-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_2471538-2820739

-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_13-snap.477-T1
Valid prediction for Augustus_model.g20749.t1
Valid prediction for HiQ_model.g20733.t1
Valid prediction for snap_scaffold_13-snap.504-T1
Valid prediction for GlimmerHMM_glimmerT_31253-T1
Couldn't classify 245951, 245988
Couldn't classify 246409, 246546
Sorry, prediction pasa_asmbl_11698.p2 fails validation.
(GTC)	 AC	245951-245988	GT	AGG
(GTA)	 AG	246147-246288	GT	TTG
(GGC)	 AG	246409-246546	GC	AGG
-recovered pasa_asmbl_11698.p2, internal, 246147, 246288
-recovered pasa_asmbl_11698.p2, internal, 246409, 246546
Valid prediction for snap_scaffold_13-snap.518-T1
Valid prediction for GlimmerHMM_glimmerT_31226-T1
Valid prediction for CodingQuarry_transcript_12904-T1
Valid prediction for snap_scaffold_13-snap.493-T1
Couldn't classify 313327, 313461
Couldn't classify 317796, 317985
Sorry, prediction pasa_asmbl_10637.p1 fails validation.
(AGT)	 GC	313327-313461	GT	AGG
(GGC)	 AG	315036-315122	GT	GGG
(CTG)	 AG	316165-316323	GT	CGG
(CTG)	 AG	317197-317378	GT	AGG
(CGG)	 AG	317796-317985	GT	AGG
-recovered pasa_asmbl_10637.p1, internal, 315036, 315122
-recovered pasa_asmbl_10637.p1, internal, 316165, 316323
-recovered pasa_asmbl_10637.p1, internal, 317197, 317378
-recovered pasa_asmbl_10637.p1, internal, 317796, 317985
Valid prediction for Augustus_model.g20748.t1
Valid prediction for snap_scaffold_13-snap.479-T1
Valid prediction for GlimmerHMM_glimmerT_31229-T1
Valid prediction for CodingQuarry_transcript_12903-T1
Valid prediction for GlimmerHMM_glimmerT_31239-T1
Valid prediction for Augustus_model.g20738.t1
Valid prediction for snap_scaffold_13-snap.502-T1
Couldn't classify 95419, 95468
Sorry, prediction pasa_asmbl_10624.p1 fails validation.
(GCC)	 CC	95419-95468	GT	AGG
(CCT)	 AG	96262-96508	GT	AGG
(CTA)	 AG	98227-98254	GT	AGG
(ACT)	 AG	98782-98931	GT	GGG
(ACA)	 AG	99067-99240	GT	GGG
(GGG)	 AG	99413-99490	GT	AGG
(CTT)	 AG	99637-99665	AG	AAA
-recovered pasa_asmbl_10624.p1, terminal, 99637, 99665
-recovered pasa_asmbl_10624.p1, internal, 96262, 96508
-recovered pasa_asmbl_10624.p1, internal, 98227, 98254
-recovered pasa_asmbl_10624.p1, internal, 98782, 98931
-recovered pasa_asmbl_10624.p1, internal, 99067, 99240
-recovered pasa_asmbl_10624.p1, internal, 99413, 99490
Valid prediction for Augustus_model.g20754.t1
Valid prediction for Augustus_model.g20742.t1
Valid prediction for GlimmerHMM_glimmerT_31232-T1
Valid prediction for GlimmerHMM_glimmerT_31230-T1
Couldn't classify 270743, 270844
Couldn't classify 276850, 276945
Sorry, prediction pasa_asmbl_10636.p1 fails validation.
(TCC)	 GC	270743-270844	GT	CTG
(ACC)	 AG	272146-272290	GT	AGG
(AGC)	 AG	272453-272586	GT	ATG
(GTG)	 AG	274653-274760	GT	AGG
(GAC)	 AG	275045-275242	GT	AGG
(GAC)	 AG	276850-276945	AC	TCA
-recovered pasa_asmbl_10636.p1, internal, 272146, 272290
-recovered pasa_asmbl_10636.p1, internal, 272453, 272586
-recovered pasa_asmbl_10636.p1, internal, 274653, 274760
-recovered pasa_asmbl_10636.p1, internal, 275045, 275242
Valid prediction for snap_scaffold_13-snap.478-T1
Couldn't classify 242815, 242920
Couldn't classify 243298, 243341
Sorry, prediction pasa_asmbl_11619.p1 fails validation.
(CAG)	 CA	242815-242920	GT	AGG
(AAA)	 AG	243020-243175	GT	AGG
(ATC)	 AG	243298-243341	GT	CGG
-recovered pasa_asmbl_11619.p1, internal, 243020, 243175
-recovered pasa_asmbl_11619.p1, internal, 243298, 243341
Valid prediction for CodingQuarry_transcript_12902-T1
Valid prediction for snap_scaffold_13-snap.482-T1
Valid prediction for GlimmerHMM_glimmerT_31246-T1
Valid prediction for snap_scaffold_13-snap.484-T1
Valid prediction for snap_scaffold_13-snap.485-T1
Valid prediction for HiQ_model.g20741.t1
Valid prediction for CodingQuarry_transcript_12900-T1
Couldn't classify 174890, 175006
Sorry, prediction pasa_asmbl_10632.p1 fails validation.
(ACA)	 GT	174890-175006	GT	CTG
(GCG)	 AG	175392-175465	GT	AAG
(TGA)	 AG	175581-175641	GT	TTG
(GTA)	 AG	175781-175850	GT	AGG
(GCA)	 AG	175941-176059	GT	CGG
(AAC)	 AG	176167-176215	GT	TGG
(ATC)	 AG	176300-176395	GT	AGG
(GTT)	 AG	176498-176580	GT	AGG
(CAC)	 AG	176670-176743	GT	TGG
(CTC)	 AG	176864-176972	GT	AGG
(TAT)	 AG	177054-177188	GT	AGG
(CTG)	 AG	177307-177407	GT	AGG
(CTC)	 AG	177554-177620	GT	AGG
(CTC)	 AG	177728-177778	GT	AGG
(CAC)	 AG	177882-177952	GT	AGG
(ACC)	 AG	178094-178189	GT	AAG
(TGA)	 AG	178273-178338	GT	AGG
(GGA)	 AG	178449-178532	GT	AAG
(GGT)	 AG	178626-178773	GT	CTG
(AAG)	 AG	178885-178969	GT	CAG
(GCC)	 AG	179084-179361	AC	GAA
add_exon() Sorry, pasa_asmbl_10632.p1 178449-178532-terminal-1 is invalid.
-recovered pasa_asmbl_10632.p1, terminal, 178449, 178532
-recovered pasa_asmbl_10632.p1, terminal, 179084, 179361
-recovered pasa_asmbl_10632.p1, internal, 175392, 175465
-recovered pasa_asmbl_10632.p1, internal, 175581, 175641
-recovered pasa_asmbl_10632.p1, internal, 175781, 175850
-recovered pasa_asmbl_10632.p1, internal, 175941, 176059
-recovered pasa_asmbl_10632.p1, internal, 176167, 176215
-recovered pasa_asmbl_10632.p1, internal, 176300, 176395
-recovered pasa_asmbl_10632.p1, internal, 176498, 176580
-recovered pasa_asmbl_10632.p1, internal, 176670, 176743
-recovered pasa_asmbl_10632.p1, internal, 176864, 176972
-recovered pasa_asmbl_10632.p1, internal, 177054, 177188
-recovered pasa_asmbl_10632.p1, internal, 177307, 177407
-recovered pasa_asmbl_10632.p1, internal, 177554, 177620
-recovered pasa_asmbl_10632.p1, internal, 177728, 177778
-recovered pasa_asmbl_10632.p1, internal, 177882, 177952
-recovered pasa_asmbl_10632.p1, internal, 178094, 178189
-recovered pasa_asmbl_10632.p1, internal, 178273, 178338
-recovered pasa_asmbl_10632.p1, internal, 178449, 178532
-recovered pasa_asmbl_10632.p1, internal, 178626, 178773
-recovered pasa_asmbl_10632.p1, internal, 178885, 178969
Valid prediction for Augustus_model.g20746.t1
Valid prediction for GlimmerHMM_glimmerT_31244-T1
Valid prediction for snap_scaffold_13-snap.516-T1
Valid prediction for CodingQuarry_transcript_12905-T1
Valid prediction for GlimmerHMM_glimmerT_31247-T1
Valid prediction for snap_scaffold_13-snap.512-T1
Valid prediction for snap_scaffold_13-snap.476-T1
Valid prediction for snap_scaffold_13-snap.517-T1
Valid prediction for snap_scaffold_13-snap.492-T1
Valid prediction for snap_scaffold_13-snap.475-T1
Valid prediction for snap_scaffold_13-snap.510-T1
Valid prediction for HiQ_model.g20737.t1
Valid prediction for HiQ_model.g20743.t1
Valid prediction for snap_scaffold_13-snap.490-T1
Valid prediction for GlimmerHMM_glimmerT_31254-T1
Valid prediction for snap_scaffold_13-snap.488-T1
Valid prediction for GlimmerHMM_glimmerT_31248-T1
Valid prediction for snap_scaffold_13-snap.494-T1
Valid prediction for snap_scaffold_13-snap.470-T1
Valid prediction for GlimmerHMM_glimmerT_31250-T1
Valid prediction for snap_scaffold_13-snap.496-T1
Valid prediction for GlimmerHMM_glimmerT_31240-T1
Valid prediction for pasa_asmbl_10615.p1
Valid prediction for GlimmerHMM_glimmerT_31233-T1
Valid prediction for Augustus_model.g20757.t1
Valid prediction for Augustus_model.g20739.t1
Valid prediction for snap_scaffold_13-snap.491-T1
Valid prediction for snap_scaffold_13-snap.508-T1
Valid prediction for pasa_asmbl_10631.p1
Valid prediction for snap_scaffold_13-snap.483-T1
Valid prediction for Augustus_model.g20756.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 GlimmerHMM_glimmerT_31225-T1
Valid prediction for HiQ_model.g20744.t1
Valid prediction for GlimmerHMM_glimmerT_31251-T1
Valid prediction for HiQ_model.g20734.t1
Valid prediction for snap_scaffold_13-snap.514-T1
Valid prediction for snap_scaffold_13-snap.471-T1
Valid prediction for CodingQuarry_transcript_12906-T1
Valid prediction for GlimmerHMM_glimmerT_31243-T1
Valid prediction for snap_scaffold_13-snap.486-T1
Valid prediction for pasa_asmbl_9473.p1
Valid prediction for GlimmerHMM_glimmerT_31238-T1
Valid prediction for CodingQuarry_transcript_12899-T1
Valid prediction for snap_scaffold_13-snap.489-T1
Valid prediction for Augustus_model.g20755.t1
Valid prediction for snap_scaffold_13-snap.497-T1
Valid prediction for Augustus_model.g20752.t1
Valid prediction for pasa_asmbl_9463.p1
Valid prediction for Augustus_model.g20747.t1
Valid prediction for snap_scaffold_13-snap.474-T1
Valid prediction for snap_scaffold_13-snap.469-T1
Valid prediction for snap_scaffold_13-snap.472-T1
Valid prediction for snap_scaffold_13-snap.509-T1
Valid prediction for pasa_asmbl_9467.p1
Valid prediction for snap_scaffold_13-snap.513-T1
Valid prediction for GlimmerHMM_glimmerT_31234-T1
Valid prediction for snap_scaffold_13-snap.503-T1
Valid prediction for HiQ_model.g20732.t1
Valid prediction for CodingQuarry_transcript_12901-T1
Valid prediction for snap_scaffold_13-snap.487-T1
Valid prediction for snap_scaffold_13-snap.501-T1
Valid prediction for GlimmerHMM_glimmerT_31241-T1
Valid prediction for Augustus_model.g20736.t1
Valid prediction for Augustus_model.g20750.t1
Valid prediction for GlimmerHMM_glimmerT_31236-T1
Valid prediction for snap_scaffold_13-snap.511-T1
Valid prediction for GlimmerHMM_glimmerT_31245-T1
Valid prediction for GlimmerHMM_glimmerT_31227-T1
Valid prediction for Augustus_model.g20735.t1
Valid prediction for HiQ_model.g20745.t1
Valid prediction for snap_scaffold_13-snap.498-T1
Valid prediction for GlimmerHMM_glimmerT_31249-T1
Valid prediction for GlimmerHMM_glimmerT_31235-T1
Valid prediction for snap_scaffold_13-snap.515-T1
Valid prediction for GlimmerHMM_glimmerT_31252-T1
Valid prediction for GlimmerHMM_glimmerT_31228-T1
Valid prediction for snap_scaffold_13-snap.499-T1
Valid prediction for snap_scaffold_13-snap.495-T1
Valid prediction for GlimmerHMM_glimmerT_31237-T1
Valid prediction for Augustus_model.g20751.t1
Valid prediction for snap_scaffold_13-snap.480-T1
Valid prediction for snap_scaffold_13-snap.507-T1
Valid prediction for snap_scaffold_13-snap.505-T1
Valid prediction for Augustus_model.g20740.t1
Valid prediction for snap_scaffold_13-snap.473-T1
Valid prediction for snap_scaffold_13-snap.506-T1
Valid prediction for snap_scaffold_13-snap.481-T1
Valid prediction for Augustus_model.g20753.t1
Valid prediction for snap_scaffold_13-snap.500-T1
Valid prediction for GlimmerHMM_glimmerT_31231-T1
Valid prediction for GlimmerHMM_glimmerT_31242-T1
Valid prediction for pasa_asmbl_9461.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 179361, rend_intergenic: 178441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194456, rend_intergenic: 190962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204172, rend_intergenic: 194580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 247204, rend_intergenic: 240429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 272905, rend_intergenic: 266853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 290535, rend_intergenic: 272983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 291844, rend_intergenic: 290620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 295105, rend_intergenic: 292759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 308183, rend_intergenic: 296566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 321231, rend_intergenic: 311854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 349202
-exon list size: 556


building trellis

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91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 179361, rend_intergenic: 178441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194456, rend_intergenic: 190962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204172, rend_intergenic: 194580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 247204, rend_intergenic: 240429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 272905, rend_intergenic: 266853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 290535, rend_intergenic: 272983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 291844, rend_intergenic: 290620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 295105, rend_intergenic: 292759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 308183, rend_intergenic: 296566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 321231, rend_intergenic: 311854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support