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  • #31
    Originally posted by catfisher View Post
    Marten, thanks for your quick reply. I editted my configure file as you suggested and run goBambus again, but still failed.
    I used the .conf as:
    # Priorities
    priority ALL 1
    # The following lines can be un-commented to specify certain
    # per-library settings

    # Redundancies
    # redundancy lib_some 1

    # allowed error
    # error MUMmer 0.5

    # overlaps allowed
    # overlaps MUMmer Y

    # Global redundancy
    redundancy 2

    # min group size
    mingroupsize 0

    The log information for goBambus is :
    Parsing links out of input file
    Step 100: running detective
    Combining XML files
    Step 200: making the xmls
    starting
    Done
    Step 300: Preparing contig links
    starting
    Done
    Step 400: Running scaffolder
    Grommit(/home/aubsxl/bin/bambus/bin/grommit -i ctg2660_BES_mapping_704.inp -o ctg2660_BES_mapping_704.out.xml -C c
    tg2660_BES_mapping_704.grommit.conf --append --logfile goBambus.log --debug 1) script failed

    The error information from goBambus.error file is:
    20100712|123807| 10451| Grommit(/home/aubsxl/bin/bambus/bin/grommit -i ctg2660_BES_mapping_704.inp -o ctg2660_BES_
    mapping_704.out.xml -C ctg2660_BES_mapping_704.grommit.conf --append --logfile goBambus.log --debug 1) script fail
    ed

    The first several lines from my mates files is:
    library libname 200 500
    HWUSI-EAS1665_0002:2:1:1022:18088#0/1 HWUSI-EAS1665_0002:2:1:1022:18088#0/2 libname
    HWUSI-EAS1665_0002:2:1:1029:11872#0/1 HWUSI-EAS1665_0002:2:1:1029:11872#0/2 libname
    HWUSI-EAS1665_0002:2:1:1029:11034#0/1 HWUSI-EAS1665_0002:2:1:1029:11034#0/2 libname
    HWUSI-EAS1665_0002:2:1:1030:19457#0/1 HWUSI-EAS1665_0002:2:1:1030:19457#0/2 libname
    HWUSI-EAS1665_0002:2:1:1031:12133#0/1 HWUSI-EAS1665_0002:2:1:1031:12133#0/2 libname

    Marten, could you look at these information and point out what's wrong with this? I have no idea. Thanks a lot,

    Kevin
    Hi, Catfisher,

    I met the exact same question as you. Have you found any solution of this question?

    Comment


    • #32
      Hi shouhua,
      I also have the same err as you. Have you figured out?

      Thanks!

      Comment


      • #33
        HI all,
        I have a question regarding the mate file. I ran velvet(with no scaffolding option) and get 4-5 nice assemblies with different k-mer's. Then I merged all these 4 assemblies into a single one using minimus2 Amos. Now I have .contig file and .bnk/ file. How can I generate the .mate file? should I use the sed command discussed in some posts. but the Id's of my .mate file and .contig file are not showing any link. My .contig file has id: #NODE_1_length_1305_cov_18.627586(0) from velvet and the .mate is with Illumina id's @HWUSI-EAS100R:6:73:941:1973#0/1 @HWUSI-EAS100R:6:73:941:1973#0/2. How can I link this information. Anybody please help.
        Regards,
        Rahul
        Rahul Sharma,
        Ph.D
        Frankfurt am Main, Germany

        Comment


        • #34
          Hii,,
          I am trying to run bambus on velvet contigs..
          i have generated .afg while assembling using velvet.. and then used the following command lines... as suggested by some forum ...
          /amos-3.0.1/src/Bank/bank-transact -cf -b j99.bnk -m velvet_asm.afg

          /amos-3.0.1/src/Bambus/Bundler/clk -b j99.bnk/

          /amos-3.0.1/src/Bambus/Bundler/Bundler -b j99.bnk

          /amos-3.0.1/src/Bambus/Bundler/MarkRepeats -b j99.bnk -redundancy 2 -agressive >repeat_fi

          /amos-3.0.1/src/Bambus/Bundler/OrientContigs -b j99.bnk -prefix j99scaff -redundancy 2 -repeats repeat_fi -all -agressive -linearize

          perl /amos-3.0.1/src/Bambus/Untangler/untangle.pl -e j99scaff.evidence.xml -s j99scaff.out.xml -o j99scaff.untangle.xml

          /amos-3.0.1/src/Bank/bank2fasta -d -b j99.bnk >bambus_contigs.fa

          perl /amos-3.0.1/src/Bambus/Untangler/printScaff.pl -e j99scaff.evidence.xml -s j99scaff.untangle.xml -l j99scaff.library -f bambus_contigs.fa -merge -o bambus_scaff

          and it has generated the following stats..

          no. valid links: 0
          no. incorrect len. links: 0
          no. incorrect ori. links: 0
          no. unchecked links: 18129

          I can see that no scaffolding is being done, since there are no valid links...
          can anyone tell me if my approach is right ... and if it is a must to use mates file

          Comment


          • #35
            Originally posted by sabiha View Post
            Hii,,
            I am trying to run bambus on velvet contigs..
            i have generated .afg while assembling using velvet.. and then used the following command lines... as suggested by some forum ...
            Why don't try SSPACE? For more details, please see http://seqanswers.com/forums/showthread.php?t=8350

            and

            Boetzer, M., Henkel, C.V., Jansen, H.J., Butler, D. and Pirovano, W. (2011) Scaffolding pre-assembled contigs using SSPACE, Bioinformatics, 27, 578-579.

            Comment


            • #36
              .. I ve already tried SSpace. Just wanted to see how bambus wrks... as it does hierarchical scaffolding

              Comment


              • #37
                sabiha,

                Does the stdout from bank-transact report any "Objects added"?

                Are your .xml files links of some sort (paired reads, etc)? I have gotten bambus to work, but used the .xml link information much earlier. Before running bambus, I used toAmos with fasta reads, a TIGR .contig file, and xml link information. Then I generated an amos bank using bank-transact on the resulting .afg file. Then ran bambus (via the goBambus script) on the bank.

                Comment


                • #38
                  MeganS,

                  Thank you for helping me out. stdout from bank-transact reported the following.
                  Messages read: 4963548
                  Objects added: 4963548
                  Objects deleted: 0
                  Objects replaced: 0

                  I have Illumina paired end reads in fastq format, which has quality scores included in the same file. I am planning to split the sequences and the quality into two files and will try using these files.

                  How did u generate the xml link information??

                  Comment

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