-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_7956815-8210883

-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: +)Couldn't classify 114951, 115142
Sorry, prediction pasa_asmbl_54137.p1 fails validation.
(AAC)	 AG	114951-115142	GT	AGG
(GTT)	 AG	115271-116470	AG	AGA
-recovered pasa_asmbl_54137.p1, terminal, 115271, 116470
-recovered pasa_asmbl_54137.p1, internal, 114951, 115142
Valid prediction for GlimmerHMM_glimmerT_23043-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_23047-T1
Valid prediction for CodingQuarry_transcript_62081-T1
Valid prediction for snap_scaffold_9-snap.1682-T1
Valid prediction for GlimmerHMM_glimmerT_23026-T1
Valid prediction for GeneMark_model.39469_t
Valid prediction for GeneMark_model.39483_t
Valid prediction for GlimmerHMM_glimmerT_23049-T1
Valid prediction for GeneMark_model.39492_t
Valid prediction for snap_scaffold_9-snap.1692-T1
Valid prediction for GeneMark_model.39486_t
Valid prediction for GeneMark_model.39480_t
Valid prediction for snap_scaffold_9-snap.1706-T1
Valid prediction for GlimmerHMM_glimmerT_23048-T1
Valid prediction for HiQ_model.g15424.t1
Valid prediction for GeneMark_model.39467_t
Valid prediction for snap_scaffold_9-snap.1676-T1
Valid prediction for GeneMark_model.39461_t
Valid prediction for GeneMark_model.39476_t
Valid prediction for snap_scaffold_9-snap.1697-T1
Valid prediction for Augustus_model.g15411.t1
Valid prediction for snap_scaffold_9-snap.1709-T1
Valid prediction for GeneMark_model.39468_t
Valid prediction for GlimmerHMM_glimmerT_23027-T1
Valid prediction for CodingQuarry_transcript_62082-T1
Valid prediction for Augustus_model.g15416.t1
Valid prediction for snap_scaffold_9-snap.1704-T1
Valid prediction for GeneMark_model.39484_t
Valid prediction for GeneMark_model.39471_t
Valid prediction for Augustus_model.g15419.t1
Valid prediction for CodingQuarry_transcript_62083-T1
Couldn't classify 191399, 191524
Sorry, prediction pasa_asmbl_54139.p1 fails validation.
(GTG)	 CT	191399-191524	GT	AGG
(GCA)	 AG	191841-192193	GT	AGG
(GAT)	 AG	192357-192569	GT	AGG
(ATT)	 AG	192818-192984	GT	AGG
(CCC)	 AG	193130-193254	GT	AGG
(GTG)	 AG	193624-193947	GC	GAG
-recovered pasa_asmbl_54139.p1, terminal, 193624, 193947
-recovered pasa_asmbl_54139.p1, internal, 191841, 192193
-recovered pasa_asmbl_54139.p1, internal, 192357, 192569
-recovered pasa_asmbl_54139.p1, internal, 192818, 192984
-recovered pasa_asmbl_54139.p1, internal, 193130, 193254
-recovered pasa_asmbl_54139.p1, internal, 193624, 193947
Valid prediction for Augustus_model.g15421.t1
Valid prediction for Augustus_model.g15404.t1
Valid prediction for snap_scaffold_9-snap.1702-T1
Valid prediction for snap_scaffold_9-snap.1710-T1
Valid prediction for Augustus_model.g15409.t1
Couldn't classify 214908, 215390
Sorry, prediction pasa_asmbl_54143.p1 fails validation.
(GAC)	 CT	214908-215390	AC	AAA
Valid prediction for Augustus_model.g15425.t1
Valid prediction for Augustus_model.g15420.t1
Valid prediction for pasa_asmbl_54144.p1
Valid prediction for GeneMark_model.39479_t
Valid prediction for snap_scaffold_9-snap.1698-T1
Valid prediction for GeneMark_model.39490_t
Valid prediction for Augustus_model.g15412.t1
Valid prediction for snap_scaffold_9-snap.1703-T1
Valid prediction for GlimmerHMM_glimmerT_23036-T1
Valid prediction for snap_scaffold_9-snap.1674-T1
Valid prediction for Augustus_model.g15423.t1
Valid prediction for Augustus_model.g15403.t1
Valid prediction for snap_scaffold_9-snap.1701-T1
Valid prediction for GlimmerHMM_glimmerT_23040-T1
Valid prediction for GlimmerHMM_glimmerT_23033-T1
Valid prediction for GlimmerHMM_glimmerT_23046-T1
Valid prediction for pasa_asmbl_54147.p1
Valid prediction for snap_scaffold_9-snap.1707-T1
Valid prediction for snap_scaffold_9-snap.1677-T1
Valid prediction for snap_scaffold_9-snap.1679-T1
Valid prediction for GlimmerHMM_glimmerT_23045-T1
Valid prediction for Augustus_model.g15401.t1
Valid prediction for pasa_asmbl_54136.p1
Valid prediction for pasa_asmbl_54142.p1
Valid prediction for snap_scaffold_9-snap.1675-T1
Valid prediction for GeneMark_model.39489_t
Valid prediction for GeneMark_model.39491_t
Valid prediction for GlimmerHMM_glimmerT_23039-T1
Valid prediction for snap_scaffold_9-snap.1681-T1
Valid prediction for snap_scaffold_9-snap.1705-T1
Valid prediction for GeneMark_model.39466_t
Valid prediction for Augustus_model.g15405.t1
Valid prediction for Augustus_model.g15417.t1
Valid prediction for GlimmerHMM_glimmerT_23050-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_9-snap.1693-T1
Valid prediction for GeneMark_model.39487_t
Valid prediction for pasa_asmbl_55080.p1
Valid prediction for HiQ_model.g15422.t1
Valid prediction for GlimmerHMM_glimmerT_23034-T1
Valid prediction for GlimmerHMM_glimmerT_23038-T1
Valid prediction for GlimmerHMM_glimmerT_23037-T1
Valid prediction for GeneMark_model.39464_t
Valid prediction for snap_scaffold_9-snap.1687-T1
Valid prediction for Augustus_model.g15418.t1
Valid prediction for Augustus_model.g15415.t1
Valid prediction for Augustus_model.g15413.t1
Valid prediction for GeneMark_model.39477_t
Valid prediction for GeneMark_model.39460_t
Valid prediction for Augustus_model.g15414.t1
Valid prediction for snap_scaffold_9-snap.1683-T1
Valid prediction for GeneMark_model.39473_t
Valid prediction for snap_scaffold_9-snap.1688-T1
Valid prediction for snap_scaffold_9-snap.1708-T1
Valid prediction for snap_scaffold_9-snap.1700-T1
Valid prediction for GlimmerHMM_glimmerT_23044-T1
Valid prediction for GlimmerHMM_glimmerT_23029-T1
Valid prediction for GeneMark_model.39478_t
Valid prediction for snap_scaffold_9-snap.1684-T1
Valid prediction for GlimmerHMM_glimmerT_23042-T1
Valid prediction for snap_scaffold_9-snap.1680-T1
Valid prediction for snap_scaffold_9-snap.1689-T1
Valid prediction for pasa_asmbl_55092.p1
Valid prediction for GeneMark_model.39465_t
Valid prediction for Augustus_model.g15408.t1
Valid prediction for GlimmerHMM_glimmerT_23031-T1
Valid prediction for CodingQuarry_transcript_62076-T1
Valid prediction for GeneMark_model.39470_t
Valid prediction for snap_scaffold_9-snap.1685-T1
Valid prediction for snap_scaffold_9-snap.1678-T1
Valid prediction for GlimmerHMM_glimmerT_23032-T1
Valid prediction for HiQ_model.g15410.t1
Valid prediction for Augustus_model.g15402.t1
Couldn't classify 92462, 92520
Sorry, prediction pasa_asmbl_55091.p1 fails validation.
(GGA)	 TG	92462-92520	GT	AGG
(GAT)	 AG	92691-92881	GT	AGG
(ACG)	 AG	93179-93305	GT	AGG
(ATG)	 AG	93550-93689	GT	AGG
(GGT)	 AG	94115-94245	GT	GGG
(GAG)	 AG	94373-94513	CT	GAC
add_exon() Sorry, pasa_asmbl_55091.p1 93550-93689-initial-1 is invalid.
-recovered pasa_asmbl_55091.p1, initial, 93550, 93689
add_exon() Sorry, pasa_asmbl_55091.p1 92691-92881-terminal-2 is invalid.
-recovered pasa_asmbl_55091.p1, terminal, 92691, 92881
add_exon() Sorry, pasa_asmbl_55091.p1 93550-93689-terminal-2 is invalid.
-recovered pasa_asmbl_55091.p1, terminal, 93550, 93689
-recovered pasa_asmbl_55091.p1, terminal, 94373, 94513
-recovered pasa_asmbl_55091.p1, internal, 92691, 92881
-recovered pasa_asmbl_55091.p1, internal, 93179, 93305
-recovered pasa_asmbl_55091.p1, internal, 93550, 93689
-recovered pasa_asmbl_55091.p1, internal, 94115, 94245
Valid prediction for snap_scaffold_9-snap.1694-T1
Valid prediction for GlimmerHMM_glimmerT_23041-T1
Valid prediction for GeneMark_model.39463_t
Couldn't classify 120236, 120291
Sorry, prediction pasa_asmbl_55087.p1 fails validation.
(ATG)	 TT	116183-116302	GT	AGG
(GAA)	 AG	116613-116756	GT	AGG
(GAA)	 AG	116955-117026	GT	AGG
(GCT)	 AG	117117-117175	GT	AAG
(TCA)	 AG	118406-118517	GT	AGG
(GAC)	 AG	118657-118739	GT	GGG
(GCT)	 AG	118992-119062	GT	GAG
(ATG)	 AG	119329-119422	GT	AAG
(GTA)	 AG	119593-119721	GT	AGG
(GTA)	 AG	119873-119964	GT	AGG
(GAC)	 AG	120236-120291	CC	GAC
-recovered pasa_asmbl_55087.p1, initial, 116183, 116302
add_exon() Sorry, pasa_asmbl_55087.p1 119329-119422-initial-1 is invalid.
-recovered pasa_asmbl_55087.p1, initial, 119329, 119422
-recovered pasa_asmbl_55087.p1, internal, 116613, 116756
-recovered pasa_asmbl_55087.p1, internal, 116955, 117026
-recovered pasa_asmbl_55087.p1, internal, 117117, 117175
-recovered pasa_asmbl_55087.p1, internal, 118406, 118517
-recovered pasa_asmbl_55087.p1, internal, 118657, 118739
-recovered pasa_asmbl_55087.p1, internal, 118992, 119062
-recovered pasa_asmbl_55087.p1, internal, 119329, 119422
-recovered pasa_asmbl_55087.p1, internal, 119593, 119721
-recovered pasa_asmbl_55087.p1, internal, 119873, 119964
Valid prediction for GlimmerHMM_glimmerT_23030-T1
Valid prediction for GlimmerHMM_glimmerT_23028-T1
Valid prediction for GeneMark_model.39485_t
Valid prediction for CodingQuarry_transcript_62077-T1
Valid prediction for snap_scaffold_9-snap.1690-T1
Valid prediction for snap_scaffold_9-snap.1686-T1
Valid prediction for Augustus_model.g15400.t1
Valid prediction for CodingQuarry_transcript_62078-T1
Valid prediction for snap_scaffold_9-snap.1696-T1
Valid prediction for snap_scaffold_9-snap.1695-T1
Valid prediction for HiQ_model.g15407.t1
Valid prediction for snap_scaffold_9-snap.1673-T1
Couldn't classify 98198, 99178
Sorry, prediction pasa_asmbl_55089.p1 fails validation.
(AGC)	 AC	98198-99178	TC	GAT
Valid prediction for GlimmerHMM_glimmerT_23035-T1
Valid prediction for GeneMark_model.39482_t
Valid prediction for GeneMark_model.39475_t
Valid prediction for GlimmerHMM_glimmerT_23025-T1
Valid prediction for pasa_asmbl_55086.p1
Valid prediction for Augustus_model.g15406.t1
Valid prediction for GeneMark_model.39474_t
Valid prediction for CodingQuarry_transcript_62080-T1
Valid prediction for snap_scaffold_9-snap.1691-T1
Valid prediction for snap_scaffold_9-snap.1699-T1
Couldn't classify 159181, 159323
Sorry, prediction pasa_asmbl_55084.p1 fails validation.
(TTA)	 TG	159181-159323	GT	GGG
(ACC)	 AG	159711-159809	GT	GCG
(GAC)	 AG	161519-161583	GT	AGG
(TGG)	 AG	161791-161948	GT	AGG
(ACA)	 AG	162024-162188	GC	GGG
(GTG)	 AG	162282-162428	GT	GTG
(GCT)	 AG	162543-162684	GT	AGG
(CAC)	 AG	163613-163825	GT	TGG
(CCA)	 AG	163946-164080	GT	TGG
(ATG)	 AG	164249-164397	GT	CTG
(GCT)	 AG	164847-164983	GT	AAG
(GAT)	 AG	165070-165200	GT	GGG
(GAG)	 AG	165335-165465	GT	CTG
(GCA)	 AG	165599-165701	GT	AGG
(ACC)	 AG	165870-165937	GT	AGG
(TAT)	 AG	166653-166698	GT	GAG
(GGA)	 AG	166810-166836	GT	AGG
(GGC)	 AG	167135-167482	GT	AGG
(GAA)	 AG	167627-167713	GT	AGG
(AGG)	 AG	168027-168065	GT	AGG
(CTG)	 AG	168182-168225	TC	GAT
add_exon() Sorry, pasa_asmbl_55084.p1 164249-164397-initial-1 is invalid.
-recovered pasa_asmbl_55084.p1, initial, 164249, 164397
add_exon() Sorry, pasa_asmbl_55084.p1 166653-166698-terminal-3 is invalid.
-recovered pasa_asmbl_55084.p1, terminal, 166653, 166698
-recovered pasa_asmbl_55084.p1, terminal, 168182, 168225
-recovered pasa_asmbl_55084.p1, internal, 159711, 159809
-recovered pasa_asmbl_55084.p1, internal, 161519, 161583
-recovered pasa_asmbl_55084.p1, internal, 161791, 161948
-recovered pasa_asmbl_55084.p1, internal, 162024, 162188
-recovered pasa_asmbl_55084.p1, internal, 162282, 162428
-recovered pasa_asmbl_55084.p1, internal, 162543, 162684
-recovered pasa_asmbl_55084.p1, internal, 163613, 163825
-recovered pasa_asmbl_55084.p1, internal, 163946, 164080
-recovered pasa_asmbl_55084.p1, internal, 164249, 164397
-recovered pasa_asmbl_55084.p1, internal, 164847, 164983
-recovered pasa_asmbl_55084.p1, internal, 165070, 165200
-recovered pasa_asmbl_55084.p1, internal, 165335, 165465
-recovered pasa_asmbl_55084.p1, internal, 165599, 165701
-recovered pasa_asmbl_55084.p1, internal, 165870, 165937
-recovered pasa_asmbl_55084.p1, internal, 166653, 166698
-recovered pasa_asmbl_55084.p1, internal, 166810, 166836
-recovered pasa_asmbl_55084.p1, internal, 167135, 167482
-recovered pasa_asmbl_55084.p1, internal, 167627, 167713
-recovered pasa_asmbl_55084.p1, internal, 168027, 168065
Valid prediction for GeneMark_model.39472_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 41333, rend_intergenic: 38338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47166, rend_intergenic: 45246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 254069
-exon list size: 485


building trellis

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98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 41333, rend_intergenic: 38338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47166, rend_intergenic: 45246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 242517 - 254069
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 242571 - 254069
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 242930 - 254069
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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