-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_1127610-1391467

-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.g132.t1
Valid prediction for snap_scaffold_1-snap.213-T1
Valid prediction for snap_scaffold_1-snap.240-T1
Valid prediction for GlimmerHMM_glimmerT_179-T1
Valid prediction for GlimmerHMM_glimmerT_163-T1
Valid prediction for GlimmerHMM_glimmerT_174-T1
Valid prediction for snap_scaffold_1-snap.237-T1
Valid prediction for GlimmerHMM_glimmerT_152-T1
Valid prediction for Augustus_model.g135.t1
Valid prediction for Augustus_model.g142.t1
Valid prediction for snap_scaffold_1-snap.241-T1
Valid prediction for GlimmerHMM_glimmerT_168-T1
Valid prediction for snap_scaffold_1-snap.217-T1
Valid prediction for GlimmerHMM_glimmerT_156-T1
Valid prediction for snap_scaffold_1-snap.226-T1
Valid prediction for snap_scaffold_1-snap.219-T1
Valid prediction for Augustus_model.g131.t1
Valid prediction for Augustus_model.g141.t1
Valid prediction for GlimmerHMM_glimmerT_183-T1
Valid prediction for snap_scaffold_1-snap.243-T1
Valid prediction for snap_scaffold_1-snap.242-T1
Valid prediction for snap_scaffold_1-snap.211-T1
Valid prediction for GlimmerHMM_glimmerT_173-T1
Valid prediction for GlimmerHMM_glimmerT_178-T1
Valid prediction for GlimmerHMM_glimmerT_164-T1
Couldn't classify 198521, 198571
Sorry, prediction pasa_asmbl_1474.p1 fails validation.
(GCC)	 TG	198521-198571	GT	AGG
(ATT)	 AG	199046-199192	GT	TGG
(CAT)	 AG	199316-199525	GT	CGG
(GTT)	 AG	199642-199798	GT	AGG
(GAA)	 AG	199923-200090	GT	TGG
(GTA)	 AG	200258-200373	CC	AGC
-recovered pasa_asmbl_1474.p1, terminal, 200258, 200373
-recovered pasa_asmbl_1474.p1, internal, 199046, 199192
-recovered pasa_asmbl_1474.p1, internal, 199316, 199525
-recovered pasa_asmbl_1474.p1, internal, 199642, 199798
-recovered pasa_asmbl_1474.p1, internal, 199923, 200090
Couldn't classify 98878, 98999
Sorry, prediction pasa_asmbl_1463.p1 fails validation.
(GTG)	 AG	98878-98999	GT	AGG
(ACT)	 AG	99444-99642	GT	TAG
(GAC)	 AG	100345-100518	GT	TGG
(ATT)	 AG	100871-100996	TT	AAT
-recovered pasa_asmbl_1463.p1, terminal, 100871, 100996
-recovered pasa_asmbl_1463.p1, internal, 98878, 98999
-recovered pasa_asmbl_1463.p1, internal, 99444, 99642
-recovered pasa_asmbl_1463.p1, internal, 100345, 100518
Valid prediction for GlimmerHMM_glimmerT_165-T1
Valid prediction for GlimmerHMM_glimmerT_171-T1
Valid prediction for pasa_asmbl_1467.p1
Valid prediction for snap_scaffold_1-snap.229-T1
Valid prediction for GlimmerHMM_glimmerT_176-T1
Valid prediction for Augustus_model.g138.t1
Valid prediction for pasa_asmbl_1464.p1
Valid prediction for snap_scaffold_1-snap.228-T1
Valid prediction for snap_scaffold_1-snap.225-T1
Valid prediction for snap_scaffold_1-snap.212-T1
Valid prediction for GlimmerHMM_glimmerT_155-T1
Valid prediction for snap_scaffold_1-snap.220-T1
Valid prediction for snap_scaffold_1-snap.210-T1
Valid prediction for GlimmerHMM_glimmerT_161-T1
Valid prediction for GlimmerHMM_glimmerT_154-T1
Valid prediction for GlimmerHMM_glimmerT_175-T1
Couldn't classify 218106, 218380
Couldn't classify 219935, 220115
Sorry, prediction pasa_asmbl_1475.p1 fails validation.
(CAA)	 AA	218106-218380	GT	GTG
(CCG)	 AG	218466-218548	GT	TGG
(AAT)	 AG	218753-218896	GT	AGG
(GTA)	 AG	219010-219171	GT	TGG
(GTC)	 AG	219404-219548	GT	AGG
(TTC)	 AG	219706-219822	GT	ATG
(CTA)	 AG	219935-220115	CC	AGC
-recovered pasa_asmbl_1475.p1, internal, 218466, 218548
-recovered pasa_asmbl_1475.p1, internal, 218753, 218896
-recovered pasa_asmbl_1475.p1, internal, 219010, 219171
-recovered pasa_asmbl_1475.p1, internal, 219404, 219548
-recovered pasa_asmbl_1475.p1, internal, 219706, 219822
Valid prediction for snap_scaffold_1-snap.246-T1
Couldn't classify 221264, 221431
Couldn't classify 222315, 222448
Sorry, prediction pasa_asmbl_1476.p1 fails validation.
(CAT)	 GA	221264-221431	GT	CGG
(GTG)	 AG	221515-221671	GT	AGG
(GCA)	 AG	221906-222073	GT	TGG
(GTA)	 AG	222315-222448	CA	GCC
-recovered pasa_asmbl_1476.p1, internal, 221515, 221671
-recovered pasa_asmbl_1476.p1, internal, 221906, 222073
Valid prediction for HiQ_model.g133.t1
Valid prediction for snap_scaffold_1-snap.236-T1
Valid prediction for snap_scaffold_1-snap.223-T1
Valid prediction for Augustus_model.g121.t1
Valid prediction for Augustus_model.g143.t1
Valid prediction for snap_scaffold_1-snap.245-T1
Valid prediction for Augustus_model.g137.t1
Valid prediction for GlimmerHMM_glimmerT_177-T1
Valid prediction for snap_scaffold_1-snap.244-T1
Couldn't classify 198379, 198448
Sorry, prediction pasa_asmbl_1471.p1 fails validation.
(ATG)	 AG	196826-196829	GT	GTG
(CCT)	 AG	197271-197408	GT	AGG
(GAA)	 AG	197490-197636	GC	CGG
(AGT)	 AG	197844-197988	GT	AGG
(GAA)	 AG	198145-198276	GT	GAG
(CTA)	 AG	198379-198448	AC	GCA
-recovered pasa_asmbl_1471.p1, initial, 196826, 196829
-recovered pasa_asmbl_1471.p1, internal, 196826, 196829
-recovered pasa_asmbl_1471.p1, internal, 197271, 197408
-recovered pasa_asmbl_1471.p1, internal, 197490, 197636
-recovered pasa_asmbl_1471.p1, internal, 197844, 197988
-recovered pasa_asmbl_1471.p1, internal, 198145, 198276
Valid prediction for snap_scaffold_1-snap.208-T1
Valid prediction for snap_scaffold_1-snap.233-T1
Valid prediction for Augustus_model.g123.t1
Valid prediction for CodingQuarry_transcript_2523-T1
Valid prediction for GlimmerHMM_glimmerT_180-T1
Valid prediction for Augustus_model.g129.t1
Valid prediction for CodingQuarry_transcript_2526-T1
Valid prediction for Augustus_model.g124.t1
Valid prediction for Augustus_model.g140.t1
Valid prediction for GlimmerHMM_glimmerT_160-T1
Valid prediction for snap_scaffold_1-snap.224-T1
Valid prediction for GlimmerHMM_glimmerT_166-T1
Valid prediction for snap_scaffold_1-snap.227-T1
Valid prediction for Augustus_model.g144.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.g128.t1
Valid prediction for snap_scaffold_1-snap.209-T1
Valid prediction for CodingQuarry_transcript_2522-T1
Valid prediction for Augustus_model.g139.t1
Valid prediction for GlimmerHMM_glimmerT_162-T1
Valid prediction for pasa_asmbl_48.p1
Valid prediction for snap_scaffold_1-snap.207-T1
Valid prediction for HiQ_model.g130.t1
Valid prediction for GlimmerHMM_glimmerT_169-T1
Valid prediction for GlimmerHMM_glimmerT_172-T1
Valid prediction for Augustus_model.g125.t1
Valid prediction for snap_scaffold_1-snap.234-T1
Valid prediction for snap_scaffold_1-snap.218-T1
Valid prediction for snap_scaffold_1-snap.238-T1
Valid prediction for GlimmerHMM_glimmerT_181-T1
Valid prediction for CodingQuarry_transcript_2524-T1
Valid prediction for Augustus_model.g122.t1
Couldn't classify 143802, 144020
Couldn't classify 144824, 144975
Sorry, prediction pasa_asmbl_55.p2 fails validation.
(TCA)	 AG	143802-144020	GT	AAG
(GTA)	 AG	144184-144376	GT	AGG
(GCT)	 AG	144824-144975	AG	CGA
-recovered pasa_asmbl_55.p2, internal, 143802, 144020
-recovered pasa_asmbl_55.p2, internal, 144184, 144376
Valid prediction for Augustus_model.g134.t1
Valid prediction for Augustus_model.g119.t1
Valid prediction for snap_scaffold_1-snap.247-T1
Valid prediction for GlimmerHMM_glimmerT_151-T1
Valid prediction for snap_scaffold_1-snap.239-T1
Valid prediction for Augustus_model.g120.t1
Valid prediction for GlimmerHMM_glimmerT_167-T1
Valid prediction for snap_scaffold_1-snap.221-T1
Valid prediction for snap_scaffold_1-snap.232-T1
Couldn't classify 119275, 119350
Sorry, prediction pasa_asmbl_61.p1 fails validation.
(GAC)	 GT	119275-119350	GT	AAG
(AAA)	 AG	119501-119856	AG	AAA
-recovered pasa_asmbl_61.p1, terminal, 119501, 119856
Valid prediction for snap_scaffold_1-snap.230-T1
Valid prediction for GlimmerHMM_glimmerT_182-T1
Valid prediction for snap_scaffold_1-snap.216-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.222-T1
Valid prediction for pasa_asmbl_57.p1
Valid prediction for snap_scaffold_1-snap.248-T1
Valid prediction for Augustus_model.g145.t1
Valid prediction for Augustus_model.g136.t1
Valid prediction for GlimmerHMM_glimmerT_153-T1
Valid prediction for snap_scaffold_1-snap.214-T1
Valid prediction for Augustus_model.g126.t1
Valid prediction for snap_scaffold_1-snap.215-T1
Valid prediction for GlimmerHMM_glimmerT_170-T1
Valid prediction for snap_scaffold_1-snap.235-T1
Valid prediction for Augustus_model.g127.t1
Valid prediction for snap_scaffold_1-snap.231-T1
Valid prediction for GlimmerHMM_glimmerT_157-T1
Couldn't classify 147767, 147979
Sorry, prediction pasa_asmbl_54.p2 fails validation.
(AGC)	 CC	147767-147979	GT	CGG
(ACG)	 AG	148405-148599	CC	GAC
-recovered pasa_asmbl_54.p2, terminal, 148405, 148599
Valid prediction for GlimmerHMM_glimmerT_159-T1
Valid prediction for GlimmerHMM_glimmerT_158-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17765, rend_intergenic: 17231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52163, rend_intergenic: 49233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53558, rend_intergenic: 52463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57567, rend_intergenic: 53597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79801, rend_intergenic: 77516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 263858
-exon list size: 401


building trellis

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97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 17765, rend_intergenic: 17231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52163, rend_intergenic: 49233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53558, rend_intergenic: 52463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57567, rend_intergenic: 53597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79801, rend_intergenic: 77516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support