-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_8593220-8778049

-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 HiQ_model.g18243.t1
Valid prediction for HiQ_model.g18246.t1
Valid prediction for Augustus_model.g18240.t1
Valid prediction for pasa_asmbl_5818.p1
Valid prediction for HiQ_model.g18245.t1
Valid prediction for CodingQuarry_transcript_8183-T1
Valid prediction for GlimmerHMM_glimmerT_27567-T1
Valid prediction for GlimmerHMM_glimmerT_27561-T1
Valid prediction for snap_scaffold_11-snap.1971-T1
Valid prediction for pasa_asmbl_5814.p1
Valid prediction for snap_scaffold_11-snap.1952-T1
Valid prediction for Augustus_model.g18260.t1
Valid prediction for GlimmerHMM_glimmerT_27563-T1
Couldn't classify 28096, 28156
Sorry, prediction pasa_asmbl_5817.p2 fails validation.
(GCT)	 AC	28096-28156	GT	AGG
(GTT)	 AG	28255-28374	GT	AGG
(GAA)	 AG	28458-28548	GT	AGG
(GGC)	 AG	28666-28753	AT	AAA
-recovered pasa_asmbl_5817.p2, terminal, 28666, 28753
-recovered pasa_asmbl_5817.p2, internal, 28255, 28374
-recovered pasa_asmbl_5817.p2, internal, 28458, 28548
Valid prediction for Augustus_model.g18257.t1
Valid prediction for CodingQuarry_transcript_8174-T1
Valid prediction for GlimmerHMM_glimmerT_27565-T1
Valid prediction for GlimmerHMM_glimmerT_27568-T1
Valid prediction for pasa_asmbl_5806.p1
Valid prediction for snap_scaffold_11-snap.1955-T1
Valid prediction for snap_scaffold_11-snap.1975-T1
Valid prediction for pasa_asmbl_5827.p1
Valid prediction for snap_scaffold_11-snap.1945-T1
Valid prediction for snap_scaffold_11-snap.1957-T1
Valid prediction for pasa_asmbl_5823.p1
Valid prediction for CodingQuarry_transcript_8173-T1
Valid prediction for Augustus_model.g18259.t1
Valid prediction for snap_scaffold_11-snap.1965-T1
Valid prediction for GlimmerHMM_glimmerT_27559-T1
Valid prediction for pasa_asmbl_5805.p2
Valid prediction for pasa_asmbl_5829.p1
Valid prediction for GlimmerHMM_glimmerT_27578-T1
Valid prediction for pasa_asmbl_5837.p1
Valid prediction for HiQ_model.g18238.t1
Valid prediction for GlimmerHMM_glimmerT_27564-T1
Valid prediction for CodingQuarry_transcript_8186-T1
Valid prediction for GlimmerHMM_glimmerT_27584-T1
Valid prediction for HiQ_model.g18239.t1
Couldn't classify 50996, 53317
Couldn't classify 53588, 54022
Sorry, prediction CodingQuarry_transcript_8180-T1 fails validation.
(ATG)	 AA	45976-46114	GT	AGG
(ATG)	 AG	47039-47115	GT	AGG
(TAC)	 AG	47245-47355	GT	ACG
(GTG)	 AG	47445-47735	GT	AGG
(GCA)	 AG	48098-48166	GT	ACG
(GAT)	 AG	48545-48710	GT	CGG
(GCA)	 AG	49099-49419	GT	AGG
(ATG)	 AG	50067-50107	GT	AGG
(AGT)	 AG	50254-50349	GT	AGG
(CTG)	 AG	50533-50721	GT	AGG
(CAC)	 AG	50996-53317	CT	AGC
(CAC)	 AC	53588-54022	GT	AGG
(GGG)	 AG	54355-54495	GT	AGG
(TTG)	 AG	55374-55567	GT	AGG
(CCA)	 AG	55836-55999	GC	AGG
(AAG)	 AG	56498-56601	GT	AGG
(GTG)	 AG	56900-56999	GT	AGG
(TGG)	 AG	58350-58431	GT	AAG
(AGT)	 AG	58732-58846	GT	AGG
(ATG)	 AG	60634-60756	GT	CGG
(TCA)	 AG	60898-61036	GT	AGG
(GAG)	 AG	61159-61376	TG	AGT
-recovered CodingQuarry_transcript_8180-T1, initial, 45976, 46114
-recovered CodingQuarry_transcript_8180-T1, initial, 47039, 47115
-recovered CodingQuarry_transcript_8180-T1, initial, 50067, 50107
-recovered CodingQuarry_transcript_8180-T1, initial, 60634, 60756
-recovered CodingQuarry_transcript_8180-T1, terminal, 58350, 58431
-recovered CodingQuarry_transcript_8180-T1, terminal, 61159, 61376
-recovered CodingQuarry_transcript_8180-T1, internal, 47039, 47115
-recovered CodingQuarry_transcript_8180-T1, internal, 47245, 47355
-recovered CodingQuarry_transcript_8180-T1, internal, 47445, 47735
-recovered CodingQuarry_transcript_8180-T1, internal, 48098, 48166
-recovered CodingQuarry_transcript_8180-T1, internal, 48545, 48710
-recovered CodingQuarry_transcript_8180-T1, internal, 49099, 49419
-recovered CodingQuarry_transcript_8180-T1, internal, 50067, 50107
-recovered CodingQuarry_transcript_8180-T1, internal, 50254, 50349
-recovered CodingQuarry_transcript_8180-T1, internal, 50533, 50721
-recovered CodingQuarry_transcript_8180-T1, internal, 54355, 54495
-recovered CodingQuarry_transcript_8180-T1, internal, 55374, 55567
-recovered CodingQuarry_transcript_8180-T1, internal, 55836, 55999
-recovered CodingQuarry_transcript_8180-T1, internal, 56498, 56601
-recovered CodingQuarry_transcript_8180-T1, internal, 56900, 56999
-recovered CodingQuarry_transcript_8180-T1, internal, 58350, 58431
-recovered CodingQuarry_transcript_8180-T1, internal, 58732, 58846
-recovered CodingQuarry_transcript_8180-T1, internal, 60634, 60756
-recovered CodingQuarry_transcript_8180-T1, internal, 60898, 61036
Valid prediction for pasa_asmbl_5834.p1
Valid prediction for snap_scaffold_11-snap.1961-T1
Valid prediction for Augustus_model.g18241.t1
Valid prediction for GlimmerHMM_glimmerT_27562-T1
Valid prediction for snap_scaffold_11-snap.1953-T1
Valid prediction for snap_scaffold_11-snap.1951-T1
Valid prediction for GlimmerHMM_glimmerT_27585-T1
Valid prediction for CodingQuarry_transcript_8185-T1
Valid prediction for pasa_asmbl_5832.p2
Valid prediction for GlimmerHMM_glimmerT_27566-T1
Valid prediction for Augustus_model.g18247.t1
Valid prediction for snap_scaffold_11-snap.1980-T1
Valid prediction for snap_scaffold_11-snap.1959-T1
Valid prediction for CodingQuarry_transcript_8181-T1
Couldn't classify 96478, 96703
Couldn't classify 96808, 96914
Sorry, prediction pasa_asmbl_6250.p1 fails validation.
(CGT)	 AG	96478-96703	GT	AGG
(GGC)	 AG	96808-96914	AC	GCA
-recovered pasa_asmbl_6250.p1, internal, 96478, 96703
Valid prediction for snap_scaffold_11-snap.1970-T1
Valid prediction for CodingQuarry_transcript_8179-T1
Valid prediction for GlimmerHMM_glimmerT_27570-T1
Valid prediction for HiQ_model.g18256.t1
Valid prediction for CodingQuarry_transcript_8175-T1
Valid prediction for CodingQuarry_transcript_8189-T1
Valid prediction for GlimmerHMM_glimmerT_27579-T1
Valid prediction for snap_scaffold_11-snap.1950-T1
Valid prediction for snap_scaffold_11-snap.1956-T1
Valid prediction for pasa_asmbl_5822.p1
Valid prediction for Augustus_model.g18248.t1
Valid prediction for CodingQuarry_transcript_8187-T1
Valid prediction for CodingQuarry_transcript_8178-T1
Valid prediction for GlimmerHMM_glimmerT_27572-T1
Valid prediction for pasa_asmbl_5819.p1
Couldn't classify 108578, 108631
Sorry, prediction pasa_asmbl_5826.p2 fails validation.
(TGC)	 AC	108578-108631	GT	ACG
(GCC)	 AG	108730-108780	GT	AGG
(ATC)	 AG	109038-109250	CT	AAC
-recovered pasa_asmbl_5826.p2, terminal, 109038, 109250
-recovered pasa_asmbl_5826.p2, internal, 108730, 108780
Valid prediction for GlimmerHMM_glimmerT_27582-T1
Valid prediction for GlimmerHMM_glimmerT_27576-T1
Valid prediction for snap_scaffold_11-snap.1977-T1
Valid prediction for HiQ_model.g18244.t1
Valid prediction for Augustus_model.g18250.t1
Valid prediction for snap_scaffold_11-snap.1944-T1
Valid prediction for GlimmerHMM_glimmerT_27577-T1
Valid prediction for HiQ_model.g18252.t1
Valid prediction for snap_scaffold_11-snap.1946-T1
Valid prediction for CodingQuarry_transcript_8172-T1
Valid prediction for Augustus_model.g18254.t1
Couldn't classify 173173, 173341
Couldn't classify 179405, 179460
Sorry, prediction pasa_asmbl_5840.p1 fails validation.
(TGG)	 AG	173173-173341	GT	AGG
(GTA)	 AG	173704-173787	GT	AGG
(ATG)	 AG	174311-174423	GT	AGG
(GTG)	 AG	174934-175033	GT	AGG
(GAA)	 AG	176277-176327	GT	AGG
(GGT)	 AG	176808-176855	GT	AGG
(TCT)	 AG	178670-178759	GT	TGG
(AGA)	 AG	179405-179460	AA	AAA
-recovered pasa_asmbl_5840.p1, initial, 174311, 174423
-recovered pasa_asmbl_5840.p1, internal, 173173, 173341
-recovered pasa_asmbl_5840.p1, internal, 173704, 173787
-recovered pasa_asmbl_5840.p1, internal, 174311, 174423
-recovered pasa_asmbl_5840.p1, internal, 174934, 175033
-recovered pasa_asmbl_5840.p1, internal, 176277, 176327
-recovered pasa_asmbl_5840.p1, internal, 176808, 176855
-recovered pasa_asmbl_5840.p1, internal, 178670, 178759
Valid prediction for GlimmerHMM_glimmerT_27556-T1
Valid prediction for GlimmerHMM_glimmerT_27571-T1
Couldn't classify 106761, 106958
Couldn't classify 108146, 108205
Sorry, prediction pasa_asmbl_5825.p2 fails validation.
(CAG)	 AG	106761-106958	GT	TGG
(GAC)	 AG	107187-107398	GT	AGG
(ACA)	 AG	107771-107936	GT	AGG
(GTG)	 AG	108146-108205	GT	AGG
add_exon() Sorry, pasa_asmbl_5825.p2 107187-107398-terminal-2 is invalid.
-recovered pasa_asmbl_5825.p2, terminal, 107187, 107398
-recovered pasa_asmbl_5825.p2, internal, 106761, 106958
-recovered pasa_asmbl_5825.p2, internal, 107187, 107398
-recovered pasa_asmbl_5825.p2, internal, 107771, 107936
-recovered pasa_asmbl_5825.p2, internal, 108146, 108205
Valid prediction for snap_scaffold_11-snap.1958-T1
Valid prediction for GlimmerHMM_glimmerT_27574-T1
Valid prediction for CodingQuarry_transcript_8188-T1
Valid prediction for snap_scaffold_11-snap.1969-T1
Valid prediction for snap_scaffold_11-snap.1949-T1
Valid prediction for Augustus_model.g18255.t1
Couldn't classify 104778, 104864
Couldn't classify 105140, 105376
Sorry, prediction pasa_asmbl_6303.p1 fails validation.
(TCG)	 CC	104778-104864	GT	AGG
(GTG)	 AG	105140-105376	AG	ACA
Valid prediction for GlimmerHMM_glimmerT_27581-T1
Valid prediction for CodingQuarry_transcript_8177-T1
Valid prediction for snap_scaffold_11-snap.1947-T1
Valid prediction for GlimmerHMM_glimmerT_27557-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_11-snap.1972-T1
Valid prediction for pasa_asmbl_6866.p1
Valid prediction for HiQ_model.g18242.t1
Valid prediction for snap_scaffold_11-snap.1960-T1
Valid prediction for pasa_asmbl_6869.p1
Valid prediction for GlimmerHMM_glimmerT_27583-T1
Valid prediction for snap_scaffold_11-snap.1973-T1
Couldn't classify 2133, 2489
Sorry, prediction pasa_asmbl_5843.p1 fails validation.
(ACA)	 CC	2133-2489	GT	GGG
Valid prediction for Augustus_model.g18249.t1
Valid prediction for GlimmerHMM_glimmerT_27580-T1
Valid prediction for CodingQuarry_transcript_8182-T1
Valid prediction for snap_scaffold_11-snap.1966-T1
Valid prediction for snap_scaffold_11-snap.1967-T1
Valid prediction for GlimmerHMM_glimmerT_27558-T1
Valid prediction for CodingQuarry_transcript_8176-T1
Valid prediction for GlimmerHMM_glimmerT_27569-T1
Valid prediction for HiQ_model.g18253.t1
Valid prediction for snap_scaffold_11-snap.1979-T1
Valid prediction for snap_scaffold_11-snap.1962-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for pasa_asmbl_6864.p1
Valid prediction for GlimmerHMM_glimmerT_27560-T1
Valid prediction for snap_scaffold_11-snap.1976-T1
Valid prediction for snap_scaffold_11-snap.1948-T1
Valid prediction for HiQ_model.g18251.t1
Valid prediction for CodingQuarry_transcript_8184-T1
Valid prediction for GlimmerHMM_glimmerT_27575-T1
Valid prediction for GlimmerHMM_glimmerT_27573-T1
Valid prediction for Augustus_model.g18258.t1
Valid prediction for snap_scaffold_11-snap.1954-T1
Valid prediction for snap_scaffold_11-snap.1964-T1
Valid prediction for snap_scaffold_11-snap.1978-T1
Valid prediction for snap_scaffold_11-snap.1963-T1
Valid prediction for snap_scaffold_11-snap.1968-T1
Valid prediction for snap_scaffold_11-snap.1974-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 61376, rend_intergenic: 54297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105438, rend_intergenic: 97624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107914, rend_intergenic: 106112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149352, rend_intergenic: 145172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178954, rend_intergenic: 172449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 184830
-exon list size: 528


building trellis

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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 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 61376, rend_intergenic: 54297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105438, rend_intergenic: 97624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107914, rend_intergenic: 106112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149352, rend_intergenic: 145172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178954, rend_intergenic: 172449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support