-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_573525-779897

-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_13-snap.119-T1
Valid prediction for snap_scaffold_13-snap.117-T1
Couldn't classify 76355, 76415
Sorry, prediction pasa_asmbl_10465.p1 fails validation.
(CTC)	 CT	76355-76415	GT	TGG
(TGA)	 AG	77054-77115	GT	AGG
(AGC)	 AG	77239-77367	GT	AGG
(GTG)	 AG	77504-77602	GT	AGG
(GAC)	 AG	77709-77791	GT	AGG
(TGA)	 AG	77945-78071	GT	AGG
(GTG)	 AG	78160-78255	GT	AAG
(GGT)	 AG	78375-78497	GT	AGG
(GTA)	 AG	78603-78767	GT	AGG
(GTG)	 AG	78893-79018	GA	AGG
-recovered pasa_asmbl_10465.p1, terminal, 77709, 77791
-recovered pasa_asmbl_10465.p1, terminal, 78893, 79018
-recovered pasa_asmbl_10465.p1, internal, 77054, 77115
-recovered pasa_asmbl_10465.p1, internal, 77239, 77367
-recovered pasa_asmbl_10465.p1, internal, 77504, 77602
-recovered pasa_asmbl_10465.p1, internal, 77709, 77791
-recovered pasa_asmbl_10465.p1, internal, 77945, 78071
-recovered pasa_asmbl_10465.p1, internal, 78160, 78255
-recovered pasa_asmbl_10465.p1, internal, 78375, 78497
-recovered pasa_asmbl_10465.p1, internal, 78603, 78767
Valid prediction for Augustus_model.g21189.t1
Valid prediction for GeneMark_model.54507_t
Valid prediction for GlimmerHMM_glimmerT_31686-T1
Valid prediction for pasa_asmbl_10467.p1
Valid prediction for GeneMark_model.54483_t
Valid prediction for GlimmerHMM_glimmerT_31668-T1
Couldn't classify 80967, 81152
Sorry, prediction pasa_asmbl_10466.p1 fails validation.
(CGG)	 AG	80967-81152	GT	AAG
(GTG)	 AG	81744-81950	GT	AGG
(ATC)	 AG	82022-82381	TG	GAT
-recovered pasa_asmbl_10466.p1, terminal, 82022, 82381
-recovered pasa_asmbl_10466.p1, internal, 80967, 81152
-recovered pasa_asmbl_10466.p1, internal, 81744, 81950
Valid prediction for snap_scaffold_13-snap.132-T1
Valid prediction for GlimmerHMM_glimmerT_31672-T1
Valid prediction for GlimmerHMM_glimmerT_31673-T1
Valid prediction for Augustus_model.g21180.t1
Valid prediction for snap_scaffold_13-snap.142-T1
Valid prediction for Augustus_model.g21186.t1
Valid prediction for Augustus_model.g21182.t1
Valid prediction for snap_scaffold_13-snap.118-T1
Couldn't classify 158706, 158807
Couldn't classify 160625, 160846
Sorry, prediction pasa_asmbl_10475.p1 fails validation.
(GCA)	 CA	158706-158807	GT	AGG
(TTG)	 AG	159007-159147	GT	AGG
(GAG)	 AG	159306-159464	GT	AGG
(GAA)	 AG	159558-159779	GT	AGG
(CTT)	 AG	160325-160453	GT	AGG
(CAG)	 AG	160625-160846	AC	GGA
-recovered pasa_asmbl_10475.p1, internal, 159007, 159147
-recovered pasa_asmbl_10475.p1, internal, 159306, 159464
-recovered pasa_asmbl_10475.p1, internal, 159558, 159779
-recovered pasa_asmbl_10475.p1, internal, 160325, 160453
Valid prediction for Augustus_model.g21169.t1
Valid prediction for pasa_asmbl_10468.p1
Valid prediction for GeneMark_model.54492_t
Valid prediction for snap_scaffold_13-snap.147-T1
Valid prediction for snap_scaffold_13-snap.122-T1
Valid prediction for CodingQuarry_transcript_12814-T1
Valid prediction for snap_scaffold_13-snap.144-T1
Valid prediction for Augustus_model.g21175.t1
Valid prediction for snap_scaffold_13-snap.126-T1
Valid prediction for snap_scaffold_13-snap.143-T1
Valid prediction for Augustus_model.g21171.t1
Valid prediction for GlimmerHMM_glimmerT_31675-T1
Valid prediction for snap_scaffold_13-snap.121-T1
Valid prediction for snap_scaffold_13-snap.130-T1
Valid prediction for snap_scaffold_13-snap.139-T1
Valid prediction for GlimmerHMM_glimmerT_31669-T1
Valid prediction for GeneMark_model.54487_t
Valid prediction for Augustus_model.g21184.t1
Valid prediction for HiQ_model.g21172.t1
Valid prediction for snap_scaffold_13-snap.146-T1
Valid prediction for snap_scaffold_13-snap.137-T1
Valid prediction for snap_scaffold_13-snap.141-T1
Valid prediction for GlimmerHMM_glimmerT_31683-T1
Valid prediction for GeneMark_model.54491_t
Valid prediction for snap_scaffold_13-snap.120-T1
Valid prediction for GlimmerHMM_glimmerT_31671-T1
Valid prediction for CodingQuarry_transcript_12813-T1
Valid prediction for CodingQuarry_transcript_12810-T1
Valid prediction for GeneMark_model.54495_t
Valid prediction for snap_scaffold_13-snap.127-T1
Valid prediction for Augustus_model.g21170.t1
Valid prediction for GeneMark_model.54505_t
Valid prediction for snap_scaffold_13-snap.138-T1
Valid prediction for snap_scaffold_13-snap.151-T1
Valid prediction for snap_scaffold_13-snap.133-T1
Couldn't classify 153024, 153183
Couldn't classify 154880, 155027
Sorry, prediction pasa_asmbl_10474.p1 fails validation.
(CAG)	 TT	153024-153183	GT	GGG
(GGC)	 AG	153532-153698	GT	AGG
(GGT)	 AG	153924-154018	GT	AGG
(GCA)	 AG	154676-154804	GT	AGG
(AAC)	 AG	154880-155027	GG	TGG
-recovered pasa_asmbl_10474.p1, internal, 153532, 153698
-recovered pasa_asmbl_10474.p1, internal, 153924, 154018
-recovered pasa_asmbl_10474.p1, internal, 154676, 154804
Valid prediction for GlimmerHMM_glimmerT_31685-T1
Valid prediction for CodingQuarry_transcript_12809-T1
Valid prediction for GlimmerHMM_glimmerT_31692-T1
Valid prediction for HiQ_model.g21173.t1
Valid prediction for GeneMark_model.54502_t
Valid prediction for GeneMark_model.54485_t
Valid prediction for GeneMark_model.54499_t
Valid prediction for GeneMark_model.54493_t
Valid prediction for snap_scaffold_13-snap.128-T1
Valid prediction for Augustus_model.g21183.t1
Valid prediction for GeneMark_model.54504_t
Couldn't classify 165123, 165331
Sorry, prediction pasa_asmbl_10482.p1 fails validation.
(ACC)	 AG	165123-165331	GT	AGG
(TAA)	 AG	165504-165655	GT	TGG
(TGC)	 AG	166895-167073	GT	AGG
(GAT)	 AG	169123-169264	GT	TGG
(GTT)	 AG	169440-169507	GG	GAG
-recovered pasa_asmbl_10482.p1, terminal, 169440, 169507
-recovered pasa_asmbl_10482.p1, internal, 165123, 165331
-recovered pasa_asmbl_10482.p1, internal, 165504, 165655
-recovered pasa_asmbl_10482.p1, internal, 166895, 167073
-recovered pasa_asmbl_10482.p1, internal, 169123, 169264
Valid prediction for snap_scaffold_13-snap.148-T1
Valid prediction for GlimmerHMM_glimmerT_31689-T1
Valid prediction for GeneMark_model.54482_t
Valid prediction for Augustus_model.g21168.t1
Valid prediction for snap_scaffold_13-snap.145-T1
Valid prediction for GeneMark_model.54509_t
Couldn't classify 140773, 140812
Couldn't classify 143035, 143207
Sorry, prediction pasa_asmbl_10473.p1 fails validation.
(GGA)	 GG	140773-140812	GT	AGG
(AAG)	 AG	140918-140950	GT	CAG
(TTC)	 AG	141052-141228	GT	AGG
(ATG)	 AG	141518-141735	GC	AGG
(AAA)	 AG	142276-142462	GT	GGG
(TTC)	 AG	142646-142864	GT	AGG
(ACG)	 AG	143035-143207	GT	AGG
add_exon() Sorry, pasa_asmbl_10473.p1 141518-141735-initial-1 is invalid.
-recovered pasa_asmbl_10473.p1, initial, 141518, 141735
-recovered pasa_asmbl_10473.p1, internal, 140918, 140950
-recovered pasa_asmbl_10473.p1, internal, 141052, 141228
-recovered pasa_asmbl_10473.p1, internal, 141518, 141735
-recovered pasa_asmbl_10473.p1, internal, 142276, 142462
-recovered pasa_asmbl_10473.p1, internal, 142646, 142864
-recovered pasa_asmbl_10473.p1, internal, 143035, 143207
Valid prediction for HiQ_model.g21179.t1
Valid prediction for snap_scaffold_13-snap.125-T1
Valid prediction for GlimmerHMM_glimmerT_31682-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 GlimmerHMM_glimmerT_31676-T1
Valid prediction for snap_scaffold_13-snap.124-T1
Valid prediction for HiQ_model.g21188.t1
Valid prediction for CodingQuarry_transcript_12812-T1
Valid prediction for Augustus_model.g21178.t1
Valid prediction for GeneMark_model.54494_t
Valid prediction for GeneMark_model.54481_t
Valid prediction for GlimmerHMM_glimmerT_31677-T1
Valid prediction for GeneMark_model.54488_t
Valid prediction for GlimmerHMM_glimmerT_31679-T1
Valid prediction for snap_scaffold_13-snap.150-T1
Valid prediction for CodingQuarry_transcript_12816-T1
Valid prediction for snap_scaffold_13-snap.134-T1
Valid prediction for pasa_asmbl_9335.p1
Valid prediction for GlimmerHMM_glimmerT_31667-T1
Valid prediction for GeneMark_model.54484_t
Valid prediction for GlimmerHMM_glimmerT_31687-T1
Valid prediction for GeneMark_model.54490_t
Valid prediction for snap_scaffold_13-snap.140-T1
Valid prediction for GeneMark_model.54498_t
Valid prediction for Augustus_model.g21177.t1
Valid prediction for GeneMark_model.54501_t
Valid prediction for GlimmerHMM_glimmerT_31684-T1
Valid prediction for GlimmerHMM_glimmerT_31670-T1
Valid prediction for Augustus_model.g21187.t1
Valid prediction for snap_scaffold_13-snap.115-T1
Valid prediction for HiQ_model.g21174.t1
Valid prediction for snap_scaffold_13-snap.135-T1
Valid prediction for snap_scaffold_13-snap.129-T1
Valid prediction for GlimmerHMM_glimmerT_31681-T1
Valid prediction for GeneMark_model.54486_t
Valid prediction for HiQ_model.g21176.t1
Valid prediction for snap_scaffold_13-snap.131-T1
Valid prediction for CodingQuarry_transcript_12815-T1
Valid prediction for GeneMark_model.54508_t
Valid prediction for GlimmerHMM_glimmerT_31690-T1
Valid prediction for GeneMark_model.54480_t
Valid prediction for GlimmerHMM_glimmerT_31688-T1
Valid prediction for snap_scaffold_13-snap.123-T1
Valid prediction for snap_scaffold_13-snap.149-T1
Valid prediction for GlimmerHMM_glimmerT_31678-T1
Valid prediction for GlimmerHMM_glimmerT_31674-T1
Valid prediction for Augustus_model.g21185.t1
Valid prediction for snap_scaffold_13-snap.136-T1
Valid prediction for CodingQuarry_transcript_12811-T1
Valid prediction for snap_scaffold_13-snap.116-T1
Valid prediction for GlimmerHMM_glimmerT_31691-T1
Valid prediction for Augustus_model.g21181.t1
Couldn't classify 104524, 104656
Sorry, prediction pasa_asmbl_9332.p1 fails validation.
(ATC)	 TC	104524-104656	GT	ACG
(TAC)	 AG	104855-105030	GT	AGG
(GTG)	 AG	105225-105431	GT	CGG
(GCT)	 AG	105549-105630	GT	CGG
(GAG)	 AG	105796-105989	GT	AGG
(AGT)	 AG	106159-106318	GT	TGG
(GTC)	 AG	106653-106810	GT	AGG
(CTG)	 AG	106928-107031	GT	AGG
(AGG)	 AG	107148-107287	GT	AGG
(TGT)	 AG	107462-107700	GG	AAG
-recovered pasa_asmbl_9332.p1, terminal, 107462, 107700
-recovered pasa_asmbl_9332.p1, internal, 104855, 105030
-recovered pasa_asmbl_9332.p1, internal, 105225, 105431
-recovered pasa_asmbl_9332.p1, internal, 105549, 105630
-recovered pasa_asmbl_9332.p1, internal, 105796, 105989
-recovered pasa_asmbl_9332.p1, internal, 106159, 106318
-recovered pasa_asmbl_9332.p1, internal, 106653, 106810
-recovered pasa_asmbl_9332.p1, internal, 106928, 107031
-recovered pasa_asmbl_9332.p1, internal, 107148, 107287
Valid prediction for GlimmerHMM_glimmerT_31680-T1
Valid prediction for GeneMark_model.54500_t
Valid prediction for GeneMark_model.54497_t
Valid prediction for pasa_asmbl_9327.p1
Valid prediction for GeneMark_model.54496_t

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

-building trellis in range 1 - 206373
-exon list size: 462


building trellis

0.2    
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10.8    
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11.9    
12.1    
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13.1    
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13.8    
14.0    
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14.9    
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20.9    
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22.0    
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22.6    
22.8    
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23.5    
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23.9    
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24.6    
24.8    
25.0    
25.2    
25.4    
25.6    
25.9    
26.1    
26.3    
26.5    
26.7    
26.9    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.2    
36.4    
36.6    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
40.9    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.6    
46.8    
47.0    
47.2    
47.4    
47.6    
47.8    
48.1    
48.3    
48.5    
48.7    
48.9    
49.1    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.9    
51.1    
51.3    
51.5    
51.7    
51.9    
52.2    
52.4    
52.6    
52.8    
53.0    
53.2    
53.4    
53.7    
53.9    
54.1    
54.3    
54.5    
54.7    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.1    
59.3    
59.5    
59.7    
59.9    
60.1    
60.3    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.4    
63.6    
63.8    
64.0    
64.2    
64.4    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 29 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 - 14881
-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
GOT 5prime partial gene.

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