-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_1685205-1950505

-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_24-snap.435-T1
Valid prediction for GlimmerHMM_glimmerT_52069-T1
Valid prediction for snap_scaffold_24-snap.434-T1
Valid prediction for Augustus_model.g34692.t1
Valid prediction for GlimmerHMM_glimmerT_52065-T1
Valid prediction for CodingQuarry_transcript_37239-T1
Valid prediction for snap_scaffold_24-snap.438-T1
Valid prediction for snap_scaffold_24-snap.417-T1
Valid prediction for Augustus_model.g34689.t1
Valid prediction for GlimmerHMM_glimmerT_52078-T1
Valid prediction for snap_scaffold_24-snap.446-T1
Valid prediction for Augustus_model.g34690.t1
Valid prediction for snap_scaffold_24-snap.409-T1
Valid prediction for snap_scaffold_24-snap.440-T1
Valid prediction for snap_scaffold_24-snap.441-T1
Valid prediction for snap_scaffold_24-snap.405-T1
Valid prediction for snap_scaffold_24-snap.429-T1
Valid prediction for GlimmerHMM_glimmerT_52082-T1
Valid prediction for GlimmerHMM_glimmerT_52061-T1
Valid prediction for Augustus_model.g34699.t1
Valid prediction for snap_scaffold_24-snap.454-T1
Valid prediction for snap_scaffold_24-snap.432-T1
Valid prediction for Augustus_model.g34691.t1
Valid prediction for snap_scaffold_24-snap.426-T1
Valid prediction for snap_scaffold_24-snap.443-T1
Couldn't classify 180777, 180818
Sorry, prediction pasa_asmbl_32082.p1 fails validation.
(AAT)	 CC	180777-180818	GT	AGG
(GTG)	 AG	181421-181786	TC	AAT
-recovered pasa_asmbl_32082.p1, terminal, 181421, 181786
Valid prediction for snap_scaffold_24-snap.424-T1
Valid prediction for snap_scaffold_24-snap.421-T1
Valid prediction for snap_scaffold_24-snap.452-T1
Valid prediction for GlimmerHMM_glimmerT_52057-T1
Valid prediction for snap_scaffold_24-snap.444-T1
Valid prediction for Augustus_model.g34688.t1
Valid prediction for GlimmerHMM_glimmerT_52066-T1
Valid prediction for snap_scaffold_24-snap.419-T1
Valid prediction for snap_scaffold_24-snap.448-T1
Valid prediction for snap_scaffold_24-snap.418-T1
Valid prediction for GlimmerHMM_glimmerT_52058-T1
Valid prediction for snap_scaffold_24-snap.450-T1
Valid prediction for GlimmerHMM_glimmerT_52067-T1
Valid prediction for GlimmerHMM_glimmerT_52063-T1
Valid prediction for snap_scaffold_24-snap.406-T1
Valid prediction for snap_scaffold_24-snap.439-T1
Valid prediction for Augustus_model.g34702.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_24-snap.451-T1
Valid prediction for snap_scaffold_24-snap.449-T1
Valid prediction for snap_scaffold_24-snap.416-T1
Valid prediction for snap_scaffold_24-snap.436-T1
Couldn't classify 116816, 116890
Couldn't classify 117665, 117746
Sorry, prediction pasa_asmbl_33246.p1 fails validation.
(ATC)	 GG	116816-116890	GT	AGG
(TGT)	 AG	117251-117374	GT	GAG
(TGC)	 AG	117528-117591	GT	AGG
(GTA)	 AG	117665-117746	GT	ATG
add_exon() Sorry, pasa_asmbl_33246.p1 117251-117374-terminal-3 is invalid.
-recovered pasa_asmbl_33246.p1, terminal, 117251, 117374
-recovered pasa_asmbl_33246.p1, internal, 117251, 117374
-recovered pasa_asmbl_33246.p1, internal, 117528, 117591
-recovered pasa_asmbl_33246.p1, internal, 117665, 117746
Valid prediction for snap_scaffold_24-snap.425-T1
Valid prediction for Augustus_model.g34694.t1
Valid prediction for Augustus_model.g34696.t1
Valid prediction for GlimmerHMM_glimmerT_52068-T1
Valid prediction for GlimmerHMM_glimmerT_52072-T1
Valid prediction for GlimmerHMM_glimmerT_52059-T1
Valid prediction for Augustus_model.g34693.t1
Valid prediction for Augustus_model.g34695.t1
Couldn't classify 5699, 5810
Sorry, prediction pasa_asmbl_32753.p1 fails validation.
(GAC)	 GA	5699-5810	GT	AGG
(GTC)	 AG	5937-6202	GT	AGG
(GGC)	 AG	6666-6841	GT	AGG
(TAA)	 AG	8638-8762	GT	AGG
(GGG)	 AG	9116-9363	AG	AGA
-recovered pasa_asmbl_32753.p1, terminal, 9116, 9363
-recovered pasa_asmbl_32753.p1, internal, 5937, 6202
-recovered pasa_asmbl_32753.p1, internal, 6666, 6841
-recovered pasa_asmbl_32753.p1, internal, 8638, 8762
Valid prediction for snap_scaffold_24-snap.447-T1
Valid prediction for Augustus_model.g34709.t1
Valid prediction for snap_scaffold_24-snap.433-T1
Valid prediction for GlimmerHMM_glimmerT_52080-T1
Valid prediction for GlimmerHMM_glimmerT_52085-T1
Valid prediction for Augustus_model.g34697.t1
Valid prediction for snap_scaffold_24-snap.413-T1
Valid prediction for GlimmerHMM_glimmerT_52060-T1
Valid prediction for GlimmerHMM_glimmerT_52070-T1
Valid prediction for snap_scaffold_24-snap.422-T1
Valid prediction for snap_scaffold_24-snap.420-T1
Valid prediction for HiQ_model.g34701.t1
Valid prediction for snap_scaffold_24-snap.453-T1
Valid prediction for GlimmerHMM_glimmerT_52074-T1
Valid prediction for HiQ_model.g34707.t1
Valid prediction for Augustus_model.g34704.t1
Valid prediction for snap_scaffold_24-snap.427-T1
Valid prediction for pasa_asmbl_32746.p1
Valid prediction for snap_scaffold_24-snap.411-T1
Couldn't classify 90982, 91028
Couldn't classify 94369, 94458
Sorry, prediction pasa_asmbl_32740.p1 fails validation.
(GCG)	 AG	90982-91028	GT	AGG
(CGA)	 AG	93213-93472	GT	TGG
(GTG)	 AG	93829-93920	GT	GTG
(ACG)	 AG	94369-94458	AG	ACA
-recovered pasa_asmbl_32740.p1, internal, 90982, 91028
-recovered pasa_asmbl_32740.p1, internal, 93213, 93472
-recovered pasa_asmbl_32740.p1, internal, 93829, 93920
Valid prediction for GlimmerHMM_glimmerT_52076-T1
Valid prediction for CodingQuarry_transcript_37241-T1
Valid prediction for Augustus_model.g34703.t1
Valid prediction for Augustus_model.g34687.t1
Valid prediction for Augustus_model.g34698.t1
Valid prediction for GlimmerHMM_glimmerT_52084-T1
Valid prediction for snap_scaffold_24-snap.415-T1
Valid prediction for snap_scaffold_24-snap.445-T1
Valid prediction for snap_scaffold_24-snap.423-T1
Valid prediction for snap_scaffold_24-snap.430-T1
Valid prediction for snap_scaffold_24-snap.412-T1
Valid prediction for Augustus_model.g34708.t1
Valid prediction for GlimmerHMM_glimmerT_52079-T1
Valid prediction for GlimmerHMM_glimmerT_52075-T1
Couldn't classify 38195, 38394
Sorry, prediction Augustus_model.g34706.t1 fails validation.
(ATG)	 TA	20466-20534	GT	AGG
(GTG)	 AG	21798-21887	GT	AGG
(ATC)	 AG	22190-22237	GT	AGG
(CAA)	 AG	22350-22445	GT	TTG
(CAT)	 AG	22903-22965	GT	AGG
(GCG)	 AG	23221-23346	GT	GGG
(GTC)	 AG	23921-23980	GT	TGG
(GCT)	 AG	24847-25050	GT	CGG
(TGG)	 AG	26385-26530	GT	TGG
(GGA)	 AG	26845-27001	GT	AGG
(AAC)	 AG	28518-28600	GT	CGG
(AGA)	 AG	31263-31335	GT	AGG
(GAC)	 AG	32534-32695	GT	TGG
(ATC)	 AG	33046-33243	GT	AGG
(GTG)	 AG	34499-34873	GT	CGG
(GAA)	 AG	34963-35031	GT	AGG
(GTG)	 AG	35197-35362	GT	CCG
(ATG)	 AG	35814-35858	GT	AGG
(TCG)	 AG	35960-36369	GT	CTG
(AAT)	 AG	36507-36579	GT	AGG
(ATC)	 AG	37479-37549	GT	AGG
(TCA)	 AG	37848-37992	GT	AGG
(GCA)	 AG	38195-38394	GT	AAG
-recovered Augustus_model.g34706.t1, initial, 20466, 20534
-recovered Augustus_model.g34706.t1, initial, 35814, 35858
-recovered Augustus_model.g34706.t1, internal, 21798, 21887
-recovered Augustus_model.g34706.t1, internal, 22190, 22237
-recovered Augustus_model.g34706.t1, internal, 22350, 22445
-recovered Augustus_model.g34706.t1, internal, 22903, 22965
-recovered Augustus_model.g34706.t1, internal, 23221, 23346
-recovered Augustus_model.g34706.t1, internal, 23921, 23980
-recovered Augustus_model.g34706.t1, internal, 24847, 25050
-recovered Augustus_model.g34706.t1, internal, 26385, 26530
-recovered Augustus_model.g34706.t1, internal, 26845, 27001
-recovered Augustus_model.g34706.t1, internal, 28518, 28600
-recovered Augustus_model.g34706.t1, internal, 31263, 31335
-recovered Augustus_model.g34706.t1, internal, 32534, 32695
-recovered Augustus_model.g34706.t1, internal, 33046, 33243
-recovered Augustus_model.g34706.t1, internal, 34499, 34873
-recovered Augustus_model.g34706.t1, internal, 34963, 35031
-recovered Augustus_model.g34706.t1, internal, 35197, 35362
-recovered Augustus_model.g34706.t1, internal, 35814, 35858
-recovered Augustus_model.g34706.t1, internal, 35960, 36369
-recovered Augustus_model.g34706.t1, internal, 36507, 36579
-recovered Augustus_model.g34706.t1, internal, 37479, 37549
-recovered Augustus_model.g34706.t1, internal, 37848, 37992
-recovered Augustus_model.g34706.t1, internal, 38195, 38394
Valid prediction for GlimmerHMM_glimmerT_52071-T1
Valid prediction for Augustus_model.g34700.t1
Valid prediction for snap_scaffold_24-snap.410-T1
Valid prediction for GlimmerHMM_glimmerT_52083-T1
Valid prediction for snap_scaffold_24-snap.407-T1
Valid prediction for snap_scaffold_24-snap.404-T1
Valid prediction for GlimmerHMM_glimmerT_52077-T1
Valid prediction for GlimmerHMM_glimmerT_52081-T1
Valid prediction for Augustus_model.g34705.t1
Couldn't classify 79199, 79356
Sorry, prediction pasa_asmbl_32742.p4 fails validation.
(GTC)	 AC	79199-79356	GT	GAG
(GTG)	 AG	79784-79955	GC	GAG
-recovered pasa_asmbl_32742.p4, terminal, 79784, 79955
-recovered pasa_asmbl_32742.p4, internal, 79784, 79955
Valid prediction for snap_scaffold_24-snap.455-T1
Valid prediction for snap_scaffold_24-snap.431-T1
Valid prediction for pasa_asmbl_32751.p1
Valid prediction for GlimmerHMM_glimmerT_52073-T1
Valid prediction for GlimmerHMM_glimmerT_52062-T1
Valid prediction for snap_scaffold_24-snap.442-T1
Valid prediction for snap_scaffold_24-snap.437-T1
Valid prediction for GlimmerHMM_glimmerT_52064-T1
Valid prediction for snap_scaffold_24-snap.414-T1
Valid prediction for snap_scaffold_24-snap.428-T1
Valid prediction for snap_scaffold_24-snap.408-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18489, rend_intergenic: 15532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20204, rend_intergenic: 18690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39621, rend_intergenic: 20464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61554, rend_intergenic: 40121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72903, rend_intergenic: 71355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82469, rend_intergenic: 72906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84159, rend_intergenic: 82571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87504, rend_intergenic: 84697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95194, rend_intergenic: 87938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120804, rend_intergenic: 112355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128674, rend_intergenic: 120869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130532, rend_intergenic: 129224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131964, rend_intergenic: 130679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149564, rend_intergenic: 132556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151227, rend_intergenic: 149785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177871, rend_intergenic: 153171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193100, rend_intergenic: 184129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199717, rend_intergenic: 198736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212264, rend_intergenic: 200498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218145, rend_intergenic: 212925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229371, rend_intergenic: 223632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236271, rend_intergenic: 229930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240441, rend_intergenic: 236367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244919, rend_intergenic: 240878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 254287, rend_intergenic: 250350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 265301
-exon list size: 510


building trellis

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89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 18489, rend_intergenic: 15532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20204, rend_intergenic: 18690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39621, rend_intergenic: 20464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61554, rend_intergenic: 40121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72903, rend_intergenic: 71355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82469, rend_intergenic: 72906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84159, rend_intergenic: 82571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87504, rend_intergenic: 84697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95194, rend_intergenic: 87938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120804, rend_intergenic: 112355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128674, rend_intergenic: 120869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130532, rend_intergenic: 129224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131964, rend_intergenic: 130679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149564, rend_intergenic: 132556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151227, rend_intergenic: 149785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177871, rend_intergenic: 153171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193100, rend_intergenic: 184129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199717, rend_intergenic: 198736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212264, rend_intergenic: 200498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218145, rend_intergenic: 212925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229371, rend_intergenic: 223632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236271, rend_intergenic: 229930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240441, rend_intergenic: 236367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244919, rend_intergenic: 240878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 254287, rend_intergenic: 250350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 17193
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-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 1 - 16773
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-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 1 - 16720
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 1 predictions from path traversal

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