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  • #16
    I know it does not have an inbuilt option for running multithread. I was wondering if anyone has a workaround it to make the program faster.

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    • #17
      Hi

      I have assembled the reads from 454 and illumina as contig1 and contig2 respectively of the same species, can somebody will help me in merging these two contig files into one file using cap3. My aim is to get larger contigs.

      Thanks in Advance

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      • #18
        Happy new year

        This is too late...
        but just want to know if u tried PCAP ?

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        • #19
          cap3 input file

          I am trying to use Cap3 at the moment but having some difficulty. I am concatenating some .fna files with some a contigs file in fasta format. However, although both files appear to be running when submitted individually, the concatenated file fails with a segmentation error. I have tried removing any empty line at the end of each file before concatenating but this didn't help. I even tried manually combining both files but it didn't help!Anyone come across a simliar problem and can share a solution.

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          • #20
            Is there any limitation to the input sequence size into CAP3.
            I want to combine assemblies from 454 and illumina using CAP3. However I find most of the contigs in singleton_file generated by cap3.
            If someone can explain...kindly help me out.
            Thanks

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            • #21
              Also having troubles with cap3, not seeing .qual file

              Hi,

              I am also having some frustrations with cap3. I can't get it to recognize my qual file associated with my fasta file. I was told that cap3 picks this file up automatically if it is in the same directory as the fasta file, as long as the name before the file extension is the same...is that true? I've tried naming just the .fna file and also adding the qual file to the command line, but I still get the message "No file of quality values (.qual) is found".

              Here are the two ways I've tried to input the files:

              $cap3 2011_4_26Reads.fna 2011_4_26Reads.qual

              $cap3 2011_4_26Reads.fna

              Any suggestions?

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              • #22
                Originally posted by grassgirl View Post
                Hi,

                I am also having some frustrations with cap3. I can't get it to recognize my qual file associated with my fasta file. I was told that cap3 picks this file up automatically if it is in the same directory as the fasta file, as long as the name before the file extension is the same...is that true? I've tried naming just the .fna file and also adding the qual file to the command line, but I still get the message "No file of quality values (.qual) is found".

                Here are the two ways I've tried to input the files:

                $cap3 2011_4_26Reads.fna 2011_4_26Reads.qual

                $cap3 2011_4_26Reads.fna

                Any suggestions?
                The file needs to be named 2011_4_26Reads.fna.qual. cap3 assumes it is the full file name, with any extension if present, then with .qual.

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                • #23
                  Thanks, kmcarr! This solutions appears to have worked. At least I'm not getting that error message when I run it the way you state above.

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