-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_1293862-1455663

-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_21856-T1
Valid prediction for snap_scaffold_17-snap.279-T1
Valid prediction for snap_scaffold_17-snap.275-T1
Valid prediction for snap_scaffold_17-snap.280-T1
Valid prediction for snap_scaffold_17-snap.289-T1
Valid prediction for GlimmerHMM_glimmerT_39735-T1
Valid prediction for HiQ_model.g26466.t1
Valid prediction for GlimmerHMM_glimmerT_39746-T1
Valid prediction for GlimmerHMM_glimmerT_39744-T1
Valid prediction for snap_scaffold_17-snap.282-T1
Valid prediction for snap_scaffold_17-snap.271-T1
Couldn't classify 58003, 58030
Sorry, prediction pasa_asmbl_18604.p1 fails validation.
(CCC)	 CC	58003-58030	GT	AGG
(CCA)	 AG	58126-58275	GT	CGG
(ATG)	 AG	58512-58649	GT	TGG
(TGG)	 AG	59500-59655	GT	TGG
(CAC)	 AG	59768-59937	AG	AGA
add_exon() Sorry, pasa_asmbl_18604.p1 58512-58649-initial-1 is invalid.
-recovered pasa_asmbl_18604.p1, initial, 58512, 58649
-recovered pasa_asmbl_18604.p1, terminal, 59768, 59937
-recovered pasa_asmbl_18604.p1, internal, 58126, 58275
-recovered pasa_asmbl_18604.p1, internal, 58512, 58649
-recovered pasa_asmbl_18604.p1, internal, 59500, 59655
Valid prediction for GlimmerHMM_glimmerT_39749-T1
Valid prediction for snap_scaffold_17-snap.290-T1
Valid prediction for snap_scaffold_17-snap.283-T1
Valid prediction for CodingQuarry_transcript_21853-T1
Valid prediction for GlimmerHMM_glimmerT_39729-T1
Valid prediction for Augustus_model.g26464.t1
Valid prediction for snap_scaffold_17-snap.274-T1
Valid prediction for pasa_asmbl_18608.p1
Valid prediction for CodingQuarry_transcript_21854-T1
Valid prediction for snap_scaffold_17-snap.267-T1
Valid prediction for HiQ_model.g26461.t1
Valid prediction for snap_scaffold_17-snap.285-T1
Valid prediction for HiQ_model.g26470.t1
Valid prediction for snap_scaffold_17-snap.269-T1
Valid prediction for GlimmerHMM_glimmerT_39738-T1
Valid prediction for GlimmerHMM_glimmerT_39740-T1
Valid prediction for Augustus_model.g26472.t1
Valid prediction for GlimmerHMM_glimmerT_39736-T1
Valid prediction for CodingQuarry_transcript_21851-T1
Valid prediction for snap_scaffold_17-snap.293-T1
Valid prediction for Augustus_model.g26468.t1
Valid prediction for GlimmerHMM_glimmerT_39731-T1
Valid prediction for GlimmerHMM_glimmerT_39734-T1
Valid prediction for GlimmerHMM_glimmerT_39747-T1
Valid prediction for snap_scaffold_17-snap.268-T1
Valid prediction for pasa_asmbl_18600.p1
Valid prediction for pasa_asmbl_18605.p2
Valid prediction for Augustus_model.g26465.t1
Valid prediction for snap_scaffold_17-snap.277-T1
Valid prediction for snap_scaffold_17-snap.265-T1
Valid prediction for snap_scaffold_17-snap.263-T1
Valid prediction for snap_scaffold_17-snap.264-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: -)Couldn't classify 37973, 38089
Sorry, prediction pasa_asmbl_17711.p1 fails validation.
(GAG)	 CA	37973-38089	GT	AAG
(CTC)	 AG	38280-38359	GT	GGG
(TTT)	 AG	38471-38528	GT	AGG
(GGA)	 AG	38612-38701	AC	AAA
-recovered pasa_asmbl_17711.p1, terminal, 38612, 38701
-recovered pasa_asmbl_17711.p1, internal, 38280, 38359
-recovered pasa_asmbl_17711.p1, internal, 38471, 38528
Valid prediction for CodingQuarry_transcript_21849-T1
Valid prediction for GlimmerHMM_glimmerT_39733-T1
Valid prediction for Augustus_model.g26473.t1
Valid prediction for Augustus_model.g26474.t1
Couldn't classify 30917, 31309
Sorry, prediction pasa_asmbl_17713.p1 fails validation.
(ACT)	 CG	30917-31309	CC	AGC
Valid prediction for GlimmerHMM_glimmerT_39743-T1
Valid prediction for GlimmerHMM_glimmerT_39745-T1
Valid prediction for CodingQuarry_transcript_21857-T1
Valid prediction for Augustus_model.g26469.t1
Valid prediction for GlimmerHMM_glimmerT_39742-T1
Valid prediction for GlimmerHMM_glimmerT_39727-T1
Couldn't classify 157680, 159002
Sorry, prediction pasa_asmbl_17691.p1 fails validation.
(ATC)	 CC	157680-159002	GC	AGG
Valid prediction for Augustus_model.g26463.t1
Valid prediction for HiQ_model.g26477.t1
Valid prediction for HiQ_model.g26459.t1
Valid prediction for GlimmerHMM_glimmerT_39755-T1
Valid prediction for snap_scaffold_17-snap.291-T1
Valid prediction for GlimmerHMM_glimmerT_39737-T1
Valid prediction for HiQ_model.g26460.t1
Valid prediction for CodingQuarry_transcript_21850-T1
Valid prediction for snap_scaffold_17-snap.287-T1
Valid prediction for snap_scaffold_17-snap.292-T1
Valid prediction for snap_scaffold_17-snap.273-T1
Couldn't classify 10262, 10427
Sorry, prediction pasa_asmbl_17715.p1 fails validation.
(ATG)	 AA	6810-6924	GT	AGG
(GTA)	 AG	7282-7411	GT	AGG
(TGA)	 AG	7509-7563	GT	AGG
(GAG)	 AG	7940-8043	GT	GAG
(GTC)	 AG	8160-8324	GT	AGG
(TAA)	 AG	8451-8604	GT	AGG
(TTC)	 AG	9230-9298	GT	AGG
(CTG)	 AG	9378-9453	GT	GAG
(TTC)	 AG	9681-9794	GT	AGG
(AGC)	 AG	10050-10098	GT	AGG
(ACC)	 AG	10262-10427	AG	AGA
-recovered pasa_asmbl_17715.p1, initial, 6810, 6924
add_exon() Sorry, pasa_asmbl_17715.p1 9378-9453-terminal-3 is invalid.
-recovered pasa_asmbl_17715.p1, terminal, 9378, 9453
-recovered pasa_asmbl_17715.p1, internal, 7282, 7411
-recovered pasa_asmbl_17715.p1, internal, 7509, 7563
-recovered pasa_asmbl_17715.p1, internal, 7940, 8043
-recovered pasa_asmbl_17715.p1, internal, 8160, 8324
-recovered pasa_asmbl_17715.p1, internal, 8451, 8604
-recovered pasa_asmbl_17715.p1, internal, 9230, 9298
-recovered pasa_asmbl_17715.p1, internal, 9378, 9453
-recovered pasa_asmbl_17715.p1, internal, 9681, 9794
-recovered pasa_asmbl_17715.p1, internal, 10050, 10098
Couldn't classify 33130, 33308
Sorry, prediction pasa_asmbl_17712.p1 fails validation.
(TCC)	 CT	33130-33308	GT	AGG
(AGA)	 AG	33628-33730	GT	AGG
(GTG)	 AG	33828-33956	AC	GAA
-recovered pasa_asmbl_17712.p1, terminal, 33828, 33956
-recovered pasa_asmbl_17712.p1, internal, 33628, 33730
Valid prediction for GlimmerHMM_glimmerT_39732-T1
Valid prediction for snap_scaffold_17-snap.270-T1
Valid prediction for snap_scaffold_17-snap.278-T1
Valid prediction for GlimmerHMM_glimmerT_39739-T1
Valid prediction for GlimmerHMM_glimmerT_39730-T1
Valid prediction for GlimmerHMM_glimmerT_39756-T1
Valid prediction for CodingQuarry_transcript_21855-T1
Valid prediction for GlimmerHMM_glimmerT_39728-T1
Valid prediction for snap_scaffold_17-snap.262-T1
Couldn't classify 157111, 157454
Sorry, prediction pasa_asmbl_17692.p1 fails validation.
(ATG)	 CC	156178-156340	GT	GGG
(GTA)	 AG	157111-157454	CA	GGC
-recovered pasa_asmbl_17692.p1, initial, 156178, 156340
Valid prediction for GlimmerHMM_glimmerT_39748-T1
Couldn't classify 28990, 29039
Couldn't classify 29998, 30093
Sorry, prediction pasa_asmbl_18481.p1 fails validation.
(GCC)	 CC	28990-29039	GT	TGG
(CCT)	 AG	29322-29472	GT	AGG
(GTG)	 AG	29998-30093	AT	ACA
-recovered pasa_asmbl_18481.p1, internal, 29322, 29472
Valid prediction for GlimmerHMM_glimmerT_39752-T1
Valid prediction for Augustus_model.g26478.t1
Valid prediction for snap_scaffold_17-snap.272-T1
Valid prediction for GlimmerHMM_glimmerT_39753-T1
Valid prediction for GlimmerHMM_glimmerT_39741-T1
Valid prediction for snap_scaffold_17-snap.284-T1
Valid prediction for Augustus_model.g26475.t1
Valid prediction for Augustus_model.g26476.t1
Valid prediction for GlimmerHMM_glimmerT_39726-T1
Valid prediction for snap_scaffold_17-snap.266-T1
Valid prediction for Augustus_model.g26467.t1
Valid prediction for snap_scaffold_17-snap.286-T1
Valid prediction for GlimmerHMM_glimmerT_39751-T1
Valid prediction for snap_scaffold_17-snap.261-T1
Valid prediction for HiQ_model.g26471.t1
Valid prediction for GlimmerHMM_glimmerT_39750-T1
Valid prediction for snap_scaffold_17-snap.260-T1
Couldn't classify 3743, 3762
Sorry, prediction pasa_asmbl_17717.p1 fails validation.
(ATG)	 GT	1014-1202	GT	AGG
(CGA)	 AG	1869-1952	GT	ATG
(GTG)	 AG	2371-2454	GT	GGG
(TGT)	 AG	2742-2855	GT	AGG
(TTG)	 AG	3304-3388	GT	AGG
(GTG)	 AG	3743-3762	AA	AGA
-recovered pasa_asmbl_17717.p1, initial, 1014, 1202
-recovered pasa_asmbl_17717.p1, internal, 1869, 1952
-recovered pasa_asmbl_17717.p1, internal, 2371, 2454
-recovered pasa_asmbl_17717.p1, internal, 2742, 2855
-recovered pasa_asmbl_17717.p1, internal, 3304, 3388
Valid prediction for Augustus_model.g26462.t1
Valid prediction for snap_scaffold_17-snap.288-T1
Valid prediction for snap_scaffold_17-snap.281-T1
Valid prediction for snap_scaffold_17-snap.276-T1
Valid prediction for GlimmerHMM_glimmerT_39754-T1
Couldn't classify 146217, 146404
Sorry, prediction pasa_asmbl_17702.p1 fails validation.
(ATG)	 GC	145548-145628	GT	AGG
(GAG)	 AG	145857-146013	GT	GGG
(ACT)	 AG	146217-146404	CC	CCC
-recovered pasa_asmbl_17702.p1, initial, 145548, 145628
-recovered pasa_asmbl_17702.p1, internal, 145857, 146013
Valid prediction for pasa_asmbl_17710.p1
Valid prediction for CodingQuarry_transcript_21859-T1
Couldn't classify 151100, 151157
Sorry, prediction pasa_asmbl_17694.p1 fails validation.
(GGA)	 GT	151100-151157	GT	AGG
(ACA)	 AG	151463-151528	GT	CGG
(ACG)	 AG	151664-151713	GT	AGG
(TTC)	 AG	151943-152006	GT	AGG
(AGG)	 AG	152167-152310	GT	GGG
(ATT)	 AG	152748-152790	GT	AAG
(GTA)	 AG	152907-152992	GT	AGG
(AGA)	 AG	153207-153247	GT	TGG
(GTC)	 AG	153669-153745	GT	TGG
(TTC)	 AG	153858-153928	GT	TGG
(ATG)	 AG	154189-154315	GT	GTG
(ACA)	 AG	155300-155402	CG	GAC
add_exon() Sorry, pasa_asmbl_17694.p1 154189-154315-initial-1 is invalid.
-recovered pasa_asmbl_17694.p1, initial, 154189, 154315
-recovered pasa_asmbl_17694.p1, terminal, 152907, 152992
-recovered pasa_asmbl_17694.p1, terminal, 155300, 155402
-recovered pasa_asmbl_17694.p1, internal, 151463, 151528
-recovered pasa_asmbl_17694.p1, internal, 151664, 151713
-recovered pasa_asmbl_17694.p1, internal, 151943, 152006
-recovered pasa_asmbl_17694.p1, internal, 152167, 152310
-recovered pasa_asmbl_17694.p1, internal, 152748, 152790
-recovered pasa_asmbl_17694.p1, internal, 152907, 152992
-recovered pasa_asmbl_17694.p1, internal, 153207, 153247
-recovered pasa_asmbl_17694.p1, internal, 153669, 153745
-recovered pasa_asmbl_17694.p1, internal, 153858, 153928
-recovered pasa_asmbl_17694.p1, internal, 154189, 154315

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10667, rend_intergenic: 6441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16852, rend_intergenic: 14943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28410, rend_intergenic: 21952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34987, rend_intergenic: 30427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59937, rend_intergenic: 45006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87672, rend_intergenic: 84750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116593, rend_intergenic: 115253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120338, rend_intergenic: 116933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137371, rend_intergenic: 132071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160684, rend_intergenic: 150279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 117266, rend_intergenic: 117263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 161802
-exon list size: 416


building trellis

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-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 10667, rend_intergenic: 6441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16852, rend_intergenic: 14943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28410, rend_intergenic: 21952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34987, rend_intergenic: 30427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59937, rend_intergenic: 45006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87672, rend_intergenic: 84750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116593, rend_intergenic: 115253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120338, rend_intergenic: 116933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137371, rend_intergenic: 132071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160684, rend_intergenic: 150279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 117266, rend_intergenic: 117263  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