Re: [Cortexassembler-variation] Cortexassembler-variation Digest, Vol 2, Issue 3
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Re: [Cortexassembler-variation] Cortexassembler-variation Digest, Vol 2, Issue 3
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From: w y <yww...@gm...> - 2012-01-14 12:04:41
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Hi Zam, It was my fault. The problem was solved. Thank you. Andrew 2012/1/14 <cor...@li...> > Send Cortexassembler-variation mailing list submissions to > cor...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > > https://lists.sourceforge.net/lists/listinfo/cortexassembler-variation > > or, via email, send a message with subject or body 'help' to > cor...@li... > > You can reach the person managing the list at > cor...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Cortexassembler-variation digest..." > > > Today's Topics: > > 1. incompatible error (w y) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 14 Jan 2012 16:42:42 +0800 > From: w y <yw...@we...> > Subject: [Cortexassembler-variation] incompatible error > To: cortex <cor...@li...> > Message-ID: > <CAMspgV==XZ3...@ma... > > > Content-Type: text/plain; charset="iso-8859-1" > > 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 > > ----- > 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 > > ----- > Sat Jan 14 06:39:39 2012 > Binary dumped > > ----- > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > > ------------------------------------------------------------------------------ > RSA(R) Conference 2012 > Mar 27 - Feb 2 > Save $400 by Jan. 27 > Register now! > http://p.sf.net/sfu/rsa-sfdev2dev2 > > ------------------------------ > > _______________________________________________ > Cortexassembler-variation mailing list > Cor...@li... > https://lists.sourceforge.net/lists/listinfo/cortexassembler-variation > > > End of Cortexassembler-variation Digest, Vol 2, Issue 3 > ******************************************************* > -- National Key Laboratory of Crop Genetic Improvement(Wuhan) 430070 |