[Cortexassembler-variation] incompatible error
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[Cortexassembler-variation] incompatible error
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From: w y <yw...@we...> - 2012-01-14 08:43:14
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Hi all
I have sequencing data of 203 samples. I builded uncleaned individual
graph for each sample and then merged all of the individual binaries into a
pooled graph with the parameter "--remove_low_coverage_supernodes 1". I
want to clean each individual by comparing it with the cleaned pool graph.
Then I got an error message as follow:
[xwb@node8 xa1326]$
/public3/xwb/solexa_seq/BGI_NCGR/cortex_var_1.0.5.3/bin/cortex_var_63_c203
--kmer_size 41 --mem_height 17 --mem_width 100
--remove_low_coverage_supernodes 1 --colour_list BGI-211-unclean.color_list
colour_list --dump_binary BGI-203-all-clean.ctx
-----
Sat Jan 14 06:38:21 2012
Starting Cortex
Command:
/public3/xwb/solexa_seq/BGI_NCGR/cortex_var_1.0.5.3/bin/cortex_var_63_c203
--kmer_size 41 --mem_height 17 --mem_width 100
--remove_low_coverage_supernodes 1 --colour_list BGI-211-unclean.color_list
colour_list --dump_binary BGI-203-all-clean.ctx
colour list is set to BGI-211-unclean.color_list
cortex_var_63_c203: [--dump_binary] filename [BGI-203-all-clean.ctx] exists!
[xwb@node8 xa1326]$ mv BGI-203-all-clean.ctx first_try/
[xwb@node8 xa1326]$
/public3/xwb/solexa_seq/BGI_NCGR/cortex_var_1.0.5.3/bin/cortex_var_63_c203
--kmer_size 41 --mem_height 17 --mem_width 100
--remove_low_coverage_supernodes 1 --colour_list BGI-211-unclean.color_list
colour_list --dump_binary BGI-203-all-clean.ctx
-----
Sat Jan 14 06:38:29 2012
Starting Cortex
Command:
/public3/xwb/solexa_seq/BGI_NCGR/cortex_var_1.0.5.3/bin/cortex_var_63_c203
--kmer_size 41 --mem_height 17 --mem_width 100
--remove_low_coverage_supernodes 1 --colour_list BGI-211-unclean.color_list
colour_list --dump_binary BGI-203-all-clean.ctx
colour list is set to BGI-211-unclean.color_list
Maximum k-mer size (compile-time setting): 63
Actual K-mer size: 41
Hash table created, number of buckets: 131072
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Sat Jan 14 06:38:29 2012
-----
Sat Jan 14 06:38:29 2012
List of colours: BGI-211-unclean.color_list (contains one filelist per
colour). Load data into consecutive colours starting at 0
Loaded next binary; total kmers in graph is now 22767
Loaded next binary; total kmers in graph is now 32366
Loaded next binary; total kmers in graph is now 37411
Loaded next binary; total kmers in graph is now 41366
Loaded next binary; total kmers in graph is now 48047
Loaded next binary; total kmers in graph is now 52526
Loaded next binary; total kmers in graph is now 55879
Loaded next binary; total kmers in graph is now 59175
Loaded next binary; total kmers in graph is now 64060
Loaded next binary; total kmers in graph is now 66626
Loaded next binary; total kmers in graph is now 69666
Loaded next binary; total kmers in graph is now 75362
Loaded next binary; total kmers in graph is now 77083
Loaded next binary; total kmers in graph is now 81297
Loaded next binary; total kmers in graph is now 83661
Loaded next binary; total kmers in graph is now 86083
Loaded next binary; total kmers in graph is now 89550
Loaded next binary; total kmers in graph is now 91017
Loaded next binary; total kmers in graph is now 93822
Loaded next binary; total kmers in graph is now 96385
Loaded next binary; total kmers in graph is now 99694
Loaded next binary; total kmers in graph is now 101107
Loaded next binary; total kmers in graph is now 102291
Loaded next binary; total kmers in graph is now 105138
Loaded next binary; total kmers in graph is now 106929
Loaded next binary; total kmers in graph is now 108591
Loaded next binary; total kmers in graph is now 110976
Loaded next binary; total kmers in graph is now 113177
Loaded next binary; total kmers in graph is now 115458
Loaded next binary; total kmers in graph is now 117983
Loaded next binary; total kmers in graph is now 122441
Loaded next binary; total kmers in graph is now 124451
Loaded next binary; total kmers in graph is now 125681
Loaded next binary; total kmers in graph is now 126878
Loaded next binary; total kmers in graph is now 129357
Loaded next binary; total kmers in graph is now 131531
Loaded next binary; total kmers in graph is now 133402
Loaded next binary; total kmers in graph is now 136230
Loaded next binary; total kmers in graph is now 139239
Loaded next binary; total kmers in graph is now 141905
Loaded next binary; total kmers in graph is now 143275
Loaded next binary; total kmers in graph is now 146672
Loaded next binary; total kmers in graph is now 149789
Loaded next binary; total kmers in graph is now 152071
Loaded next binary; total kmers in graph is now 155431
Loaded next binary; total kmers in graph is now 157177
Loaded next binary; total kmers in graph is now 158641
Loaded next binary; total kmers in graph is now 161144
Loaded next binary; total kmers in graph is now 162721
Loaded next binary; total kmers in graph is now 165230
Loaded next binary; total kmers in graph is now 167404
Loaded next binary; total kmers in graph is now 171258
Loaded next binary; total kmers in graph is now 174242
Loaded next binary; total kmers in graph is now 176664
Loaded next binary; total kmers in graph is now 178109
Loaded next binary; total kmers in graph is now 179621
Loaded next binary; total kmers in graph is now 183080
Loaded next binary; total kmers in graph is now 184308
Loaded next binary; total kmers in graph is now 186840
Loaded next binary; total kmers in graph is now 189077
Loaded next binary; total kmers in graph is now 190685
Loaded next binary; total kmers in graph is now 193500
Loaded next binary; total kmers in graph is now 195646
Loaded next binary; total kmers in graph is now 199109
Loaded next binary; total kmers in graph is now 200801
Loaded next binary; total kmers in graph is now 203224
Loaded next binary; total kmers in graph is now 204817
Loaded next binary; total kmers in graph is now 206443
Loaded next binary; total kmers in graph is now 207823
Loaded next binary; total kmers in graph is now 210392
Loaded next binary; total kmers in graph is now 211673
Loaded next binary; total kmers in graph is now 213965
Loaded next binary; total kmers in graph is now 216451
Loaded next binary; total kmers in graph is now 219080
Loaded next binary; total kmers in graph is now 221138
Loaded next binary; total kmers in graph is now 222421
Loaded next binary; total kmers in graph is now 223871
Loaded next binary; total kmers in graph is now 226932
Loaded next binary; total kmers in graph is now 228422
Loaded next binary; total kmers in graph is now 229918
Loaded next binary; total kmers in graph is now 232287
Loaded next binary; total kmers in graph is now 234695
Loaded next binary; total kmers in graph is now 236351
Loaded next binary; total kmers in graph is now 237901
Loaded next binary; total kmers in graph is now 239630
Loaded next binary; total kmers in graph is now 242343
Loaded next binary; total kmers in graph is now 245181
Loaded next binary; total kmers in graph is now 246607
Loaded next binary; total kmers in graph is now 250624
Loaded next binary; total kmers in graph is now 253823
Loaded next binary; total kmers in graph is now 256329
Loaded next binary; total kmers in graph is now 257659
Loaded next binary; total kmers in graph is now 262796
Loaded next binary; total kmers in graph is now 264864
Loaded next binary; total kmers in graph is now 267321
Loaded next binary; total kmers in graph is now 269634
Loaded next binary; total kmers in graph is now 273173
Loaded next binary; total kmers in graph is now 277487
Loaded next binary; total kmers in graph is now 278522
Loaded next binary; total kmers in graph is now 281063
Loaded next binary; total kmers in graph is now 285782
Loaded next binary; total kmers in graph is now 287787
Loaded next binary; total kmers in graph is now 290553
Loaded next binary; total kmers in graph is now 293259
Loaded next binary; total kmers in graph is now 295971
Loaded next binary; total kmers in graph is now 297148
Loaded next binary; total kmers in graph is now 298921
Loaded next binary; total kmers in graph is now 300536
Loaded next binary; total kmers in graph is now 301999
Loaded next binary; total kmers in graph is now 304524
Loaded next binary; total kmers in graph is now 305434
Loaded next binary; total kmers in graph is now 306990
Loaded next binary; total kmers in graph is now 308284
Loaded next binary; total kmers in graph is now 310515
Loaded next binary; total kmers in graph is now 311637
Loaded next binary; total kmers in graph is now 313175
Loaded next binary; total kmers in graph is now 314616
Loaded next binary; total kmers in graph is now 316389
Loaded next binary; total kmers in graph is now 317761
Loaded next binary; total kmers in graph is now 319910
Loaded next binary; total kmers in graph is now 322054
Loaded next binary; total kmers in graph is now 323139
Loaded next binary; total kmers in graph is now 324855
Loaded next binary; total kmers in graph is now 327307
Loaded next binary; total kmers in graph is now 328925
Loaded next binary; total kmers in graph is now 331554
Loaded next binary; total kmers in graph is now 332922
Loaded next binary; total kmers in graph is now 335022
Loaded next binary; total kmers in graph is now 337108
Loaded next binary; total kmers in graph is now 338717
Loaded next binary; total kmers in graph is now 339977
Loaded next binary; total kmers in graph is now 341436
Loaded next binary; total kmers in graph is now 343882
Loaded next binary; total kmers in graph is now 345598
Loaded next binary; total kmers in graph is now 346811
Loaded next binary; total kmers in graph is now 348513
Loaded next binary; total kmers in graph is now 350895
Loaded next binary; total kmers in graph is now 352561
Loaded next binary; total kmers in graph is now 354833
Loaded next binary; total kmers in graph is now 356768
Loaded next binary; total kmers in graph is now 358614
Loaded next binary; total kmers in graph is now 359984
Loaded next binary; total kmers in graph is now 362040
Loaded next binary; total kmers in graph is now 362901
Loaded next binary; total kmers in graph is now 365440
Loaded next binary; total kmers in graph is now 366804
Loaded next binary; total kmers in graph is now 368567
Loaded next binary; total kmers in graph is now 370585
Loaded next binary; total kmers in graph is now 371982
Loaded next binary; total kmers in graph is now 373144
Loaded next binary; total kmers in graph is now 374375
Loaded next binary; total kmers in graph is now 375606
Loaded next binary; total kmers in graph is now 377440
Loaded next binary; total kmers in graph is now 378810
Loaded next binary; total kmers in graph is now 379565
Loaded next binary; total kmers in graph is now 380437
Loaded next binary; total kmers in graph is now 381815
Loaded next binary; total kmers in graph is now 382664
Loaded next binary; total kmers in graph is now 384275
Loaded next binary; total kmers in graph is now 385551
Loaded next binary; total kmers in graph is now 386886
Loaded next binary; total kmers in graph is now 388872
Loaded next binary; total kmers in graph is now 390189
Loaded next binary; total kmers in graph is now 390924
Loaded next binary; total kmers in graph is now 392236
Loaded next binary; total kmers in graph is now 393605
Loaded next binary; total kmers in graph is now 395231
Loaded next binary; total kmers in graph is now 396548
Loaded next binary; total kmers in graph is now 397668
Loaded next binary; total kmers in graph is now 399317
Loaded next binary; total kmers in graph is now 400101
Loaded next binary; total kmers in graph is now 401453
Loaded next binary; total kmers in graph is now 402692
Loaded next binary; total kmers in graph is now 404067
Loaded next binary; total kmers in graph is now 405598
Loaded next binary; total kmers in graph is now 407399
Loaded next binary; total kmers in graph is now 409371
Loaded next binary; total kmers in graph is now 412168
Loaded next binary; total kmers in graph is now 413327
Loaded next binary; total kmers in graph is now 414596
Loaded next binary; total kmers in graph is now 415702
Loaded next binary; total kmers in graph is now 417744
Loaded next binary; total kmers in graph is now 419690
Loaded next binary; total kmers in graph is now 421309
Loaded next binary; total kmers in graph is now 422236
Loaded next binary; total kmers in graph is now 423203
Loaded next binary; total kmers in graph is now 424510
Loaded next binary; total kmers in graph is now 425970
Loaded next binary; total kmers in graph is now 427800
Loaded next binary; total kmers in graph is now 429053
Loaded next binary; total kmers in graph is now 430986
Loaded next binary; total kmers in graph is now 431656
Loaded next binary; total kmers in graph is now 433148
Loaded next binary; total kmers in graph is now 434068
Loaded next binary; total kmers in graph is now 435313
Loaded next binary; total kmers in graph is now 436008
Loaded next binary; total kmers in graph is now 437131
Loaded next binary; total kmers in graph is now 438891
Loaded next binary; total kmers in graph is now 439999
Loaded next binary; total kmers in graph is now 441646
Loaded next binary; total kmers in graph is now 443600
Loaded next binary; total kmers in graph is now 445225
Loaded next binary; total kmers in graph is now 446503
-----
Sat Jan 14 06:39:16 2012
Finished loading single_colour binaries
Total kmers in table: 446503
****************************************
SUMMARY:
Colour: MeanReadLen TotalSeq
0 89 10401241
1 0 0
2 0 0
3 0 0
4 0 0
5 0 0
6 0 0
7 0 0
8 0 0
9 0 0
10 0 0
11 0 0
12 0 0
13 0 0
14 0 0
15 0 0
16 0 0
17 0 0
18 0 0
19 0 0
20 0 0
21 0 0
22 0 0
23 0 0
24 0 0
25 0 0
26 0 0
27 0 0
28 0 0
29 0 0
30 0 0
31 0 0
32 0 0
33 0 0
34 0 0
35 0 0
36 0 0
37 0 0
38 0 0
39 0 0
40 0 0
41 0 0
42 0 0
43 0 0
44 0 0
45 0 0
46 0 0
47 0 0
48 0 0
49 0 0
50 0 0
51 0 0
52 0 0
53 0 0
54 0 0
55 0 0
56 0 0
57 0 0
58 0 0
59 0 0
60 0 0
61 0 0
62 0 0
63 0 0
64 0 0
65 0 0
66 0 0
67 0 0
68 0 0
69 0 0
70 0 0
71 0 0
72 0 0
73 0 0
74 0 0
75 0 0
76 0 0
77 0 0
78 0 0
79 0 0
80 0 0
81 0 0
82 0 0
83 0 0
84 0 0
85 0 0
86 0 0
87 0 0
88 0 0
89 0 0
90 0 0
91 0 0
92 0 0
93 0 0
94 0 0
95 0 0
96 0 0
97 0 0
98 0 0
99 0 0
100 0 0
101 0 0
102 0 0
103 0 0
104 0 0
105 0 0
106 0 0
107 0 0
108 0 0
109 0 0
110 0 0
111 0 0
112 0 0
113 0 0
114 0 0
115 0 0
116 0 0
117 0 0
118 0 0
119 0 0
120 0 0
121 0 0
122 0 0
123 0 0
124 0 0
125 0 0
126 0 0
127 0 0
128 0 0
129 0 0
130 0 0
131 0 0
132 0 0
133 0 0
134 0 0
135 0 0
136 0 0
137 0 0
138 0 0
139 0 0
140 0 0
141 0 0
142 0 0
143 0 0
144 0 0
145 0 0
146 0 0
147 0 0
148 0 0
149 0 0
150 0 0
151 0 0
152 0 0
153 0 0
154 0 0
155 0 0
156 0 0
157 0 0
158 0 0
159 0 0
160 0 0
161 0 0
162 0 0
163 0 0
164 0 0
165 0 0
166 0 0
167 0 0
168 0 0
169 0 0
170 0 0
171 0 0
172 0 0
173 0 0
174 0 0
175 0 0
176 0 0
177 0 0
178 0 0
179 0 0
180 0 0
181 0 0
182 0 0
183 0 0
184 0 0
185 0 0
186 0 0
187 0 0
188 0 0
189 0 0
190 0 0
191 0 0
192 0 0
193 0 0
194 0 0
195 0 0
196 0 0
197 0 0
198 0 0
199 0 0
200 0 0
201 0 0
202 0 0
****************************************
Clip tips first
Remove low coverage supernodes covg (<= 1)
-----
Sat Jan 14 06:39:35 2012
Error correction done
-----
Sat Jan 14 06:39:35 2012
Dump multicolour binary with 203 colours (compile-time setting)
129800 kmers dumped
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Sat Jan 14 06:39:39 2012
Binary dumped
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Sat Jan 14 06:39:39 2012
Cortex completed - have a nice day!
[xwb@node8 xa1326]$ ../bin/cortex_var_63_c2 --kmer_size 41 --mem_height 17
--mem_width 100 --multicolour_bin BGI-203-all-clean.ctx --colour_list
unclean_colour_list --load_colours_only_where_overlap_clean_colour 0
--successively_dump_cleaned_colours cleaned
-----
Sat Jan 14 06:40:47 2012
Starting Cortex
Command: ../bin/cortex_var_63_c2 --kmer_size 41 --mem_height 17 --mem_width
100 --multicolour_bin BGI-203-all-clean.ctx --colour_list
unclean_colour_list --load_colours_only_where_overlap_clean_colour 0
--successively_dump_cleaned_colours cleaned
colour list is set to unclean_colour_list
You are loading binary with 203 colours into a graph with 2 colours -
incompatible
Error in cmd-line input: This binary BGI-203-all-clean.ctx is not
compatible with the current de Bruijn graph parameters
Could anyone help?
Best regards
Andrew
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