-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_1073097-1273359

-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 HiQ_model.g38631.t1
Valid prediction for snap_scaffold_27-snap.251-T1
Valid prediction for GlimmerHMM_glimmerT_57985-T1
Valid prediction for snap_scaffold_27-snap.267-T1
Valid prediction for GlimmerHMM_glimmerT_57982-T1
Valid prediction for HiQ_model.g38628.t1
Valid prediction for snap_scaffold_27-snap.272-T1
Valid prediction for snap_scaffold_27-snap.274-T1
Valid prediction for snap_scaffold_27-snap.255-T1
Valid prediction for CodingQuarry_transcript_41680-T1
Valid prediction for GlimmerHMM_glimmerT_57996-T1
Valid prediction for GeneMark_model.100948_t
Valid prediction for snap_scaffold_27-snap.265-T1
Couldn't classify 34833, 34946
Sorry, prediction pasa_asmbl_35956.p1 fails validation.
(GTG)	 CT	34833-34946	GT	AGG
(GAG)	 AG	35322-35396	GT	AGG
(GCT)	 AG	35619-35834	GT	ATG
(GCC)	 AG	36022-36126	GT	AGG
(GCC)	 AG	37889-38077	GT	TGG
(AAA)	 AG	38590-38673	GT	ATG
(GCG)	 AG	40967-41086	GT	CGG
(GAG)	 AG	41264-41353	AG	GAA
-recovered pasa_asmbl_35956.p1, terminal, 41264, 41353
-recovered pasa_asmbl_35956.p1, internal, 35322, 35396
-recovered pasa_asmbl_35956.p1, internal, 35619, 35834
-recovered pasa_asmbl_35956.p1, internal, 36022, 36126
-recovered pasa_asmbl_35956.p1, internal, 37889, 38077
-recovered pasa_asmbl_35956.p1, internal, 38590, 38673
-recovered pasa_asmbl_35956.p1, internal, 40967, 41086
Valid prediction for GlimmerHMM_glimmerT_57989-T1
Valid prediction for snap_scaffold_27-snap.241-T1
Valid prediction for GeneMark_model.100962_t
Valid prediction for GeneMark_model.100957_t
Valid prediction for CodingQuarry_transcript_41681-T1
Valid prediction for GeneMark_model.100964_t
Valid prediction for GlimmerHMM_glimmerT_57984-T1
Valid prediction for GlimmerHMM_glimmerT_57994-T1
Valid prediction for GeneMark_model.100978_t
Valid prediction for GeneMark_model.100959_t
Valid prediction for snap_scaffold_27-snap.262-T1
Valid prediction for Augustus_model.g38630.t1
Valid prediction for snap_scaffold_27-snap.244-T1
Valid prediction for snap_scaffold_27-snap.261-T1
Valid prediction for snap_scaffold_27-snap.250-T1
Valid prediction for GlimmerHMM_glimmerT_57999-T1
Valid prediction for GlimmerHMM_glimmerT_57995-T1
Valid prediction for snap_scaffold_27-snap.266-T1
Valid prediction for GlimmerHMM_glimmerT_57992-T1
Valid prediction for GeneMark_model.100954_t
Valid prediction for snap_scaffold_27-snap.277-T1
Valid prediction for snap_scaffold_27-snap.259-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GeneMark_model.100985_t
Valid prediction for GlimmerHMM_glimmerT_57980-T1
Valid prediction for GeneMark_model.100955_t
Valid prediction for HiQ_model.g38629.t1
Valid prediction for snap_scaffold_27-snap.258-T1
Valid prediction for snap_scaffold_27-snap.242-T1
Valid prediction for Augustus_model.g38634.t1
Valid prediction for GeneMark_model.100956_t
Valid prediction for GlimmerHMM_glimmerT_57981-T1
Valid prediction for CodingQuarry_transcript_41679-T1
Couldn't classify 31066, 31096
Couldn't classify 32555, 32617
Sorry, prediction pasa_asmbl_35955.p1 fails validation.
(CTC)	 GC	31066-31096	GT	AGG
(CGG)	 AG	31215-31353	GT	AAG
(GCC)	 AG	31693-31846	GT	AGG
(GTG)	 AG	32196-32390	GT	AGG
(GTG)	 AG	32555-32617	GC	CAG
-recovered pasa_asmbl_35955.p1, internal, 31215, 31353
-recovered pasa_asmbl_35955.p1, internal, 31693, 31846
-recovered pasa_asmbl_35955.p1, internal, 32196, 32390
-recovered pasa_asmbl_35955.p1, internal, 32555, 32617
Valid prediction for snap_scaffold_27-snap.253-T1
Valid prediction for GeneMark_model.100966_t
Couldn't classify 26233, 26341
Couldn't classify 27745, 27976
Sorry, prediction pasa_asmbl_35954.p1 fails validation.
(GAC)	 CT	26233-26341	GT	AGG
(AGA)	 AG	26559-26686	GT	AGG
(GTG)	 AG	27473-27552	GT	AGG
(GGG)	 AG	27745-27976	GG	GAG
-recovered pasa_asmbl_35954.p1, internal, 26559, 26686
-recovered pasa_asmbl_35954.p1, internal, 27473, 27552
Valid prediction for GeneMark_model.100960_t
Valid prediction for GlimmerHMM_glimmerT_57986-T1
Valid prediction for GeneMark_model.100951_t
Valid prediction for pasa_asmbl_35947.p1
Valid prediction for GeneMark_model.100976_t
Valid prediction for GeneMark_model.100949_t
Valid prediction for GeneMark_model.100973_t
Valid prediction for GeneMark_model.100981_t
Valid prediction for GeneMark_model.100950_t
Valid prediction for snap_scaffold_27-snap.268-T1
Valid prediction for CodingQuarry_transcript_41682-T1
Valid prediction for GlimmerHMM_glimmerT_58001-T1
Valid prediction for GlimmerHMM_glimmerT_57983-T1
Valid prediction for snap_scaffold_27-snap.256-T1
Valid prediction for GeneMark_model.100979_t
Valid prediction for snap_scaffold_27-snap.278-T1
Couldn't classify 20099, 20261
Sorry, prediction pasa_asmbl_35951.p1 fails validation.
(TCC)	 TC	20099-20261	GC	AGG
(TGA)	 AG	21879-22214	GT	AGG
(CTC)	 AG	22532-22597	GT	AGG
(AAC)	 AG	23039-23118	GT	TTG
(CTG)	 AG	24059-24170	GT	ACG
(GAG)	 AG	24333-24366	GT	TGG
(TCT)	 AG	24476-24560	AG	AGA
-recovered pasa_asmbl_35951.p1, terminal, 24476, 24560
-recovered pasa_asmbl_35951.p1, internal, 21879, 22214
-recovered pasa_asmbl_35951.p1, internal, 22532, 22597
-recovered pasa_asmbl_35951.p1, internal, 23039, 23118
-recovered pasa_asmbl_35951.p1, internal, 24059, 24170
-recovered pasa_asmbl_35951.p1, internal, 24333, 24366
Valid prediction for Augustus_model.g38635.t1
Valid prediction for snap_scaffold_27-snap.246-T1
Valid prediction for GlimmerHMM_glimmerT_57990-T1
Valid prediction for snap_scaffold_27-snap.240-T1
Valid prediction for CodingQuarry_transcript_41678-T1
Valid prediction for snap_scaffold_27-snap.254-T1
Valid prediction for GeneMark_model.100969_t
Valid prediction for GlimmerHMM_glimmerT_57991-T1
Valid prediction for GeneMark_model.100983_t
Valid prediction for GeneMark_model.100961_t
Valid prediction for GeneMark_model.100987_t
Valid prediction for Augustus_model.g38636.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.g38627.t1
Valid prediction for GeneMark_model.100984_t
Valid prediction for Augustus_model.g38632.t1
Valid prediction for GlimmerHMM_glimmerT_57993-T1
Valid prediction for snap_scaffold_27-snap.238-T1
Valid prediction for GeneMark_model.100972_t
Valid prediction for Augustus_model.g38638.t1
Valid prediction for GeneMark_model.100977_t
Valid prediction for GeneMark_model.100986_t
Couldn't classify 132212, 132364
Couldn't classify 134425, 134562
Sorry, prediction pasa_asmbl_36698.p2 fails validation.
(CTG)	 TG	132212-132364	GT	AGG
(GTG)	 AG	132631-132759	GT	AGG
(GTG)	 AG	134425-134562	GT	CCG
-recovered pasa_asmbl_36698.p2, internal, 132631, 132759
-recovered pasa_asmbl_36698.p2, internal, 134425, 134562
Valid prediction for snap_scaffold_27-snap.263-T1
Valid prediction for GeneMark_model.100953_t
Valid prediction for snap_scaffold_27-snap.252-T1
Valid prediction for Augustus_model.g38639.t1
Valid prediction for GeneMark_model.100958_t
Valid prediction for GeneMark_model.100965_t
Valid prediction for GeneMark_model.100947_t
Valid prediction for snap_scaffold_27-snap.269-T1
Valid prediction for snap_scaffold_27-snap.270-T1
Valid prediction for Augustus_model.g38626.t1
Couldn't classify 137227, 137314
Sorry, prediction pasa_asmbl_36694.p1 fails validation.
(CAG)	 AG	137227-137314	GT	GGG
(CCA)	 AG	137489-137726	GT	AGG
(ACA)	 AG	138473-138662	GT	TGG
(CTG)	 AG	138816-138942	GT	TAG
(TTG)	 AG	139061-139254	GT	AGG
(GAA)	 AG	139380-139490	GT	AGG
(ATC)	 AG	139619-139711	GT	AGG
(CAA)	 AG	141265-141378	GT	GGG
(GTG)	 AG	141641-141768	GT	ACG
(GGA)	 AG	141945-142169	GT	CAG
(ATC)	 AG	143513-143598	GT	AGG
(ATA)	 AG	143806-143948	GT	AGG
(GTG)	 AG	144052-144185	GT	GAG
(GAT)	 AG	144461-144647	CG	GAC
-recovered pasa_asmbl_36694.p1, terminal, 144461, 144647
-recovered pasa_asmbl_36694.p1, internal, 137227, 137314
-recovered pasa_asmbl_36694.p1, internal, 137489, 137726
-recovered pasa_asmbl_36694.p1, internal, 138473, 138662
-recovered pasa_asmbl_36694.p1, internal, 138816, 138942
-recovered pasa_asmbl_36694.p1, internal, 139061, 139254
-recovered pasa_asmbl_36694.p1, internal, 139380, 139490
-recovered pasa_asmbl_36694.p1, internal, 139619, 139711
-recovered pasa_asmbl_36694.p1, internal, 141265, 141378
-recovered pasa_asmbl_36694.p1, internal, 141641, 141768
-recovered pasa_asmbl_36694.p1, internal, 141945, 142169
-recovered pasa_asmbl_36694.p1, internal, 143513, 143598
-recovered pasa_asmbl_36694.p1, internal, 143806, 143948
-recovered pasa_asmbl_36694.p1, internal, 144052, 144185
Valid prediction for GlimmerHMM_glimmerT_57988-T1
Valid prediction for GeneMark_model.100988_t
Valid prediction for snap_scaffold_27-snap.264-T1
Valid prediction for GeneMark_model.100952_t
Valid prediction for snap_scaffold_27-snap.276-T1
Valid prediction for GeneMark_model.100971_t
Valid prediction for snap_scaffold_27-snap.257-T1
Valid prediction for GlimmerHMM_glimmerT_57998-T1
Valid prediction for snap_scaffold_27-snap.247-T1
Valid prediction for GeneMark_model.100982_t
Valid prediction for snap_scaffold_27-snap.243-T1
Valid prediction for Augustus_model.g38641.t1
Valid prediction for snap_scaffold_27-snap.271-T1
Valid prediction for snap_scaffold_27-snap.245-T1
Valid prediction for snap_scaffold_27-snap.237-T1
Valid prediction for GeneMark_model.100975_t
Valid prediction for GlimmerHMM_glimmerT_57978-T1
Valid prediction for GeneMark_model.100980_t
Valid prediction for Augustus_model.g38640.t1
Valid prediction for snap_scaffold_27-snap.248-T1
Valid prediction for Augustus_model.g38633.t1
Valid prediction for GeneMark_model.100967_t
Valid prediction for GlimmerHMM_glimmerT_58000-T1
Valid prediction for Augustus_model.g38637.t1
Valid prediction for GeneMark_model.100968_t
Valid prediction for snap_scaffold_27-snap.249-T1
Valid prediction for GeneMark_model.100970_t
Valid prediction for GeneMark_model.100974_t
Valid prediction for snap_scaffold_27-snap.260-T1
Valid prediction for GlimmerHMM_glimmerT_57997-T1
Valid prediction for snap_scaffold_27-snap.239-T1
Valid prediction for GlimmerHMM_glimmerT_57987-T1
Valid prediction for GeneMark_model.100963_t
Valid prediction for snap_scaffold_27-snap.273-T1
Valid prediction for snap_scaffold_27-snap.275-T1
Couldn't classify 135698, 135877
Couldn't classify 136727, 136762
Sorry, prediction pasa_asmbl_36697.p2 fails validation.
(AAG)	 GC	135698-135877	GT	CGG
(GAG)	 AG	136281-136463	GT	AGG
(GTG)	 AG	136727-136762	AG	CCA
-recovered pasa_asmbl_36697.p2, internal, 136281, 136463
Valid prediction for GlimmerHMM_glimmerT_57979-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 32855, rend_intergenic: 31011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38878, rend_intergenic: 36018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65946, rend_intergenic: 60525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96158, rend_intergenic: 93570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99516, rend_intergenic: 98998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102726, rend_intergenic: 100565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117524, rend_intergenic: 106773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167430, rend_intergenic: 161601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174402, rend_intergenic: 172856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178770, rend_intergenic: 174468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195443, rend_intergenic: 183758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 200263
-exon list size: 612


building trellis

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83.6    
83.7    
83.9    
84.0    
84.2    
84.4    
84.5    
84.7    
84.9    
85.0    
85.2    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
87.0    
87.1    
87.3    
87.5    
87.6    
87.8    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
88.9    
89.1    
89.3    
89.4    
89.6    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 32855, rend_intergenic: 31011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38878, rend_intergenic: 36018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65946, rend_intergenic: 60525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96158, rend_intergenic: 93570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99516, rend_intergenic: 98998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102726, rend_intergenic: 100565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117524, rend_intergenic: 106773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167430, rend_intergenic: 161601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174402, rend_intergenic: 172856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178770, rend_intergenic: 174468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195443, rend_intergenic: 183758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support