-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_2817941-3009119

-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_48495-T1
Valid prediction for GlimmerHMM_glimmerT_48482-T1
Valid prediction for GlimmerHMM_glimmerT_48493-T1
Valid prediction for GeneMark_model.84193_t
Valid prediction for GeneMark_model.84206_t
Valid prediction for GlimmerHMM_glimmerT_48490-T1
Valid prediction for GlimmerHMM_glimmerT_48472-T1
Valid prediction for snap_scaffold_21-snap.520-T1
Valid prediction for GlimmerHMM_glimmerT_48494-T1
Valid prediction for GlimmerHMM_glimmerT_48487-T1
Valid prediction for GeneMark_model.84203_t
Valid prediction for snap_scaffold_21-snap.512-T1
Valid prediction for Augustus_model.g32424.t1
Valid prediction for GlimmerHMM_glimmerT_48475-T1
Valid prediction for CodingQuarry_transcript_32417-T1
Valid prediction for Augustus_model.g32437.t1
Valid prediction for GeneMark_model.84191_t
Valid prediction for snap_scaffold_21-snap.536-T1
Valid prediction for snap_scaffold_21-snap.509-T1
Valid prediction for pasa_asmbl_28450.p1
Valid prediction for Augustus_model.g32428.t1
Valid prediction for GlimmerHMM_glimmerT_48479-T1
Valid prediction for GeneMark_model.84184_t
Valid prediction for snap_scaffold_21-snap.511-T1
Valid prediction for snap_scaffold_21-snap.537-T1
Valid prediction for GlimmerHMM_glimmerT_48483-T1
Valid prediction for Augustus_model.g32432.t1
Valid prediction for Augustus_model.g32421.t1
Valid prediction for GeneMark_model.84212_t
Valid prediction for snap_scaffold_21-snap.532-T1
Valid prediction for Augustus_model.g32427.t1
Couldn't classify 135143, 135163
Sorry, prediction CodingQuarry_transcript_32419-T1 fails validation.
(ATG)	 AC	132668-132730	GT	AGG
(AAC)	 AG	133963-134131	GT	CGG
(GTT)	 AG	134374-134457	GT	TGG
(GCA)	 AG	134615-134724	GT	CTG
(GTC)	 AG	134867-134992	GT	AAG
(AGA)	 GG	135143-135163	AT	AGA
-recovered CodingQuarry_transcript_32419-T1, initial, 132668, 132730
-recovered CodingQuarry_transcript_32419-T1, internal, 133963, 134131
-recovered CodingQuarry_transcript_32419-T1, internal, 134374, 134457
-recovered CodingQuarry_transcript_32419-T1, internal, 134615, 134724
-recovered CodingQuarry_transcript_32419-T1, internal, 134867, 134992
Valid prediction for snap_scaffold_21-snap.517-T1
Valid prediction for GeneMark_model.84188_t
Valid prediction for snap_scaffold_21-snap.527-T1
Valid prediction for GeneMark_model.84195_t
Valid prediction for GeneMark_model.84192_t
Valid prediction for snap_scaffold_21-snap.523-T1
Valid prediction for snap_scaffold_21-snap.522-T1
Valid prediction for snap_scaffold_21-snap.518-T1
Valid prediction for snap_scaffold_21-snap.528-T1
Valid prediction for GeneMark_model.84211_t
Valid prediction for Augustus_model.g32426.t1
Valid prediction for HiQ_model.g32443.t1
Valid prediction for GeneMark_model.84209_t
Valid prediction for GlimmerHMM_glimmerT_48478-T1
Valid prediction for snap_scaffold_21-snap.539-T1
Valid prediction for CodingQuarry_transcript_32418-T1
Valid prediction for GlimmerHMM_glimmerT_48477-T1
Valid prediction for GeneMark_model.84204_t
Valid prediction for HiQ_model.g32436.t1
Valid prediction for Augustus_model.g32434.t1
Valid prediction for GlimmerHMM_glimmerT_48491-T1
Valid prediction for GeneMark_model.84198_t
Valid prediction for snap_scaffold_21-snap.515-T1
Valid prediction for GeneMark_model.84217_t
Valid prediction for snap_scaffold_21-snap.535-T1
Valid prediction for Augustus_model.g32423.t1
Valid prediction for GeneMark_model.84199_t
Valid prediction for snap_scaffold_21-snap.531-T1
Valid prediction for snap_scaffold_21-snap.521-T1
Valid prediction for GeneMark_model.84207_t
Valid prediction for GlimmerHMM_glimmerT_48485-T1
Couldn't classify 60056, 60139
Couldn't classify 60472, 60637
Sorry, prediction pasa_asmbl_28997.p1 fails validation.
(AGC)	 CC	60056-60139	GT	CGG
(GAT)	 AG	60305-60381	GT	AAG
(GTA)	 AG	60472-60637	AC	ACA
-recovered pasa_asmbl_28997.p1, internal, 60305, 60381

-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_21-snap.538-T1
Valid prediction for GeneMark_model.84201_t
Valid prediction for snap_scaffold_21-snap.546-T1
Valid prediction for snap_scaffold_21-snap.533-T1
Valid prediction for GeneMark_model.84185_t
Valid prediction for GeneMark_model.84200_t
Valid prediction for GeneMark_model.84216_t
Valid prediction for Augustus_model.g32441.t1
Valid prediction for GlimmerHMM_glimmerT_48496-T1
Valid prediction for GlimmerHMM_glimmerT_48484-T1
Valid prediction for Augustus_model.g32439.t1
Valid prediction for pasa_asmbl_27520.p1
Valid prediction for snap_scaffold_21-snap.549-T1
Valid prediction for GeneMark_model.84196_t
Valid prediction for Augustus_model.g32444.t1
Valid prediction for GeneMark_model.84215_t
Valid prediction for snap_scaffold_21-snap.534-T1
Valid prediction for GeneMark_model.84187_t
Valid prediction for Augustus_model.g32429.t1
Valid prediction for Augustus_model.g32433.t1
Couldn't classify 13101, 13221
Sorry, prediction pasa_asmbl_27526.p1 fails validation.
(ATG)	 CG	11012-11048	GT	AGG
(GGG)	 AG	11223-11328	GT	AGG
(CTC)	 AG	11495-11630	GC	AGG
(GAC)	 AG	11900-12145	GT	TGG
(GTG)	 AG	12781-12971	GT	AGG
(CAT)	 AG	13101-13221	CT	CCC
-recovered pasa_asmbl_27526.p1, initial, 11012, 11048
-recovered pasa_asmbl_27526.p1, internal, 11223, 11328
-recovered pasa_asmbl_27526.p1, internal, 11495, 11630
-recovered pasa_asmbl_27526.p1, internal, 11900, 12145
-recovered pasa_asmbl_27526.p1, internal, 12781, 12971
Valid prediction for GlimmerHMM_glimmerT_48498-T1
Valid prediction for snap_scaffold_21-snap.513-T1
Valid prediction for GeneMark_model.84218_t
Valid prediction for GlimmerHMM_glimmerT_48476-T1
Valid prediction for Augustus_model.g32440.t1
Valid prediction for Augustus_model.g32431.t1
Couldn't classify 15535, 15669
Couldn't classify 16291, 16434
Sorry, prediction pasa_asmbl_27525.p1 fails validation.
(AAC)	 AG	15535-15669	GT	AGG
(GTC)	 AG	16023-16121	GT	AGG
(GAT)	 AG	16291-16434	GA	TGG
-recovered pasa_asmbl_27525.p1, internal, 15535, 15669
-recovered pasa_asmbl_27525.p1, internal, 16023, 16121
Valid prediction for GeneMark_model.84202_t
Valid prediction for GeneMark_model.84194_t
Valid prediction for Augustus_model.g32442.t1
Valid prediction for GlimmerHMM_glimmerT_48473-T1
Valid prediction for snap_scaffold_21-snap.524-T1
Valid prediction for HiQ_model.g32435.t1
Valid prediction for snap_scaffold_21-snap.519-T1
Valid prediction for snap_scaffold_21-snap.544-T1
Valid prediction for GeneMark_model.84205_t
Valid prediction for GeneMark_model.84219_t
Couldn't classify 7640, 7651
Sorry, prediction pasa_asmbl_27527.p1 fails validation.
(AGG)	 GG	7640-7651	GT	GGG
(ACT)	 AG	7742-8068	GT	GGG
(GGG)	 AG	8170-8283	CT	GAC
-recovered pasa_asmbl_27527.p1, terminal, 8170, 8283
-recovered pasa_asmbl_27527.p1, internal, 7742, 8068
Valid prediction for Augustus_model.g32430.t1
Valid prediction for GlimmerHMM_glimmerT_48481-T1
Couldn't classify 22415, 22444
Sorry, prediction pasa_asmbl_27524.p1 fails validation.
(CTG)	 AC	22415-22444	GT	CAG
(GTG)	 AG	22976-23128	GT	CTG
(GTG)	 AG	24599-24744	GT	AGG
(CTT)	 AG	25019-25148	GT	AGG
(GTG)	 AG	27976-28060	GT	GGG
(AGC)	 AG	28198-28284	GT	AGG
(ACA)	 AG	30518-30672	GT	CGG
(CTT)	 AG	32609-32683	GC	GAG
-recovered pasa_asmbl_27524.p1, terminal, 24599, 24744
-recovered pasa_asmbl_27524.p1, terminal, 32609, 32683
-recovered pasa_asmbl_27524.p1, internal, 22976, 23128
-recovered pasa_asmbl_27524.p1, internal, 24599, 24744
-recovered pasa_asmbl_27524.p1, internal, 25019, 25148
-recovered pasa_asmbl_27524.p1, internal, 27976, 28060
-recovered pasa_asmbl_27524.p1, internal, 28198, 28284
-recovered pasa_asmbl_27524.p1, internal, 30518, 30672
-recovered pasa_asmbl_27524.p1, internal, 32609, 32683
Valid prediction for snap_scaffold_21-snap.547-T1
Valid prediction for GlimmerHMM_glimmerT_48486-T1
Valid prediction for GeneMark_model.84210_t
Valid prediction for GeneMark_model.84189_t
Valid prediction for GeneMark_model.84208_t
Valid prediction for snap_scaffold_21-snap.545-T1
Valid prediction for GeneMark_model.84186_t
Valid prediction for snap_scaffold_21-snap.540-T1
Valid prediction for GlimmerHMM_glimmerT_48489-T1
Valid prediction for GlimmerHMM_glimmerT_48480-T1
Valid prediction for GlimmerHMM_glimmerT_48492-T1
Valid prediction for snap_scaffold_21-snap.548-T1
Valid prediction for snap_scaffold_21-snap.542-T1
Valid prediction for snap_scaffold_21-snap.543-T1
Valid prediction for snap_scaffold_21-snap.541-T1
Valid prediction for GeneMark_model.84214_t
Valid prediction for HiQ_model.g32425.t1
Valid prediction for GeneMark_model.84197_t
Valid prediction for GlimmerHMM_glimmerT_48488-T1
Valid prediction for Augustus_model.g32422.t1
Couldn't classify 4568, 4738
Couldn't classify 5178, 5234
Sorry, prediction pasa_asmbl_27528.p1 fails validation.
(CGT)	 GC	4568-4738	GT	AGG
(GAC)	 AG	4926-5066	GT	AGG
(AAC)	 AG	5178-5234	TG	GCT
-recovered pasa_asmbl_27528.p1, internal, 4926, 5066
Valid prediction for snap_scaffold_21-snap.530-T1
Valid prediction for snap_scaffold_21-snap.516-T1
Couldn't classify 174366, 175496
Sorry, prediction pasa_asmbl_27517.p1 fails validation.
(CCA)	 GA	174366-175496	AA	GAA
Valid prediction for snap_scaffold_21-snap.510-T1
Valid prediction for GlimmerHMM_glimmerT_48474-T1
Valid prediction for GlimmerHMM_glimmerT_48497-T1
Valid prediction for snap_scaffold_21-snap.525-T1
Valid prediction for snap_scaffold_21-snap.514-T1
Valid prediction for GeneMark_model.84190_t
Valid prediction for snap_scaffold_21-snap.526-T1
Valid prediction for Augustus_model.g32438.t1
Valid prediction for snap_scaffold_21-snap.529-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22596, rend_intergenic: 19876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33462, rend_intergenic: 31528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91628, rend_intergenic: 89140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127230, rend_intergenic: 119788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 191179
-exon list size: 591


building trellis

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98.7    
98.8    
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99.2    
99.3    
99.5    
99.7    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 22596, rend_intergenic: 19876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33462, rend_intergenic: 31528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91628, rend_intergenic: 89140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127230, rend_intergenic: 119788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support