-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_4965368-5119960

-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 GlimmerHMM_glimmerT_27068-T1
Valid prediction for CodingQuarry_transcript_8060-T1
Valid prediction for Augustus_model.g17900.t1
Valid prediction for HiQ_model.g17903.t1
Valid prediction for Augustus_model.g17913.t1
Valid prediction for GlimmerHMM_glimmerT_27076-T1
Valid prediction for snap_scaffold_11-snap.1213-T1
Valid prediction for Augustus_model.g17914.t1
Valid prediction for Augustus_model.g17912.t1
Valid prediction for GlimmerHMM_glimmerT_27063-T1
Couldn't classify 15704, 15791
Sorry, prediction pasa_asmbl_5535.p1 fails validation.
(AAG)	 GT	15704-15791	GT	AGG
(ACC)	 AG	17126-17338	GT	AGG
(ATG)	 AG	17504-17719	GT	AGG
(ACG)	 AG	18073-18294	GT	AGG
(ACG)	 AG	19703-19891	GT	TGG
(AGA)	 AG	20268-20381	GT	AGG
(GGG)	 AG	20518-20708	GT	AGG
(CCC)	 AG	20869-21051	CA	GAC
add_exon() Sorry, pasa_asmbl_5535.p1 17504-17719-initial-1 is invalid.
-recovered pasa_asmbl_5535.p1, initial, 17504, 17719
add_exon() Sorry, pasa_asmbl_5535.p1 18073-18294-terminal-1 is invalid.
-recovered pasa_asmbl_5535.p1, terminal, 18073, 18294
-recovered pasa_asmbl_5535.p1, terminal, 20869, 21051
-recovered pasa_asmbl_5535.p1, internal, 17126, 17338
-recovered pasa_asmbl_5535.p1, internal, 17504, 17719
-recovered pasa_asmbl_5535.p1, internal, 18073, 18294
-recovered pasa_asmbl_5535.p1, internal, 19703, 19891
-recovered pasa_asmbl_5535.p1, internal, 20268, 20381
-recovered pasa_asmbl_5535.p1, internal, 20518, 20708
Valid prediction for snap_scaffold_11-snap.1235-T1
Valid prediction for GlimmerHMM_glimmerT_27061-T1
Valid prediction for GlimmerHMM_glimmerT_27064-T1
Valid prediction for snap_scaffold_11-snap.1209-T1
Valid prediction for pasa_asmbl_5537.p1
Valid prediction for snap_scaffold_11-snap.1205-T1
Valid prediction for snap_scaffold_11-snap.1216-T1
Valid prediction for GlimmerHMM_glimmerT_27066-T1
Valid prediction for snap_scaffold_11-snap.1232-T1
Valid prediction for snap_scaffold_11-snap.1215-T1
Valid prediction for snap_scaffold_11-snap.1197-T1
Valid prediction for snap_scaffold_11-snap.1199-T1
Valid prediction for Augustus_model.g17915.t1
Valid prediction for snap_scaffold_11-snap.1198-T1
Valid prediction for CodingQuarry_transcript_8062-T1
Valid prediction for snap_scaffold_11-snap.1229-T1
Valid prediction for GlimmerHMM_glimmerT_27065-T1
Valid prediction for snap_scaffold_11-snap.1208-T1
Valid prediction for snap_scaffold_11-snap.1223-T1
Valid prediction for snap_scaffold_11-snap.1204-T1
Valid prediction for GlimmerHMM_glimmerT_27078-T1
Valid prediction for Augustus_model.g17902.t1
Valid prediction for snap_scaffold_11-snap.1221-T1
Valid prediction for GlimmerHMM_glimmerT_27077-T1
Valid prediction for snap_scaffold_11-snap.1234-T1
Valid prediction for snap_scaffold_11-snap.1228-T1
Couldn't classify 137718, 137729
Sorry, prediction pasa_asmbl_5541.p1 fails validation.
(GAA)	 AG	137718-137729	GT	TGG
(GCA)	 AG	138207-138245	GT	GGG
(GAG)	 AG	138371-138480	GT	GAG
(GAG)	 AG	138577-138632	GT	AAG
(AAA)	 AG	138738-138793	GT	TGG
(GAG)	 AG	139180-139306	GT	GGG
(CGG)	 AG	139452-139592	GT	CGG
(GCA)	 AG	139682-139728	CA	AAC
add_exon() Sorry, pasa_asmbl_5541.p1 138577-138632-terminal-2 is invalid.
-recovered pasa_asmbl_5541.p1, terminal, 138577, 138632
-recovered pasa_asmbl_5541.p1, terminal, 139682, 139728
-recovered pasa_asmbl_5541.p1, internal, 137718, 137729
-recovered pasa_asmbl_5541.p1, internal, 138207, 138245
-recovered pasa_asmbl_5541.p1, internal, 138371, 138480
-recovered pasa_asmbl_5541.p1, internal, 138577, 138632
-recovered pasa_asmbl_5541.p1, internal, 138738, 138793
-recovered pasa_asmbl_5541.p1, internal, 139180, 139306
-recovered pasa_asmbl_5541.p1, internal, 139452, 139592
Valid prediction for snap_scaffold_11-snap.1226-T1
Couldn't classify 146729, 146738
Sorry, prediction pasa_asmbl_5543.p1 fails validation.
(CTG)	 CT	146729-146738	GT	AGG
(ATT)	 AG	146844-148400	GT	GGG
(AAA)	 AG	148895-149203	GT	AGG
(GAA)	 AG	149339-149470	GT	GGG
(GCT)	 AG	150022-150185	GT	AGG
(GAC)	 AG	150743-151084	AA	GAA
-recovered pasa_asmbl_5543.p1, terminal, 150743, 151084
-recovered pasa_asmbl_5543.p1, internal, 146844, 148400
-recovered pasa_asmbl_5543.p1, internal, 148895, 149203
-recovered pasa_asmbl_5543.p1, internal, 149339, 149470
-recovered pasa_asmbl_5543.p1, internal, 150022, 150185
Valid prediction for snap_scaffold_11-snap.1224-T1
Valid prediction for snap_scaffold_11-snap.1230-T1
Valid prediction for snap_scaffold_11-snap.1219-T1
Valid prediction for snap_scaffold_11-snap.1214-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.g17906.t1
Valid prediction for snap_scaffold_11-snap.1218-T1
Valid prediction for pasa_asmbl_6649.p1
Valid prediction for GlimmerHMM_glimmerT_27070-T1
Valid prediction for Augustus_model.g17904.t1
Valid prediction for snap_scaffold_11-snap.1227-T1
Valid prediction for snap_scaffold_11-snap.1207-T1
Valid prediction for HiQ_model.g17909.t1
Couldn't classify 87953, 88080
Couldn't classify 88972, 89104
Sorry, prediction pasa_asmbl_7311.p1 fails validation.
(GGG)	 AG	87953-88080	GT	ATG
(AGA)	 AG	88479-88568	GT	AAG
(GAA)	 AG	88972-89104	GG	ACG
-recovered pasa_asmbl_7311.p1, internal, 87953, 88080
-recovered pasa_asmbl_7311.p1, internal, 88479, 88568
Valid prediction for snap_scaffold_11-snap.1231-T1
Valid prediction for snap_scaffold_11-snap.1206-T1
Valid prediction for snap_scaffold_11-snap.1212-T1
Couldn't classify 20762, 20952
Sorry, prediction pasa_asmbl_6651.p1 fails validation.
(GGG)	 GG	20762-20952	GT	AGG
(GCT)	 AG	21251-21369	GT	CGG
(GGC)	 AG	21555-21717	GT	AGG
(GTC)	 AG	21903-22017	GT	AGG
(AAC)	 AG	22229-22466	GT	CGG
(GGG)	 AG	22703-22949	GT	GGG
(GGT)	 AG	23136-23312	GT	AAG
(GTA)	 AG	23402-23552	GT	AGG
(GTG)	 AG	23759-24088	AC	AGA
-recovered pasa_asmbl_6651.p1, terminal, 23759, 24088
-recovered pasa_asmbl_6651.p1, internal, 21251, 21369
-recovered pasa_asmbl_6651.p1, internal, 21555, 21717
-recovered pasa_asmbl_6651.p1, internal, 21903, 22017
-recovered pasa_asmbl_6651.p1, internal, 22229, 22466
-recovered pasa_asmbl_6651.p1, internal, 22703, 22949
-recovered pasa_asmbl_6651.p1, internal, 23136, 23312
-recovered pasa_asmbl_6651.p1, internal, 23402, 23552
Valid prediction for snap_scaffold_11-snap.1203-T1
Valid prediction for snap_scaffold_11-snap.1202-T1
Valid prediction for snap_scaffold_11-snap.1210-T1
Valid prediction for snap_scaffold_11-snap.1220-T1
Valid prediction for Augustus_model.g17908.t1
Valid prediction for Augustus_model.g17910.t1
Valid prediction for GlimmerHMM_glimmerT_27069-T1
Valid prediction for GlimmerHMM_glimmerT_27073-T1
Valid prediction for GlimmerHMM_glimmerT_27071-T1
Valid prediction for Augustus_model.g17907.t1
Valid prediction for GlimmerHMM_glimmerT_27060-T1
Valid prediction for HiQ_model.g17911.t1
Valid prediction for snap_scaffold_11-snap.1201-T1
Valid prediction for GlimmerHMM_glimmerT_27067-T1
Valid prediction for GlimmerHMM_glimmerT_27074-T1
Valid prediction for CodingQuarry_transcript_8061-T1
Valid prediction for snap_scaffold_11-snap.1233-T1
Valid prediction for snap_scaffold_11-snap.1196-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_11-snap.1200-T1
Valid prediction for snap_scaffold_11-snap.1217-T1
Valid prediction for GlimmerHMM_glimmerT_27075-T1
Couldn't classify 29339, 29458
Sorry, prediction pasa_asmbl_6650.p1 fails validation.
(ATG)	 TC	25606-25669	GT	TGG
(TGA)	 AG	26914-26992	GT	CTG
(GCT)	 AG	27374-27431	GT	AGG
(GAG)	 AG	27704-27796	GT	AGG
(GCC)	 AG	27913-28007	GT	AGG
(GCC)	 AG	28151-28217	GT	AGG
(GAG)	 AG	28339-28611	GT	AGG
(AGG)	 AG	28931-29041	GT	CGG
(ATA)	 AG	29339-29458	AC	CCA
-recovered pasa_asmbl_6650.p1, initial, 25606, 25669
-recovered pasa_asmbl_6650.p1, internal, 26914, 26992
-recovered pasa_asmbl_6650.p1, internal, 27374, 27431
-recovered pasa_asmbl_6650.p1, internal, 27704, 27796
-recovered pasa_asmbl_6650.p1, internal, 27913, 28007
-recovered pasa_asmbl_6650.p1, internal, 28151, 28217
-recovered pasa_asmbl_6650.p1, internal, 28339, 28611
-recovered pasa_asmbl_6650.p1, internal, 28931, 29041
Valid prediction for snap_scaffold_11-snap.1211-T1
Couldn't classify 46851, 47096
Sorry, prediction pasa_asmbl_6648.p1 fails validation.
(TAT)	 AT	46851-47096	GT	AGG
(GTC)	 AG	48018-48095	GT	AGG
(GCT)	 AG	48349-48495	GT	TGG
(GGT)	 AG	48618-48779	GT	TGG
(GCG)	 AG	48912-48989	GT	TGG
(GTC)	 AG	49192-49375	GT	CGG
(GGA)	 AG	49522-49593	GT	AGG
(GGA)	 AG	49718-49789	GT	TGG
(ATT)	 AG	49948-50115	GT	ACG
(ACA)	 AG	50330-50532	GT	AGG
(TCA)	 AG	50855-50965	GT	AGG
(CCA)	 AG	51098-51274	GG	GAG
-recovered pasa_asmbl_6648.p1, terminal, 51098, 51274
-recovered pasa_asmbl_6648.p1, internal, 48018, 48095
-recovered pasa_asmbl_6648.p1, internal, 48349, 48495
-recovered pasa_asmbl_6648.p1, internal, 48618, 48779
-recovered pasa_asmbl_6648.p1, internal, 48912, 48989
-recovered pasa_asmbl_6648.p1, internal, 49192, 49375
-recovered pasa_asmbl_6648.p1, internal, 49522, 49593
-recovered pasa_asmbl_6648.p1, internal, 49718, 49789
-recovered pasa_asmbl_6648.p1, internal, 49948, 50115
-recovered pasa_asmbl_6648.p1, internal, 50330, 50532
-recovered pasa_asmbl_6648.p1, internal, 50855, 50965
Valid prediction for Augustus_model.g17901.t1
Valid prediction for GlimmerHMM_glimmerT_27072-T1
Valid prediction for snap_scaffold_11-snap.1222-T1
Valid prediction for GlimmerHMM_glimmerT_27062-T1
Valid prediction for Augustus_model.g17905.t1
Valid prediction for snap_scaffold_11-snap.1225-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7212, rend_intergenic: 1960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21051, rend_intergenic: 7237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27143, rend_intergenic: 23816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40245, rend_intergenic: 28634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52548, rend_intergenic: 44496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83993, rend_intergenic: 59458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90173, rend_intergenic: 84282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95283, rend_intergenic: 92372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100813, rend_intergenic: 96360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109547, rend_intergenic: 105397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127836, rend_intergenic: 117719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134970, rend_intergenic: 132075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143439, rend_intergenic: 141553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146243, rend_intergenic: 144997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148408, rend_intergenic: 146826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150997, rend_intergenic: 148766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 154593
-exon list size: 482


building trellis

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99.8    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 7212, rend_intergenic: 1960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21051, rend_intergenic: 7237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27143, rend_intergenic: 23816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40245, rend_intergenic: 28634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52548, rend_intergenic: 44496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83993, rend_intergenic: 59458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90173, rend_intergenic: 84282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95283, rend_intergenic: 92372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100813, rend_intergenic: 96360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109547, rend_intergenic: 105397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127836, rend_intergenic: 117719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134970, rend_intergenic: 132075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143439, rend_intergenic: 141553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146243, rend_intergenic: 144997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148408, rend_intergenic: 146826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150997, rend_intergenic: 148766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support