-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_3327841-3652085

-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_1-snap.535-T1
Valid prediction for CodingQuarry_transcript_2568-T1
Valid prediction for Augustus_model.g337.t1
Valid prediction for HiQ_model.g336.t1
Valid prediction for Augustus_model.g348.t1
Valid prediction for GlimmerHMM_glimmerT_417-T1
Valid prediction for CodingQuarry_transcript_2570-T1
Valid prediction for GlimmerHMM_glimmerT_427-T1
Valid prediction for GlimmerHMM_glimmerT_428-T1
Valid prediction for CodingQuarry_transcript_2560-T1
Valid prediction for snap_scaffold_1-snap.529-T1
Valid prediction for snap_scaffold_1-snap.532-T1
Valid prediction for snap_scaffold_1-snap.556-T1
Valid prediction for snap_scaffold_1-snap.530-T1
Valid prediction for CodingQuarry_transcript_2564-T1
Valid prediction for snap_scaffold_1-snap.544-T1
Valid prediction for GlimmerHMM_glimmerT_432-T1
Valid prediction for Augustus_model.g339.t1
Valid prediction for CodingQuarry_transcript_2559-T1
Valid prediction for Augustus_model.g344.t1
Valid prediction for GeneMark_model.473_t
Valid prediction for pasa_asmbl_1604.p1
Valid prediction for snap_scaffold_1-snap.554-T1
Valid prediction for snap_scaffold_1-snap.531-T1
Couldn't classify 315709, 315733
Sorry, prediction pasa_asmbl_1619.p1 fails validation.
(GAG)	 CG	315709-315733	GT	CCG
(GGG)	 AG	316188-316501	GT	AGG
(ATC)	 AG	316659-316864	GT	AGG
(CGA)	 AG	317169-317418	GT	TGG
(AAT)	 AG	317678-317717	GT	CAG
(CCC)	 AG	318124-318280	GT	AGG
(CCA)	 AG	318385-318439	GT	CGG
(TAC)	 AG	318555-318789	GT	TGG
(GGA)	 AG	319337-319428	GT	CAG
(CAG)	 AG	319779-319829	GT	TGG
(CCC)	 AG	319986-320076	GT	GGG
(GTG)	 AG	320521-320925	GT	AGG
(GGT)	 AG	321254-321358	GT	AGG
(GTG)	 AG	321747-321814	GT	AGG
(TCC)	 AG	322165-322359	GT	AGG
(GGT)	 AG	322508-322603	GA	AAG
-recovered pasa_asmbl_1619.p1, terminal, 322508, 322603
-recovered pasa_asmbl_1619.p1, internal, 316188, 316501
-recovered pasa_asmbl_1619.p1, internal, 316659, 316864
-recovered pasa_asmbl_1619.p1, internal, 317169, 317418
-recovered pasa_asmbl_1619.p1, internal, 317678, 317717
-recovered pasa_asmbl_1619.p1, internal, 318124, 318280
-recovered pasa_asmbl_1619.p1, internal, 318385, 318439
-recovered pasa_asmbl_1619.p1, internal, 318555, 318789
-recovered pasa_asmbl_1619.p1, internal, 319337, 319428
-recovered pasa_asmbl_1619.p1, internal, 319779, 319829
-recovered pasa_asmbl_1619.p1, internal, 319986, 320076
-recovered pasa_asmbl_1619.p1, internal, 320521, 320925
-recovered pasa_asmbl_1619.p1, internal, 321254, 321358
-recovered pasa_asmbl_1619.p1, internal, 321747, 321814
-recovered pasa_asmbl_1619.p1, internal, 322165, 322359
Valid prediction for GlimmerHMM_glimmerT_437-T1
Valid prediction for HiQ_model.g338.t1
Valid prediction for GlimmerHMM_glimmerT_441-T1
Valid prediction for pasa_asmbl_1615.p1
Valid prediction for GeneMark_model.486_t
Valid prediction for Augustus_model.g332.t1
Valid prediction for GlimmerHMM_glimmerT_431-T1
Valid prediction for GlimmerHMM_glimmerT_440-T1
Valid prediction for GlimmerHMM_glimmerT_430-T1
Valid prediction for snap_scaffold_1-snap.533-T1
Valid prediction for GlimmerHMM_glimmerT_414-T1
Valid prediction for GlimmerHMM_glimmerT_421-T1
Couldn't classify 236012, 236133
Sorry, prediction pasa_asmbl_1602.p1 fails validation.
(CGC)	 AG	236012-236133	GT	AGG
(CTC)	 AG	236268-236431	GT	AGG
(GCA)	 AG	238821-239080	GT	AGG
(GTG)	 AG	240220-240344	GT	CGG
(GAA)	 AG	240925-240994	GT	AGG
(AAG)	 AG	241232-242321	GT	AAG
(ATT)	 AG	243126-243192	GT	GCG
(GAA)	 AG	243590-243761	GT	AGG
(GAG)	 AG	243965-244009	GT	AAG
(CAT)	 AG	244130-244246	GC	AAG
-recovered pasa_asmbl_1602.p1, terminal, 244130, 244246
-recovered pasa_asmbl_1602.p1, internal, 236012, 236133
-recovered pasa_asmbl_1602.p1, internal, 236268, 236431
-recovered pasa_asmbl_1602.p1, internal, 238821, 239080
-recovered pasa_asmbl_1602.p1, internal, 240220, 240344
-recovered pasa_asmbl_1602.p1, internal, 240925, 240994
-recovered pasa_asmbl_1602.p1, internal, 241232, 242321
-recovered pasa_asmbl_1602.p1, internal, 243126, 243192
-recovered pasa_asmbl_1602.p1, internal, 243590, 243761
-recovered pasa_asmbl_1602.p1, internal, 243965, 244009
-recovered pasa_asmbl_1602.p1, internal, 244130, 244246
Valid prediction for pasa_asmbl_1610.p2
Valid prediction for GeneMark_model.497_t
Valid prediction for pasa_asmbl_1596.p1
Valid prediction for snap_scaffold_1-snap.545-T1
Couldn't classify 314020, 314079
Couldn't classify 315481, 315612
Sorry, prediction pasa_asmbl_1617.p1 fails validation.
(GTA)	 CA	314020-314079	GT	GTG
(CTC)	 AG	314265-314335	GT	AGG
(TGT)	 AG	314994-315180	GT	TGG
(TCC)	 AG	315481-315612	CC	CAC
-recovered pasa_asmbl_1617.p1, internal, 314265, 314335
-recovered pasa_asmbl_1617.p1, internal, 314994, 315180
Valid prediction for snap_scaffold_1-snap.540-T1
Valid prediction for snap_scaffold_1-snap.543-T1
Valid prediction for HiQ_model.g353.t1
Valid prediction for snap_scaffold_1-snap.557-T1
Valid prediction for GeneMark_model.495_t
Valid prediction for GeneMark_model.478_t
Valid prediction for GlimmerHMM_glimmerT_425-T1
Valid prediction for Augustus_model.g345.t1
Valid prediction for GeneMark_model.487_t
Valid prediction for Augustus_model.g343.t1
Valid prediction for snap_scaffold_1-snap.537-T1
Valid prediction for GlimmerHMM_glimmerT_423-T1
Valid prediction for GlimmerHMM_glimmerT_429-T1
Valid prediction for GeneMark_model.492_t
Valid prediction for GeneMark_model.468_t
Valid prediction for pasa_asmbl_1599.p1
Valid prediction for GeneMark_model.483_t
Couldn't classify 308927, 308956
Couldn't classify 313567, 313631
Sorry, prediction pasa_asmbl_2767.p1 fails validation.
(GTT)	 CA	308927-308956	GT	GTG
(ATT)	 AG	309789-309926	GT	AGG
(GCA)	 AG	310415-310492	GT	AGG
(TTG)	 AG	311328-311438	GT	CGG
(ACC)	 AG	312971-313133	GT	AGG
(GGC)	 AG	313320-313406	GT	AGG
(GAT)	 AG	313567-313631	TA	GGT
-recovered pasa_asmbl_2767.p1, internal, 309789, 309926
-recovered pasa_asmbl_2767.p1, internal, 310415, 310492
-recovered pasa_asmbl_2767.p1, internal, 311328, 311438
-recovered pasa_asmbl_2767.p1, internal, 312971, 313133
-recovered pasa_asmbl_2767.p1, internal, 313320, 313406
Valid prediction for GeneMark_model.464_t
Valid prediction for CodingQuarry_transcript_2566-T1
Valid prediction for pasa_asmbl_1611.p1
Valid prediction for HiQ_model.g351.t1
Valid prediction for CodingQuarry_transcript_2569-T1
Valid prediction for GeneMark_model.471_t
Valid prediction for snap_scaffold_1-snap.539-T1
Valid prediction for GeneMark_model.480_t
Valid prediction for Augustus_model.g350.t1
Valid prediction for GlimmerHMM_glimmerT_435-T1
Valid prediction for snap_scaffold_1-snap.542-T1
Valid prediction for snap_scaffold_1-snap.555-T1
Valid prediction for GeneMark_model.482_t
Valid prediction for GeneMark_model.481_t
Valid prediction for snap_scaffold_1-snap.521-T1
Valid prediction for HiQ_model.g352.t1
Valid prediction for Augustus_model.g341.t1
Valid prediction for GeneMark_model.485_t
Valid prediction for GlimmerHMM_glimmerT_439-T1
Valid prediction for GlimmerHMM_glimmerT_438-T1
Valid prediction for GeneMark_model.475_t
Valid prediction for GlimmerHMM_glimmerT_422-T1
Valid prediction for GeneMark_model.494_t
Valid prediction for snap_scaffold_1-snap.551-T1
Valid prediction for GeneMark_model.476_t
Valid prediction for GlimmerHMM_glimmerT_416-T1
Couldn't classify 103104, 103166
Sorry, prediction pasa_asmbl_1592.p1 fails validation.
(TTA)	 TT	103104-103166	GT	AGG
(GGC)	 AG	103597-103773	GT	AGG
(GCA)	 AG	104062-104182	GT	AGG
(GAA)	 AG	104433-104493	GT	AGG
(GCG)	 AG	104584-104716	GT	AGG
(AGC)	 AG	106240-106373	GT	ATG
(GAA)	 AG	106565-106667	GT	AGG
(CTG)	 AG	106822-106968	GT	CTG
(GGG)	 AG	107232-107326	GT	AAG
(CCT)	 AG	107462-107522	GT	AGG
(GTA)	 AG	108690-108779	AC	AAA
add_exon() Sorry, pasa_asmbl_1592.p1 104433-104493-terminal-3 is invalid.
-recovered pasa_asmbl_1592.p1, terminal, 104433, 104493
-recovered pasa_asmbl_1592.p1, terminal, 108690, 108779
-recovered pasa_asmbl_1592.p1, internal, 103597, 103773
-recovered pasa_asmbl_1592.p1, internal, 104062, 104182
-recovered pasa_asmbl_1592.p1, internal, 104433, 104493
-recovered pasa_asmbl_1592.p1, internal, 104584, 104716
-recovered pasa_asmbl_1592.p1, internal, 106240, 106373
-recovered pasa_asmbl_1592.p1, internal, 106565, 106667
-recovered pasa_asmbl_1592.p1, internal, 106822, 106968
-recovered pasa_asmbl_1592.p1, internal, 107232, 107326
-recovered pasa_asmbl_1592.p1, internal, 107462, 107522
Valid prediction for snap_scaffold_1-snap.541-T1
Valid prediction for snap_scaffold_1-snap.538-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_1-snap.528-T1
Valid prediction for snap_scaffold_1-snap.548-T1
Valid prediction for snap_scaffold_1-snap.523-T1
Valid prediction for GeneMark_model.467_t
Valid prediction for GeneMark_model.496_t
Valid prediction for GlimmerHMM_glimmerT_420-T1
Valid prediction for Augustus_model.g342.t1
Valid prediction for HiQ_model.g349.t1
Valid prediction for snap_scaffold_1-snap.522-T1
Valid prediction for GeneMark_model.472_t
Valid prediction for snap_scaffold_1-snap.536-T1
Valid prediction for Augustus_model.g346.t1
Valid prediction for GeneMark_model.490_t
Valid prediction for GeneMark_model.465_t
Valid prediction for GeneMark_model.491_t
Valid prediction for snap_scaffold_1-snap.525-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.547-T1
Valid prediction for GeneMark_model.488_t
Valid prediction for snap_scaffold_1-snap.527-T1
Valid prediction for GeneMark_model.484_t
Valid prediction for pasa_asmbl_169.p2
Valid prediction for pasa_asmbl_166.p1
Valid prediction for snap_scaffold_1-snap.524-T1
Valid prediction for snap_scaffold_1-snap.550-T1
Valid prediction for GeneMark_model.469_t
Valid prediction for GlimmerHMM_glimmerT_419-T1
Valid prediction for GlimmerHMM_glimmerT_434-T1
Valid prediction for GeneMark_model.466_t
Valid prediction for CodingQuarry_transcript_2567-T1
Valid prediction for snap_scaffold_1-snap.552-T1
Valid prediction for snap_scaffold_1-snap.549-T1
Valid prediction for GeneMark_model.489_t
Valid prediction for GeneMark_model.477_t
Valid prediction for Augustus_model.g334.t1
Valid prediction for GlimmerHMM_glimmerT_418-T1
Valid prediction for Augustus_model.g347.t1
Valid prediction for GlimmerHMM_glimmerT_436-T1
Valid prediction for snap_scaffold_1-snap.520-T1
Valid prediction for Augustus_model.g333.t1
Valid prediction for GlimmerHMM_glimmerT_413-T1
Valid prediction for GeneMark_model.470_t
Valid prediction for GeneMark_model.474_t
Valid prediction for GlimmerHMM_glimmerT_415-T1
Valid prediction for snap_scaffold_1-snap.546-T1
Valid prediction for snap_scaffold_1-snap.553-T1
Valid prediction for GlimmerHMM_glimmerT_426-T1
Valid prediction for snap_scaffold_1-snap.526-T1
Valid prediction for GlimmerHMM_glimmerT_424-T1
Valid prediction for snap_scaffold_1-snap.534-T1
Couldn't classify 144101, 144163
Sorry, prediction pasa_asmbl_155.p1 fails validation.
(CCC)	 AA	144101-144163	GT	AGG
(AAG)	 AG	145684-145827	GT	AGG
(GTA)	 AG	148136-148180	GT	AGG
(GGA)	 AG	149873-149914	GT	CGG
(AAA)	 AG	150769-150852	GT	AAG
(AAA)	 AG	150983-151081	GT	AGG
(AAA)	 AG	151454-151531	GT	AGG
(AAA)	 AG	152010-152087	GT	AGG
(GAT)	 AG	152383-152487	GT	CGG
(GAG)	 AG	152635-152751	GT	AGG
(CCC)	 AG	153096-153191	GT	CGG
(CCT)	 AG	153355-153432	GT	AGG
(AAA)	 AG	153545-153637	GT	AGG
(GAT)	 AG	154293-154397	GT	CGG
(GAA)	 AG	154638-154754	GT	AGG
(CCA)	 AG	155225-155419	GT	AGG
(CTC)	 AG	155543-155647	GT	AGG
(GAG)	 AG	155818-155910	GT	AGG
(GCC)	 AG	156337-156375	GT	AGG
(AAA)	 AG	156564-156692	GT	AGG
(ACT)	 AG	156821-156907	GT	AGG
(GGC)	 AG	157276-157305	GT	AAG
(AAA)	 AG	157486-157584	AC	AGA
-recovered pasa_asmbl_155.p1, terminal, 157486, 157584
-recovered pasa_asmbl_155.p1, internal, 145684, 145827
-recovered pasa_asmbl_155.p1, internal, 148136, 148180
-recovered pasa_asmbl_155.p1, internal, 149873, 149914
-recovered pasa_asmbl_155.p1, internal, 150769, 150852
-recovered pasa_asmbl_155.p1, internal, 150983, 151081
-recovered pasa_asmbl_155.p1, internal, 151454, 151531
-recovered pasa_asmbl_155.p1, internal, 152010, 152087
-recovered pasa_asmbl_155.p1, internal, 152383, 152487
-recovered pasa_asmbl_155.p1, internal, 152635, 152751
-recovered pasa_asmbl_155.p1, internal, 153096, 153191
-recovered pasa_asmbl_155.p1, internal, 153355, 153432
-recovered pasa_asmbl_155.p1, internal, 153545, 153637
-recovered pasa_asmbl_155.p1, internal, 154293, 154397
-recovered pasa_asmbl_155.p1, internal, 154638, 154754
-recovered pasa_asmbl_155.p1, internal, 155225, 155419
-recovered pasa_asmbl_155.p1, internal, 155543, 155647
-recovered pasa_asmbl_155.p1, internal, 155818, 155910
-recovered pasa_asmbl_155.p1, internal, 156337, 156375
-recovered pasa_asmbl_155.p1, internal, 156564, 156692
-recovered pasa_asmbl_155.p1, internal, 156821, 156907
-recovered pasa_asmbl_155.p1, internal, 157276, 157305
Valid prediction for GlimmerHMM_glimmerT_433-T1
Valid prediction for HiQ_model.g335.t1
Valid prediction for GeneMark_model.493_t
Valid prediction for CodingQuarry_transcript_2565-T1
Valid prediction for Augustus_model.g340.t1
Couldn't classify 227689, 227781
Couldn't classify 228084, 228235
Sorry, prediction CodingQuarry_transcript_2558-T1 fails validation.
(ATG)	 AC	222514-222529	GT	GAG
(AGC)	 AG	223377-223498	GT	ATG
(AAT)	 AG	223617-223707	GT	AGG
(ATG)	 AG	223823-223970	GT	AAG
(GTT)	 AG	224528-224708	GT	ACG
(GAC)	 AG	225966-226043	GT	AGG
(ATC)	 AG	226378-226458	GT	CTG
(GTC)	 AG	226940-227173	GT	AGG
(GGT)	 AG	227689-227781	CT	TCC
(TGG)	 AC	228084-228235	GT	AGG
(TGC)	 AG	228325-228412	GT	AGG
(GTG)	 AG	228576-228686	GT	CTG
(GAT)	 AG	228892-229065	GT	CGG
(GTC)	 AG	229178-229322	GT	AGG
(ACT)	 AG	229568-229674	TC	GAT
-recovered CodingQuarry_transcript_2558-T1, initial, 222514, 222529
add_exon() Sorry, CodingQuarry_transcript_2558-T1 223823-223970-initial-1 is invalid.
-recovered CodingQuarry_transcript_2558-T1, initial, 223823, 223970
-recovered CodingQuarry_transcript_2558-T1, terminal, 229568, 229674
-recovered CodingQuarry_transcript_2558-T1, internal, 223377, 223498
-recovered CodingQuarry_transcript_2558-T1, internal, 223617, 223707
-recovered CodingQuarry_transcript_2558-T1, internal, 223823, 223970
-recovered CodingQuarry_transcript_2558-T1, internal, 224528, 224708
-recovered CodingQuarry_transcript_2558-T1, internal, 225966, 226043
-recovered CodingQuarry_transcript_2558-T1, internal, 226378, 226458
-recovered CodingQuarry_transcript_2558-T1, internal, 226940, 227173
-recovered CodingQuarry_transcript_2558-T1, internal, 228325, 228412
-recovered CodingQuarry_transcript_2558-T1, internal, 228576, 228686
-recovered CodingQuarry_transcript_2558-T1, internal, 228892, 229065
-recovered CodingQuarry_transcript_2558-T1, internal, 229178, 229322

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)
-building DP trellis

-building trellis in range 1 - 324245
-exon list size: 555


building trellis

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45.6    
45.8    
46.0    
46.1    
46.3    
46.5    
46.7    
46.9    
47.0    
47.2    
47.4    
47.6    
47.8    
47.9    
48.1    
48.3    
48.5    
48.7    
48.8    
49.0    
49.2    
49.4    
49.6    
49.7    
49.9    
50.1    
50.3    
50.4    
50.6    
50.8    
51.0    
51.2    
51.3    
51.5    
51.7    
51.9    
52.1    
52.2    
52.4    
52.6    
52.8    
53.0    
53.1    
53.3    
53.5    
53.7    
53.9    
54.0    
54.2    
54.4    
54.6    
54.8    
54.9    
55.1    
55.3    
55.5    
55.7    
55.8    
56.0    
56.2    
56.4    
56.6    
56.7    
56.9    
57.1    
57.3    
57.5    
57.6    
57.8    
58.0    
58.2    
58.3    
58.5    
58.7    
58.9    
59.1    
59.2    
59.4    
59.6    
59.8    
60.0    
60.1    
60.3    
60.5    
60.7    
60.9    
61.0    
61.2    
61.4    
61.6    
61.8    
61.9    
62.1    
62.3    
62.5    
62.7    
62.8    
63.0    
63.2    
63.4    
63.6    
63.7    
63.9    
64.1    
64.3    
64.5    
64.6    
64.8    
65.0    
65.2    
65.4    
65.5    
65.7    
65.9    
66.1    
66.2    
66.4    
66.6    
66.8    
67.0    
67.1    
67.3    
67.5    
67.7    
67.9    
68.0    
68.2    
68.4    
68.6    
68.8    
68.9    
69.1    
69.3    
69.5    
69.7    
69.8    
70.0    
70.2    
70.4    
70.6    
70.7    
70.9    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.2    
72.4    
72.5    
72.7    
72.9    
73.1    
73.2    
73.4    
73.6    
73.8    
74.0    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
75.9    
76.1    
76.3    
76.5    
76.7    
76.8    
77.0    
77.2    
77.4    
77.6    
77.7    
77.9    
78.1    
78.3    
78.5    
78.6    
78.8    
79.0    
79.2    
79.4    
79.5    
79.7    
79.9    
80.1    
80.3    
80.4    
80.6    
80.8    
81.0    
81.1    
81.3    
81.5    
81.7    
81.9    
82.0    
82.2    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.5    
83.7    
83.8    
84.0    
84.2    
84.4    
84.6    
84.7    
84.9    
85.1    
85.3    
85.5    
85.6    
85.8    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.1    
87.3    
87.4    
87.6    
87.8    
88.0    
88.2    
88.3    
88.5    
88.7    
88.9    
89.0    
89.2    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 28 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 22199
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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
	-no exons in range 1 - 14734