-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_7736435-7922682

-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.g36209.t1
Valid prediction for GlimmerHMM_glimmerT_54566-T1
Valid prediction for GlimmerHMM_glimmerT_54551-T1
Valid prediction for Augustus_model.g36191.t1
Valid prediction for snap_scaffold_25-snap.1693-T1
Valid prediction for snap_scaffold_25-snap.1674-T1
Valid prediction for Augustus_model.g36192.t1
Valid prediction for Augustus_model.g36195.t1
Valid prediction for CodingQuarry_transcript_38792-T1
Valid prediction for snap_scaffold_25-snap.1676-T1
Valid prediction for snap_scaffold_25-snap.1679-T1
Valid prediction for snap_scaffold_25-snap.1707-T1
Valid prediction for GlimmerHMM_glimmerT_54553-T1
Valid prediction for GlimmerHMM_glimmerT_54546-T1
Valid prediction for snap_scaffold_25-snap.1697-T1
Valid prediction for GlimmerHMM_glimmerT_54549-T1
Valid prediction for GlimmerHMM_glimmerT_54575-T1
Valid prediction for snap_scaffold_25-snap.1710-T1
Valid prediction for GlimmerHMM_glimmerT_54576-T1
Valid prediction for snap_scaffold_25-snap.1713-T1
Valid prediction for Augustus_model.g36207.t1
Valid prediction for GlimmerHMM_glimmerT_54574-T1
Valid prediction for GlimmerHMM_glimmerT_54570-T1
Valid prediction for snap_scaffold_25-snap.1673-T1
Valid prediction for HiQ_model.g36201.t1
Valid prediction for GlimmerHMM_glimmerT_54562-T1
Valid prediction for snap_scaffold_25-snap.1681-T1
Valid prediction for GlimmerHMM_glimmerT_54547-T1
Valid prediction for Augustus_model.g36199.t1
Couldn't classify 62810, 62874
Sorry, prediction pasa_asmbl_33678.p1 fails validation.
(ATG)	 CC	61955-62031	GT	AGG
(GTT)	 AG	62319-62460	GT	AGG
(GTG)	 AG	62553-62700	GT	AGG
(ACG)	 AG	62810-62874	CC	AGC
-recovered pasa_asmbl_33678.p1, initial, 61955, 62031
-recovered pasa_asmbl_33678.p1, internal, 62319, 62460
-recovered pasa_asmbl_33678.p1, internal, 62553, 62700
Valid prediction for GlimmerHMM_glimmerT_54559-T1
Valid prediction for snap_scaffold_25-snap.1701-T1
Valid prediction for Augustus_model.g36196.t1
Valid prediction for snap_scaffold_25-snap.1718-T1
Valid prediction for snap_scaffold_25-snap.1706-T1
Valid prediction for GlimmerHMM_glimmerT_54571-T1
Valid prediction for GlimmerHMM_glimmerT_54563-T1
Valid prediction for snap_scaffold_25-snap.1685-T1
Valid prediction for GlimmerHMM_glimmerT_54573-T1
Valid prediction for snap_scaffold_25-snap.1716-T1
Couldn't classify 161551, 161577
Couldn't classify 163363, 163403
Sorry, prediction pasa_asmbl_33688.p2 fails validation.
(GAC)	 TG	161551-161577	GT	GGG
(GTC)	 AG	161855-161917	GT	ACG
(GTG)	 AG	162150-162248	GT	TGG
(AAC)	 AG	162555-162654	GT	TGG
(GTG)	 AG	162974-163084	GT	CGG
(AGC)	 AG	163363-163403	AA	AGA
-recovered pasa_asmbl_33688.p2, internal, 161855, 161917
-recovered pasa_asmbl_33688.p2, internal, 162150, 162248
-recovered pasa_asmbl_33688.p2, internal, 162555, 162654
-recovered pasa_asmbl_33688.p2, internal, 162974, 163084
Valid prediction for snap_scaffold_25-snap.1690-T1
Valid prediction for CodingQuarry_transcript_38793-T1
Valid prediction for Augustus_model.g36204.t1
Valid prediction for snap_scaffold_25-snap.1699-T1
Couldn't classify 64082, 64187
Sorry, prediction pasa_asmbl_33929.p1 fails validation.
(GGG)	 AG	64082-64187	GT	GGG
(CGT)	 AG	64384-64478	GT	GGG
(ATC)	 AG	64601-64712	GT	TGG
(GGG)	 AG	64797-64945	AG	AGA
-recovered pasa_asmbl_33929.p1, terminal, 64797, 64945
-recovered pasa_asmbl_33929.p1, internal, 64082, 64187
-recovered pasa_asmbl_33929.p1, internal, 64384, 64478
-recovered pasa_asmbl_33929.p1, internal, 64601, 64712
Couldn't classify 86203, 86265
Couldn't classify 89022, 89051
Sorry, prediction pasa_asmbl_33679.p1 fails validation.
(CAC)	 AG	86203-86265	GT	ACG
(AGT)	 AG	88486-88590	GT	AGG
(GCC)	 AG	88697-88825	GT	AGG
(AAC)	 AG	89022-89051	GT	CTG
-recovered pasa_asmbl_33679.p1, internal, 86203, 86265
-recovered pasa_asmbl_33679.p1, internal, 88486, 88590
-recovered pasa_asmbl_33679.p1, internal, 88697, 88825
-recovered pasa_asmbl_33679.p1, internal, 89022, 89051
Valid prediction for GlimmerHMM_glimmerT_54556-T1
Couldn't classify 129769, 129827
Sorry, prediction pasa_asmbl_33683.p1 fails validation.
(GCG)	 CA	129769-129827	GT	AGG
(TTC)	 AG	129994-130131	GT	AGG
(TGT)	 AG	130747-130846	GT	AGG
(GAG)	 AG	131090-131209	GT	AGG
(AGA)	 AG	131405-131575	GT	AGG
(GCC)	 AG	131774-131891	GT	CAG
(ATG)	 AG	133780-133922	TC	AAT
-recovered pasa_asmbl_33683.p1, terminal, 133780, 133922
-recovered pasa_asmbl_33683.p1, internal, 129994, 130131
-recovered pasa_asmbl_33683.p1, internal, 130747, 130846
-recovered pasa_asmbl_33683.p1, internal, 131090, 131209
-recovered pasa_asmbl_33683.p1, internal, 131405, 131575
-recovered pasa_asmbl_33683.p1, internal, 131774, 131891
Valid prediction for pasa_asmbl_33681.p1
Couldn't classify 166008, 166035
Sorry, prediction pasa_asmbl_33689.p1 fails validation.
(GTT)	 AC	166008-166035	GT	AGG
(ATA)	 AG	166177-166928	CT	GAC
-recovered pasa_asmbl_33689.p1, terminal, 166177, 166928
Valid prediction for Augustus_model.g36202.t1
Valid prediction for GlimmerHMM_glimmerT_54552-T1
Valid prediction for GlimmerHMM_glimmerT_54565-T1
Valid prediction for GlimmerHMM_glimmerT_54557-T1
Couldn't classify 175785, 175843
Couldn't classify 176499, 176561
Sorry, prediction pasa_asmbl_33691.p1 fails validation.
(ACC)	 GG	175785-175843	GT	AGG
(GGA)	 AG	176028-176193	GT	AGG
(GAG)	 AG	176341-176421	GT	GGG
(GAT)	 AG	176499-176561	GG	ACG
-recovered pasa_asmbl_33691.p1, internal, 176028, 176193
-recovered pasa_asmbl_33691.p1, internal, 176341, 176421
Valid prediction for GlimmerHMM_glimmerT_54564-T1
Valid prediction for snap_scaffold_25-snap.1675-T1
Valid prediction for GlimmerHMM_glimmerT_54560-T1
Valid prediction for Augustus_model.g36203.t1
Valid prediction for snap_scaffold_25-snap.1687-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_25-snap.1684-T1
Valid prediction for snap_scaffold_25-snap.1678-T1
Valid prediction for snap_scaffold_25-snap.1689-T1
Valid prediction for HiQ_model.g36194.t1
Valid prediction for snap_scaffold_25-snap.1714-T1
Valid prediction for snap_scaffold_25-snap.1705-T1
Valid prediction for snap_scaffold_25-snap.1691-T1
Valid prediction for snap_scaffold_25-snap.1682-T1
Valid prediction for snap_scaffold_25-snap.1680-T1
Valid prediction for HiQ_model.g36208.t1
Valid prediction for pasa_asmbl_34410.p1
Valid prediction for snap_scaffold_25-snap.1700-T1
Valid prediction for GlimmerHMM_glimmerT_54568-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_54555-T1
Valid prediction for Augustus_model.g36198.t1
Valid prediction for snap_scaffold_25-snap.1708-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_54567-T1
Valid prediction for GlimmerHMM_glimmerT_54545-T1
Valid prediction for snap_scaffold_25-snap.1672-T1
Valid prediction for snap_scaffold_25-snap.1704-T1
Valid prediction for snap_scaffold_25-snap.1711-T1
Valid prediction for snap_scaffold_25-snap.1686-T1
Valid prediction for Augustus_model.g36190.t1
Valid prediction for GlimmerHMM_glimmerT_54544-T1
Valid prediction for Augustus_model.g36197.t1
Valid prediction for snap_scaffold_25-snap.1715-T1
Couldn't classify 87613, 87715
Couldn't classify 87812, 88071
Sorry, prediction pasa_asmbl_34411.p1 fails validation.
(AGG)	 CC	87613-87715	GT	GGG
(GCT)	 AG	87812-88071	AC	CCA
Valid prediction for snap_scaffold_25-snap.1677-T1
Couldn't classify 35659, 36522
Sorry, prediction pasa_asmbl_33687.p1 fails validation.
(CCC)	 GA	35659-36522	TT	TGT
Valid prediction for GlimmerHMM_glimmerT_54548-T1
Valid prediction for snap_scaffold_25-snap.1719-T1
Valid prediction for Augustus_model.g36210.t1
Valid prediction for snap_scaffold_25-snap.1694-T1
Valid prediction for HiQ_model.g36193.t1
Valid prediction for GlimmerHMM_glimmerT_54554-T1
Valid prediction for snap_scaffold_25-snap.1696-T1
Valid prediction for Augustus_model.g36200.t1
Valid prediction for snap_scaffold_25-snap.1698-T1
Valid prediction for snap_scaffold_25-snap.1695-T1
Valid prediction for snap_scaffold_25-snap.1692-T1
Valid prediction for GlimmerHMM_glimmerT_54569-T1
Valid prediction for snap_scaffold_25-snap.1709-T1
Valid prediction for GlimmerHMM_glimmerT_54577-T1
Valid prediction for CodingQuarry_transcript_38797-T1
Valid prediction for Augustus_model.g36206.t1
Valid prediction for GlimmerHMM_glimmerT_54550-T1
Valid prediction for pasa_asmbl_34406.p2
Valid prediction for CodingQuarry_transcript_38796-T1
Valid prediction for snap_scaffold_25-snap.1717-T1
Valid prediction for Augustus_model.g36189.t1
Valid prediction for GlimmerHMM_glimmerT_54578-T1
Valid prediction for snap_scaffold_25-snap.1688-T1
Valid prediction for snap_scaffold_25-snap.1712-T1
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g36205.t1
Valid prediction for snap_scaffold_25-snap.1702-T1
Valid prediction for pasa_asmbl_34418.p1
Valid prediction for GlimmerHMM_glimmerT_54558-T1
Valid prediction for CodingQuarry_transcript_38791-T1
Valid prediction for snap_scaffold_25-snap.1683-T1
Valid prediction for CodingQuarry_transcript_38795-T1
Valid prediction for GlimmerHMM_glimmerT_54572-T1
Valid prediction for snap_scaffold_25-snap.1703-T1
Valid prediction for GlimmerHMM_glimmerT_54561-T1
Valid prediction for pasa_asmbl_34414.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23094, rend_intergenic: 7486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27075, rend_intergenic: 23692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34019, rend_intergenic: 30346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42440, rend_intergenic: 34557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47718, rend_intergenic: 42912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54903, rend_intergenic: 51363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58404, rend_intergenic: 54907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64945, rend_intergenic: 60082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68239, rend_intergenic: 66438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70012, rend_intergenic: 68239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82012, rend_intergenic: 72765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94194, rend_intergenic: 82085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101646, rend_intergenic: 95486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104747, rend_intergenic: 104024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105369, rend_intergenic: 104842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118724, rend_intergenic: 105952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127914, rend_intergenic: 124030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133922, rend_intergenic: 132350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139628, rend_intergenic: 135591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166928, rend_intergenic: 161711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178903, rend_intergenic: 173713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184585, rend_intergenic: 180959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 186248
-exon list size: 535


building trellis

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90.3    
90.5    
90.7    
90.9    
91.1    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 23094, rend_intergenic: 7486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27075, rend_intergenic: 23692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34019, rend_intergenic: 30346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42440, rend_intergenic: 34557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47718, rend_intergenic: 42912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54903, rend_intergenic: 51363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58404, rend_intergenic: 54907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64945, rend_intergenic: 60082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68239, rend_intergenic: 66438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70012, rend_intergenic: 68239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82012, rend_intergenic: 72765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94194, rend_intergenic: 82085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101646, rend_intergenic: 95486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104747, rend_intergenic: 104024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105369, rend_intergenic: 104842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118724, rend_intergenic: 105952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127914, rend_intergenic: 124030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133922, rend_intergenic: 132350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139628, rend_intergenic: 135591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166928, rend_intergenic: 161711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178903, rend_intergenic: 173713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184585, rend_intergenic: 180959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support