-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_10035046-10205787

-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 GlimmerHMM_glimmerT_37602-T1
Valid prediction for GlimmerHMM_glimmerT_37601-T1
Valid prediction for GeneMark_model.64731_t
Valid prediction for snap_scaffold_15-snap.2094-T1
Valid prediction for snap_scaffold_15-snap.2092-T1
Valid prediction for GlimmerHMM_glimmerT_37592-T1
Valid prediction for Augustus_model.g25209.t1
Valid prediction for Augustus_model.g25208.t1
Valid prediction for GeneMark_model.64728_t
Valid prediction for Augustus_model.g25202.t1
Valid prediction for GlimmerHMM_glimmerT_37594-T1
Valid prediction for snap_scaffold_15-snap.2072-T1
Valid prediction for snap_scaffold_15-snap.2093-T1
Valid prediction for GlimmerHMM_glimmerT_37604-T1
Valid prediction for snap_scaffold_15-snap.2074-T1
Valid prediction for GeneMark_model.64715_t
Valid prediction for Augustus_model.g25213.t1
Valid prediction for Augustus_model.g25207.t1
Valid prediction for GlimmerHMM_glimmerT_37588-T1
Valid prediction for GlimmerHMM_glimmerT_37608-T1
Valid prediction for GeneMark_model.64725_t
Valid prediction for Augustus_model.g25200.t1
Valid prediction for GlimmerHMM_glimmerT_37599-T1
Couldn't classify 100563, 100693
Couldn't classify 103945, 104076
Sorry, prediction pasa_asmbl_14385.p1 fails validation.
(AAC)	 AC	100563-100693	GT	AGG
(GAC)	 AG	101039-101126	GT	AGG
(GAC)	 AG	102026-102067	GT	TTG
(TCG)	 AG	103072-103191	GT	TGG
(GGG)	 AG	103371-103430	GT	ACG
(TCT)	 AG	103549-103617	GT	TGG
(ATG)	 AG	103945-104076	AG	GGA
-recovered pasa_asmbl_14385.p1, internal, 101039, 101126
-recovered pasa_asmbl_14385.p1, internal, 102026, 102067
-recovered pasa_asmbl_14385.p1, internal, 103072, 103191
-recovered pasa_asmbl_14385.p1, internal, 103371, 103430
-recovered pasa_asmbl_14385.p1, internal, 103549, 103617
Valid prediction for GeneMark_model.64729_t
Valid prediction for GlimmerHMM_glimmerT_37605-T1
Valid prediction for GeneMark_model.64720_t
Couldn't classify 105561, 105600
Couldn't classify 106355, 106629
Sorry, prediction pasa_asmbl_14386.p1 fails validation.
(CCG)	 TC	105561-105600	GT	GGG
(GTA)	 AG	105771-105857	GT	GGG
(GAG)	 AG	106355-106629	TC	CCT
-recovered pasa_asmbl_14386.p1, internal, 105771, 105857
Valid prediction for GeneMark_model.64698_t
Couldn't classify 145408, 145437
Sorry, prediction pasa_asmbl_14390.p1 fails validation.
(CGG)	 AC	145408-145437	GT	TGG
(ACT)	 AG	145649-145739	GT	GGG
(GCA)	 AG	145886-145973	GT	AGG
(TGG)	 AG	146132-146735	GA	AGG
-recovered pasa_asmbl_14390.p1, terminal, 146132, 146735
-recovered pasa_asmbl_14390.p1, internal, 145649, 145739
-recovered pasa_asmbl_14390.p1, internal, 145886, 145973
Valid prediction for GlimmerHMM_glimmerT_37600-T1
Valid prediction for CodingQuarry_transcript_18079-T1
Valid prediction for snap_scaffold_15-snap.2095-T1
Valid prediction for snap_scaffold_15-snap.2101-T1
Valid prediction for GeneMark_model.64726_t
Valid prediction for snap_scaffold_15-snap.2099-T1
Valid prediction for GeneMark_model.64703_t
Valid prediction for GeneMark_model.64714_t
Valid prediction for GeneMark_model.64705_t
Valid prediction for GeneMark_model.64717_t
Valid prediction for Augustus_model.g25214.t1
Valid prediction for snap_scaffold_15-snap.2090-T1
Valid prediction for snap_scaffold_15-snap.2098-T1
Valid prediction for HiQ_model.g25203.t1
Valid prediction for snap_scaffold_15-snap.2077-T1
Valid prediction for GeneMark_model.64700_t
Valid prediction for snap_scaffold_15-snap.2097-T1
Valid prediction for snap_scaffold_15-snap.2096-T1
Valid prediction for Augustus_model.g25211.t1
Valid prediction for GeneMark_model.64722_t
Valid prediction for GlimmerHMM_glimmerT_37606-T1
Valid prediction for Augustus_model.g25206.t1
Valid prediction for GeneMark_model.64701_t
Valid prediction for snap_scaffold_15-snap.2091-T1
Valid prediction for snap_scaffold_15-snap.2081-T1
Valid prediction for snap_scaffold_15-snap.2083-T1
Valid prediction for pasa_asmbl_14384.p1
Valid prediction for snap_scaffold_15-snap.2075-T1
Valid prediction for GeneMark_model.64711_t
Valid prediction for GeneMark_model.64723_t
Valid prediction for GlimmerHMM_glimmerT_37603-T1
Couldn't classify 143779, 143847
Couldn't classify 144479, 144528
Sorry, prediction pasa_asmbl_14874.p1 fails validation.
(GAT)	 AG	143779-143847	GT	AGG
(ATG)	 AG	144014-144139	GT	AGG
(AAG)	 AG	144228-144336	GT	AGG
(CAA)	 AG	144479-144528	AA	CCA
-recovered pasa_asmbl_14874.p1, initial, 144014, 144139
-recovered pasa_asmbl_14874.p1, internal, 143779, 143847
-recovered pasa_asmbl_14874.p1, internal, 144014, 144139
-recovered pasa_asmbl_14874.p1, internal, 144228, 144336
Valid prediction for snap_scaffold_15-snap.2079-T1
Valid prediction for GeneMark_model.64707_t
Valid prediction for GeneMark_model.64727_t
Valid prediction for snap_scaffold_15-snap.2084-T1
Valid prediction for GlimmerHMM_glimmerT_37589-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_15-snap.2089-T1
Valid prediction for GlimmerHMM_glimmerT_37596-T1
Valid prediction for GeneMark_model.64718_t
Valid prediction for GeneMark_model.64708_t
Valid prediction for GlimmerHMM_glimmerT_37590-T1
Valid prediction for Augustus_model.g25201.t1
Valid prediction for snap_scaffold_15-snap.2078-T1
Valid prediction for snap_scaffold_15-snap.2082-T1
Valid prediction for snap_scaffold_15-snap.2088-T1
Valid prediction for GeneMark_model.64730_t
Valid prediction for GeneMark_model.64724_t
Valid prediction for GeneMark_model.64702_t
Valid prediction for snap_scaffold_15-snap.2086-T1
Valid prediction for GeneMark_model.64710_t
Valid prediction for Augustus_model.g25205.t1
Valid prediction for GlimmerHMM_glimmerT_37591-T1
Valid prediction for GlimmerHMM_glimmerT_37593-T1
Valid prediction for GeneMark_model.64699_t
Valid prediction for Augustus_model.g25212.t1
Valid prediction for GeneMark_model.64704_t
Valid prediction for GeneMark_model.64716_t
Valid prediction for Augustus_model.g25210.t1
Valid prediction for snap_scaffold_15-snap.2076-T1
Valid prediction for GlimmerHMM_glimmerT_37598-T1
Valid prediction for snap_scaffold_15-snap.2100-T1
Valid prediction for GlimmerHMM_glimmerT_37595-T1
Valid prediction for GeneMark_model.64712_t
Valid prediction for GeneMark_model.64721_t
Couldn't classify 106128, 106293
Sorry, prediction pasa_asmbl_15440.p1 fails validation.
(AGC)	 GC	106128-106293	GT	AGG
(CCA)	 AG	106911-106996	GT	AGG
(GAC)	 AG	107113-107286	TG	AGT
-recovered pasa_asmbl_15440.p1, terminal, 107113, 107286
-recovered pasa_asmbl_15440.p1, internal, 106911, 106996
Valid prediction for Augustus_model.g25204.t1
Couldn't classify 105189, 105211
Sorry, prediction pasa_asmbl_15441.p1 fails validation.
(ATG)	 CC	101646-101794	GT	AGG
(CCC)	 AG	102066-102189	GT	TGG
(AGG)	 AG	102492-102569	GT	AGG
(GAG)	 AG	103459-103735	GT	CAG
(AGG)	 AG	104678-104730	GT	TGG
(GAT)	 AG	104844-104916	GT	AGG
(GTA)	 AG	105189-105211	GA	GAG
-recovered pasa_asmbl_15441.p1, initial, 101646, 101794
-recovered pasa_asmbl_15441.p1, internal, 102066, 102189
-recovered pasa_asmbl_15441.p1, internal, 102492, 102569
-recovered pasa_asmbl_15441.p1, internal, 103459, 103735
-recovered pasa_asmbl_15441.p1, internal, 104678, 104730
-recovered pasa_asmbl_15441.p1, internal, 104844, 104916
Valid prediction for GlimmerHMM_glimmerT_37597-T1
Valid prediction for GlimmerHMM_glimmerT_37607-T1
Valid prediction for GlimmerHMM_glimmerT_37587-T1
Valid prediction for snap_scaffold_15-snap.2073-T1
Valid prediction for snap_scaffold_15-snap.2087-T1
Valid prediction for GeneMark_model.64709_t
Valid prediction for GeneMark_model.64719_t
Valid prediction for snap_scaffold_15-snap.2080-T1
Valid prediction for GeneMark_model.64697_t
Valid prediction for GeneMark_model.64713_t
Valid prediction for snap_scaffold_15-snap.2085-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6265, rend_intergenic: 5145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18104, rend_intergenic: 6279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26756, rend_intergenic: 21097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35764, rend_intergenic: 28066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48496, rend_intergenic: 40908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55742, rend_intergenic: 48964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166915, rend_intergenic: 164197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 170742
-exon list size: 474


building trellis

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-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 6265, rend_intergenic: 5145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18104, rend_intergenic: 6279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26756, rend_intergenic: 21097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35764, rend_intergenic: 28066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48496, rend_intergenic: 40908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55742, rend_intergenic: 48964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166915, rend_intergenic: 164197  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