-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_1938839-2170172

-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 snap_scaffold_24-snap.482-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.461-T1
Valid prediction for snap_scaffold_24-snap.491-T1
Valid prediction for GlimmerHMM_glimmerT_52105-T1
Valid prediction for snap_scaffold_24-snap.479-T1
Valid prediction for snap_scaffold_24-snap.460-T1
Valid prediction for snap_scaffold_24-snap.497-T1
Valid prediction for GlimmerHMM_glimmerT_52107-T1
Valid prediction for snap_scaffold_24-snap.487-T1
Valid prediction for snap_scaffold_24-snap.476-T1
Valid prediction for snap_scaffold_24-snap.468-T1
Valid prediction for snap_scaffold_24-snap.484-T1
Valid prediction for snap_scaffold_24-snap.500-T1
Valid prediction for snap_scaffold_24-snap.457-T1
Valid prediction for snap_scaffold_24-snap.471-T1
Valid prediction for snap_scaffold_24-snap.458-T1
Valid prediction for snap_scaffold_24-snap.462-T1
Valid prediction for snap_scaffold_24-snap.480-T1
Valid prediction for snap_scaffold_24-snap.478-T1
Valid prediction for Augustus_model.g34714.t1
Valid prediction for snap_scaffold_24-snap.459-T1
Valid prediction for snap_scaffold_24-snap.485-T1
Valid prediction for snap_scaffold_24-snap.474-T1
Valid prediction for snap_scaffold_24-snap.495-T1
Valid prediction for Augustus_model.g34719.t1
Valid prediction for GlimmerHMM_glimmerT_52098-T1
Valid prediction for snap_scaffold_24-snap.473-T1
Valid prediction for Augustus_model.g34711.t1
Valid prediction for snap_scaffold_24-snap.469-T1
Valid prediction for snap_scaffold_24-snap.488-T1
Valid prediction for snap_scaffold_24-snap.466-T1
Valid prediction for snap_scaffold_24-snap.496-T1
Valid prediction for GlimmerHMM_glimmerT_52087-T1
Valid prediction for snap_scaffold_24-snap.493-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.g34725.t1
Valid prediction for GlimmerHMM_glimmerT_52091-T1
Valid prediction for CodingQuarry_transcript_37243-T1
Valid prediction for snap_scaffold_24-snap.467-T1
Couldn't classify 225366, 225477
Sorry, prediction pasa_asmbl_32753.p1 fails validation.
(GAC)	 GA	225366-225477	GT	AGG
(GTC)	 AG	225604-225869	GT	AGG
(GGC)	 AG	226333-226508	GT	AGG
(TAA)	 AG	228305-228429	GT	AGG
(GGG)	 AG	228783-229030	AG	AGA
-recovered pasa_asmbl_32753.p1, terminal, 228783, 229030
-recovered pasa_asmbl_32753.p1, internal, 225604, 225869
-recovered pasa_asmbl_32753.p1, internal, 226333, 226508
-recovered pasa_asmbl_32753.p1, internal, 228305, 228429
Valid prediction for snap_scaffold_24-snap.501-T1
Valid prediction for snap_scaffold_24-snap.483-T1
Valid prediction for GlimmerHMM_glimmerT_52086-T1
Couldn't classify 214343, 214507
Sorry, prediction pasa_asmbl_32759.p1 fails validation.
(GGA)	 AC	214343-214507	GT	CGG
(GAG)	 AG	215308-215392	GT	CAG
(TAT)	 AG	215599-215709	GT	AGG
(GTT)	 AG	216262-216325	GT	AGG
(GTC)	 AG	216407-216547	GT	TTG
(TCC)	 AG	216866-216944	GT	GGG
(GAG)	 AG	217065-217156	GT	AGG
(CTT)	 AG	217336-217471	GT	GGG
(TTG)	 AG	217783-217857	GC	GAG
-recovered pasa_asmbl_32759.p1, terminal, 217783, 217857
-recovered pasa_asmbl_32759.p1, internal, 215308, 215392
-recovered pasa_asmbl_32759.p1, internal, 215599, 215709
-recovered pasa_asmbl_32759.p1, internal, 216262, 216325
-recovered pasa_asmbl_32759.p1, internal, 216407, 216547
-recovered pasa_asmbl_32759.p1, internal, 216866, 216944
-recovered pasa_asmbl_32759.p1, internal, 217065, 217156
-recovered pasa_asmbl_32759.p1, internal, 217336, 217471
-recovered pasa_asmbl_32759.p1, internal, 217783, 217857
Valid prediction for snap_scaffold_24-snap.481-T1
Valid prediction for pasa_asmbl_32763.p1
Valid prediction for GlimmerHMM_glimmerT_52100-T1
Valid prediction for snap_scaffold_24-snap.477-T1
Valid prediction for GlimmerHMM_glimmerT_52103-T1
Valid prediction for GlimmerHMM_glimmerT_52106-T1
Valid prediction for snap_scaffold_24-snap.504-T1
Valid prediction for GlimmerHMM_glimmerT_52109-T1
Valid prediction for snap_scaffold_24-snap.472-T1
Valid prediction for Augustus_model.g34717.t1
Couldn't classify 201529, 201630
Couldn't classify 206822, 206860
Sorry, prediction pasa_asmbl_33250.p1 fails validation.
(GGA)	 GG	201529-201630	GT	CTG
(GAG)	 AG	204620-204715	GT	AGG
(CTC)	 AG	205096-205143	GT	GAG
(AAA)	 AG	206110-206139	GT	TTG
(AGT)	 AG	206261-206311	GT	AGG
(GAT)	 AG	206822-206860	GT	TAG
-recovered pasa_asmbl_33250.p1, internal, 204620, 204715
-recovered pasa_asmbl_33250.p1, internal, 205096, 205143
-recovered pasa_asmbl_33250.p1, internal, 206110, 206139
-recovered pasa_asmbl_33250.p1, internal, 206261, 206311
-recovered pasa_asmbl_33250.p1, internal, 206822, 206860
Valid prediction for snap_scaffold_24-snap.463-T1
Valid prediction for GlimmerHMM_glimmerT_52089-T1
Valid prediction for Augustus_model.g34715.t1
Valid prediction for snap_scaffold_24-snap.475-T1
Valid prediction for snap_scaffold_24-snap.492-T1
Valid prediction for Augustus_model.g34726.t1
Valid prediction for Augustus_model.g34721.t1
Valid prediction for GlimmerHMM_glimmerT_52090-T1
Valid prediction for CodingQuarry_transcript_37242-T1
Valid prediction for GlimmerHMM_glimmerT_52088-T1
Valid prediction for Augustus_model.g34720.t1
Valid prediction for Augustus_model.g34718.t1
Valid prediction for Augustus_model.g34710.t1
Valid prediction for GlimmerHMM_glimmerT_52104-T1
Valid prediction for snap_scaffold_24-snap.489-T1
Valid prediction for CodingQuarry_transcript_37244-T1
Valid prediction for snap_scaffold_24-snap.498-T1
Couldn't classify 173539, 173678
Sorry, prediction pasa_asmbl_32768.p1 fails validation.
(ATG)	 CG	171477-171552	GT	GGG
(GTG)	 AG	171666-171843	GT	AGG
(AGA)	 AG	172247-172431	GT	GGG
(CGT)	 AG	172743-172895	GT	CTG
(GCT)	 AG	173211-173300	GT	AGG
(AGG)	 AG	173539-173678	GG	GCG
-recovered pasa_asmbl_32768.p1, initial, 171477, 171552
-recovered pasa_asmbl_32768.p1, internal, 171666, 171843
-recovered pasa_asmbl_32768.p1, internal, 172247, 172431
-recovered pasa_asmbl_32768.p1, internal, 172743, 172895
-recovered pasa_asmbl_32768.p1, internal, 173211, 173300
Valid prediction for GlimmerHMM_glimmerT_52097-T1
Valid prediction for Augustus_model.g34723.t1
Valid prediction for Augustus_model.g34709.t1
Couldn't classify 100485, 100703
Sorry, prediction pasa_asmbl_32772.p3 fails validation.
(TGT)	 CG	100485-100703	GT	TGG
(ATG)	 AG	101226-101353	GT	AGG
(AGG)	 AG	104246-104261	AC	GAA
-recovered pasa_asmbl_32772.p3, initial, 101226, 101353
-recovered pasa_asmbl_32772.p3, terminal, 104246, 104261
-recovered pasa_asmbl_32772.p3, internal, 101226, 101353
Valid prediction for GlimmerHMM_glimmerT_52095-T1
Valid prediction for GlimmerHMM_glimmerT_52108-T1
Valid prediction for GlimmerHMM_glimmerT_52094-T1
Valid prediction for Augustus_model.g34724.t1
Valid prediction for snap_scaffold_24-snap.456-T1
Couldn't classify 106804, 106929
Sorry, prediction pasa_asmbl_32769.p1 fails validation.
(GTT)	 AG	106804-106929	GT	AGG
(GCA)	 AG	107204-107345	GT	GGG
(GTG)	 AG	108019-108197	GT	AGG
(GCC)	 AG	108307-108846	GA	AGG
-recovered pasa_asmbl_32769.p1, terminal, 108307, 108846
-recovered pasa_asmbl_32769.p1, internal, 106804, 106929
-recovered pasa_asmbl_32769.p1, internal, 107204, 107345
-recovered pasa_asmbl_32769.p1, internal, 108019, 108197
Valid prediction for GlimmerHMM_glimmerT_52101-T1
Valid prediction for Augustus_model.g34713.t1
Valid prediction for snap_scaffold_24-snap.494-T1
Valid prediction for snap_scaffold_24-snap.470-T1
Valid prediction for GlimmerHMM_glimmerT_52102-T1
Valid prediction for GlimmerHMM_glimmerT_52099-T1
Valid prediction for snap_scaffold_24-snap.486-T1
Valid prediction for Augustus_model.g34712.t1
Valid prediction for GlimmerHMM_glimmerT_52093-T1
Valid prediction for GlimmerHMM_glimmerT_52092-T1
Valid prediction for snap_scaffold_24-snap.465-T1
Couldn't classify 85863, 86183
Sorry, prediction pasa_asmbl_32774.p1 fails validation.
(GCG)	 AG	85863-86183	AG	TGA
Valid prediction for Augustus_model.g34716.t1
Valid prediction for Augustus_model.g34722.t1
Valid prediction for snap_scaffold_24-snap.503-T1
Valid prediction for snap_scaffold_24-snap.455-T1
Valid prediction for GlimmerHMM_glimmerT_52096-T1
Valid prediction for snap_scaffold_24-snap.490-T1
Valid prediction for snap_scaffold_24-snap.499-T1
Valid prediction for snap_scaffold_24-snap.502-T1
Valid prediction for snap_scaffold_24-snap.464-T1
Valid prediction for Augustus_model.g34708.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 37847, rend_intergenic: 11668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38024, rend_intergenic: 37863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62709, rend_intergenic: 59243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64323, rend_intergenic: 63188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77422, rend_intergenic: 65458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78178, rend_intergenic: 77459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81612, rend_intergenic: 78250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88587, rend_intergenic: 85379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95421, rend_intergenic: 92610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106204, rend_intergenic: 103977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121810, rend_intergenic: 109285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128752, rend_intergenic: 122489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133793, rend_intergenic: 128890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145734, rend_intergenic: 134154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148917, rend_intergenic: 147189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153646, rend_intergenic: 149622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159455, rend_intergenic: 153647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167986, rend_intergenic: 159746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170488, rend_intergenic: 168718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171265, rend_intergenic: 170620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175029, rend_intergenic: 172073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179853, rend_intergenic: 175507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188833, rend_intergenic: 179873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195855, rend_intergenic: 193083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215909, rend_intergenic: 199251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217196, rend_intergenic: 216507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 231334
-exon list size: 543


building trellis

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95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 37847, rend_intergenic: 11668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38024, rend_intergenic: 37863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62709, rend_intergenic: 59243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64323, rend_intergenic: 63188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77422, rend_intergenic: 65458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78178, rend_intergenic: 77459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81612, rend_intergenic: 78250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88587, rend_intergenic: 85379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95421, rend_intergenic: 92610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106204, rend_intergenic: 103977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121810, rend_intergenic: 109285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128752, rend_intergenic: 122489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133793, rend_intergenic: 128890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145734, rend_intergenic: 134154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148917, rend_intergenic: 147189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153646, rend_intergenic: 149622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159455, rend_intergenic: 153647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167986, rend_intergenic: 159746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170488, rend_intergenic: 168718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171265, rend_intergenic: 170620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175029, rend_intergenic: 172073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179853, rend_intergenic: 175507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188833, rend_intergenic: 179873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195855, rend_intergenic: 193083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215909, rend_intergenic: 199251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217196, rend_intergenic: 216507  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

-building DP trellis

-building trellis in range 217218 - 231334
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 219831 - 231334
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support