-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_6498775-6633730

-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 GeneMark_model.85084_t
Valid prediction for GeneMark_model.85069_t
Valid prediction for GeneMark_model.85072_t
Valid prediction for snap_scaffold_21-snap.1342-T1
Valid prediction for GlimmerHMM_glimmerT_49090-T1
Valid prediction for snap_scaffold_21-snap.1352-T1
Valid prediction for GlimmerHMM_glimmerT_49083-T1
Valid prediction for snap_scaffold_21-snap.1353-T1
Valid prediction for GeneMark_model.85098_t
Valid prediction for pasa_asmbl_28678.p1
Valid prediction for CodingQuarry_transcript_32532-T1
Valid prediction for pasa_asmbl_28674.p1
Valid prediction for snap_scaffold_21-snap.1336-T1
Valid prediction for snap_scaffold_21-snap.1362-T1
Valid prediction for GeneMark_model.85095_t
Valid prediction for HiQ_model.g32896.t1
Valid prediction for GlimmerHMM_glimmerT_49080-T1
Valid prediction for GeneMark_model.85094_t
Valid prediction for GeneMark_model.85088_t
Valid prediction for CodingQuarry_transcript_32523-T1
Valid prediction for snap_scaffold_21-snap.1358-T1
Valid prediction for CodingQuarry_transcript_32530-T1
Valid prediction for Augustus_model.g32901.t1
Valid prediction for GeneMark_model.85075_t
Valid prediction for CodingQuarry_transcript_32526-T1
Valid prediction for snap_scaffold_21-snap.1333-T1
Valid prediction for snap_scaffold_21-snap.1332-T1
Valid prediction for Augustus_model.g32893.t1
Valid prediction for GeneMark_model.85100_t
Valid prediction for snap_scaffold_21-snap.1355-T1
Valid prediction for GeneMark_model.85081_t
Valid prediction for HiQ_model.g32905.t1
Valid prediction for snap_scaffold_21-snap.1331-T1
Valid prediction for GeneMark_model.85091_t
Couldn't classify 8747, 8962
Sorry, prediction pasa_asmbl_28676.p1 fails validation.
(CAT)	 TC	8747-8962	GT	AGG
(CCG)	 AG	9089-9283	GG	AGG
-recovered pasa_asmbl_28676.p1, terminal, 9089, 9283
Valid prediction for Augustus_model.g32889.t1
Valid prediction for snap_scaffold_21-snap.1344-T1
Valid prediction for GlimmerHMM_glimmerT_49065-T1
Valid prediction for GlimmerHMM_glimmerT_49066-T1
Valid prediction for Augustus_model.g32911.t1
Valid prediction for GeneMark_model.85103_t
Valid prediction for HiQ_model.g32910.t1
Valid prediction for GeneMark_model.85105_t
Valid prediction for HiQ_model.g32890.t1
Valid prediction for CodingQuarry_transcript_32525-T1
Valid prediction for snap_scaffold_21-snap.1340-T1
Valid prediction for CodingQuarry_transcript_32528-T1
Valid prediction for GlimmerHMM_glimmerT_49093-T1
Valid prediction for GeneMark_model.85086_t
Valid prediction for Augustus_model.g32892.t1
Valid prediction for GlimmerHMM_glimmerT_49094-T1
Valid prediction for Augustus_model.g32908.t1
Valid prediction for snap_scaffold_21-snap.1329-T1
Valid prediction for pasa_asmbl_28689.p1
Valid prediction for GeneMark_model.85090_t
Couldn't classify 117609, 118173
Sorry, prediction pasa_asmbl_28691.p1 fails validation.
(AGT)	 AG	117609-118173	GT	AGG
(GTG)	 AG	118343-118839	GT	AGG
(ATT)	 AG	118919-119098	GT	AGG
(ATC)	 AG	119191-119432	GT	AGG
(GAA)	 AG	119518-119649	GT	AAG
(CCA)	 AG	119745-120078	GT	CGG
(GTT)	 AG	120223-120426	CT	AAC
-recovered pasa_asmbl_28691.p1, terminal, 120223, 120426
-recovered pasa_asmbl_28691.p1, internal, 117609, 118173
-recovered pasa_asmbl_28691.p1, internal, 118343, 118839
-recovered pasa_asmbl_28691.p1, internal, 118919, 119098
-recovered pasa_asmbl_28691.p1, internal, 119191, 119432
-recovered pasa_asmbl_28691.p1, internal, 119518, 119649
-recovered pasa_asmbl_28691.p1, internal, 119745, 120078
Valid prediction for pasa_asmbl_28681.p1
Valid prediction for GeneMark_model.85068_t
Valid prediction for GlimmerHMM_glimmerT_49076-T1
Valid prediction for snap_scaffold_21-snap.1335-T1
Valid prediction for GlimmerHMM_glimmerT_49079-T1
Valid prediction for snap_scaffold_21-snap.1363-T1
Valid prediction for HiQ_model.g32906.t1
Valid prediction for snap_scaffold_21-snap.1350-T1
Valid prediction for snap_scaffold_21-snap.1347-T1
Valid prediction for GlimmerHMM_glimmerT_49077-T1
Valid prediction for snap_scaffold_21-snap.1345-T1
Valid prediction for GlimmerHMM_glimmerT_49084-T1
Valid prediction for GlimmerHMM_glimmerT_49067-T1
Valid prediction for GlimmerHMM_glimmerT_49069-T1
Valid prediction for Augustus_model.g32912.t1
Valid prediction for Augustus_model.g32899.t1
Valid prediction for GeneMark_model.85093_t
Valid prediction for CodingQuarry_transcript_32524-T1
Valid prediction for GeneMark_model.85104_t
Valid prediction for GeneMark_model.85077_t
Valid prediction for Augustus_model.g32904.t1
Valid prediction for GlimmerHMM_glimmerT_49074-T1
Valid prediction for snap_scaffold_21-snap.1356-T1
Valid prediction for snap_scaffold_21-snap.1351-T1
Couldn't classify 132810, 132884
Sorry, prediction pasa_asmbl_28699.p1 fails validation.
(GTG)	 TG	132810-132884	GT	AAG
(GTA)	 AG	133019-133153	GT	AGG
(TTT)	 AG	133283-133356	GT	AGG
(CAA)	 AG	133481-133577	TC	GAT
-recovered pasa_asmbl_28699.p1, terminal, 133481, 133577
-recovered pasa_asmbl_28699.p1, internal, 133019, 133153
-recovered pasa_asmbl_28699.p1, internal, 133283, 133356
Valid prediction for GlimmerHMM_glimmerT_49092-T1
Valid prediction for snap_scaffold_21-snap.1361-T1
Valid prediction for CodingQuarry_transcript_32527-T1
Valid prediction for GeneMark_model.85102_t
Valid prediction for CodingQuarry_transcript_32522-T1
Valid prediction for HiQ_model.g32888.t1
Couldn't classify 86201, 86243
Sorry, prediction pasa_asmbl_28686.p1 fails validation.
(ATT)	 TC	86201-86243	GT	AGG
(ACC)	 AG	86707-86821	GT	AGG
(GTT)	 AG	86966-87056	GT	GGG
(CTG)	 AG	87289-87396	GT	AGG
(GAC)	 AG	87536-87627	GT	GAG
(GTC)	 AG	88427-88501	GT	AAG
(CTC)	 AG	89858-89887	GT	AGG
(TAT)	 AG	90017-90099	GT	CAG
(ATC)	 AG	90275-90399	CA	GAC
-recovered pasa_asmbl_28686.p1, terminal, 90275, 90399
-recovered pasa_asmbl_28686.p1, internal, 86707, 86821
-recovered pasa_asmbl_28686.p1, internal, 86966, 87056
-recovered pasa_asmbl_28686.p1, internal, 87289, 87396
-recovered pasa_asmbl_28686.p1, internal, 87536, 87627
-recovered pasa_asmbl_28686.p1, internal, 88427, 88501
-recovered pasa_asmbl_28686.p1, internal, 89858, 89887
-recovered pasa_asmbl_28686.p1, internal, 90017, 90099
Valid prediction for GeneMark_model.85071_t
Valid prediction for GlimmerHMM_glimmerT_49087-T1
Valid prediction for snap_scaffold_21-snap.1330-T1
Valid prediction for GlimmerHMM_glimmerT_49070-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 104722, 104805
Sorry, prediction pasa_asmbl_27752.p1 fails validation.
(TCG)	 GC	104722-104805	GT	AGG
(GTG)	 AG	105006-105164	GT	AGG
(GTC)	 AG	105571-105824	GT	AAG
(GGT)	 AG	106142-106343	GT	AGG
(CTT)	 AG	106466-106498	GT	AGG
-recovered pasa_asmbl_27752.p1, terminal, 106466, 106498
-recovered pasa_asmbl_27752.p1, internal, 105006, 105164
-recovered pasa_asmbl_27752.p1, internal, 105571, 105824
-recovered pasa_asmbl_27752.p1, internal, 106142, 106343
-recovered pasa_asmbl_27752.p1, internal, 106466, 106498
Valid prediction for HiQ_model.g32898.t1
Valid prediction for snap_scaffold_21-snap.1364-T1
Valid prediction for HiQ_model.g32895.t1
Valid prediction for GlimmerHMM_glimmerT_49078-T1
Valid prediction for GeneMark_model.85082_t
Valid prediction for snap_scaffold_21-snap.1360-T1
Valid prediction for GeneMark_model.85070_t
Valid prediction for Augustus_model.g32894.t1
Valid prediction for GlimmerHMM_glimmerT_49088-T1
Valid prediction for snap_scaffold_21-snap.1339-T1
Valid prediction for GeneMark_model.85089_t
Valid prediction for snap_scaffold_21-snap.1354-T1
Valid prediction for Augustus_model.g32891.t1
Valid prediction for GeneMark_model.85076_t
Valid prediction for GlimmerHMM_glimmerT_49072-T1
Valid prediction for GeneMark_model.85078_t
Valid prediction for HiQ_model.g32909.t1
Valid prediction for GeneMark_model.85092_t
Valid prediction for GeneMark_model.85096_t
Valid prediction for GeneMark_model.85099_t
Valid prediction for GeneMark_model.85073_t
Valid prediction for snap_scaffold_21-snap.1343-T1
Valid prediction for Augustus_model.g32897.t1
Valid prediction for Augustus_model.g32903.t1
Valid prediction for GeneMark_model.85083_t
Valid prediction for GlimmerHMM_glimmerT_49075-T1
Valid prediction for GeneMark_model.85101_t
Valid prediction for GeneMark_model.85067_t
Valid prediction for GeneMark_model.85079_t
Valid prediction for snap_scaffold_21-snap.1348-T1
Valid prediction for snap_scaffold_21-snap.1346-T1
Valid prediction for snap_scaffold_21-snap.1359-T1
Valid prediction for GeneMark_model.85087_t
Valid prediction for snap_scaffold_21-snap.1349-T1
Valid prediction for GeneMark_model.85097_t
Valid prediction for CodingQuarry_transcript_32533-T1
Valid prediction for GlimmerHMM_glimmerT_49089-T1
Valid prediction for Augustus_model.g32902.t1
Valid prediction for GlimmerHMM_glimmerT_49071-T1
Valid prediction for GlimmerHMM_glimmerT_49086-T1
Valid prediction for CodingQuarry_transcript_32529-T1
Couldn't classify 39187, 39261
Sorry, prediction CodingQuarry_transcript_32531-T1 fails validation.
(ATG)	 GC	39187-39261	GA	AGG
(AGG)	 AG	39286-39375	GG	GAG
-recovered CodingQuarry_transcript_32531-T1, terminal, 39286, 39375
Valid prediction for snap_scaffold_21-snap.1357-T1
Valid prediction for GlimmerHMM_glimmerT_49082-T1
Valid prediction for GlimmerHMM_glimmerT_49081-T1
Valid prediction for GlimmerHMM_glimmerT_49068-T1
Valid prediction for Augustus_model.g32900.t1
Valid prediction for GlimmerHMM_glimmerT_49073-T1
Couldn't classify 74436, 74466
Sorry, prediction pasa_asmbl_27758.p1 fails validation.
(CAT)	 AC	74436-74466	GT	AGG
(GGG)	 AG	74547-74702	GT	CTG
(ACG)	 AG	74818-75061	GT	AGG
(GGT)	 AG	75192-75292	GT	AGG
(ATA)	 AG	75375-75496	AC	AAA
-recovered pasa_asmbl_27758.p1, terminal, 75375, 75496
-recovered pasa_asmbl_27758.p1, internal, 74547, 74702
-recovered pasa_asmbl_27758.p1, internal, 74818, 75061
-recovered pasa_asmbl_27758.p1, internal, 75192, 75292
Valid prediction for snap_scaffold_21-snap.1338-T1
Valid prediction for snap_scaffold_21-snap.1334-T1
Valid prediction for snap_scaffold_21-snap.1341-T1
Valid prediction for GlimmerHMM_glimmerT_49091-T1
Valid prediction for GeneMark_model.85085_t
Valid prediction for pasa_asmbl_27754.p1
Couldn't classify 85726, 85823
Sorry, prediction pasa_asmbl_27755.p1 fails validation.
(GTC)	 CA	85726-85823	GT	AGG
(AAT)	 AG	86422-86584	GT	AAG
(AGC)	 AG	86830-87061	GT	TGG
(GCA)	 AG	88304-88389	GT	AGG
(GAG)	 AG	88620-88828	GT	CGG
(ACG)	 AG	89269-89386	GT	AGG
(GCT)	 AG	89513-89654	GT	AGG
(CCC)	 AG	89847-90013	GT	AGG
(GTG)	 AG	90126-90225	GT	GGG
(GTA)	 AG	90316-90554	GT	AGG
(AGA)	 AG	90763-90777	GG	GAG
add_exon() Sorry, pasa_asmbl_27755.p1 89513-89654-terminal-3 is invalid.
-recovered pasa_asmbl_27755.p1, terminal, 89513, 89654
-recovered pasa_asmbl_27755.p1, terminal, 90763, 90777
-recovered pasa_asmbl_27755.p1, internal, 86422, 86584
-recovered pasa_asmbl_27755.p1, internal, 86830, 87061
-recovered pasa_asmbl_27755.p1, internal, 88304, 88389
-recovered pasa_asmbl_27755.p1, internal, 88620, 88828
-recovered pasa_asmbl_27755.p1, internal, 89269, 89386
-recovered pasa_asmbl_27755.p1, internal, 89513, 89654
-recovered pasa_asmbl_27755.p1, internal, 89847, 90013
-recovered pasa_asmbl_27755.p1, internal, 90126, 90225
-recovered pasa_asmbl_27755.p1, internal, 90316, 90554
Valid prediction for CodingQuarry_transcript_32534-T1
Valid prediction for pasa_asmbl_27763.p1
Valid prediction for Augustus_model.g32907.t1
Valid prediction for GeneMark_model.85074_t
Valid prediction for GlimmerHMM_glimmerT_49085-T1
Valid prediction for GeneMark_model.85080_t
Valid prediction for snap_scaffold_21-snap.1337-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 46744, rend_intergenic: 44050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61249, rend_intergenic: 55690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70713, rend_intergenic: 68251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79991, rend_intergenic: 73162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108177, rend_intergenic: 104586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111871, rend_intergenic: 110137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118830, rend_intergenic: 116306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133577, rend_intergenic: 125070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 134956
-exon list size: 534


building trellis

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86.6    
86.8    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.1    
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    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 46744, rend_intergenic: 44050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61249, rend_intergenic: 55690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70713, rend_intergenic: 68251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79991, rend_intergenic: 73162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108177, rend_intergenic: 104586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111871, rend_intergenic: 110137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118830, rend_intergenic: 116306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133577, rend_intergenic: 125070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support