-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_5308959-5515097

-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.g6230.t1
Valid prediction for GlimmerHMM_glimmerT_9568-T1
Valid prediction for GlimmerHMM_glimmerT_9579-T1
Valid prediction for snap_scaffold_4-snap.1189-T1
Valid prediction for GeneMark_model.15656_t
Couldn't classify 118165, 118225
Sorry, prediction pasa_asmbl_42675.p1 fails validation.
(AGC)	 GC	118165-118225	GT	CGG
(ACG)	 AG	118320-118414	GT	AGG
(GGT)	 AG	118637-118753	GT	AGG
(GAT)	 AG	118878-119039	GT	AGG
(GAG)	 AG	119473-119621	GT	AGG
(TCT)	 AG	119756-119891	GT	AGG
(GTA)	 AG	120049-120156	GA	GAG
-recovered pasa_asmbl_42675.p1, terminal, 120049, 120156
-recovered pasa_asmbl_42675.p1, internal, 118320, 118414
-recovered pasa_asmbl_42675.p1, internal, 118637, 118753
-recovered pasa_asmbl_42675.p1, internal, 118878, 119039
-recovered pasa_asmbl_42675.p1, internal, 119473, 119621
-recovered pasa_asmbl_42675.p1, internal, 119756, 119891
Valid prediction for CodingQuarry_transcript_48890-T1
Couldn't classify 68774, 69184
Sorry, prediction pasa_asmbl_42673.p1 fails validation.
(ATG)	 CA	68505-68594	GT	AGG
(GAT)	 AG	68774-69184	CA	CTC
-recovered pasa_asmbl_42673.p1, initial, 68505, 68594
Valid prediction for snap_scaffold_4-snap.1202-T1
Couldn't classify 157491, 157907
Sorry, prediction pasa_asmbl_42677.p1 fails validation.
(CAA)	 AC	157491-157907	GA	AAG
Couldn't classify 131008, 131069
Sorry, prediction pasa_asmbl_42676.p1 fails validation.
(GCC)	 TG	131008-131069	GT	TGG
(CTG)	 AG	131334-131485	GT	AGG
(GAA)	 AG	131896-132209	GA	AAG
-recovered pasa_asmbl_42676.p1, terminal, 131896, 132209
-recovered pasa_asmbl_42676.p1, internal, 131334, 131485
Valid prediction for Augustus_model.g6244.t1
Valid prediction for GeneMark_model.15669_t
Valid prediction for GeneMark_model.15655_t
Valid prediction for snap_scaffold_4-snap.1206-T1
Valid prediction for GeneMark_model.15657_t
Valid prediction for HiQ_model.g6238.t1
Valid prediction for GeneMark_model.15662_t
Valid prediction for Augustus_model.g6235.t1
Valid prediction for snap_scaffold_4-snap.1183-T1
Valid prediction for GlimmerHMM_glimmerT_9571-T1
Valid prediction for Augustus_model.g6236.t1
Valid prediction for snap_scaffold_4-snap.1181-T1
Valid prediction for Augustus_model.g6233.t1
Valid prediction for snap_scaffold_4-snap.1196-T1
Valid prediction for GeneMark_model.15649_t
Couldn't classify 160473, 160486
Sorry, prediction pasa_asmbl_42679.p1 fails validation.
(GCA)	 CA	160473-160486	GT	AGG
(GAT)	 AG	161021-161103	GT	GGG
(CGC)	 AG	161201-161253	GT	CAG
(ATC)	 AG	161337-161412	GT	AGG
(TCC)	 AG	161563-161669	GT	CGG
(AGG)	 AG	161827-161895	GT	GAG
-recovered pasa_asmbl_42679.p1, terminal, 161827, 161895
-recovered pasa_asmbl_42679.p1, internal, 161021, 161103
-recovered pasa_asmbl_42679.p1, internal, 161201, 161253
-recovered pasa_asmbl_42679.p1, internal, 161337, 161412
-recovered pasa_asmbl_42679.p1, internal, 161563, 161669
-recovered pasa_asmbl_42679.p1, internal, 161827, 161895
Valid prediction for Augustus_model.g6228.t1
Valid prediction for snap_scaffold_4-snap.1178-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for HiQ_model.g6227.t1
Valid prediction for snap_scaffold_4-snap.1191-T1
Valid prediction for pasa_asmbl_42671.p1
Valid prediction for HiQ_model.g6240.t1
Valid prediction for GlimmerHMM_glimmerT_9575-T1
Valid prediction for GeneMark_model.15658_t
Valid prediction for snap_scaffold_4-snap.1187-T1
Valid prediction for CodingQuarry_transcript_48892-T1
Valid prediction for GlimmerHMM_glimmerT_9569-T1
Valid prediction for pasa_asmbl_42685.p1
Valid prediction for snap_scaffold_4-snap.1201-T1
Valid prediction for GeneMark_model.15660_t
Valid prediction for snap_scaffold_4-snap.1185-T1
Valid prediction for GlimmerHMM_glimmerT_9576-T1
Valid prediction for HiQ_model.g6232.t1
Valid prediction for snap_scaffold_4-snap.1190-T1
Valid prediction for HiQ_model.g6242.t1
Valid prediction for GlimmerHMM_glimmerT_9586-T1
Couldn't classify 158070, 159191
Sorry, prediction pasa_asmbl_42678.p1 fails validation.
(GAG)	 AT	158070-159191	AC	AAA
Valid prediction for snap_scaffold_4-snap.1194-T1
Valid prediction for snap_scaffold_4-snap.1184-T1
Valid prediction for GeneMark_model.15668_t
Valid prediction for GeneMark_model.15671_t
Valid prediction for CodingQuarry_transcript_48891-T1
Valid prediction for Augustus_model.g6239.t1
Valid prediction for GeneMark_model.15665_t
Valid prediction for GlimmerHMM_glimmerT_9578-T1
Valid prediction for GeneMark_model.15647_t
Valid prediction for GeneMark_model.15653_t
Valid prediction for GeneMark_model.15650_t
Valid prediction for snap_scaffold_4-snap.1205-T1
Valid prediction for GlimmerHMM_glimmerT_9567-T1
Valid prediction for GlimmerHMM_glimmerT_9564-T1
Couldn't classify 166818, 166830
Sorry, prediction pasa_asmbl_42684.p1 fails validation.
(TCG)	 CC	166818-166830	GT	AGG
(GCC)	 AG	167011-167220	GT	AGG
(GAC)	 AG	167323-167469	GT	AGG
(CTG)	 AG	167853-168001	TA	AGT
-recovered pasa_asmbl_42684.p1, terminal, 167853, 168001
-recovered pasa_asmbl_42684.p1, internal, 167011, 167220
-recovered pasa_asmbl_42684.p1, internal, 167323, 167469
Valid prediction for snap_scaffold_4-snap.1195-T1
Valid prediction for GeneMark_model.15651_t
Valid prediction for snap_scaffold_4-snap.1186-T1
Valid prediction for CodingQuarry_transcript_48886-T1
Valid prediction for GlimmerHMM_glimmerT_9573-T1
Valid prediction for GeneMark_model.15663_t
Valid prediction for GlimmerHMM_glimmerT_9583-T1
Valid prediction for GlimmerHMM_glimmerT_9581-T1
Valid prediction for CodingQuarry_transcript_48884-T1
Valid prediction for pasa_asmbl_42686.p1
Valid prediction for pasa_asmbl_42688.p1
Couldn't classify 113201, 113262
Couldn't classify 113987, 114017
Sorry, prediction pasa_asmbl_43560.p2 fails validation.
(TGG)	 TG	113201-113262	GT	AGG
(AGA)	 AG	113439-113563	GT	GGG
(GAG)	 AG	113700-113817	GT	CAG
(AGT)	 AG	113987-114017	AA	AGA
-recovered pasa_asmbl_43560.p2, internal, 113439, 113563
-recovered pasa_asmbl_43560.p2, internal, 113700, 113817
Valid prediction for GlimmerHMM_glimmerT_9582-T1
Valid prediction for GlimmerHMM_glimmerT_9570-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.g6231.t1
Couldn't classify 137966, 138056
Couldn't classify 138890, 138985
Sorry, prediction pasa_asmbl_41339.p1 fails validation.
(AGA)	 AG	137966-138056	GT	TGG
(CGG)	 AG	138380-138507	GT	ATG
(GGT)	 AG	138890-138985	TT	CTT
-recovered pasa_asmbl_41339.p1, internal, 137966, 138056
-recovered pasa_asmbl_41339.p1, internal, 138380, 138507
Valid prediction for CodingQuarry_transcript_48889-T1
Valid prediction for GeneMark_model.15648_t
Valid prediction for GeneMark_model.15673_t
Valid prediction for Augustus_model.g6243.t1
Valid prediction for GlimmerHMM_glimmerT_9563-T1
Valid prediction for snap_scaffold_4-snap.1198-T1
Valid prediction for snap_scaffold_4-snap.1207-T1
Couldn't classify 192012, 192069
Couldn't classify 192592, 192728
Sorry, prediction pasa_asmbl_42297.p1 fails validation.
(CTG)	 AG	192012-192069	GT	AGG
(AAC)	 AG	192195-192264	GT	AGG
(GGG)	 AG	192375-192496	GT	AGG
(GAA)	 AG	192592-192728	AC	CAA
-recovered pasa_asmbl_42297.p1, internal, 192012, 192069
-recovered pasa_asmbl_42297.p1, internal, 192195, 192264
-recovered pasa_asmbl_42297.p1, internal, 192375, 192496
Valid prediction for GeneMark_model.15654_t
Valid prediction for CodingQuarry_transcript_48887-T1
Valid prediction for CodingQuarry_transcript_48883-T1
Valid prediction for snap_scaffold_4-snap.1180-T1
Valid prediction for GeneMark_model.15667_t
Valid prediction for snap_scaffold_4-snap.1176-T1
Valid prediction for snap_scaffold_4-snap.1182-T1
Valid prediction for snap_scaffold_4-snap.1179-T1
Valid prediction for GeneMark_model.15664_t
Valid prediction for GlimmerHMM_glimmerT_9566-T1
Valid prediction for GeneMark_model.15661_t
Couldn't classify 59656, 59783
Couldn't classify 61947, 62984
Sorry, prediction pasa_asmbl_41343.p1 fails validation.
(TCA)	 GC	59656-59783	GT	CCG
(GAA)	 AG	59941-60064	GT	AGG
(ATC)	 AG	60193-60270	GT	AGG
(TGG)	 AG	60441-60538	GT	GGG
(CAA)	 AG	60671-60815	GT	CGG
(GTG)	 AG	61353-61487	GT	AAG
(GAT)	 AG	61651-61779	GT	AGG
(ATC)	 AG	61947-62984	CT	ACC
-recovered pasa_asmbl_41343.p1, internal, 59941, 60064
-recovered pasa_asmbl_41343.p1, internal, 60193, 60270
-recovered pasa_asmbl_41343.p1, internal, 60441, 60538
-recovered pasa_asmbl_41343.p1, internal, 60671, 60815
-recovered pasa_asmbl_41343.p1, internal, 61353, 61487
-recovered pasa_asmbl_41343.p1, internal, 61651, 61779
Valid prediction for GlimmerHMM_glimmerT_9572-T1
Valid prediction for Augustus_model.g6225.t1
Valid prediction for GlimmerHMM_glimmerT_9585-T1
Valid prediction for GlimmerHMM_glimmerT_9565-T1
Couldn't classify 168624, 168731
Sorry, prediction pasa_asmbl_41336.p1 fails validation.
(ATA)	 AG	168624-168731	GT	AGG
(TGT)	 AG	168961-169073	GT	CTG
(GAA)	 AG	169354-169423	GT	AGG
(ACC)	 AG	169518-169613	TT	AAT
-recovered pasa_asmbl_41336.p1, terminal, 169518, 169613
-recovered pasa_asmbl_41336.p1, internal, 168624, 168731
-recovered pasa_asmbl_41336.p1, internal, 168961, 169073
-recovered pasa_asmbl_41336.p1, internal, 169354, 169423
Valid prediction for GeneMark_model.15646_t
Valid prediction for GeneMark_model.15652_t
Couldn't classify 63117, 63317
Sorry, prediction pasa_asmbl_41341.p1 fails validation.
(CCA)	 GC	63117-63317	GT	AGG
(GTG)	 AG	63345-63584	GT	AGG
(GAG)	 AG	63709-63757	GT	TGG
(ATC)	 AG	63834-64173	GT	CGG
(ATT)	 AG	65218-65944	GT	AGG
(TGC)	 AG	66114-66248	GT	AGG
(GAG)	 AG	66639-66775	GT	AGG
(GCA)	 AG	67339-67450	GT	AGG
(TTC)	 AG	68861-68935	GT	AGG
(ATG)	 AG	69059-69160	GT	AGG
(CTA)	 AG	69856-70017	TC	AGT
-recovered pasa_asmbl_41341.p1, initial, 69059, 69160
-recovered pasa_asmbl_41341.p1, terminal, 69856, 70017
-recovered pasa_asmbl_41341.p1, internal, 63345, 63584
-recovered pasa_asmbl_41341.p1, internal, 63709, 63757
-recovered pasa_asmbl_41341.p1, internal, 63834, 64173
-recovered pasa_asmbl_41341.p1, internal, 65218, 65944
-recovered pasa_asmbl_41341.p1, internal, 66114, 66248
-recovered pasa_asmbl_41341.p1, internal, 66639, 66775
-recovered pasa_asmbl_41341.p1, internal, 67339, 67450
-recovered pasa_asmbl_41341.p1, internal, 68861, 68935
-recovered pasa_asmbl_41341.p1, internal, 69059, 69160
Valid prediction for CodingQuarry_transcript_48888-T1
Valid prediction for GeneMark_model.15670_t
Valid prediction for Augustus_model.g6229.t1
Valid prediction for GeneMark_model.15659_t
Valid prediction for snap_scaffold_4-snap.1188-T1
Couldn't classify 28947, 29095
Couldn't classify 29824, 29901
Sorry, prediction pasa_asmbl_42330.p1 fails validation.
(GAC)	 CA	28947-29095	GT	GGG
(ACA)	 AG	29452-29515	GT	GAG
(ATC)	 AG	29631-29714	GT	AGG
(GGT)	 AG	29824-29901	AA	GTA
-recovered pasa_asmbl_42330.p1, internal, 29452, 29515
-recovered pasa_asmbl_42330.p1, internal, 29631, 29714
Valid prediction for snap_scaffold_4-snap.1203-T1
Couldn't classify 141197, 141319
Sorry, prediction pasa_asmbl_41337.p1 fails validation.
(GAG)	 CT	141197-141319	GT	CCG
(GAC)	 AG	141400-141526	GT	GGG
(AGA)	 AG	141637-141748	GT	AGG
(GTC)	 AG	141962-142025	GG	GAG
-recovered pasa_asmbl_41337.p1, terminal, 141637, 141748
-recovered pasa_asmbl_41337.p1, terminal, 141962, 142025
-recovered pasa_asmbl_41337.p1, internal, 141400, 141526
-recovered pasa_asmbl_41337.p1, internal, 141637, 141748
Valid prediction for Augustus_model.g6237.t1
Couldn't classify 55486, 55803
Sorry, prediction pasa_asmbl_42296.p1 fails validation.
(CTA)	 CA	55486-55803	AA	AGA
Valid prediction for GeneMark_model.15666_t
Valid prediction for snap_scaffold_4-snap.1193-T1
Valid prediction for Augustus_model.g6226.t1
Valid prediction for GlimmerHMM_glimmerT_9580-T1
Valid prediction for GlimmerHMM_glimmerT_9577-T1
Valid prediction for Augustus_model.g6241.t1
Valid prediction for HiQ_model.g6234.t1
Valid prediction for snap_scaffold_4-snap.1177-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.15672_t
Valid prediction for GlimmerHMM_glimmerT_9584-T1
Valid prediction for snap_scaffold_4-snap.1192-T1
Valid prediction for snap_scaffold_4-snap.1200-T1
Valid prediction for GlimmerHMM_glimmerT_9574-T1
Valid prediction for pasa_asmbl_41340.p1
Valid prediction for snap_scaffold_4-snap.1199-T1
Valid prediction for snap_scaffold_4-snap.1197-T1
Valid prediction for snap_scaffold_4-snap.1204-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18910, rend_intergenic: 12922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80406, rend_intergenic: 75508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 206139
-exon list size: 528


building trellis

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80.4    
80.6    
80.8    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 18910, rend_intergenic: 12922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80406, rend_intergenic: 75508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13003
-exon list size: 20


building trellis

4.5    
9.1    
13.6    
18.2    
22.7    
27.3    
31.8    
36.4    
40.9    
45.5    
50.0    
54.5    
59.1    
63.6    
68.2    
72.7    
77.3    
81.8    
86.4    
90.9    
95.5    
-found 2 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support