-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_5646958-5852727

-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 Augustus_model.g32998.t1
Valid prediction for GlimmerHMM_glimmerT_49492-T1
Valid prediction for snap_scaffold_22-snap.1062-T1
Valid prediction for snap_scaffold_22-snap.1071-T1
Valid prediction for GlimmerHMM_glimmerT_49495-T1
Valid prediction for Augustus_model.g32997.t1
Valid prediction for snap_scaffold_22-snap.1060-T1
Couldn't classify 108213, 108271
Couldn't classify 109024, 109291
Sorry, prediction pasa_asmbl_30058.p1 fails validation.
(AAG)	 AC	108213-108271	GT	AGG
(GGC)	 AG	108458-108564	GT	GAG
(TCC)	 AG	108673-108826	GT	ACG
(GAG)	 AG	109024-109291	GT	CCG
-recovered pasa_asmbl_30058.p1, internal, 108458, 108564
-recovered pasa_asmbl_30058.p1, internal, 108673, 108826
-recovered pasa_asmbl_30058.p1, internal, 109024, 109291
Valid prediction for snap_scaffold_22-snap.1067-T1
Valid prediction for snap_scaffold_22-snap.1065-T1
Valid prediction for Augustus_model.g33001.t1
Valid prediction for GlimmerHMM_glimmerT_49476-T1
Valid prediction for GlimmerHMM_glimmerT_49478-T1
Valid prediction for Augustus_model.g33002.t1
Valid prediction for Augustus_model.g32992.t1
Valid prediction for GlimmerHMM_glimmerT_49474-T1
Valid prediction for Augustus_model.g32990.t1
Couldn't classify 112760, 112981
Sorry, prediction pasa_asmbl_30060.p1 fails validation.
(CCG)	 CC	112760-112981	GT	CCG
(GGG)	 AG	113120-113297	GT	CAG
(GGA)	 AG	113564-113910	GT	CGG
(GCC)	 AG	114047-114298	GG	GAG
-recovered pasa_asmbl_30060.p1, terminal, 114047, 114298
-recovered pasa_asmbl_30060.p1, internal, 113120, 113297
-recovered pasa_asmbl_30060.p1, internal, 113564, 113910
Valid prediction for GlimmerHMM_glimmerT_49494-T1
Valid prediction for GlimmerHMM_glimmerT_49497-T1
Valid prediction for snap_scaffold_22-snap.1049-T1
Valid prediction for Augustus_model.g32993.t1
Valid prediction for snap_scaffold_22-snap.1092-T1
Valid prediction for snap_scaffold_22-snap.1055-T1
Valid prediction for GlimmerHMM_glimmerT_49493-T1
Valid prediction for snap_scaffold_22-snap.1077-T1
Valid prediction for GlimmerHMM_glimmerT_49480-T1
Valid prediction for Augustus_model.g32996.t1
Valid prediction for Augustus_model.g32994.t1
Couldn't classify 120674, 120725
Sorry, prediction pasa_asmbl_30061.p1 fails validation.
(GGG)	 CC	120674-120725	GT	AGG
(AGG)	 AG	120829-120953	GT	ACG
(GTG)	 AG	121651-121787	GT	GGG
(ATC)	 AG	122044-122519	GT	ATG
(TAA)	 AG	122666-122737	GT	TGG
(TCA)	 AG	123123-123293	GC	AGG
(GAG)	 AG	123404-123534	CC	GAC
-recovered pasa_asmbl_30061.p1, terminal, 123404, 123534
-recovered pasa_asmbl_30061.p1, internal, 120829, 120953
-recovered pasa_asmbl_30061.p1, internal, 121651, 121787
-recovered pasa_asmbl_30061.p1, internal, 122044, 122519
-recovered pasa_asmbl_30061.p1, internal, 122666, 122737
-recovered pasa_asmbl_30061.p1, internal, 123123, 123293
Couldn't classify 159045, 159190
Couldn't classify 167671, 167814
Sorry, prediction pasa_asmbl_30062.p1 fails validation.
(GAC)	 CA	159045-159190	GT	AGG
(TCG)	 AG	159480-159609	GT	TGG
(GAT)	 AG	160009-160114	GT	AGG
(AGC)	 AG	160589-160835	GT	TGG
(TCT)	 AG	161845-161941	GT	AGG
(TCT)	 AG	162122-162230	GT	AGG
(TGA)	 AG	162661-162767	GT	AGG
(GAA)	 AG	162881-162930	GT	AGG
(GAG)	 AG	164063-164227	GT	AGG
(TCT)	 AG	164517-164582	GT	GGG
(TGG)	 AG	164771-164825	GT	CGG
(AGT)	 AG	164924-164987	GT	AGG
(ACA)	 AG	165065-165166	GT	TGG
(GGT)	 AG	165264-165361	GT	AGG
(ACT)	 AG	165778-165915	GT	TGG
(CCC)	 AG	166051-166128	GT	AGG
(ATG)	 AG	167671-167814	TC	CCT
-recovered pasa_asmbl_30062.p1, internal, 159480, 159609
-recovered pasa_asmbl_30062.p1, internal, 160009, 160114
-recovered pasa_asmbl_30062.p1, internal, 160589, 160835
-recovered pasa_asmbl_30062.p1, internal, 161845, 161941
-recovered pasa_asmbl_30062.p1, internal, 162122, 162230
-recovered pasa_asmbl_30062.p1, internal, 162661, 162767
-recovered pasa_asmbl_30062.p1, internal, 162881, 162930
-recovered pasa_asmbl_30062.p1, internal, 164063, 164227
-recovered pasa_asmbl_30062.p1, internal, 164517, 164582
-recovered pasa_asmbl_30062.p1, internal, 164771, 164825
-recovered pasa_asmbl_30062.p1, internal, 164924, 164987
-recovered pasa_asmbl_30062.p1, internal, 165065, 165166
-recovered pasa_asmbl_30062.p1, internal, 165264, 165361
-recovered pasa_asmbl_30062.p1, internal, 165778, 165915
-recovered pasa_asmbl_30062.p1, internal, 166051, 166128
Valid prediction for snap_scaffold_22-snap.1090-T1
Valid prediction for snap_scaffold_22-snap.1086-T1
Valid prediction for GlimmerHMM_glimmerT_49481-T1
Valid prediction for GlimmerHMM_glimmerT_49488-T1
Valid prediction for snap_scaffold_22-snap.1089-T1
Valid prediction for GlimmerHMM_glimmerT_49479-T1
Valid prediction for snap_scaffold_22-snap.1081-T1
Valid prediction for snap_scaffold_22-snap.1064-T1
Valid prediction for HiQ_model.g33005.t1
Valid prediction for snap_scaffold_22-snap.1075-T1
Valid prediction for snap_scaffold_22-snap.1057-T1
Valid prediction for snap_scaffold_22-snap.1053-T1
Valid prediction for CodingQuarry_transcript_34159-T1
Valid prediction for snap_scaffold_22-snap.1069-T1
Valid prediction for snap_scaffold_22-snap.1094-T1
Valid prediction for GlimmerHMM_glimmerT_49475-T1
Valid prediction for snap_scaffold_22-snap.1058-T1
Valid prediction for snap_scaffold_22-snap.1083-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.g33006.t1
Valid prediction for snap_scaffold_22-snap.1050-T1
Valid prediction for Augustus_model.g32995.t1
Valid prediction for snap_scaffold_22-snap.1087-T1
Valid prediction for GlimmerHMM_glimmerT_49498-T1
Valid prediction for Augustus_model.g32991.t1
Valid prediction for snap_scaffold_22-snap.1056-T1
Valid prediction for GlimmerHMM_glimmerT_49499-T1
Valid prediction for snap_scaffold_22-snap.1085-T1
Valid prediction for snap_scaffold_22-snap.1080-T1
Valid prediction for snap_scaffold_22-snap.1088-T1
Valid prediction for GlimmerHMM_glimmerT_49482-T1
Valid prediction for GlimmerHMM_glimmerT_49484-T1
Valid prediction for GlimmerHMM_glimmerT_49489-T1
Valid prediction for snap_scaffold_22-snap.1063-T1
Valid prediction for GlimmerHMM_glimmerT_49477-T1
Couldn't classify 22652, 22891
Sorry, prediction pasa_asmbl_29288.p1 fails validation.
(AGT)	 CC	22652-22891	GT	TGG
(CTG)	 AG	23428-23636	GT	AGG
(ACC)	 AG	24796-24847	CC	GAC
-recovered pasa_asmbl_29288.p1, terminal, 24796, 24847
-recovered pasa_asmbl_29288.p1, internal, 23428, 23636
Valid prediction for snap_scaffold_22-snap.1095-T1
Valid prediction for snap_scaffold_22-snap.1096-T1
Valid prediction for snap_scaffold_22-snap.1079-T1
Valid prediction for Augustus_model.g33008.t1
Valid prediction for GlimmerHMM_glimmerT_49496-T1
Valid prediction for Augustus_model.g33003.t1
Valid prediction for Augustus_model.g33000.t1
Valid prediction for GlimmerHMM_glimmerT_49473-T1
Valid prediction for GlimmerHMM_glimmerT_49490-T1
Valid prediction for GlimmerHMM_glimmerT_49487-T1
Valid prediction for snap_scaffold_22-snap.1084-T1
Valid prediction for snap_scaffold_22-snap.1078-T1
Valid prediction for snap_scaffold_22-snap.1054-T1
Valid prediction for snap_scaffold_22-snap.1070-T1
Valid prediction for Augustus_model.g33007.t1
Valid prediction for GlimmerHMM_glimmerT_49483-T1
Valid prediction for GlimmerHMM_glimmerT_49485-T1
Valid prediction for snap_scaffold_22-snap.1074-T1
Valid prediction for snap_scaffold_22-snap.1059-T1
Valid prediction for snap_scaffold_22-snap.1091-T1
Valid prediction for snap_scaffold_22-snap.1051-T1
Valid prediction for Augustus_model.g33004.t1
Valid prediction for snap_scaffold_22-snap.1076-T1
Valid prediction for snap_scaffold_22-snap.1066-T1
Valid prediction for GlimmerHMM_glimmerT_49491-T1
Valid prediction for snap_scaffold_22-snap.1073-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_49486-T1
Valid prediction for snap_scaffold_22-snap.1082-T1
Valid prediction for snap_scaffold_22-snap.1052-T1
Valid prediction for Augustus_model.g32999.t1
Valid prediction for snap_scaffold_22-snap.1072-T1
Valid prediction for snap_scaffold_22-snap.1093-T1
Valid prediction for snap_scaffold_22-snap.1061-T1
Couldn't classify 6255, 6331
Couldn't classify 20452, 20589
Sorry, prediction pasa_asmbl_29290.p1 fails validation.
(GAT)	 AG	6255-6331	GT	AGG
(GGG)	 AG	8834-9020	GT	GGG
(GTT)	 AG	11091-11156	GT	TGG
(TAT)	 AG	11852-11923	GT	AGG
(TTC)	 AG	12574-12740	GT	ACG
(GGG)	 AG	13458-13542	GT	TGG
(GAC)	 AG	14283-14425	GT	GGG
(GCA)	 AG	14519-14696	GT	AGG
(GAG)	 AG	15865-15954	GT	AAG
(TTG)	 AG	16241-16436	GT	TGG
(GTG)	 AG	17239-17347	GT	AGG
(CGA)	 AG	18027-18231	GC	AGG
(GTG)	 AG	18433-18510	GT	GGG
(GTA)	 AG	20452-20589	CG	CGC
-recovered pasa_asmbl_29290.p1, internal, 6255, 6331
-recovered pasa_asmbl_29290.p1, internal, 8834, 9020
-recovered pasa_asmbl_29290.p1, internal, 11091, 11156
-recovered pasa_asmbl_29290.p1, internal, 11852, 11923
-recovered pasa_asmbl_29290.p1, internal, 12574, 12740
-recovered pasa_asmbl_29290.p1, internal, 13458, 13542
-recovered pasa_asmbl_29290.p1, internal, 14283, 14425
-recovered pasa_asmbl_29290.p1, internal, 14519, 14696
-recovered pasa_asmbl_29290.p1, internal, 15865, 15954
-recovered pasa_asmbl_29290.p1, internal, 16241, 16436
-recovered pasa_asmbl_29290.p1, internal, 17239, 17347
-recovered pasa_asmbl_29290.p1, internal, 18027, 18231
-recovered pasa_asmbl_29290.p1, internal, 18433, 18510
Valid prediction for snap_scaffold_22-snap.1068-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12909, rend_intergenic: 3737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21752, rend_intergenic: 18803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22978, rend_intergenic: 22338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31906, rend_intergenic: 30620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48933, rend_intergenic: 45672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50245, rend_intergenic: 49250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53181, rend_intergenic: 50263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74339, rend_intergenic: 72179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75803, rend_intergenic: 75255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87057, rend_intergenic: 83375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96024, rend_intergenic: 87178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114298, rend_intergenic: 105979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123534, rend_intergenic: 116990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136505, rend_intergenic: 130975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155064, rend_intergenic: 145791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162432, rend_intergenic: 155262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167901, rend_intergenic: 164039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191452, rend_intergenic: 190346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197014, rend_intergenic: 194840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205770
-exon list size: 449


building trellis

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30.4    
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31.9    
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32.8    
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33.9    
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34.4    
34.6    
34.8    
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-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 12909, rend_intergenic: 3737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21752, rend_intergenic: 18803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22978, rend_intergenic: 22338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31906, rend_intergenic: 30620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48933, rend_intergenic: 45672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50245, rend_intergenic: 49250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53181, rend_intergenic: 50263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74339, rend_intergenic: 72179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75803, rend_intergenic: 75255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87057, rend_intergenic: 83375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96024, rend_intergenic: 87178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114298, rend_intergenic: 105979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123534, rend_intergenic: 116990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136505, rend_intergenic: 130975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155064, rend_intergenic: 145791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162432, rend_intergenic: 155262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167901, rend_intergenic: 164039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191452, rend_intergenic: 190346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197014, rend_intergenic: 194840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support