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  • newbler ace to amos bnk

    does anyone know how to convert a newbler derived ace file to amos bnk so i can use amosvalidate. I know the standard command to do this using toAmos, however, we i do this lose mate pair information.
    I tried using toAmos with a traceinfo file derived from sff_extract which seemed to work but when i ran amosvalidate i encountered the following error

    Command: /usr/local/bioinf/Amos/bin/asmQC -b 454Contigs.bnk -scaff -recompute -update -numsd 2 exited with status:1


    can anyone help?

    regards

    Brian

  • #2
    in case anyone is interested



    Unfortunately, we don't support 454 mates at this time, so I recommend you skip
    the mate analysis of amosvalidate. Copy the amosvalidate script to a new
    location:

    $ cp /path/to/amos/bin/amosvalidate amosvalidate-nomates

    Edit the script to remove the mate analysis by commenting out steps 300-340

    ## Analyzing mate-pairs
    ## 300: $(BINDIR)/asmQC -b $(PREF).bnk -scaff -recompute -update -numsd 2
    ## 310: $(BINDIR)/asmQC -b $(PREF).bnk -scaff -recompute -update -numsd 2
    ## 320: $(BINDIR)/asmQC -b $(PREF).bnk -scaff -feat -numsd 3 -shortcvg -1 -longcvg
    -1
    ## 330: $(BINDIR)/cestat-cov -i -f 4 $(PREF).bnk > $(PREF).ce.feat
    ## 340: $(BINDIR)/loadFeatures -i $(PREF).bnk $(PREF).ce.feat

    Then try the new script
    $ amosvalidate-nomates 454Contigs

    Good luck!

    Michael Schatz


    Which leads me to ask if there is any program which can be used to validate 454 mate pair assemblies

    Comment


    • #3
      Hi All,
      I am attempting to use amosalidate to perform assembly forensics. I am stuck, however, as everytime I follow the instructions on the amos wiki to convert my newbler .ace file to a .bnk, I get the following error:

      $ toAmos -ace 454Contigs.ace.1 -o - | bank-transact -m - -o 454Contigs.bnk -c
      bank-transact: invalid option -- o
      ERROR: The -b option is mandatory
      ERROR: Bank directory is not accessible, No such file or directory


      .USAGE.
      bank-transact [options] -b <bank path> -m <message path>
      Try 'bank-transact -h' for more information.




      Any suggestions? Thanks a bunch!

      Comment


      • #4
        hi me shahid plz can any body help me i m using velvet for denovo and producing afg file and from that afg file creating amos bank file but when i run amos validate command on that bnk folder it give error like this:
        Doing step 100: Creating FastA
        Command: /usr/local/amos/bin/bank2fasta -b /home/shahid/denovo_run2/bank/assembly.bnk/.bnk > /home/shahid/denovo_run2/bank/assembly.bnk/.fasta exited with status: 1

        so any body can help me what this error come and any suggestion for solution.thanks

        Comment


        • #5
          Originally posted by shahid.manzoor View Post
          hi me shahid plz can any body help me i m using velvet for denovo and producing afg file and from that afg file creating amos bank file but when i run amos validate command on that bnk folder it give error like this:
          Doing step 100: Creating FastA
          Command: /usr/local/amos/bin/bank2fasta -b /home/shahid/denovo_run2/bank/assembly.bnk/.bnk > /home/shahid/denovo_run2/bank/assembly.bnk/.fasta exited with status: 1

          so any body can help me what this error come and any suggestion for solution.thanks
          A similar error is returned when i use amosvalidate!
          github:
          https://github.com/Bioinformatics-and-Genomics

          Comment


          • #6
            I have the same problem exactly the same problem as shahid.manzoor. I do velvet assembly with create .afg file option, put it in the AMOS bank, no problem. When I do amosvalidate I get the same response unfortunately...

            Does anyone know how to do it the right way?

            Comment


            • #7
              Originally posted by AppleInformatics View Post
              I am attempting to use amosalidate to perform assembly forensics. I am stuck, however, as everytime I follow the instructions on the amos wiki to convert my newbler .ace file to a .bnk, I get the following error:

              [I]$ toAmos -ace 454Contigs.ace.1 -o - | bank-transact -m - -o 454Contigs.bnk -c
              bank-transact: invalid option -- o
              ERROR: The -b option is mandatory
              ERROR: Bank directory is not accessible, No such file or directory
              I know this is an old thread, but thought I would add what I've done recently to convert Newbler ACE files to AMOS bank:

              Code:
              toAmos -ace newbler_assembly.ace -o - | bank-transact -m - -b newbler_assembly.bnk -c

              Comment


              • #8
                Originally posted by Irsan_Kooi View Post
                I have the same problem exactly the same problem as shahid.manzoor. I do velvet assembly with create .afg file option, put it in the AMOS bank, no problem. When I do amosvalidate I get the same response unfortunately...

                Does anyone know how to do it the right way?
                Hi,
                I know it's an old thread but I ran into the same problem. It seems as if the solution is the following:
                I guess you used tab-complete to write the bank name?
                So you would have something like this as an input:
                Code:
                amosvalidate assembly.bnk/
                just cut off the "/". So:
                Code:
                amosvalidate assembly.bnk
                seems to work for me.

                Maybe this helps someone running into similar problems.

                Comment

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