-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_9413726-9582099

-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 snap_scaffold_19-snap.1885-T1
Valid prediction for GlimmerHMM_glimmerT_45684-T1
Valid prediction for HiQ_model.g30485.t1
Valid prediction for snap_scaffold_19-snap.1855-T1
Valid prediction for snap_scaffold_19-snap.1888-T1
Valid prediction for GeneMark_model.79733_t
Valid prediction for snap_scaffold_19-snap.1860-T1
Valid prediction for GlimmerHMM_glimmerT_45692-T1
Valid prediction for HiQ_model.g30493.t1
Valid prediction for GlimmerHMM_glimmerT_45680-T1
Valid prediction for GeneMark_model.79734_t
Valid prediction for Augustus_model.g30479.t1
Valid prediction for pasa_asmbl_22413.p1
Valid prediction for snap_scaffold_19-snap.1881-T1
Valid prediction for snap_scaffold_19-snap.1868-T1
Valid prediction for GeneMark_model.79743_t
Valid prediction for GlimmerHMM_glimmerT_45682-T1
Valid prediction for GlimmerHMM_glimmerT_45675-T1
Valid prediction for snap_scaffold_19-snap.1854-T1
Valid prediction for snap_scaffold_19-snap.1858-T1
Valid prediction for Augustus_model.g30491.t1
Valid prediction for GlimmerHMM_glimmerT_45697-T1
Valid prediction for GlimmerHMM_glimmerT_45691-T1
Couldn't classify 6707, 6760
Sorry, prediction pasa_asmbl_22387.p1 fails validation.
(CTG)	 AC	6707-6760	GT	AGG
(GGC)	 AG	6890-7006	GT	GGG
(GAT)	 AG	7186-7347	GT	AGG
(GAT)	 AG	7543-7691	GT	AGG
(CTT)	 AG	7839-7974	GT	AGG
(ATG)	 AG	9099-9200	CC	GAC
-recovered pasa_asmbl_22387.p1, terminal, 9099, 9200
-recovered pasa_asmbl_22387.p1, internal, 6890, 7006
-recovered pasa_asmbl_22387.p1, internal, 7186, 7347
-recovered pasa_asmbl_22387.p1, internal, 7543, 7691
-recovered pasa_asmbl_22387.p1, internal, 7839, 7974
Valid prediction for GlimmerHMM_glimmerT_45699-T1
Valid prediction for pasa_asmbl_22406.p1
Valid prediction for GlimmerHMM_glimmerT_45683-T1
Valid prediction for CodingQuarry_transcript_25719-T1
Valid prediction for snap_scaffold_19-snap.1872-T1
Valid prediction for GeneMark_model.79738_t
Valid prediction for snap_scaffold_19-snap.1865-T1
Valid prediction for GlimmerHMM_glimmerT_45678-T1
Valid prediction for CodingQuarry_transcript_25716-T1
Valid prediction for GeneMark_model.79726_t
Valid prediction for GeneMark_model.79744_t
Valid prediction for snap_scaffold_19-snap.1877-T1
Valid prediction for CodingQuarry_transcript_25718-T1
Valid prediction for pasa_asmbl_22402.p1
Valid prediction for snap_scaffold_19-snap.1867-T1
Valid prediction for snap_scaffold_19-snap.1879-T1
Valid prediction for snap_scaffold_19-snap.1883-T1
Valid prediction for GlimmerHMM_glimmerT_45685-T1
Valid prediction for pasa_asmbl_22396.p1
Valid prediction for GlimmerHMM_glimmerT_45681-T1
Valid prediction for Augustus_model.g30481.t1
Valid prediction for GeneMark_model.79725_t
Valid prediction for GeneMark_model.79749_t
Valid prediction for snap_scaffold_19-snap.1862-T1
Valid prediction for GeneMark_model.79735_t
Valid prediction for Augustus_model.g30477.t1
Couldn't classify 18101, 18141
Sorry, prediction pasa_asmbl_22391.p1 fails validation.
(ATG)	 CT	17184-17369	GT	AGG
(GAG)	 AG	17476-17712	GT	TGG
(GTG)	 AG	17804-17942	GT	AGG
(AAC)	 AG	18101-18141	GA	GAG
-recovered pasa_asmbl_22391.p1, initial, 17184, 17369
-recovered pasa_asmbl_22391.p1, internal, 17476, 17712
-recovered pasa_asmbl_22391.p1, internal, 17804, 17942
Valid prediction for Augustus_model.g30483.t1
Valid prediction for CodingQuarry_transcript_25712-T1
Valid prediction for GlimmerHMM_glimmerT_45673-T1
Valid prediction for GeneMark_model.79729_t
Couldn't classify 4475, 4529
Couldn't classify 5307, 5344
Sorry, prediction pasa_asmbl_22385.p1 fails validation.
(AAG)	 TC	4475-4529	GT	TGG
(GCT)	 AG	4760-4869	GT	TGG
(GAG)	 AG	5019-5136	GT	AGG
(GGG)	 AG	5307-5344	CG	AGC
-recovered pasa_asmbl_22385.p1, internal, 4760, 4869
-recovered pasa_asmbl_22385.p1, internal, 5019, 5136
Valid prediction for snap_scaffold_19-snap.1861-T1
Couldn't classify 9573, 9884
Sorry, prediction pasa_asmbl_22389.p1 fails validation.
(ACC)	 TC	9573-9884	GG	GAG
Valid prediction for GeneMark_model.79731_t
Valid prediction for HiQ_model.g30488.t1
Valid prediction for GeneMark_model.79741_t
Valid prediction for GlimmerHMM_glimmerT_45674-T1
Valid prediction for Augustus_model.g30480.t1
Couldn't classify 6666, 6673
Sorry, prediction pasa_asmbl_22386.p1 fails validation.
(ATG)	 CC	5920-5922	GT	TGG
(GTC)	 AG	6051-6160	GT	AAG
(GAC)	 AG	6293-6465	GT	GGG
(ACA)	 AG	6666-6673	AC	TGA
-recovered pasa_asmbl_22386.p1, initial, 5920, 5922
-recovered pasa_asmbl_22386.p1, terminal, 6051, 6160
-recovered pasa_asmbl_22386.p1, internal, 6051, 6160
-recovered pasa_asmbl_22386.p1, internal, 6293, 6465
Valid prediction for Augustus_model.g30484.t1
Valid prediction for GlimmerHMM_glimmerT_45671-T1
Valid prediction for GeneMark_model.79742_t
Valid prediction for GeneMark_model.79747_t
Valid prediction for snap_scaffold_19-snap.1874-T1
Valid prediction for pasa_asmbl_22405.p2
Valid prediction for GeneMark_model.79739_t
Couldn't classify 24334, 24535
Sorry, prediction pasa_asmbl_22392.p1 fails validation.
(CAG)	 CC	24334-24535	GT	AGG
(AGA)	 AG	24818-24921	GT	AGG
(ACT)	 AG	25021-25101	CC	GAC
-recovered pasa_asmbl_22392.p1, terminal, 25021, 25101
-recovered pasa_asmbl_22392.p1, internal, 24818, 24921
Valid prediction for snap_scaffold_19-snap.1856-T1
Couldn't classify 51537, 51711
Couldn't classify 52114, 52605
Sorry, prediction pasa_asmbl_22404.p1 fails validation.
(AAT)	 GA	51537-51711	GT	AGG
(ATG)	 AG	51837-51985	GT	TGG
(GCT)	 AG	52114-52605	GA	CTG
add_exon() Sorry, pasa_asmbl_22404.p1 51837-51985-initial-1 is invalid.
-recovered pasa_asmbl_22404.p1, initial, 51837, 51985
-recovered pasa_asmbl_22404.p1, internal, 51837, 51985
Valid prediction for snap_scaffold_19-snap.1875-T1
Valid prediction for GlimmerHMM_glimmerT_45679-T1
Valid prediction for snap_scaffold_19-snap.1869-T1
Valid prediction for GlimmerHMM_glimmerT_45677-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_45687-T1
Valid prediction for GlimmerHMM_glimmerT_45690-T1
Valid prediction for snap_scaffold_19-snap.1871-T1
Couldn't classify 27721, 28392
Sorry, prediction pasa_asmbl_21550.p1 fails validation.
(ATG)	 AG	27721-28392	TG	GCT
Valid prediction for GlimmerHMM_glimmerT_45686-T1
Valid prediction for GlimmerHMM_glimmerT_45694-T1
Valid prediction for GeneMark_model.79751_t
Valid prediction for GeneMark_model.79745_t
Valid prediction for GlimmerHMM_glimmerT_45688-T1
Couldn't classify 56213, 56251
Sorry, prediction pasa_asmbl_21547.p1 fails validation.
(ATG)	 TG	55273-55327	GT	GGG
(ATG)	 AG	55432-55553	GT	AGG
(AAC)	 AG	55660-55700	GT	AGG
(GAT)	 AG	55948-56047	GT	AGG
(TTG)	 AG	56213-56251	GC	AGG
-recovered pasa_asmbl_21547.p1, initial, 55273, 55327
add_exon() Sorry, pasa_asmbl_21547.p1 55432-55553-initial-1 is invalid.
-recovered pasa_asmbl_21547.p1, initial, 55432, 55553
-recovered pasa_asmbl_21547.p1, internal, 55432, 55553
-recovered pasa_asmbl_21547.p1, internal, 55660, 55700
-recovered pasa_asmbl_21547.p1, internal, 55948, 56047
-recovered pasa_asmbl_21547.p1, internal, 56213, 56251
Valid prediction for CodingQuarry_transcript_25714-T1
Valid prediction for GeneMark_model.79748_t
Valid prediction for GlimmerHMM_glimmerT_45693-T1
Valid prediction for GlimmerHMM_glimmerT_45695-T1
Valid prediction for HiQ_model.g30487.t1
Valid prediction for GeneMark_model.79732_t
Valid prediction for GeneMark_model.79727_t
Valid prediction for CodingQuarry_transcript_25715-T1
Valid prediction for snap_scaffold_19-snap.1870-T1
Valid prediction for Augustus_model.g30494.t1
Valid prediction for snap_scaffold_19-snap.1876-T1
Valid prediction for Augustus_model.g30478.t1
Valid prediction for snap_scaffold_19-snap.1859-T1
Valid prediction for GeneMark_model.79728_t
Valid prediction for GlimmerHMM_glimmerT_45696-T1
Valid prediction for snap_scaffold_19-snap.1878-T1
Valid prediction for snap_scaffold_19-snap.1864-T1
Valid prediction for Augustus_model.g30482.t1
Valid prediction for snap_scaffold_19-snap.1886-T1
Valid prediction for GlimmerHMM_glimmerT_45701-T1
Valid prediction for Augustus_model.g30490.t1
Valid prediction for GlimmerHMM_glimmerT_45700-T1
Valid prediction for snap_scaffold_19-snap.1882-T1
Valid prediction for CodingQuarry_transcript_25713-T1
Valid prediction for GlimmerHMM_glimmerT_45689-T1
Valid prediction for Augustus_model.g30486.t1
Valid prediction for snap_scaffold_19-snap.1857-T1
Valid prediction for snap_scaffold_19-snap.1873-T1
Valid prediction for snap_scaffold_19-snap.1880-T1
Valid prediction for GeneMark_model.79730_t
Valid prediction for snap_scaffold_19-snap.1866-T1
Valid prediction for Augustus_model.g30492.t1
Valid prediction for snap_scaffold_19-snap.1887-T1
Valid prediction for GeneMark_model.79737_t
Valid prediction for pasa_asmbl_21540.p1
Valid prediction for snap_scaffold_19-snap.1863-T1
Valid prediction for GeneMark_model.79724_t
Valid prediction for snap_scaffold_19-snap.1884-T1
Valid prediction for GlimmerHMM_glimmerT_45672-T1
Valid prediction for GeneMark_model.79750_t
Valid prediction for GeneMark_model.79740_t
Valid prediction for Augustus_model.g30489.t1
Valid prediction for GlimmerHMM_glimmerT_45698-T1
Valid prediction for GeneMark_model.79736_t
Couldn't classify 57821, 57854
Couldn't classify 59184, 59364
Sorry, prediction pasa_asmbl_21545.p1 fails validation.
(CTG)	 CC	57821-57854	GT	CTG
(CTC)	 AG	58073-58221	GT	AGG
(GAG)	 AG	58312-58443	GT	GGG
(GGC)	 AG	58541-58670	GT	AGG
(GGG)	 AG	58810-58987	GT	TGG
(GAG)	 AG	59184-59364	TG	CCT
-recovered pasa_asmbl_21545.p1, internal, 58073, 58221
-recovered pasa_asmbl_21545.p1, internal, 58312, 58443
-recovered pasa_asmbl_21545.p1, internal, 58541, 58670
-recovered pasa_asmbl_21545.p1, internal, 58810, 58987
Valid prediction for GlimmerHMM_glimmerT_45702-T1
Valid prediction for snap_scaffold_19-snap.1853-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_45676-T1
Couldn't classify 56504, 56558
Couldn't classify 57438, 57517
Sorry, prediction pasa_asmbl_21546.p1 fails validation.
(GAC)	 TG	56504-56558	GT	AGG
(GGT)	 AG	56761-56891	GT	AGG
(ATG)	 AG	57079-57158	GT	AGG
(TGA)	 AG	57249-57313	GT	GGG
(AAT)	 AG	57438-57517	GA	AAG
-recovered pasa_asmbl_21546.p1, initial, 57079, 57158
-recovered pasa_asmbl_21546.p1, internal, 56761, 56891
-recovered pasa_asmbl_21546.p1, internal, 57079, 57158
-recovered pasa_asmbl_21546.p1, internal, 57249, 57313
Valid prediction for Augustus_model.g30495.t1
Valid prediction for GeneMark_model.79746_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23416, rend_intergenic: 17812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42184, rend_intergenic: 37495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67785, rend_intergenic: 64246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85701, rend_intergenic: 72456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91764, rend_intergenic: 90289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102741, rend_intergenic: 101311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 168374
-exon list size: 518


building trellis

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-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 23416, rend_intergenic: 17812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42184, rend_intergenic: 37495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67785, rend_intergenic: 64246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85701, rend_intergenic: 72456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91764, rend_intergenic: 90289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102741, rend_intergenic: 101311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 140655 - 168374
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 141604 - 168374
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-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 141604 - 156668
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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

-building DP trellis

-building trellis in range 141604 - 152586
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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 156708 - 168374
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

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