-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_11041293-11253827

-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.g33430.t1
Valid prediction for GlimmerHMM_glimmerT_49815-T1
Valid prediction for pasa_asmbl_28924.p1
Valid prediction for GlimmerHMM_glimmerT_49825-T1
Valid prediction for GlimmerHMM_glimmerT_49833-T1
Valid prediction for GeneMark_model.86319_t
Valid prediction for GeneMark_model.86298_t
Valid prediction for snap_scaffold_21-snap.2398-T1
Valid prediction for HiQ_model.g33438.t1
Valid prediction for GlimmerHMM_glimmerT_49819-T1
Valid prediction for Augustus_model.g33435.t1
Valid prediction for GeneMark_model.86304_t
Valid prediction for snap_scaffold_21-snap.2413-T1
Valid prediction for snap_scaffold_21-snap.2416-T1
Valid prediction for GeneMark_model.86328_t
Valid prediction for snap_scaffold_21-snap.2399-T1
Valid prediction for GeneMark_model.86296_t
Valid prediction for GeneMark_model.86320_t
Valid prediction for GlimmerHMM_glimmerT_49828-T1
Valid prediction for snap_scaffold_21-snap.2403-T1
Valid prediction for GeneMark_model.86286_t
Valid prediction for GeneMark_model.86290_t
Valid prediction for GeneMark_model.86300_t
Valid prediction for snap_scaffold_21-snap.2405-T1
Valid prediction for pasa_asmbl_28923.p1
Valid prediction for GlimmerHMM_glimmerT_49823-T1
Valid prediction for GeneMark_model.86314_t
Valid prediction for GeneMark_model.86321_t
Valid prediction for GeneMark_model.86318_t
Valid prediction for Augustus_model.g33436.t1
Valid prediction for snap_scaffold_21-snap.2411-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.86292_t
Valid prediction for snap_scaffold_21-snap.2420-T1
Valid prediction for GlimmerHMM_glimmerT_49831-T1
Valid prediction for GeneMark_model.86285_t
Valid prediction for snap_scaffold_21-snap.2408-T1
Valid prediction for CodingQuarry_transcript_32679-T1
Valid prediction for snap_scaffold_21-snap.2410-T1
Valid prediction for snap_scaffold_21-snap.2429-T1
Valid prediction for snap_scaffold_21-snap.2417-T1
Valid prediction for GeneMark_model.86324_t
Valid prediction for GlimmerHMM_glimmerT_49817-T1
Valid prediction for HiQ_model.g33437.t1
Valid prediction for GeneMark_model.86287_t
Valid prediction for snap_scaffold_21-snap.2424-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_49830-T1
Valid prediction for GeneMark_model.86301_t
Valid prediction for GlimmerHMM_glimmerT_49818-T1
Valid prediction for Augustus_model.g33439.t1
Valid prediction for Augustus_model.g33432.t1
Valid prediction for snap_scaffold_21-snap.2425-T1
Valid prediction for snap_scaffold_21-snap.2423-T1
Valid prediction for snap_scaffold_21-snap.2419-T1
Valid prediction for GlimmerHMM_glimmerT_49829-T1
Valid prediction for GeneMark_model.86297_t
Valid prediction for snap_scaffold_21-snap.2421-T1
Valid prediction for snap_scaffold_21-snap.2414-T1
Valid prediction for snap_scaffold_21-snap.2422-T1
Valid prediction for GeneMark_model.86308_t
Valid prediction for GlimmerHMM_glimmerT_49826-T1
Valid prediction for GeneMark_model.86313_t
Valid prediction for GeneMark_model.86311_t
Valid prediction for GeneMark_model.86310_t
Valid prediction for GeneMark_model.86302_t

-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_21-snap.2412-T1
Valid prediction for Augustus_model.g33440.t1
Valid prediction for snap_scaffold_21-snap.2395-T1
Valid prediction for snap_scaffold_21-snap.2402-T1
Valid prediction for GlimmerHMM_glimmerT_49814-T1
Couldn't classify 11814, 11930
Couldn't classify 12749, 12829
Sorry, prediction pasa_asmbl_28126.p2 fails validation.
(GTG)	 GC	11814-11930	GT	AGG
(AAA)	 AG	12032-12130	GT	TTG
(CTT)	 AG	12222-12290	GT	AGG
(AGG)	 AG	12749-12829	CA	AGC
-recovered pasa_asmbl_28126.p2, internal, 12032, 12130
-recovered pasa_asmbl_28126.p2, internal, 12222, 12290
Valid prediction for GlimmerHMM_glimmerT_49820-T1
Valid prediction for Augustus_model.g33433.t1
Valid prediction for GeneMark_model.86312_t
Valid prediction for snap_scaffold_21-snap.2400-T1
Valid prediction for GeneMark_model.86315_t
Valid prediction for GlimmerHMM_glimmerT_49824-T1
Valid prediction for CodingQuarry_transcript_32684-T1
Valid prediction for snap_scaffold_21-snap.2401-T1
Valid prediction for snap_scaffold_21-snap.2404-T1
Valid prediction for GlimmerHMM_glimmerT_49813-T1
Valid prediction for GeneMark_model.86307_t
Valid prediction for GeneMark_model.86309_t
Valid prediction for Augustus_model.g33434.t1
Valid prediction for GeneMark_model.86323_t
Valid prediction for snap_scaffold_21-snap.2393-T1
Valid prediction for snap_scaffold_21-snap.2406-T1
Valid prediction for snap_scaffold_21-snap.2427-T1
Valid prediction for Augustus_model.g33428.t1
Valid prediction for Augustus_model.g33427.t1
Valid prediction for GlimmerHMM_glimmerT_49834-T1
Valid prediction for GeneMark_model.86327_t
Valid prediction for GeneMark_model.86284_t
Couldn't classify 19987, 20000
Couldn't classify 22632, 22754
Sorry, prediction pasa_asmbl_28123.p1 fails validation.
(GCT)	 GT	19987-20000	GT	AGG
(CGA)	 AG	20151-20319	GT	AGG
(ATC)	 AG	21061-21273	GT	TGG
(AAG)	 AG	21436-21586	GT	AGG
(TTC)	 AG	21707-21822	GT	AGG
(AGC)	 AG	22412-22498	GT	AGG
(AAC)	 AG	22632-22754	GG	CAG
-recovered pasa_asmbl_28123.p1, internal, 20151, 20319
-recovered pasa_asmbl_28123.p1, internal, 21061, 21273
-recovered pasa_asmbl_28123.p1, internal, 21436, 21586
-recovered pasa_asmbl_28123.p1, internal, 21707, 21822
-recovered pasa_asmbl_28123.p1, internal, 22412, 22498
Valid prediction for Augustus_model.g33431.t1
Valid prediction for GeneMark_model.86295_t
Couldn't classify 29703, 29733
Sorry, prediction pasa_asmbl_28120.p2 fails validation.
(TCT)	 GT	29703-29733	GT	GGG
(AGT)	 AG	29996-30110	GT	TGG
(TCC)	 AG	30356-30542	CC	GAC
-recovered pasa_asmbl_28120.p2, terminal, 30356, 30542
-recovered pasa_asmbl_28120.p2, internal, 29996, 30110
Valid prediction for snap_scaffold_21-snap.2428-T1
Valid prediction for Augustus_model.g33441.t1
Valid prediction for GeneMark_model.86289_t
Valid prediction for GeneMark_model.86288_t
Valid prediction for snap_scaffold_21-snap.2391-T1
Valid prediction for GlimmerHMM_glimmerT_49822-T1
Valid prediction for GeneMark_model.86306_t
Valid prediction for CodingQuarry_transcript_32683-T1
Valid prediction for snap_scaffold_21-snap.2394-T1
Valid prediction for CodingQuarry_transcript_32682-T1
Valid prediction for GeneMark_model.86329_t
Couldn't classify 8242, 8415
Couldn't classify 9985, 10074
Sorry, prediction pasa_asmbl_28127.p1 fails validation.
(AGG)	 TC	8242-8415	GC	AGG
(GTG)	 AG	8519-8686	GT	AGG
(GTC)	 AG	9396-9557	GT	TGG
(CTG)	 AG	9985-10074	GA	GCG
-recovered pasa_asmbl_28127.p1, internal, 8519, 8686
-recovered pasa_asmbl_28127.p1, internal, 9396, 9557
Valid prediction for GlimmerHMM_glimmerT_49816-T1
Valid prediction for GeneMark_model.86325_t
Valid prediction for GlimmerHMM_glimmerT_49836-T1
Valid prediction for snap_scaffold_21-snap.2418-T1
Valid prediction for CodingQuarry_transcript_32681-T1
Valid prediction for snap_scaffold_21-snap.2397-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GeneMark_model.86317_t
Valid prediction for snap_scaffold_21-snap.2409-T1
Valid prediction for GeneMark_model.86326_t
Valid prediction for snap_scaffold_21-snap.2396-T1
Valid prediction for snap_scaffold_21-snap.2426-T1
Valid prediction for GlimmerHMM_glimmerT_49821-T1
Couldn't classify 18288, 18746
Sorry, prediction pasa_asmbl_28124.p1 fails validation.
(CCA)	 AC	18288-18746	GT	TCG
Valid prediction for GlimmerHMM_glimmerT_49832-T1
Couldn't classify 192231, 192363
Sorry, prediction pasa_asmbl_28114.p2 fails validation.
(GCA)	 TT	192231-192363	GT	AGG
(ACA)	 AG	194790-195166	GG	GAG
-recovered pasa_asmbl_28114.p2, terminal, 194790, 195166
Valid prediction for GeneMark_model.86291_t
Valid prediction for GeneMark_model.86316_t
Valid prediction for GeneMark_model.86330_t
Valid prediction for GeneMark_model.86283_t
Valid prediction for snap_scaffold_21-snap.2407-T1
Valid prediction for Augustus_model.g33426.t1
Couldn't classify 24200, 24254
Couldn't classify 27871, 28052
Sorry, prediction pasa_asmbl_28121.p1 fails validation.
(GAA)	 TG	24200-24254	GT	AGG
(ATG)	 AG	24570-24685	GT	CGG
(ATG)	 AG	24851-25298	GT	CAG
(GTG)	 AG	25407-25676	GC	AGG
(GTC)	 AG	26121-26218	GT	AGG
(GGC)	 AG	26677-26824	GT	AGG
(AGA)	 AG	27034-27182	GT	AGG
(TTC)	 AG	27457-27571	GT	CGG
(GTG)	 AG	27871-28052	CT	GAC
add_exon() Sorry, pasa_asmbl_28121.p1 24570-24685-initial-1 is invalid.
-recovered pasa_asmbl_28121.p1, initial, 24570, 24685
-recovered pasa_asmbl_28121.p1, initial, 24851, 25298
-recovered pasa_asmbl_28121.p1, internal, 24570, 24685
-recovered pasa_asmbl_28121.p1, internal, 24851, 25298
-recovered pasa_asmbl_28121.p1, internal, 25407, 25676
-recovered pasa_asmbl_28121.p1, internal, 26121, 26218
-recovered pasa_asmbl_28121.p1, internal, 26677, 26824
-recovered pasa_asmbl_28121.p1, internal, 27034, 27182
-recovered pasa_asmbl_28121.p1, internal, 27457, 27571
Valid prediction for GeneMark_model.86293_t
Valid prediction for GlimmerHMM_glimmerT_49827-T1
Valid prediction for snap_scaffold_21-snap.2392-T1
Valid prediction for GeneMark_model.86303_t
Valid prediction for Augustus_model.g33429.t1
Valid prediction for GlimmerHMM_glimmerT_49835-T1
Valid prediction for GeneMark_model.86299_t
Valid prediction for GeneMark_model.86305_t
Valid prediction for GeneMark_model.86294_t
Valid prediction for snap_scaffold_21-snap.2415-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 72531, rend_intergenic: 68478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79594, rend_intergenic: 78414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100669, rend_intergenic: 96219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120180, rend_intergenic: 115337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126139, rend_intergenic: 121544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152399, rend_intergenic: 149910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188457, rend_intergenic: 181654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206632, rend_intergenic: 203388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 175410, rend_intergenic: 175407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 212535
-exon list size: 556


building trellis

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-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 72531, rend_intergenic: 68478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79594, rend_intergenic: 78414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100669, rend_intergenic: 96219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120180, rend_intergenic: 115337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126139, rend_intergenic: 121544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152399, rend_intergenic: 149910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188457, rend_intergenic: 181654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206632, rend_intergenic: 203388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 175410, rend_intergenic: 175407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10732
-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 1 - 10299
-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