-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_6692844-6880011

-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.g31993.t1
Valid prediction for GlimmerHMM_glimmerT_47924-T1
Valid prediction for snap_scaffold_21-snap.1380-T1
Valid prediction for Augustus_model.g31978.t1
Valid prediction for pasa_asmbl_28700.p1
Valid prediction for Augustus_model.g31988.t1
Couldn't classify 33080, 33388
Couldn't classify 35061, 35162
Sorry, prediction pasa_asmbl_28696.p1 fails validation.
(GAC)	 GT	33080-33388	GT	CAG
(TTG)	 AG	33810-33929	GT	AGG
(GTC)	 AG	34010-34168	GT	AGG
(GAT)	 AG	34334-34425	GT	AAG
(GAA)	 AG	34517-34637	GT	AGG
(GAG)	 AG	35061-35162	AA	ACA
-recovered pasa_asmbl_28696.p1, internal, 33810, 33929
-recovered pasa_asmbl_28696.p1, internal, 34010, 34168
-recovered pasa_asmbl_28696.p1, internal, 34334, 34425
-recovered pasa_asmbl_28696.p1, internal, 34517, 34637
Valid prediction for CodingQuarry_transcript_32592-T1
Valid prediction for snap_scaffold_21-snap.1385-T1
Valid prediction for snap_scaffold_21-snap.1375-T1
Valid prediction for GlimmerHMM_glimmerT_47927-T1
Valid prediction for GlimmerHMM_glimmerT_47934-T1
Valid prediction for Augustus_model.g31986.t1
Valid prediction for snap_scaffold_21-snap.1377-T1
Valid prediction for CodingQuarry_transcript_32596-T1
Valid prediction for Augustus_model.g31987.t1
Valid prediction for HiQ_model.g31991.t1
Valid prediction for HiQ_model.g31995.t1
Valid prediction for snap_scaffold_21-snap.1386-T1
Couldn't classify 31232, 31316
Sorry, prediction pasa_asmbl_28695.p1 fails validation.
(GGG)	 AG	31232-31316	GT	TGG
(GGT)	 AG	31511-31652	GT	AGG
(AAT)	 AG	31780-31885	TT	GAT
-recovered pasa_asmbl_28695.p1, terminal, 31780, 31885
-recovered pasa_asmbl_28695.p1, internal, 31232, 31316
-recovered pasa_asmbl_28695.p1, internal, 31511, 31652
Valid prediction for snap_scaffold_21-snap.1398-T1
Valid prediction for snap_scaffold_21-snap.1407-T1
Valid prediction for CodingQuarry_transcript_32597-T1
Valid prediction for GlimmerHMM_glimmerT_47935-T1
Valid prediction for snap_scaffold_21-snap.1381-T1
Valid prediction for snap_scaffold_21-snap.1378-T1
Valid prediction for GlimmerHMM_glimmerT_47932-T1
Valid prediction for GlimmerHMM_glimmerT_47943-T1
Valid prediction for snap_scaffold_21-snap.1389-T1
Valid prediction for GlimmerHMM_glimmerT_47929-T1
Valid prediction for GlimmerHMM_glimmerT_47941-T1
Valid prediction for CodingQuarry_transcript_32593-T1
Couldn't classify 30999, 31039
Sorry, prediction pasa_asmbl_28694.p1 fails validation.
(ATG)	 CA	29700-29754	GT	AGG
(GTG)	 AG	29863-30007	GT	AGG
(AGA)	 AG	30108-30222	GT	AGG
(TCT)	 AG	30341-30385	GT	AGG
(CCT)	 AG	30736-30886	GT	AGG
(GAC)	 AG	30999-31039	AC	GGA
-recovered pasa_asmbl_28694.p1, initial, 29700, 29754
-recovered pasa_asmbl_28694.p1, internal, 29863, 30007
-recovered pasa_asmbl_28694.p1, internal, 30108, 30222
-recovered pasa_asmbl_28694.p1, internal, 30341, 30385
-recovered pasa_asmbl_28694.p1, internal, 30736, 30886
Valid prediction for snap_scaffold_21-snap.1396-T1
Valid prediction for HiQ_model.g31979.t1
Valid prediction for Augustus_model.g31989.t1
Valid prediction for GlimmerHMM_glimmerT_47926-T1
Valid prediction for GlimmerHMM_glimmerT_47930-T1
Couldn't classify 19773, 19867
Sorry, prediction pasa_asmbl_28692.p1 fails validation.
(AAG)	 GA	19773-19867	GT	AGG
(GAC)	 AG	20696-20835	GT	ATG
(TTC)	 AG	21045-21090	GT	TGG
(TGA)	 AG	21208-21302	GT	TGG
(TTC)	 AG	21418-21488	GT	AGG
(GAG)	 AG	21767-21907	GT	GAG
(CCA)	 AG	22030-22061	GT	TGG
(GGC)	 AG	22220-22314	GT	GGG
(CTT)	 AG	22496-22579	GT	CGG
(TTC)	 AG	22702-22766	CA	AGC
-recovered pasa_asmbl_28692.p1, terminal, 22702, 22766
-recovered pasa_asmbl_28692.p1, internal, 20696, 20835
-recovered pasa_asmbl_28692.p1, internal, 21045, 21090
-recovered pasa_asmbl_28692.p1, internal, 21208, 21302
-recovered pasa_asmbl_28692.p1, internal, 21418, 21488
-recovered pasa_asmbl_28692.p1, internal, 21767, 21907
-recovered pasa_asmbl_28692.p1, internal, 22030, 22061
-recovered pasa_asmbl_28692.p1, internal, 22220, 22314
-recovered pasa_asmbl_28692.p1, internal, 22496, 22579
Valid prediction for snap_scaffold_21-snap.1410-T1
Valid prediction for HiQ_model.g31981.t1
Valid prediction for snap_scaffold_21-snap.1388-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g32002.t1
Valid prediction for Augustus_model.g31992.t1
Valid prediction for pasa_asmbl_28693.p1
Valid prediction for snap_scaffold_21-snap.1394-T1
Valid prediction for Augustus_model.g31984.t1
Valid prediction for pasa_asmbl_28689.p1
Valid prediction for snap_scaffold_21-snap.1411-T1
Valid prediction for GlimmerHMM_glimmerT_47919-T1
Valid prediction for GlimmerHMM_glimmerT_47917-T1
Valid prediction for snap_scaffold_21-snap.1390-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_21-snap.1379-T1
Valid prediction for GlimmerHMM_glimmerT_47918-T1
Valid prediction for pasa_asmbl_29027.p1
Valid prediction for snap_scaffold_21-snap.1404-T1
Valid prediction for GlimmerHMM_glimmerT_47920-T1
Valid prediction for Augustus_model.g31980.t1
Valid prediction for HiQ_model.g31977.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 GlimmerHMM_glimmerT_47933-T1
Valid prediction for snap_scaffold_21-snap.1400-T1
Valid prediction for snap_scaffold_21-snap.1401-T1
Valid prediction for snap_scaffold_21-snap.1373-T1
Couldn't classify 58838, 58971
Sorry, prediction pasa_asmbl_28158.p1 fails validation.
(ATG)	 CC	55871-56053	GT	CGG
(GAC)	 AG	56799-56864	GT	AGG
(GAG)	 AG	56976-57081	GT	AGG
(CCA)	 AG	57233-57358	GT	CTG
(GTA)	 AG	57496-57630	GT	AGG
(CTC)	 AG	57721-57899	GT	AGG
(GTG)	 AG	58000-58108	GT	CGG
(ATG)	 AG	58319-58418	GT	TGG
(GAA)	 AG	58563-58672	GT	TGG
(CTG)	 AG	58838-58971	GC	GGG
-recovered pasa_asmbl_28158.p1, initial, 55871, 56053
add_exon() Sorry, pasa_asmbl_28158.p1 58319-58418-initial-1 is invalid.
-recovered pasa_asmbl_28158.p1, initial, 58319, 58418
-recovered pasa_asmbl_28158.p1, internal, 56799, 56864
-recovered pasa_asmbl_28158.p1, internal, 56976, 57081
-recovered pasa_asmbl_28158.p1, internal, 57233, 57358
-recovered pasa_asmbl_28158.p1, internal, 57496, 57630
-recovered pasa_asmbl_28158.p1, internal, 57721, 57899
-recovered pasa_asmbl_28158.p1, internal, 58000, 58108
-recovered pasa_asmbl_28158.p1, internal, 58319, 58418
-recovered pasa_asmbl_28158.p1, internal, 58563, 58672
-recovered pasa_asmbl_28158.p1, internal, 58838, 58971
Couldn't classify 148251, 148295
Sorry, prediction pasa_asmbl_27743.p1 fails validation.
(ATG)	 TC	147480-147607	GT	TGG
(CCC)	 AG	147985-148120	GT	AGG
(GTG)	 AG	148251-148295	CC	GCC
-recovered pasa_asmbl_27743.p1, initial, 147480, 147607
-recovered pasa_asmbl_27743.p1, internal, 147985, 148120
Valid prediction for snap_scaffold_21-snap.1399-T1
Valid prediction for snap_scaffold_21-snap.1387-T1
Valid prediction for GlimmerHMM_glimmerT_47922-T1
Valid prediction for snap_scaffold_21-snap.1376-T1
Valid prediction for Augustus_model.g32000.t1
Valid prediction for GlimmerHMM_glimmerT_47928-T1
Couldn't classify 20074, 20132
Sorry, prediction pasa_asmbl_27750.p3 fails validation.
(GAG)	 GG	20074-20132	GT	CGG
(GCT)	 AG	20320-20362	GT	AGG
(GGG)	 AG	20517-20735	AA	AAA
-recovered pasa_asmbl_27750.p3, terminal, 20517, 20735
-recovered pasa_asmbl_27750.p3, internal, 20320, 20362
Valid prediction for GlimmerHMM_glimmerT_47925-T1
Valid prediction for Augustus_model.g31999.t1
Valid prediction for GlimmerHMM_glimmerT_47938-T1
Couldn't classify 50859, 50915
Sorry, prediction pasa_asmbl_27747.p1 fails validation.
(GAG)	 AT	50859-50915	GT	AGG
(GTG)	 AG	51007-51107	GT	GGG
(ATT)	 AG	51260-51389	GT	AGG
(CTC)	 AG	51484-51639	GT	AGG
(GTG)	 AG	51883-51954	GT	AGG
(GGA)	 AG	52186-52272	GT	AGG
(GAG)	 AG	52551-52694	GT	AGG
(AGG)	 AG	52867-52956	GT	AGG
(ACG)	 AG	53049-53143	GT	AGG
(TCT)	 AG	53273-53368	GT	AGG
(TTT)	 AG	53562-53607	GT	ATG
(AAC)	 AG	53704-53791	GT	AGG
(AAT)	 AG	53951-54021	GT	CGG
(GGA)	 AG	54242-54250	AT	AGA
-recovered pasa_asmbl_27747.p1, terminal, 54242, 54250
-recovered pasa_asmbl_27747.p1, internal, 51007, 51107
-recovered pasa_asmbl_27747.p1, internal, 51260, 51389
-recovered pasa_asmbl_27747.p1, internal, 51484, 51639
-recovered pasa_asmbl_27747.p1, internal, 51883, 51954
-recovered pasa_asmbl_27747.p1, internal, 52186, 52272
-recovered pasa_asmbl_27747.p1, internal, 52551, 52694
-recovered pasa_asmbl_27747.p1, internal, 52867, 52956
-recovered pasa_asmbl_27747.p1, internal, 53049, 53143
-recovered pasa_asmbl_27747.p1, internal, 53273, 53368
-recovered pasa_asmbl_27747.p1, internal, 53562, 53607
-recovered pasa_asmbl_27747.p1, internal, 53704, 53791
-recovered pasa_asmbl_27747.p1, internal, 53951, 54021
Valid prediction for snap_scaffold_21-snap.1383-T1
Valid prediction for GlimmerHMM_glimmerT_47939-T1
Valid prediction for GlimmerHMM_glimmerT_47942-T1
Valid prediction for snap_scaffold_21-snap.1403-T1
Valid prediction for Augustus_model.g31997.t1
Couldn't classify 81961, 82233
Sorry, prediction pasa_asmbl_27746.p1 fails validation.
(ATG)	 TA	81355-81529	GT	TGG
(GTA)	 AG	81642-81838	GT	AGG
(GAG)	 AG	81961-82233	TA	ACT
-recovered pasa_asmbl_27746.p1, initial, 81355, 81529
-recovered pasa_asmbl_27746.p1, internal, 81642, 81838
Valid prediction for snap_scaffold_21-snap.1408-T1
Valid prediction for Augustus_model.g31998.t1
Valid prediction for GlimmerHMM_glimmerT_47916-T1
Valid prediction for snap_scaffold_21-snap.1393-T1
Valid prediction for pasa_asmbl_28189.p1
Valid prediction for snap_scaffold_21-snap.1406-T1
Valid prediction for GlimmerHMM_glimmerT_47915-T1
Valid prediction for snap_scaffold_21-snap.1405-T1
Valid prediction for Augustus_model.g31983.t1
Valid prediction for Augustus_model.g31982.t1
Valid prediction for snap_scaffold_21-snap.1392-T1
Valid prediction for Augustus_model.g31996.t1
Valid prediction for GlimmerHMM_glimmerT_47936-T1
Valid prediction for Augustus_model.g31994.t1
Valid prediction for snap_scaffold_21-snap.1382-T1
Valid prediction for snap_scaffold_21-snap.1374-T1
Valid prediction for GlimmerHMM_glimmerT_47921-T1
Valid prediction for Augustus_model.g31990.t1
Valid prediction for snap_scaffold_21-snap.1397-T1
Valid prediction for snap_scaffold_21-snap.1395-T1
Valid prediction for GlimmerHMM_glimmerT_47923-T1
Valid prediction for GlimmerHMM_glimmerT_47931-T1
Valid prediction for snap_scaffold_21-snap.1391-T1
Valid prediction for Augustus_model.g32001.t1
Valid prediction for GlimmerHMM_glimmerT_47940-T1
Valid prediction for snap_scaffold_21-snap.1384-T1
Valid prediction for Augustus_model.g31985.t1
Valid prediction for snap_scaffold_21-snap.1402-T1
Valid prediction for snap_scaffold_21-snap.1409-T1
Valid prediction for GlimmerHMM_glimmerT_47937-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 66176, rend_intergenic: 62443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74907, rend_intergenic: 70035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98518, rend_intergenic: 87900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118105, rend_intergenic: 107078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139417, rend_intergenic: 134037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141690, rend_intergenic: 139497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150596, rend_intergenic: 143484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 187168
-exon list size: 504


building trellis

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96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 48 predictions from path traversal
Error with prediction: snap lend_intergenic: 66176, rend_intergenic: 62443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74907, rend_intergenic: 70035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98518, rend_intergenic: 87900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118105, rend_intergenic: 107078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139417, rend_intergenic: 134037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141690, rend_intergenic: 139497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150596, rend_intergenic: 143484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 46 predictions persist after filtering for low support