-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_11445624-11690576

-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_21-snap.2497-T1
Valid prediction for GlimmerHMM_glimmerT_48638-T1
Valid prediction for snap_scaffold_21-snap.2489-T1
Valid prediction for snap_scaffold_21-snap.2468-T1
Valid prediction for snap_scaffold_21-snap.2473-T1
Valid prediction for GlimmerHMM_glimmerT_48635-T1
Valid prediction for GlimmerHMM_glimmerT_48662-T1
Valid prediction for snap_scaffold_21-snap.2471-T1
Valid prediction for snap_scaffold_21-snap.2501-T1
Valid prediction for Augustus_model.g32499.t1
Valid prediction for GlimmerHMM_glimmerT_48669-T1
Valid prediction for snap_scaffold_21-snap.2490-T1
Valid prediction for GlimmerHMM_glimmerT_48656-T1
Valid prediction for snap_scaffold_21-snap.2461-T1
Valid prediction for snap_scaffold_21-snap.2509-T1
Valid prediction for GlimmerHMM_glimmerT_48647-T1
Valid prediction for GlimmerHMM_glimmerT_48642-T1
Valid prediction for GlimmerHMM_glimmerT_48652-T1
Valid prediction for snap_scaffold_21-snap.2469-T1
Valid prediction for snap_scaffold_21-snap.2474-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_21-snap.2484-T1
Valid prediction for snap_scaffold_21-snap.2498-T1
Valid prediction for snap_scaffold_21-snap.2510-T1
Valid prediction for snap_scaffold_21-snap.2487-T1
Valid prediction for snap_scaffold_21-snap.2482-T1
Valid prediction for Augustus_model.g32503.t1
Valid prediction for snap_scaffold_21-snap.2478-T1
Valid prediction for snap_scaffold_21-snap.2465-T1
Valid prediction for snap_scaffold_21-snap.2506-T1
Valid prediction for snap_scaffold_21-snap.2492-T1
Valid prediction for GlimmerHMM_glimmerT_48639-T1
Valid prediction for GlimmerHMM_glimmerT_48645-T1
Valid prediction for GlimmerHMM_glimmerT_48637-T1
Valid prediction for Augustus_model.g32510.t1
Valid prediction for snap_scaffold_21-snap.2466-T1
Valid prediction for snap_scaffold_21-snap.2475-T1
Valid prediction for GlimmerHMM_glimmerT_48634-T1
Valid prediction for snap_scaffold_21-snap.2460-T1
Valid prediction for GlimmerHMM_glimmerT_48661-T1
Valid prediction for snap_scaffold_21-snap.2508-T1
Valid prediction for Augustus_model.g32497.t1
Valid prediction for GlimmerHMM_glimmerT_48649-T1
Valid prediction for GlimmerHMM_glimmerT_48664-T1
Valid prediction for GlimmerHMM_glimmerT_48655-T1
Valid prediction for snap_scaffold_21-snap.2486-T1
Valid prediction for snap_scaffold_21-snap.2488-T1
Valid prediction for snap_scaffold_21-snap.2479-T1
Valid prediction for snap_scaffold_21-snap.2477-T1
Valid prediction for GlimmerHMM_glimmerT_48641-T1
Valid prediction for snap_scaffold_21-snap.2499-T1
Valid prediction for snap_scaffold_21-snap.2496-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.g32509.t1
Valid prediction for snap_scaffold_21-snap.2505-T1
Valid prediction for Augustus_model.g32500.t1
Valid prediction for snap_scaffold_21-snap.2458-T1
Valid prediction for GlimmerHMM_glimmerT_48654-T1
Valid prediction for Augustus_model.g32506.t1
Valid prediction for snap_scaffold_21-snap.2495-T1
Couldn't classify 15392, 15522
Sorry, prediction pasa_asmbl_28138.p1 fails validation.
(AAG)	 AG	15392-15522	GT	AGG
(GCC)	 AG	17295-17364	GT	CGG
(GCC)	 AG	17592-17754	GT	AGG
(ACA)	 AG	19868-20217	AC	AAA
-recovered pasa_asmbl_28138.p1, terminal, 19868, 20217
-recovered pasa_asmbl_28138.p1, internal, 15392, 15522
-recovered pasa_asmbl_28138.p1, internal, 17295, 17364
-recovered pasa_asmbl_28138.p1, internal, 17592, 17754
Valid prediction for snap_scaffold_21-snap.2483-T1
Valid prediction for GlimmerHMM_glimmerT_48659-T1
Valid prediction for GlimmerHMM_glimmerT_48660-T1
Valid prediction for CodingQuarry_transcript_32751-T1
Valid prediction for pasa_asmbl_28132.p1
Valid prediction for GlimmerHMM_glimmerT_48658-T1
Valid prediction for GlimmerHMM_glimmerT_48667-T1
Valid prediction for Augustus_model.g32507.t1
Valid prediction for snap_scaffold_21-snap.2485-T1
Valid prediction for GlimmerHMM_glimmerT_48632-T1
Valid prediction for snap_scaffold_21-snap.2500-T1
Valid prediction for GlimmerHMM_glimmerT_48663-T1
Valid prediction for snap_scaffold_21-snap.2467-T1
Valid prediction for snap_scaffold_21-snap.2459-T1
Valid prediction for snap_scaffold_21-snap.2503-T1
Valid prediction for snap_scaffold_21-snap.2463-T1
Valid prediction for Augustus_model.g32502.t1
Valid prediction for GlimmerHMM_glimmerT_48643-T1
Valid prediction for GlimmerHMM_glimmerT_48657-T1
Valid prediction for Augustus_model.g32504.t1
Valid prediction for snap_scaffold_21-snap.2462-T1
Valid prediction for snap_scaffold_21-snap.2481-T1
Valid prediction for GlimmerHMM_glimmerT_48668-T1
Valid prediction for snap_scaffold_21-snap.2470-T1
Valid prediction for GlimmerHMM_glimmerT_48644-T1
Valid prediction for snap_scaffold_21-snap.2491-T1
Valid prediction for Augustus_model.g32498.t1
Valid prediction for snap_scaffold_21-snap.2494-T1
Valid prediction for GlimmerHMM_glimmerT_48666-T1
Valid prediction for snap_scaffold_21-snap.2476-T1
Valid prediction for GlimmerHMM_glimmerT_48646-T1
Valid prediction for GlimmerHMM_glimmerT_48633-T1
Valid prediction for GlimmerHMM_glimmerT_48648-T1
Valid prediction for GlimmerHMM_glimmerT_48651-T1
Valid prediction for CodingQuarry_transcript_32750-T1
Valid prediction for GlimmerHMM_glimmerT_48665-T1
Valid prediction for GlimmerHMM_glimmerT_48640-T1
Valid prediction for snap_scaffold_21-snap.2464-T1
Couldn't classify 14783, 15223
Sorry, prediction pasa_asmbl_28140.p1 fails validation.
(AAT)	 CT	14783-15223	TC	CCT
Valid prediction for Augustus_model.g32505.t1
Valid prediction for Augustus_model.g32508.t1
Valid prediction for GlimmerHMM_glimmerT_48653-T1
Valid prediction for GlimmerHMM_glimmerT_48650-T1
Valid prediction for snap_scaffold_21-snap.2493-T1
Couldn't classify 57121, 57269
Couldn't classify 59531, 59609
Sorry, prediction pasa_asmbl_28136.p1 fails validation.
(ATC)	 CC	57121-57269	GT	AGG
(TTT)	 AG	57614-57710	GT	AGG
(GGG)	 AG	57792-57925	GT	AGG
(ACG)	 AG	59113-59244	GT	GGG
(CAC)	 AG	59531-59609	AG	GGA
-recovered pasa_asmbl_28136.p1, internal, 57614, 57710
-recovered pasa_asmbl_28136.p1, internal, 57792, 57925
-recovered pasa_asmbl_28136.p1, internal, 59113, 59244
Valid prediction for snap_scaffold_21-snap.2502-T1
Valid prediction for snap_scaffold_21-snap.2472-T1
Valid prediction for Augustus_model.g32501.t1
Valid prediction for GlimmerHMM_glimmerT_48636-T1
Valid prediction for snap_scaffold_21-snap.2504-T1
Valid prediction for snap_scaffold_21-snap.2507-T1
Valid prediction for snap_scaffold_21-snap.2480-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 35918, rend_intergenic: 32221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54358, rend_intergenic: 36120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58861, rend_intergenic: 54793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69676, rend_intergenic: 62155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75859, rend_intergenic: 71193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78098, rend_intergenic: 76152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97077, rend_intergenic: 78786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108887, rend_intergenic: 99138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114394, rend_intergenic: 112254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126027, rend_intergenic: 121563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146713, rend_intergenic: 130562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151905, rend_intergenic: 147306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166649, rend_intergenic: 153069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171596, rend_intergenic: 166882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175514, rend_intergenic: 172502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205930, rend_intergenic: 183998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209079, rend_intergenic: 207906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216974, rend_intergenic: 214315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226059, rend_intergenic: 224828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229782, rend_intergenic: 227029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236811, rend_intergenic: 232490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 244953
-exon list size: 485


building trellis

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-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 35918, rend_intergenic: 32221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54358, rend_intergenic: 36120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58861, rend_intergenic: 54793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69676, rend_intergenic: 62155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75859, rend_intergenic: 71193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78098, rend_intergenic: 76152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97077, rend_intergenic: 78786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108887, rend_intergenic: 99138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114394, rend_intergenic: 112254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126027, rend_intergenic: 121563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146713, rend_intergenic: 130562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151905, rend_intergenic: 147306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166649, rend_intergenic: 153069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171596, rend_intergenic: 166882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175514, rend_intergenic: 172502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205930, rend_intergenic: 183998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209079, rend_intergenic: 207906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216974, rend_intergenic: 214315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226059, rend_intergenic: 224828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229782, rend_intergenic: 227029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236811, rend_intergenic: 232490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support