-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_13428149-13727091

-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 CodingQuarry_transcript_18209-T1
Valid prediction for Augustus_model.g24806.t1
Valid prediction for Augustus_model.g24822.t1
Valid prediction for GlimmerHMM_glimmerT_37268-T1
Valid prediction for snap_scaffold_15-snap.2723-T1
Valid prediction for snap_scaffold_15-snap.2717-T1
Valid prediction for GlimmerHMM_glimmerT_37266-T1
Couldn't classify 220947, 221786
Sorry, prediction pasa_asmbl_15645.p1 fails validation.
(GAT)	 CA	220947-221786	AG	AGA
Valid prediction for pasa_asmbl_15652.p1
Valid prediction for Augustus_model.g24807.t1
Valid prediction for GlimmerHMM_glimmerT_37253-T1
Valid prediction for snap_scaffold_15-snap.2736-T1
Valid prediction for snap_scaffold_15-snap.2693-T1
Valid prediction for GlimmerHMM_glimmerT_37243-T1
Valid prediction for snap_scaffold_15-snap.2735-T1
Valid prediction for Augustus_model.g24833.t1
Valid prediction for snap_scaffold_15-snap.2718-T1
Valid prediction for GlimmerHMM_glimmerT_37264-T1
Valid prediction for GlimmerHMM_glimmerT_37245-T1
Valid prediction for GlimmerHMM_glimmerT_37249-T1
Valid prediction for Augustus_model.g24820.t1
Valid prediction for snap_scaffold_15-snap.2715-T1
Valid prediction for GlimmerHMM_glimmerT_37244-T1
Valid prediction for GlimmerHMM_glimmerT_37247-T1
Valid prediction for snap_scaffold_15-snap.2697-T1
Valid prediction for snap_scaffold_15-snap.2688-T1
Valid prediction for snap_scaffold_15-snap.2709-T1
Valid prediction for GlimmerHMM_glimmerT_37261-T1
Valid prediction for snap_scaffold_15-snap.2712-T1
Valid prediction for GlimmerHMM_glimmerT_37274-T1
Valid prediction for GlimmerHMM_glimmerT_37257-T1
Valid prediction for snap_scaffold_15-snap.2720-T1
Valid prediction for snap_scaffold_15-snap.2716-T1
Valid prediction for Augustus_model.g24805.t1
Couldn't classify 229309, 229397
Couldn't classify 233281, 233385
Sorry, prediction pasa_asmbl_15647.p1 fails validation.
(CAG)	 TC	229309-229397	GT	AGG
(GCA)	 AG	230811-230931	GT	AGG
(CAG)	 AG	231281-231466	GT	AGG
(ATG)	 AG	231701-231853	GT	AGG
(CTG)	 AG	232422-232576	GT	AGG
(CTT)	 AG	232898-233015	GT	AGG
(CTG)	 AG	233114-233164	GT	TGG
(GCA)	 AG	233281-233385	GA	AGG
-recovered pasa_asmbl_15647.p1, initial, 231701, 231853
-recovered pasa_asmbl_15647.p1, internal, 230811, 230931
-recovered pasa_asmbl_15647.p1, internal, 231281, 231466
-recovered pasa_asmbl_15647.p1, internal, 231701, 231853
-recovered pasa_asmbl_15647.p1, internal, 232422, 232576
-recovered pasa_asmbl_15647.p1, internal, 232898, 233015
-recovered pasa_asmbl_15647.p1, internal, 233114, 233164
Valid prediction for snap_scaffold_15-snap.2719-T1
Valid prediction for GlimmerHMM_glimmerT_37259-T1
Valid prediction for snap_scaffold_15-snap.2725-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_18208-T1
Valid prediction for snap_scaffold_15-snap.2692-T1
Valid prediction for GlimmerHMM_glimmerT_37260-T1
Valid prediction for pasa_asmbl_15650.p2
Valid prediction for GlimmerHMM_glimmerT_37262-T1
Valid prediction for snap_scaffold_15-snap.2727-T1
Valid prediction for Augustus_model.g24808.t1
Valid prediction for Augustus_model.g24824.t1
Valid prediction for Augustus_model.g24809.t1
Valid prediction for GlimmerHMM_glimmerT_37246-T1
Valid prediction for snap_scaffold_15-snap.2733-T1
Valid prediction for snap_scaffold_15-snap.2691-T1
Valid prediction for Augustus_model.g24811.t1
Valid prediction for GlimmerHMM_glimmerT_37258-T1
Valid prediction for Augustus_model.g24818.t1
Valid prediction for snap_scaffold_15-snap.2694-T1
Valid prediction for snap_scaffold_15-snap.2732-T1
Valid prediction for GlimmerHMM_glimmerT_37271-T1
Valid prediction for Augustus_model.g24823.t1
Valid prediction for snap_scaffold_15-snap.2721-T1
Valid prediction for snap_scaffold_15-snap.2708-T1
Valid prediction for Augustus_model.g24821.t1
Valid prediction for snap_scaffold_15-snap.2690-T1
Valid prediction for snap_scaffold_15-snap.2689-T1
Valid prediction for GlimmerHMM_glimmerT_37256-T1
Valid prediction for Augustus_model.g24827.t1
Valid prediction for snap_scaffold_15-snap.2714-T1
Valid prediction for snap_scaffold_15-snap.2722-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 snap_scaffold_15-snap.2724-T1
Valid prediction for GlimmerHMM_glimmerT_37255-T1
Valid prediction for CodingQuarry_transcript_18202-T1
Couldn't classify 19054, 19145
Sorry, prediction pasa_asmbl_14658.p1 fails validation.
(ATG)	 AG	15966-16158	GT	AGG
(GTG)	 AG	17437-17568	GT	AGG
(TGC)	 AG	18545-18697	GT	AGG
(AGT)	 AG	19054-19145	GA	CTG
-recovered pasa_asmbl_14658.p1, initial, 15966, 16158
-recovered pasa_asmbl_14658.p1, internal, 15966, 16158
-recovered pasa_asmbl_14658.p1, internal, 17437, 17568
-recovered pasa_asmbl_14658.p1, internal, 18545, 18697
Valid prediction for snap_scaffold_15-snap.2703-T1
Couldn't classify 19927, 20328
Sorry, prediction pasa_asmbl_14656.p2 fails validation.
(CCT)	 CT	19927-20328	CT	AAC
Valid prediction for snap_scaffold_15-snap.2711-T1
Valid prediction for snap_scaffold_15-snap.2705-T1
Valid prediction for Augustus_model.g24831.t1
Valid prediction for snap_scaffold_15-snap.2740-T1
Valid prediction for snap_scaffold_15-snap.2738-T1
Valid prediction for Augustus_model.g24826.t1
Valid prediction for snap_scaffold_15-snap.2698-T1
Valid prediction for snap_scaffold_15-snap.2713-T1
Valid prediction for snap_scaffold_15-snap.2702-T1
Valid prediction for snap_scaffold_15-snap.2730-T1
Valid prediction for snap_scaffold_15-snap.2731-T1
Valid prediction for GlimmerHMM_glimmerT_37242-T1
Valid prediction for GlimmerHMM_glimmerT_37248-T1
Valid prediction for Augustus_model.g24804.t1
Couldn't classify 208660, 208701
Sorry, prediction pasa_asmbl_14636.p1 fails validation.
(GCA)	 CA	208660-208701	GT	AGG
(GTT)	 AG	209471-209578	GT	AAG
(GGC)	 AG	209820-209972	GT	CAG
(TCA)	 AG	211420-211485	AC	AGA
-recovered pasa_asmbl_14636.p1, terminal, 211420, 211485
-recovered pasa_asmbl_14636.p1, internal, 209471, 209578
-recovered pasa_asmbl_14636.p1, internal, 209820, 209972
Valid prediction for GlimmerHMM_glimmerT_37267-T1
Valid prediction for snap_scaffold_15-snap.2699-T1
Valid prediction for snap_scaffold_15-snap.2701-T1
Valid prediction for GlimmerHMM_glimmerT_37250-T1
Couldn't classify 161392, 161493
Couldn't classify 168637, 168687
Sorry, prediction pasa_asmbl_14641.p1 fails validation.
(GTG)	 AG	161392-161493	GT	AGG
(GAG)	 AG	161969-162143	GT	GTG
(CTG)	 AG	164059-164258	GT	AGG
(ATA)	 AG	165184-165348	GT	CTG
(CTC)	 AG	165647-165839	GT	AGG
(CTA)	 AG	168219-168349	GT	AGG
(GTG)	 AG	168637-168687	CA	CCC
-recovered pasa_asmbl_14641.p1, internal, 161392, 161493
-recovered pasa_asmbl_14641.p1, internal, 161969, 162143
-recovered pasa_asmbl_14641.p1, internal, 164059, 164258
-recovered pasa_asmbl_14641.p1, internal, 165184, 165348
-recovered pasa_asmbl_14641.p1, internal, 165647, 165839
-recovered pasa_asmbl_14641.p1, internal, 168219, 168349
Valid prediction for Augustus_model.g24828.t1
Valid prediction for snap_scaffold_15-snap.2687-T1
Valid prediction for GlimmerHMM_glimmerT_37269-T1
Valid prediction for GlimmerHMM_glimmerT_37251-T1
Valid prediction for Augustus_model.g24825.t1
Couldn't classify 228635, 230605
Sorry, prediction pasa_asmbl_14635.p1 fails validation.
(CAC)	 CC	228635-230605	GA	GAG
Valid prediction for Augustus_model.g24832.t1
Valid prediction for snap_scaffold_15-snap.2729-T1
Valid prediction for Augustus_model.g24810.t1
Valid prediction for GlimmerHMM_glimmerT_37265-T1
Couldn't classify 40378, 40446
Couldn't classify 46780, 46934
Sorry, prediction pasa_asmbl_14653.p1 fails validation.
(CTG)	 GA	40378-40446	GT	AGG
(CTG)	 AG	42112-42271	GT	GGG
(GAG)	 AG	42723-42879	GT	CTG
(GGC)	 AG	44079-44131	GT	AGG
(GTC)	 AG	46780-46934	GT	AGG
add_exon() Sorry, pasa_asmbl_14653.p1 44079-44131-terminal-2 is invalid.
-recovered pasa_asmbl_14653.p1, terminal, 44079, 44131
-recovered pasa_asmbl_14653.p1, internal, 42112, 42271
-recovered pasa_asmbl_14653.p1, internal, 42723, 42879
-recovered pasa_asmbl_14653.p1, internal, 44079, 44131
-recovered pasa_asmbl_14653.p1, internal, 46780, 46934
Valid prediction for GlimmerHMM_glimmerT_37252-T1
Valid prediction for snap_scaffold_15-snap.2700-T1
Valid prediction for snap_scaffold_15-snap.2707-T1
Valid prediction for GlimmerHMM_glimmerT_37263-T1
Valid prediction for Augustus_model.g24829.t1
Valid prediction for HiQ_model.g24817.t1
Valid prediction for snap_scaffold_15-snap.2737-T1
Valid prediction for Augustus_model.g24815.t1
Valid prediction for snap_scaffold_15-snap.2739-T1
Valid prediction for snap_scaffold_15-snap.2734-T1
Valid prediction for Augustus_model.g24830.t1
Valid prediction for GlimmerHMM_glimmerT_37273-T1
Valid prediction for Augustus_model.g24814.t1
Valid prediction for Augustus_model.g24819.t1
Valid prediction for snap_scaffold_15-snap.2695-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_15-snap.2726-T1
Valid prediction for snap_scaffold_15-snap.2696-T1
Valid prediction for CodingQuarry_transcript_18203-T1
Valid prediction for snap_scaffold_15-snap.2704-T1
Valid prediction for snap_scaffold_15-snap.2710-T1
Valid prediction for GlimmerHMM_glimmerT_37272-T1
Valid prediction for GlimmerHMM_glimmerT_37270-T1
Valid prediction for Augustus_model.g24812.t1
Valid prediction for GlimmerHMM_glimmerT_37254-T1
Valid prediction for Augustus_model.g24816.t1
Valid prediction for snap_scaffold_15-snap.2728-T1
Couldn't classify 174644, 174826
Sorry, prediction pasa_asmbl_14637.p1 fails validation.
(ATT)	 GG	174644-174826	GT	AGG
(TAC)	 AG	176585-176674	GT	TGG
(GAG)	 AG	177970-178521	GA	GAG
-recovered pasa_asmbl_14637.p1, terminal, 177970, 178521
-recovered pasa_asmbl_14637.p1, internal, 176585, 176674
Valid prediction for CodingQuarry_transcript_18204-T1
Couldn't classify 168793, 169090
Sorry, prediction pasa_asmbl_14639.p1 fails validation.
(CCC)	 CC	168793-169090	GT	AGG
(TGT)	 AG	169186-169940	GT	TGG
(GAG)	 AG	170383-170520	GT	AGG
(GTG)	 AG	170735-170868	GT	TGG
(GAC)	 AG	171026-171192	GT	TGG
(GTG)	 AG	171489-171688	GT	GGG
(CTA)	 AG	172183-172224	TT	GAT
-recovered pasa_asmbl_14639.p1, terminal, 172183, 172224
-recovered pasa_asmbl_14639.p1, internal, 169186, 169940
-recovered pasa_asmbl_14639.p1, internal, 170383, 170520
-recovered pasa_asmbl_14639.p1, internal, 170735, 170868
-recovered pasa_asmbl_14639.p1, internal, 171026, 171192
-recovered pasa_asmbl_14639.p1, internal, 171489, 171688
Valid prediction for Augustus_model.g24813.t1
Valid prediction for snap_scaffold_15-snap.2706-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 49203, rend_intergenic: 43456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139997, rend_intergenic: 134312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166977, rend_intergenic: 163946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171301, rend_intergenic: 167160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221786, rend_intergenic: 210088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231018, rend_intergenic: 223990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235010, rend_intergenic: 232844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 265521, rend_intergenic: 249521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 298943
-exon list size: 494


building trellis

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-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 49203, rend_intergenic: 43456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139997, rend_intergenic: 134312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166977, rend_intergenic: 163946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171301, rend_intergenic: 167160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221786, rend_intergenic: 210088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231018, rend_intergenic: 223990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235010, rend_intergenic: 232844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 265521, rend_intergenic: 249521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 36 predictions persist after filtering for low support