap.2070-T1
Valid prediction for CodingQuarry_transcript_23876-T1
Valid prediction for snap_scaffold_18-snap.2058-T1
Valid prediction for snap_scaffold_18-snap.2034-T1
Valid prediction for Augustus_model.g28625.t1
Valid prediction for snap_scaffold_18-snap.2025-T1
Valid prediction for GlimmerHMM_glimmerT_42937-T1
Valid prediction for snap_scaffold_18-snap.2016-T1
Couldn't classify 56757, 56920
Couldn't classify 63356, 63638
Sorry, prediction pasa_asmbl_20082.p1 fails validation.
(CTC)	 TC	56757-56920	GT	AGG
(TGC)	 AG	58740-58806	GT	GGG
(AAG)	 AG	58915-58992	GT	AGG
(GAG)	 AG	59071-59169	GT	TGG
(GAT)	 AG	61388-61473	GT	AGG
(TCA)	 AG	63356-63638	TC	CGT
-recovered pasa_asmbl_20082.p1, internal, 58740, 58806
-recovered pasa_asmbl_20082.p1, internal, 58915, 58992
-recovered pasa_asmbl_20082.p1, internal, 59071, 59169
-recovered pasa_asmbl_20082.p1, internal, 61388, 61473
Valid prediction for snap_scaffold_18-snap.2029-T1
Couldn't classify 90843, 91259
Sorry, prediction pasa_asmbl_20075.p1 fails validation.
(ATG)	 AG	90843-91259	TC	GTT
Valid prediction for snap_scaffold_18-snap.2017-T1
Valid prediction for snap_scaffold_18-snap.2022-T1
Valid prediction for GlimmerHMM_glimmerT_42928-T1
Valid prediction for Augustus_model.g28624.t1
Valid prediction for snap_scaffold_18-snap.2060-T1
Valid prediction for Augustus_model.g28623.t1
Valid prediction for GlimmerHMM_glimmerT_42931-T1
Valid prediction for snap_scaffold_18-snap.2075-T1
Valid prediction for snap_scaffold_18-snap.2045-T1
Valid prediction for snap_scaffold_18-snap.2047-T1
Valid prediction for GlimmerHMM_glimmerT_42926-T1
Valid prediction for GlimmerHMM_glimmerT_42936-T1
Valid prediction for snap_scaffold_18-snap.2024-T1
Valid prediction for Augustus_model.g28620.t1
Valid prediction for snap_scaffold_18-snap.2030-T1
Valid prediction for snap_scaffold_18-snap.2053-T1
Valid prediction for Augustus_model.g28619.t1
Valid prediction for GlimmerHMM_glimmerT_42943-T1
Valid prediction for snap_scaffold_18-snap.2032-T1
Valid prediction for snap_scaffold_18-snap.2061-T1
Valid prediction for snap_scaffold_18-snap.2036-T1
Valid prediction for GlimmerHMM_glimmerT_42942-T1
Valid prediction for snap_scaffold_18-snap.2013-T1
Valid prediction for GlimmerHMM_glimmerT_42922-T1
Valid prediction for GlimmerHMM_glimmerT_42925-T1
Valid prediction for snap_scaffold_18-snap.2073-T1
Valid prediction for Augustus_model.g28618.t1
Valid prediction for snap_scaffold_18-snap.2011-T1
Valid prediction for snap_scaffold_18-snap.2044-T1
Valid prediction for GlimmerHMM_glimmerT_42938-T1
Couldn't classify 63837, 64293
Sorry, prediction pasa_asmbl_20078.p1 fails validation.
(TCC)	 TC	63837-64293	GT	AGG
(ACC)	 AG	66056-66157	GT	AGG
(ACA)	 AG	67133-67256	GT	GGG
(GGT)	 AG	67366-67375	AC	AGA
-recovered pasa_asmbl_20078.p1, terminal, 67366, 67375
-recovered pasa_asmbl_20078.p1, internal, 66056, 66157
-recovered pasa_asmbl_20078.p1, internal, 67133, 67256
Valid prediction for snap_scaffold_18-snap.2018-T1
Valid prediction for snap_scaffold_18-snap.2038-T1
Valid prediction for snap_scaffold_18-snap.2065-T1
Valid prediction for snap_scaffold_18-snap.2072-T1
Valid prediction for CodingQuarry_transcript_23875-T1
Valid prediction for snap_scaffold_18-snap.2019-T1
Valid prediction for GlimmerHMM_glimmerT_42920-T1
Valid prediction for Augustus_model.g28629.t1
Valid prediction for snap_scaffold_18-snap.2067-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15548, rend_intergenic: 13171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21306, rend_intergenic: 17903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35702, rend_intergenic: 24524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54394, rend_intergenic: 49115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59197, rend_intergenic: 54601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73468, rend_intergenic: 60433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91733, rend_intergenic: 80540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95159, rend_intergenic: 91999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104897, rend_intergenic: 97595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112627, rend_intergenic: 106763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121457, rend_intergenic: 116762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127685, rend_intergenic: 127448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130142, rend_intergenic: 128393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133543, rend_intergenic: 132964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135400, rend_intergenic: 133591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144146, rend_intergenic: 136279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172326, rend_intergenic: 155932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177957, rend_intergenic: 176875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181227, rend_intergenic: 178064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195182, rend_intergenic: 186075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199374, rend_intergenic: 196328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204677, rend_intergenic: 199544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222789, rend_intergenic: 209291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230814, rend_intergenic: 222844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 246014, rend_intergenic: 233630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253719, rend_intergenic: 246326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 259496, rend_intergenic: 254885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 263794, rend_intergenic: 259673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 267325, rend_intergenic: 264015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 267868, rend_intergenic: 267399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 272684, rend_intergenic: 268689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 276715
-exon list size: 533


building trellis

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-found 44 predictions from path traversal
Error with prediction: snap lend_intergenic: 15548, rend_intergenic: 13171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21306, rend_intergenic: 17903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35702, rend_intergenic: 24524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54394, rend_intergenic: 49115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59197, rend_intergenic: 54601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73468, rend_intergenic: 60433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91733, rend_intergenic: 80540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95159, rend_intergenic: 91999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104897, rend_intergenic: 97595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112627, rend_intergenic: 106763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121457, rend_intergenic: 116762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127685, rend_intergenic: 127448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130142, rend_intergenic: 128393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133543, rend_intergenic: 132964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135400, rend_intergenic: 133591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144146, rend_intergenic: 136279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172326, rend_intergenic: 155932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177957, rend_intergenic: 176875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181227, rend_intergenic: 178064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195182, rend_intergenic: 186075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199374, rend_intergenic: 196328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204677, rend_intergenic: 199544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222789, rend_intergenic: 209291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230814, rend_intergenic: 222844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 246014, rend_intergenic: 233630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253719, rend_intergenic: 246326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 259496, rend_intergenic: 254885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 263794, rend_intergenic: 259673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 267325, rend_intergenic: 264015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 267868, rend_intergenic: 267399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 272684, rend_intergenic: 268689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support