-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_11392714-11763538

-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_20-snap.2411-T1
Valid prediction for snap_scaffold_20-snap.2389-T1
Valid prediction for GlimmerHMM_glimmerT_46868-T1
Valid prediction for snap_scaffold_20-snap.2395-T1
Couldn't classify 337774, 337801
Sorry, prediction pasa_asmbl_27093.p1 fails validation.
(TTG)	 GG	337774-337801	GT	AGG
(GTT)	 AG	338580-338716	GT	AGG
(ATT)	 AG	338839-338916	GT	AGG
(CAG)	 AG	340298-340480	CA	AAC
-recovered pasa_asmbl_27093.p1, terminal, 340298, 340480
-recovered pasa_asmbl_27093.p1, internal, 338580, 338716
-recovered pasa_asmbl_27093.p1, internal, 338839, 338916
Valid prediction for snap_scaffold_20-snap.2392-T1
Valid prediction for Augustus_model.g31186.t1
Valid prediction for Augustus_model.g31173.t1
Valid prediction for CodingQuarry_transcript_30689-T1
Valid prediction for snap_scaffold_20-snap.2378-T1
Valid prediction for Augustus_model.g31168.t1
Valid prediction for snap_scaffold_20-snap.2410-T1
Valid prediction for GlimmerHMM_glimmerT_46872-T1
Valid prediction for Augustus_model.g31165.t1
Valid prediction for Augustus_model.g31169.t1
Valid prediction for snap_scaffold_20-snap.2412-T1
Valid prediction for pasa_asmbl_27082.p1
Valid prediction for Augustus_model.g31172.t1
Valid prediction for pasa_asmbl_27046.p1
Valid prediction for CodingQuarry_transcript_30674-T1
Valid prediction for GlimmerHMM_glimmerT_46861-T1
Valid prediction for snap_scaffold_20-snap.2397-T1
Valid prediction for GlimmerHMM_glimmerT_46856-T1
Valid prediction for HiQ_model.g31154.t1
Valid prediction for GlimmerHMM_glimmerT_46839-T1
Couldn't classify 82795, 82926
Sorry, prediction pasa_asmbl_27049.p1 fails validation.
(CTT)	 TT	82795-82926	GT	AGG
(TGT)	 AG	83050-83218	GT	GGG
(GTA)	 AG	83368-83496	GT	AGG
(GGC)	 AG	83653-83788	GT	AAG
(ACC)	 AG	83931-84051	CA	AGC
-recovered pasa_asmbl_27049.p1, terminal, 83931, 84051
-recovered pasa_asmbl_27049.p1, internal, 83050, 83218
-recovered pasa_asmbl_27049.p1, internal, 83368, 83496
-recovered pasa_asmbl_27049.p1, internal, 83653, 83788
Valid prediction for Augustus_model.g31156.t1
Valid prediction for snap_scaffold_20-snap.2425-T1
Valid prediction for Augustus_model.g31183.t1
Valid prediction for Augustus_model.g31195.t1
Valid prediction for snap_scaffold_20-snap.2385-T1
Valid prediction for GlimmerHMM_glimmerT_46845-T1
Valid prediction for CodingQuarry_transcript_30679-T1
Couldn't classify 258035, 258385
Sorry, prediction pasa_asmbl_27084.p1 fails validation.
(CTC)	 AC	258035-258385	AA	AAA
Couldn't classify 255830, 256057
Couldn't classify 257525, 257605
Sorry, prediction pasa_asmbl_27083.p1 fails validation.
(AGT)	 CC	255830-256057	GT	AGG
(GTT)	 AG	256489-256617	GT	AGG
(GAG)	 AG	256967-257104	GT	AGG
(TTA)	 AG	257525-257605	GG	CAG
-recovered pasa_asmbl_27083.p1, internal, 256489, 256617
-recovered pasa_asmbl_27083.p1, internal, 256967, 257104
Valid prediction for GlimmerHMM_glimmerT_46866-T1
Valid prediction for HiQ_model.g31153.t1
Valid prediction for snap_scaffold_20-snap.2407-T1
Valid prediction for Augustus_model.g31163.t1
Valid prediction for CodingQuarry_transcript_30690-T1
Couldn't classify 335657, 335715
Couldn't classify 337634, 337698
Sorry, prediction pasa_asmbl_27092.p1 fails validation.
(GTG)	 AT	335657-335715	GT	GAG
(GTG)	 AG	335848-336010	GT	GGG
(CAT)	 AG	336427-336532	GT	TGG
(GAC)	 AG	337634-337698	TC	CCT
-recovered pasa_asmbl_27092.p1, internal, 335848, 336010
-recovered pasa_asmbl_27092.p1, internal, 336427, 336532
Valid prediction for snap_scaffold_20-snap.2391-T1
Valid prediction for GlimmerHMM_glimmerT_46852-T1
Valid prediction for GlimmerHMM_glimmerT_46840-T1
Valid prediction for GlimmerHMM_glimmerT_46851-T1
Valid prediction for snap_scaffold_20-snap.2388-T1
Valid prediction for CodingQuarry_transcript_30676-T1
Couldn't classify 94392, 94606
Sorry, prediction pasa_asmbl_27062.p1 fails validation.
(ACA)	 CA	94392-94606	GC	AGG
(GCC)	 AG	97179-97372	GT	AGG
(GAG)	 AG	97612-97712	AC	GAA
-recovered pasa_asmbl_27062.p1, terminal, 97612, 97712
-recovered pasa_asmbl_27062.p1, internal, 97179, 97372
Valid prediction for Augustus_model.g31191.t1
Valid prediction for GlimmerHMM_glimmerT_46863-T1
Valid prediction for Augustus_model.g31161.t1
Valid prediction for snap_scaffold_20-snap.2401-T1
Valid prediction for snap_scaffold_20-snap.2384-T1
Couldn't classify 90747, 91433
Sorry, prediction pasa_asmbl_27058.p1 fails validation.
(ATG)	 AG	89764-89817	GT	ATG
(GAC)	 AG	90747-91433	GA	CAG
-recovered pasa_asmbl_27058.p1, initial, 89764, 89817
-recovered pasa_asmbl_27058.p1, internal, 89764, 89817
Valid prediction for snap_scaffold_20-snap.2377-T1
Valid prediction for Augustus_model.g31159.t1
Couldn't classify 124687, 124757
Sorry, prediction pasa_asmbl_27068.p1 fails validation.
(ATG)	 AC	118289-118291	GT	TGG
(GAG)	 AG	118409-118598	GT	TGG
(ACA)	 AG	121196-121279	GT	ATG
(ATG)	 AG	121360-121545	GT	AGG
(GCT)	 AG	122071-122203	GT	ATG
(GTA)	 AG	122419-122611	GT	AGG
(GCC)	 AG	123292-123635	GT	AGG
(GTT)	 AG	123821-123990	GT	AGG
(GAG)	 AG	124687-124757	TT	CCT
-recovered pasa_asmbl_27068.p1, initial, 118289, 118291
add_exon() Sorry, pasa_asmbl_27068.p1 121360-121545-initial-1 is invalid.
-recovered pasa_asmbl_27068.p1, initial, 121360, 121545
-recovered pasa_asmbl_27068.p1, internal, 118409, 118598
-recovered pasa_asmbl_27068.p1, internal, 121196, 121279
-recovered pasa_asmbl_27068.p1, internal, 121360, 121545
-recovered pasa_asmbl_27068.p1, internal, 122071, 122203
-recovered pasa_asmbl_27068.p1, internal, 122419, 122611
-recovered pasa_asmbl_27068.p1, internal, 123292, 123635
-recovered pasa_asmbl_27068.p1, internal, 123821, 123990
Valid prediction for CodingQuarry_transcript_30678-T1
Valid prediction for GlimmerHMM_glimmerT_46844-T1
Valid prediction for pasa_asmbl_27041.p1
Valid prediction for snap_scaffold_20-snap.2416-T1
Valid prediction for Augustus_model.g31171.t1
Valid prediction for Augustus_model.g31155.t1
Valid prediction for GlimmerHMM_glimmerT_46860-T1
Valid prediction for Augustus_model.g31178.t1
Valid prediction for HiQ_model.g31175.t1
Valid prediction for CodingQuarry_transcript_30675-T1
Valid prediction for snap_scaffold_20-snap.2390-T1
Valid prediction for snap_scaffold_20-snap.2399-T1
Valid prediction for Augustus_model.g31170.t1
Valid prediction for CodingQuarry_transcript_30672-T1
Valid prediction for snap_scaffold_20-snap.2422-T1
Valid prediction for GlimmerHMM_glimmerT_46850-T1
Valid prediction for HiQ_model.g31181.t1
Valid prediction for snap_scaffold_20-snap.2379-T1
Valid prediction for CodingQuarry_transcript_30677-T1
Valid prediction for Augustus_model.g31162.t1
Couldn't classify 128089, 128253
Sorry, prediction pasa_asmbl_27071.p1 fails validation.
(CCA)	 GT	128089-128253	GT	AGG
(GTA)	 AG	129732-129985	GT	AGG
(GTC)	 AG	130254-130399	GT	AGG
(GTG)	 AG	131674-131771	GT	ATG
(GTT)	 AG	131865-131977	GT	AGG
(GGT)	 AG	132111-132258	AT	AAA
add_exon() Sorry, pasa_asmbl_27071.p1 130254-130399-terminal-2 is invalid.
-recovered pasa_asmbl_27071.p1, terminal, 130254, 130399
-recovered pasa_asmbl_27071.p1, terminal, 132111, 132258
-recovered pasa_asmbl_27071.p1, internal, 129732, 129985
-recovered pasa_asmbl_27071.p1, internal, 130254, 130399
-recovered pasa_asmbl_27071.p1, internal, 131674, 131771
-recovered pasa_asmbl_27071.p1, internal, 131865, 131977
Valid prediction for Augustus_model.g31188.t1
Valid prediction for GlimmerHMM_glimmerT_46853-T1
Valid prediction for snap_scaffold_20-snap.2380-T1
Valid prediction for snap_scaffold_20-snap.2394-T1
Valid prediction for Augustus_model.g31196.t1
Valid prediction for Augustus_model.g31189.t1
Valid prediction for snap_scaffold_20-snap.2396-T1
Valid prediction for HiQ_model.g31176.t1
Valid prediction for pasa_asmbl_27073.p1
Valid prediction for GlimmerHMM_glimmerT_46847-T1
Valid prediction for Augustus_model.g31167.t1
Valid prediction for CodingQuarry_transcript_30673-T1
Valid prediction for Augustus_model.g31180.t1
Couldn't classify 325848, 325888
Couldn't classify 329843, 329915
Sorry, prediction pasa_asmbl_27167.p1 fails validation.
(AGA)	 TA	325848-325888	GT	TAG
(TGT)	 AG	327149-327239	GT	ACG
(GGC)	 AG	328175-328212	GT	AAG
(GGA)	 AG	328545-328687	GT	GGG
(AAA)	 AG	329653-329704	GT	GGG
(GAC)	 AG	329843-329915	CA	GAC
-recovered pasa_asmbl_27167.p1, terminal, 328175, 328212
-recovered pasa_asmbl_27167.p1, internal, 327149, 327239
-recovered pasa_asmbl_27167.p1, internal, 328175, 328212
-recovered pasa_asmbl_27167.p1, internal, 328545, 328687
-recovered pasa_asmbl_27167.p1, internal, 329653, 329704
Couldn't classify 241433, 241608
Sorry, prediction pasa_asmbl_27081.p1 fails validation.
(ATG)	 GG	236857-236919	GT	AGG
(ATC)	 AG	238454-238616	GT	AGG
(AAA)	 AG	240015-240163	GT	GGG
(CTT)	 AG	240585-240704	GT	AGG
(GCT)	 AG	240822-240917	GT	GGG
(GAC)	 AG	241105-241204	GT	AGG
(GCA)	 AG	241433-241608	AA	GAA
-recovered pasa_asmbl_27081.p1, initial, 236857, 236919
add_exon() Sorry, pasa_asmbl_27081.p1 241105-241204-terminal-3 is invalid.
-recovered pasa_asmbl_27081.p1, terminal, 241105, 241204
-recovered pasa_asmbl_27081.p1, internal, 238454, 238616
-recovered pasa_asmbl_27081.p1, internal, 240015, 240163
-recovered pasa_asmbl_27081.p1, internal, 240585, 240704
-recovered pasa_asmbl_27081.p1, internal, 240822, 240917
-recovered pasa_asmbl_27081.p1, internal, 241105, 241204
Valid prediction for Augustus_model.g31174.t1
Valid prediction for snap_scaffold_20-snap.2424-T1
Valid prediction for snap_scaffold_20-snap.2423-T1
Valid prediction for HiQ_model.g31164.t1
Valid prediction for Augustus_model.g31160.t1
Valid prediction for snap_scaffold_20-snap.2413-T1
Valid prediction for snap_scaffold_20-snap.2383-T1
Valid prediction for snap_scaffold_20-snap.2398-T1
Valid prediction for GlimmerHMM_glimmerT_46849-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 Augustus_model.g31187.t1
Valid prediction for GlimmerHMM_glimmerT_46841-T1
Valid prediction for GlimmerHMM_glimmerT_46871-T1
Valid prediction for GlimmerHMM_glimmerT_46848-T1
Valid prediction for snap_scaffold_20-snap.2415-T1
Valid prediction for snap_scaffold_20-snap.2386-T1
Valid prediction for GlimmerHMM_glimmerT_46854-T1
Valid prediction for pasa_asmbl_26169.p2
Valid prediction for Augustus_model.g31185.t1
Valid prediction for snap_scaffold_20-snap.2420-T1
Valid prediction for snap_scaffold_20-snap.2393-T1
Valid prediction for GlimmerHMM_glimmerT_46869-T1
Valid prediction for pasa_asmbl_26187.p1
Valid prediction for snap_scaffold_20-snap.2376-T1
Valid prediction for GlimmerHMM_glimmerT_46846-T1
Valid prediction for snap_scaffold_20-snap.2404-T1
Valid prediction for snap_scaffold_20-snap.2405-T1
Valid prediction for GlimmerHMM_glimmerT_46859-T1
Valid prediction for pasa_asmbl_26193.p1
Valid prediction for snap_scaffold_20-snap.2387-T1
Valid prediction for GlimmerHMM_glimmerT_46864-T1
Valid prediction for CodingQuarry_transcript_30683-T1
Valid prediction for GlimmerHMM_glimmerT_46857-T1
Couldn't classify 218703, 218767
Sorry, prediction pasa_asmbl_26153.p1 fails validation.
(ATG)	 AA	215553-215652	GT	AGG
(ACT)	 AG	215741-215857	GT	AGG
(TTC)	 AG	215948-216015	GT	AGG
(GTG)	 AG	216145-216389	GT	AGG
(GAA)	 AG	216472-216524	GT	AGG
(GTT)	 AG	217850-218007	GT	TGG
(GTC)	 AG	218536-218581	GT	TTG
(TTA)	 AG	218703-218767	TA	AGT
-recovered pasa_asmbl_26153.p1, initial, 215553, 215652
-recovered pasa_asmbl_26153.p1, internal, 215741, 215857
-recovered pasa_asmbl_26153.p1, internal, 215948, 216015
-recovered pasa_asmbl_26153.p1, internal, 216145, 216389
-recovered pasa_asmbl_26153.p1, internal, 216472, 216524
-recovered pasa_asmbl_26153.p1, internal, 217850, 218007
-recovered pasa_asmbl_26153.p1, internal, 218536, 218581
Valid prediction for GlimmerHMM_glimmerT_46867-T1
Valid prediction for Augustus_model.g31152.t1
Valid prediction for GlimmerHMM_glimmerT_46842-T1
Valid prediction for CodingQuarry_transcript_30680-T1
Valid prediction for Augustus_model.g31157.t1
Valid prediction for snap_scaffold_20-snap.2417-T1
Valid prediction for snap_scaffold_20-snap.2408-T1
Valid prediction for GlimmerHMM_glimmerT_46855-T1
Valid prediction for CodingQuarry_transcript_30681-T1
Valid prediction for GlimmerHMM_glimmerT_46858-T1
Valid prediction for GlimmerHMM_glimmerT_46843-T1
Valid prediction for snap_scaffold_20-snap.2381-T1
Valid prediction for HiQ_model.g31192.t1
Valid prediction for CodingQuarry_transcript_30688-T1
Valid prediction for HiQ_model.g31179.t1
Valid prediction for Augustus_model.g31193.t1
Valid prediction for GlimmerHMM_glimmerT_46862-T1
Valid prediction for snap_scaffold_20-snap.2426-T1
Valid prediction for snap_scaffold_20-snap.2414-T1
Valid prediction for snap_scaffold_20-snap.2419-T1
Valid prediction for snap_scaffold_20-snap.2400-T1
Valid prediction for Augustus_model.g31158.t1
Valid prediction for HiQ_model.g31197.t1
Valid prediction for Augustus_model.g31190.t1
Valid prediction for snap_scaffold_20-snap.2409-T1
Valid prediction for pasa_asmbl_26183.p1
Valid prediction for HiQ_model.g31182.t1
Valid prediction for CodingQuarry_transcript_30682-T1
Valid prediction for CodingQuarry_transcript_30686-T1
Valid prediction for snap_scaffold_20-snap.2402-T1
Valid prediction for Augustus_model.g31198.t1
Valid prediction for HiQ_model.g31194.t1
Valid prediction for Augustus_model.g31177.t1
Valid prediction for GlimmerHMM_glimmerT_46873-T1
Valid prediction for snap_scaffold_20-snap.2421-T1
Valid prediction for Augustus_model.g31166.t1
Valid prediction for pasa_asmbl_26180.p1
Valid prediction for CodingQuarry_transcript_30687-T1
Valid prediction for snap_scaffold_20-snap.2403-T1
Valid prediction for HiQ_model.g31184.t1
Valid prediction for snap_scaffold_20-snap.2418-T1
Valid prediction for snap_scaffold_20-snap.2406-T1
Valid prediction for snap_scaffold_20-snap.2382-T1
Valid prediction for pasa_asmbl_26159.p1
Valid prediction for GlimmerHMM_glimmerT_46870-T1
Valid prediction for GlimmerHMM_glimmerT_46865-T1

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

-building trellis in range 1 - 370825
-exon list size: 549


building trellis

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28.3    
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28.9    
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34.8    
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44.8    
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52.8    
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58.1    
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58.8    
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60.1    
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61.2    
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62.1    
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62.4    
62.6    
62.8    
63.0    
63.2    
63.3    
63.5    
63.7    
63.9    
64.1    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.3    
65.5    
65.7    
65.9    
66.1    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.3    
67.5    
67.7    
67.9    
68.1    
68.2    
68.4    
68.6    
68.8    
69.0    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.2    
70.4    
70.6    
70.8    
71.0    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.2    
72.4    
72.6    
72.8    
73.0    
73.1    
73.3    
73.5    
73.7    
73.9    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.9    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.6    
78.8    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.6    
80.8    
80.9    
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    
84.8    
84.9    
85.1    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.5    
87.7    
87.8    
88.0    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.8    
90.0    
90.2    
90.4    
90.6    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.7    
96.9    
97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 52 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 51 predictions persist after filtering for low support