-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_9851178-10176535

-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 CodingQuarry_transcript_28653-T1
Valid prediction for snap_scaffold_2-snap.1964-T1
Valid prediction for GlimmerHMM_glimmerT_4390-T1
Valid prediction for snap_scaffold_2-snap.1982-T1
Valid prediction for Augustus_model.g2942.t1
Valid prediction for GlimmerHMM_glimmerT_4385-T1
Valid prediction for GlimmerHMM_glimmerT_4392-T1
Valid prediction for snap_scaffold_2-snap.1985-T1
Valid prediction for Augustus_model.g2936.t1
Valid prediction for CodingQuarry_transcript_28654-T1
Valid prediction for snap_scaffold_2-snap.1977-T1
Valid prediction for snap_scaffold_2-snap.1954-T1
Valid prediction for GlimmerHMM_glimmerT_4388-T1
Valid prediction for GlimmerHMM_glimmerT_4375-T1
Valid prediction for Augustus_model.g2932.t1
Valid prediction for Augustus_model.g2939.t1
Valid prediction for snap_scaffold_2-snap.1950-T1
Valid prediction for snap_scaffold_2-snap.1966-T1
Valid prediction for snap_scaffold_2-snap.1956-T1
Valid prediction for GlimmerHMM_glimmerT_4379-T1
Valid prediction for GlimmerHMM_glimmerT_4382-T1
Valid prediction for snap_scaffold_2-snap.1960-T1
Valid prediction for GlimmerHMM_glimmerT_4391-T1
Valid prediction for snap_scaffold_2-snap.1963-T1
Valid prediction for snap_scaffold_2-snap.1974-T1
Valid prediction for Augustus_model.g2946.t1
Valid prediction for snap_scaffold_2-snap.1961-T1
Valid prediction for HiQ_model.g2943.t1
Valid prediction for GlimmerHMM_glimmerT_4386-T1
Valid prediction for GlimmerHMM_glimmerT_4369-T1
Valid prediction for snap_scaffold_2-snap.1978-T1
Valid prediction for snap_scaffold_2-snap.1965-T1
Valid prediction for GlimmerHMM_glimmerT_4370-T1
Valid prediction for CodingQuarry_transcript_28656-T1
Valid prediction for GlimmerHMM_glimmerT_4387-T1
Valid prediction for GlimmerHMM_glimmerT_4393-T1
Valid prediction for Augustus_model.g2945.t1
Valid prediction for pasa_asmbl_24693.p1
Valid prediction for snap_scaffold_2-snap.1955-T1
Valid prediction for Augustus_model.g2944.t1
Valid prediction for snap_scaffold_2-snap.1983-T1
Valid prediction for GlimmerHMM_glimmerT_4371-T1
Valid prediction for GlimmerHMM_glimmerT_4383-T1
Couldn't classify 57885, 57960
Sorry, prediction pasa_asmbl_24692.p1 fails validation.
(TGC)	 CG	57885-57960	GT	AGG
(ACC)	 AG	58199-58299	GT	AGG
(GTG)	 AG	58413-58616	GT	AGG
(TTT)	 AG	59193-59389	GT	AAG
(CAA)	 AG	59513-59579	GT	AGG
(GAG)	 AG	59762-59952	GT	CAG
(TTT)	 AG	60152-60304	GT	AGG
(CTC)	 AG	60644-60849	GT	AGG
(AGA)	 AG	61283-61351	GT	CGG
(AAG)	 AG	61458-61582	GT	GAG
add_exon() Sorry, pasa_asmbl_24692.p1 60644-60849-terminal-2 is invalid.
-recovered pasa_asmbl_24692.p1, terminal, 60644, 60849
-recovered pasa_asmbl_24692.p1, terminal, 61458, 61582
-recovered pasa_asmbl_24692.p1, internal, 58199, 58299
-recovered pasa_asmbl_24692.p1, internal, 58413, 58616
-recovered pasa_asmbl_24692.p1, internal, 59193, 59389
-recovered pasa_asmbl_24692.p1, internal, 59513, 59579
-recovered pasa_asmbl_24692.p1, internal, 59762, 59952
-recovered pasa_asmbl_24692.p1, internal, 60152, 60304
-recovered pasa_asmbl_24692.p1, internal, 60644, 60849
-recovered pasa_asmbl_24692.p1, internal, 61283, 61351
-recovered pasa_asmbl_24692.p1, internal, 61458, 61582
Couldn't classify 53180, 53336
Couldn't classify 54173, 54232
Sorry, prediction pasa_asmbl_24691.p1 fails validation.
(GCC)	 AC	53180-53336	GT	AGG
(GTG)	 AG	53431-53558	GT	AAG
(GCG)	 AG	53677-53895	GT	AGG
(ATG)	 AG	54173-54232	AG	GGA
-recovered pasa_asmbl_24691.p1, internal, 53431, 53558
-recovered pasa_asmbl_24691.p1, internal, 53677, 53895
Valid prediction for snap_scaffold_2-snap.1967-T1
Valid prediction for Augustus_model.g2941.t1
Valid prediction for pasa_asmbl_24696.p1
Valid prediction for GlimmerHMM_glimmerT_4374-T1
Valid prediction for snap_scaffold_2-snap.1970-T1
Valid prediction for Augustus_model.g2935.t1
Valid prediction for Augustus_model.g2937.t1
Valid prediction for snap_scaffold_2-snap.1980-T1
Valid prediction for snap_scaffold_2-snap.1951-T1
Valid prediction for GlimmerHMM_glimmerT_4376-T1
Valid prediction for snap_scaffold_2-snap.1976-T1
Valid prediction for CodingQuarry_transcript_28655-T1
Valid prediction for GlimmerHMM_glimmerT_4368-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_2-snap.1969-T1
Valid prediction for snap_scaffold_2-snap.1957-T1
Valid prediction for HiQ_model.g2931.t1
Valid prediction for snap_scaffold_2-snap.1968-T1
Valid prediction for GlimmerHMM_glimmerT_4381-T1
Valid prediction for snap_scaffold_2-snap.1981-T1
Valid prediction for GlimmerHMM_glimmerT_4394-T1
Valid prediction for GlimmerHMM_glimmerT_4377-T1
Valid prediction for snap_scaffold_2-snap.1949-T1
Valid prediction for snap_scaffold_2-snap.1962-T1
Valid prediction for snap_scaffold_2-snap.1948-T1
Valid prediction for snap_scaffold_2-snap.1947-T1
Valid prediction for snap_scaffold_2-snap.1975-T1
Valid prediction for GlimmerHMM_glimmerT_4367-T1
Valid prediction for Augustus_model.g2930.t1
Valid prediction for snap_scaffold_2-snap.1973-T1
Couldn't classify 309820, 309916
Sorry, prediction pasa_asmbl_23398.p1 fails validation.
(ATG)	 CC	301139-301297	GT	AGG
(CTG)	 AG	302579-302728	GT	AGG
(ATG)	 AG	302971-303102	GT	ATG
(CAA)	 AG	303460-303630	GT	TGG
(CTT)	 AG	304074-304189	GT	AGG
(CCA)	 AG	304303-304498	GT	CGG
(GGC)	 AG	304856-305045	GT	TGG
(GAG)	 AG	305259-305322	GT	AGG
(GGC)	 AG	305547-305750	GT	AGG
(TAG)	 AG	307447-307537	GT	CGG
(GAG)	 AG	307624-307738	GT	AGG
(AGA)	 AG	307969-308157	GT	GGG
(GCT)	 AG	308399-308598	GT	AGG
(GTG)	 AG	308883-308990	GT	AGG
(CAC)	 AG	309240-309308	GT	AGG
(GTG)	 AG	309428-309576	GT	AGG
(GCA)	 AG	309820-309916	AG	AGA
-recovered pasa_asmbl_23398.p1, initial, 301139, 301297
-recovered pasa_asmbl_23398.p1, initial, 302971, 303102
-recovered pasa_asmbl_23398.p1, internal, 302579, 302728
-recovered pasa_asmbl_23398.p1, internal, 302971, 303102
-recovered pasa_asmbl_23398.p1, internal, 303460, 303630
-recovered pasa_asmbl_23398.p1, internal, 304074, 304189
-recovered pasa_asmbl_23398.p1, internal, 304303, 304498
-recovered pasa_asmbl_23398.p1, internal, 304856, 305045
-recovered pasa_asmbl_23398.p1, internal, 305259, 305322
-recovered pasa_asmbl_23398.p1, internal, 305547, 305750
-recovered pasa_asmbl_23398.p1, internal, 307447, 307537
-recovered pasa_asmbl_23398.p1, internal, 307624, 307738
-recovered pasa_asmbl_23398.p1, internal, 307969, 308157
-recovered pasa_asmbl_23398.p1, internal, 308399, 308598
-recovered pasa_asmbl_23398.p1, internal, 308883, 308990
-recovered pasa_asmbl_23398.p1, internal, 309240, 309308
-recovered pasa_asmbl_23398.p1, internal, 309428, 309576
Valid prediction for GlimmerHMM_glimmerT_4389-T1
Valid prediction for snap_scaffold_2-snap.1959-T1
Valid prediction for GlimmerHMM_glimmerT_4378-T1
Valid prediction for snap_scaffold_2-snap.1953-T1
Valid prediction for Augustus_model.g2940.t1
Valid prediction for GlimmerHMM_glimmerT_4364-T1
Valid prediction for CodingQuarry_transcript_28652-T1
Valid prediction for snap_scaffold_2-snap.1952-T1
Valid prediction for GlimmerHMM_glimmerT_4372-T1
Valid prediction for GlimmerHMM_glimmerT_4380-T1
Couldn't classify 316175, 316338
Sorry, prediction pasa_asmbl_23394.p1 fails validation.
(AAG)	 GC	316175-316338	GT	TCG
(GTC)	 AG	316556-316720	GT	AGG
(GTT)	 AG	317012-317129	GT	AGG
(ATG)	 AG	317328-317498	GT	AGG
(CAA)	 AG	317953-318152	GT	GAG
(TGA)	 AG	318426-318513	AA	GAA
-recovered pasa_asmbl_23394.p1, initial, 317328, 317498
-recovered pasa_asmbl_23394.p1, terminal, 318426, 318513
-recovered pasa_asmbl_23394.p1, internal, 316556, 316720
-recovered pasa_asmbl_23394.p1, internal, 317012, 317129
-recovered pasa_asmbl_23394.p1, internal, 317328, 317498
-recovered pasa_asmbl_23394.p1, internal, 317953, 318152
Valid prediction for snap_scaffold_2-snap.1979-T1
Valid prediction for Augustus_model.g2933.t1
Valid prediction for Augustus_model.g2938.t1
Valid prediction for GlimmerHMM_glimmerT_4365-T1
Couldn't classify 181871, 182173
Sorry, prediction pasa_asmbl_23405.p1 fails validation.
(GTT)	 AT	181871-182173	GA	AGG
Valid prediction for snap_scaffold_2-snap.1972-T1
Couldn't classify 310565, 310606
Couldn't classify 315837, 315972
Sorry, prediction pasa_asmbl_23395.p1 fails validation.
(CGC)	 CT	310565-310606	GT	AAG
(GGT)	 AG	310902-311067	GT	AGG
(AGA)	 AG	312720-312777	GT	AAG
(CTC)	 AG	313083-313137	GT	AGG
(GCT)	 AG	313229-313428	GT	ATG
(TTC)	 AG	314193-314300	GT	CAG
(AGG)	 AG	315837-315972	GG	AAG
-recovered pasa_asmbl_23395.p1, internal, 310902, 311067
-recovered pasa_asmbl_23395.p1, internal, 312720, 312777
-recovered pasa_asmbl_23395.p1, internal, 313083, 313137
-recovered pasa_asmbl_23395.p1, internal, 313229, 313428
-recovered pasa_asmbl_23395.p1, internal, 314193, 314300
Valid prediction for snap_scaffold_2-snap.1958-T1
Valid prediction for Augustus_model.g2934.t1
Valid prediction for GlimmerHMM_glimmerT_4384-T1
Couldn't classify 284808, 284824
Sorry, prediction pasa_asmbl_23400.p1 fails validation.
(CTC)	 CA	284808-284824	GT	AGG
(CAT)	 AG	285280-285773	GT	AGG
(GCA)	 AG	286070-286229	GT	AGG
(ATA)	 AG	286758-286963	GT	AGG
(GGG)	 AG	287044-287152	GT	ATG
(GTA)	 AG	287664-287827	GT	TGG
(GTA)	 AG	288017-288131	GT	GGG
(GTA)	 AG	288494-288619	GT	AGG
(GTG)	 AG	288827-288945	GT	GGG
(GTA)	 AG	289088-289240	GT	TGG
(GCG)	 AG	289414-289637	GG	AAG
add_exon() Sorry, pasa_asmbl_23400.p1 285280-285773-terminal-2 is invalid.
-recovered pasa_asmbl_23400.p1, terminal, 285280, 285773
-recovered pasa_asmbl_23400.p1, terminal, 289414, 289637
-recovered pasa_asmbl_23400.p1, internal, 285280, 285773
-recovered pasa_asmbl_23400.p1, internal, 286070, 286229
-recovered pasa_asmbl_23400.p1, internal, 286758, 286963
-recovered pasa_asmbl_23400.p1, internal, 287044, 287152
-recovered pasa_asmbl_23400.p1, internal, 287664, 287827
-recovered pasa_asmbl_23400.p1, internal, 288017, 288131
-recovered pasa_asmbl_23400.p1, internal, 288494, 288619
-recovered pasa_asmbl_23400.p1, internal, 288827, 288945
-recovered pasa_asmbl_23400.p1, internal, 289088, 289240
Valid prediction for GlimmerHMM_glimmerT_4366-T1
Valid prediction for snap_scaffold_2-snap.1971-T1
Valid prediction for GlimmerHMM_glimmerT_4373-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22916, rend_intergenic: 18632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26327, rend_intergenic: 24014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76384, rend_intergenic: 73507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87974, rend_intergenic: 85996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 268999, rend_intergenic: 262599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 300139, rend_intergenic: 295866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 304112, rend_intergenic: 301823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 307659, rend_intergenic: 304540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 325358
-exon list size: 494


building trellis

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-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 22916, rend_intergenic: 18632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26327, rend_intergenic: 24014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76384, rend_intergenic: 73507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87974, rend_intergenic: 85996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 268999, rend_intergenic: 262599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 300139, rend_intergenic: 295866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 304112, rend_intergenic: 301823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 307659, rend_intergenic: 304540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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

-building DP trellis

-building trellis in range 310702 - 325358
-exon list size: 39


building trellis

2.4    
4.9    
7.3    
9.8    
12.2    
14.6    
17.1    
19.5    
22.0    
24.4    
26.8    
29.3    
31.7    
34.1    
36.6    
39.0    
41.5    
43.9    
46.3    
48.8    
51.2    
53.7    
56.1    
58.5    
61.0    
63.4    
65.9    
68.3    
70.7    
73.2    
75.6    
78.0    
80.5    
82.9    
85.4    
87.8    
90.2    
92.7    
95.1    
97.6    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support