-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_10472998-10677877

-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 GeneMark_model.52887_t
Valid prediction for Augustus_model.g20420.t1
Valid prediction for snap_scaffold_12-snap.2020-T1
Valid prediction for Augustus_model.g20431.t1
Couldn't classify 82122, 82241
Sorry, prediction pasa_asmbl_9168.p1 fails validation.
(AAA)	 AG	82122-82241	GT	ATG
(GAG)	 AG	82363-82417	GT	TGG
(GCG)	 AG	82524-82694	GT	AGG
(CCC)	 AG	83058-83197	AG	AAA
-recovered pasa_asmbl_9168.p1, terminal, 83058, 83197
-recovered pasa_asmbl_9168.p1, internal, 82122, 82241
-recovered pasa_asmbl_9168.p1, internal, 82363, 82417
-recovered pasa_asmbl_9168.p1, internal, 82524, 82694
Valid prediction for GlimmerHMM_glimmerT_30633-T1
Valid prediction for snap_scaffold_12-snap.2007-T1
Couldn't classify 176467, 177066
Sorry, prediction pasa_asmbl_8921.p1 fails validation.
(TCT)	 CC	176467-177066	GT	AAG
Valid prediction for GlimmerHMM_glimmerT_30623-T1
Valid prediction for GlimmerHMM_glimmerT_30630-T1
Valid prediction for snap_scaffold_12-snap.1997-T1
Valid prediction for pasa_asmbl_8918.p1
Valid prediction for GeneMark_model.52872_t
Valid prediction for GeneMark_model.52894_t
Couldn't classify 172275, 172371
Couldn't classify 172963, 173105
Sorry, prediction pasa_asmbl_8920.p1 fails validation.
(GGC)	 CT	172275-172371	GT	AGG
(AAA)	 AG	172679-172783	GT	GAG
(TTC)	 AG	172963-173105	CG	AGC
-recovered pasa_asmbl_8920.p1, terminal, 172679, 172783
-recovered pasa_asmbl_8920.p1, internal, 172679, 172783
Valid prediction for GlimmerHMM_glimmerT_30625-T1
Valid prediction for snap_scaffold_12-snap.2028-T1
Valid prediction for GeneMark_model.52879_t
Valid prediction for GlimmerHMM_glimmerT_30632-T1
Valid prediction for snap_scaffold_12-snap.2030-T1
Valid prediction for GlimmerHMM_glimmerT_30615-T1
Valid prediction for GlimmerHMM_glimmerT_30614-T1
Valid prediction for HiQ_model.g20421.t1
Valid prediction for pasa_asmbl_8903.p1
Valid prediction for CodingQuarry_transcript_10354-T1
Valid prediction for GlimmerHMM_glimmerT_30627-T1
Valid prediction for GlimmerHMM_glimmerT_30621-T1
Valid prediction for pasa_asmbl_8898.p1
Valid prediction for HiQ_model.g20417.t1
Valid prediction for GeneMark_model.52891_t
Valid prediction for snap_scaffold_12-snap.2031-T1
Valid prediction for snap_scaffold_12-snap.2024-T1
Valid prediction for pasa_asmbl_8915.p1
Valid prediction for snap_scaffold_12-snap.2016-T1
Valid prediction for snap_scaffold_12-snap.2026-T1
Valid prediction for HiQ_model.g20426.t1
Valid prediction for HiQ_model.g20425.t1
Valid prediction for snap_scaffold_12-snap.2013-T1
Valid prediction for snap_scaffold_12-snap.2023-T1
Valid prediction for GeneMark_model.52888_t
Valid prediction for GlimmerHMM_glimmerT_30620-T1
Valid prediction for GlimmerHMM_glimmerT_30622-T1
Couldn't classify 80987, 81253
Couldn't classify 81799, 81966
Sorry, prediction CodingQuarry_transcript_10346-T1 fails validation.
(ATG)	 AC	80987-81253	NN	NNN
(ACC)	 CC	81799-81966	GT	GAG
(AAA)	 AG	82122-82241	GT	ATG
(GAG)	 AG	82363-82417	GT	TGG
(GCG)	 AG	82524-82694	GT	AGG
(CCC)	 AG	83058-83197	AG	AAA
-recovered CodingQuarry_transcript_10346-T1, terminal, 83058, 83197
-recovered CodingQuarry_transcript_10346-T1, internal, 82122, 82241
-recovered CodingQuarry_transcript_10346-T1, internal, 82363, 82417
-recovered CodingQuarry_transcript_10346-T1, internal, 82524, 82694
Valid prediction for GeneMark_model.52870_t
Valid prediction for snap_scaffold_12-snap.2010-T1
Valid prediction for Augustus_model.g20412.t1
Valid prediction for Augustus_model.g20429.t1
Valid prediction for CodingQuarry_transcript_10345-T1
Valid prediction for CodingQuarry_transcript_10353-T1
Valid prediction for HiQ_model.g20428.t1
Valid prediction for GeneMark_model.52873_t
Valid prediction for snap_scaffold_12-snap.2022-T1
Valid prediction for CodingQuarry_transcript_10348-T1
Couldn't classify 102941, 103109
Sorry, prediction CodingQuarry_transcript_10349-T1 fails validation.
(ATG)	 TA	99457-99567	GT	TAG
(CTG)	 AG	100206-100268	GT	TGG
(CTG)	 AG	101513-101602	GT	TAG
(GAT)	 AG	101892-101957	GT	ATG
(GTT)	 AG	102132-102220	GT	AAG
(AGA)	 AG	102385-102456	GT	AAG
(GGC)	 TG	102941-103109	GT	TGG
(ACC)	 AG	103270-103407	GT	AGG
(GGT)	 AG	103507-103650	GC	AGG
-recovered CodingQuarry_transcript_10349-T1, initial, 99457, 99567
-recovered CodingQuarry_transcript_10349-T1, terminal, 103507, 103650
-recovered CodingQuarry_transcript_10349-T1, internal, 100206, 100268
-recovered CodingQuarry_transcript_10349-T1, internal, 101513, 101602
-recovered CodingQuarry_transcript_10349-T1, internal, 101892, 101957
-recovered CodingQuarry_transcript_10349-T1, internal, 102132, 102220
-recovered CodingQuarry_transcript_10349-T1, internal, 102385, 102456
-recovered CodingQuarry_transcript_10349-T1, internal, 103270, 103407
-recovered CodingQuarry_transcript_10349-T1, internal, 103507, 103650
Valid prediction for snap_scaffold_12-snap.2017-T1
Valid prediction for Augustus_model.g20418.t1
Valid prediction for snap_scaffold_12-snap.2019-T1
Valid prediction for pasa_asmbl_8905.p1
Valid prediction for pasa_asmbl_8907.p1
Valid prediction for snap_scaffold_12-snap.2003-T1
Valid prediction for snap_scaffold_12-snap.2021-T1
Valid prediction for GeneMark_model.52885_t
Valid prediction for snap_scaffold_12-snap.2025-T1
Valid prediction for snap_scaffold_12-snap.2009-T1
Valid prediction for snap_scaffold_12-snap.2011-T1
Valid prediction for HiQ_model.g20423.t1
Valid prediction for GlimmerHMM_glimmerT_30629-T1
Valid prediction for snap_scaffold_12-snap.2001-T1
Valid prediction for CodingQuarry_transcript_10352-T1
Valid prediction for GlimmerHMM_glimmerT_30619-T1
Valid prediction for CodingQuarry_transcript_10350-T1
Valid prediction for GlimmerHMM_glimmerT_30636-T1
Valid prediction for GeneMark_model.52877_t
Valid prediction for GeneMark_model.52881_t
Valid prediction for pasa_asmbl_8892.p1
Valid prediction for GeneMark_model.52875_t

-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 GlimmerHMM_glimmerT_30626-T1
Valid prediction for Augustus_model.g20424.t1
Valid prediction for Augustus_model.g20433.t1
Valid prediction for Augustus_model.g20413.t1
Valid prediction for GlimmerHMM_glimmerT_30635-T1
Valid prediction for snap_scaffold_12-snap.2005-T1
Valid prediction for GlimmerHMM_glimmerT_30618-T1
Valid prediction for GlimmerHMM_glimmerT_30616-T1
Valid prediction for snap_scaffold_12-snap.2032-T1
Valid prediction for CodingQuarry_transcript_10344-T1
Valid prediction for Augustus_model.g20435.t1
Valid prediction for snap_scaffold_12-snap.2034-T1
Valid prediction for pasa_asmbl_7884.p1
Valid prediction for GeneMark_model.52893_t
Valid prediction for GlimmerHMM_glimmerT_30628-T1
Valid prediction for Augustus_model.g20411.t1
Valid prediction for GeneMark_model.52876_t
Valid prediction for GlimmerHMM_glimmerT_30631-T1
Valid prediction for HiQ_model.g20419.t1
Valid prediction for GeneMark_model.52882_t
Valid prediction for GlimmerHMM_glimmerT_30634-T1
Valid prediction for Augustus_model.g20434.t1
Valid prediction for GlimmerHMM_glimmerT_30624-T1
Valid prediction for GlimmerHMM_glimmerT_30613-T1
Valid prediction for snap_scaffold_12-snap.2004-T1
Valid prediction for snap_scaffold_12-snap.2018-T1
Valid prediction for GeneMark_model.52874_t
Couldn't classify 158482, 158553
Sorry, prediction pasa_asmbl_7885.p1 fails validation.
(GAC)	 TG	158482-158553	GT	AGG
(GTC)	 AG	158780-158896	GT	TGG
(GGA)	 AG	159006-159187	GT	GAG
(TGT)	 AG	159392-159503	GT	AGG
(CTG)	 AG	159695-159804	GT	AGG
(TGG)	 AG	160021-160156	GT	GGG
(GTG)	 AG	160248-160358	GT	AGG
(TTC)	 AG	160709-160874	GT	CAG
(ACG)	 AG	161028-161263	GT	TGG
(GGA)	 AG	162234-162257	GT	AGG
(GAG)	 AG	163666-163785	GC	AGG
(GAG)	 AG	163926-164010	GT	TCG
(CTG)	 AG	164311-164438	GT	AGG
(CTG)	 AG	164555-164666	GT	AGG
(CCA)	 AG	164856-164980	GG	GAG
add_exon() Sorry, pasa_asmbl_7885.p1 164555-164666-terminal-3 is invalid.
-recovered pasa_asmbl_7885.p1, terminal, 164555, 164666
-recovered pasa_asmbl_7885.p1, terminal, 164856, 164980
-recovered pasa_asmbl_7885.p1, internal, 158780, 158896
-recovered pasa_asmbl_7885.p1, internal, 159006, 159187
-recovered pasa_asmbl_7885.p1, internal, 159392, 159503
-recovered pasa_asmbl_7885.p1, internal, 159695, 159804
-recovered pasa_asmbl_7885.p1, internal, 160021, 160156
-recovered pasa_asmbl_7885.p1, internal, 160248, 160358
-recovered pasa_asmbl_7885.p1, internal, 160709, 160874
-recovered pasa_asmbl_7885.p1, internal, 161028, 161263
-recovered pasa_asmbl_7885.p1, internal, 162234, 162257
-recovered pasa_asmbl_7885.p1, internal, 163666, 163785
-recovered pasa_asmbl_7885.p1, internal, 163926, 164010
-recovered pasa_asmbl_7885.p1, internal, 164311, 164438
-recovered pasa_asmbl_7885.p1, internal, 164555, 164666
Couldn't classify 85208, 85981
Sorry, prediction pasa_asmbl_7894.p1 fails validation.
(GCT)	 GC	85208-85981	GA	AGG
Valid prediction for HiQ_model.g20422.t1
Valid prediction for GeneMark_model.52878_t
Valid prediction for snap_scaffold_12-snap.2033-T1
Couldn't classify 150462, 150498
Couldn't classify 151154, 151506
Sorry, prediction pasa_asmbl_7889.p1 fails validation.
(GGC)	 CT	150462-150498	GT	TGG
(TTC)	 AG	150615-150686	GT	TGG
(GTC)	 AG	151154-151506	AT	CCA
-recovered pasa_asmbl_7889.p1, internal, 150615, 150686
Valid prediction for Augustus_model.g20414.t1
Valid prediction for GlimmerHMM_glimmerT_30638-T1
Valid prediction for snap_scaffold_12-snap.1998-T1
Valid prediction for snap_scaffold_12-snap.2002-T1
Valid prediction for Augustus_model.g20415.t1
Valid prediction for snap_scaffold_12-snap.2014-T1
Valid prediction for snap_scaffold_12-snap.1999-T1
Valid prediction for snap_scaffold_12-snap.2012-T1
Valid prediction for GlimmerHMM_glimmerT_30617-T1
Valid prediction for CodingQuarry_transcript_10347-T1
Valid prediction for snap_scaffold_12-snap.2008-T1
Valid prediction for Augustus_model.g20416.t1
Valid prediction for HiQ_model.g20430.t1
Valid prediction for snap_scaffold_12-snap.2006-T1
Couldn't classify 82766, 82793
Sorry, prediction pasa_asmbl_7895.p1 fails validation.
(AAC)	 CA	82766-82793	GT	CGG
(ATC)	 AG	83131-83226	GT	AGG
(ACG)	 AG	83346-83482	GT	GGG
(GAA)	 AG	83662-83743	GT	AGG
(ACT)	 AG	83833-83988	GT	AGG
(ATG)	 AG	84133-84218	AT	AGA
-recovered pasa_asmbl_7895.p1, terminal, 83662, 83743
-recovered pasa_asmbl_7895.p1, terminal, 84133, 84218
-recovered pasa_asmbl_7895.p1, internal, 83131, 83226
-recovered pasa_asmbl_7895.p1, internal, 83346, 83482
-recovered pasa_asmbl_7895.p1, internal, 83662, 83743
-recovered pasa_asmbl_7895.p1, internal, 83833, 83988
Valid prediction for GeneMark_model.52871_t
Valid prediction for GlimmerHMM_glimmerT_30637-T1
Valid prediction for snap_scaffold_12-snap.2015-T1
Valid prediction for GeneMark_model.52884_t
Couldn't classify 158439, 158553
Sorry, prediction pasa_asmbl_8354.p1 fails validation.
(ATG)	 CC	157908-158011	GT	AGG
(GTT)	 AG	158210-158311	GT	GGG
(TTT)	 AG	158439-158553	GT	AGG
-recovered pasa_asmbl_8354.p1, initial, 157908, 158011
-recovered pasa_asmbl_8354.p1, internal, 158210, 158311
-recovered pasa_asmbl_8354.p1, internal, 158439, 158553
Valid prediction for HiQ_model.g20427.t1
Valid prediction for pasa_asmbl_7890.p1
Valid prediction for GeneMark_model.52890_t
Valid prediction for GeneMark_model.52892_t
Valid prediction for snap_scaffold_12-snap.2029-T1
Valid prediction for pasa_asmbl_7891.p1
Valid prediction for GeneMark_model.52883_t
Valid prediction for Augustus_model.g20432.t1
Valid prediction for CodingQuarry_transcript_10351-T1
Valid prediction for snap_scaffold_12-snap.2000-T1
Valid prediction for snap_scaffold_12-snap.2035-T1
Valid prediction for snap_scaffold_12-snap.2027-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 31513, rend_intergenic: 28359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35136, rend_intergenic: 31848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36338, rend_intergenic: 35282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81956, rend_intergenic: 80987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161459, rend_intergenic: 160430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168256, rend_intergenic: 165473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169492, rend_intergenic: 168613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 204880
-exon list size: 496


building trellis

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91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 31513, rend_intergenic: 28359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35136, rend_intergenic: 31848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36338, rend_intergenic: 35282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81956, rend_intergenic: 80987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161459, rend_intergenic: 160430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168256, rend_intergenic: 165473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169492, rend_intergenic: 168613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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