Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • MaSuRCA install error

    I'm attempting to install the MaSuRCA assembly tool using the simple instructions on the quickstart guide. Basically, the instructions say to untar the package, cd into the resulting directory, and then run ./install.sh.

    When I do this, the very end of the output gives a set of errors that apparently have to do with jellyfish. I'm not sure how to interpret this. Has anyone else seen this? I'm pasting just the part of the output that contains the errors and occurs at the very end of the process. There were not any obvious errors before this point:

    # Output
    In file included from sub_commands/count_main.cc:39:
    ./include/jellyfish/mer_qual_iterator.hpp: In member function âvoid jellyfish::mer_qual_iterator<SequencePool, MerType>::init_from_job()â:
    ./include/jellyfish/mer_qual_iterator.hpp:108: error: âstruct std::basic_string<char, std::char_traits<char>, std::allocator<char> >â has no member named âcbeginâ
    ./include/jellyfish/mer_qual_iterator.hpp:109: error: âstruct std::basic_string<char, std::char_traits<char>, std::allocator<char> >â has no member named âcendâ
    ./include/jellyfish/mer_qual_iterator.hpp:111: error: âstruct std::basic_string<char, std::char_traits<char>, std::allocator<char> >â has no member named âcbeginâ
    ./include/jellyfish/mer_qual_iterator.hpp:112: error: âstruct std::basic_string<char, std::char_traits<char>, std::allocator<char> >â has no member named âcendâ
    make[1]: *** [sub_commands/count_main.o] Error 1
    make[1]: *** Waiting for unfinished jobs....
    make[1]: Leaving directory `/raid4/cgrb/MaSuRCA-2.2.0/jellyfish'
    make: *** [install] Error 2

  • #2
    This particular excerpt does not raise any obvious flags. Can you post the earliest instances of "Error" from this output?

    If it is easier, you can paste the whole output via pastebin (http://pastebin.com/). Remember to remove any identifying IP addresses/host names/account names etc.

    Comment


    • #3
      Here's the entire output...

      OK, I tried pasting the entire output in pastebin. How do I link the pastebin page back to this thread?

      I titled the pastebin "MaSuRCA install error output".

      Comment


      • #4
        Here the pastebin link for your output: http://pastebin.com/zLDXsks7 Verify that it is right.

        Comment


        • #5
          Yup, that's the one.

          Comment


          • #6
            Can you tell us what OS you are using and if it is 32- or 64-bit? This is a real server (and not a virtual machine).

            Comment


            • #7
              OS

              The OS is Linux - x86_64 GNU/Linux

              Comment

              Latest Articles

              Collapse

              • seqadmin
                Quality Control Essentials for Next-Generation Sequencing Workflows
                by seqadmin




                Like all molecular biology applications, next-generation sequencing (NGS) workflows require diligent quality control (QC) measures to ensure accurate and reproducible results. Proper QC begins at nucleic acid extraction and continues all the way through to data analysis. This article outlines the key QC steps in an NGS workflow, along with the commonly used tools and techniques.

                Nucleic Acid Quality Control
                Preparing for NGS starts with isolating the...
                02-10-2025, 01:58 PM
              • seqadmin
                An Introduction to the Technologies Transforming Precision Medicine
                by seqadmin


                In recent years, precision medicine has become a major focus for researchers and healthcare professionals. This approach offers personalized treatment and wellness plans by utilizing insights from each person's unique biology and lifestyle to deliver more effective care. Its advancement relies on innovative technologies that enable a deeper understanding of individual variability. In a joint documentary with our colleagues at Biocompare, we examined the foundational principles of precision...
                01-27-2025, 07:46 AM

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, 02-07-2025, 09:30 AM
              0 responses
              72 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 02-05-2025, 10:34 AM
              0 responses
              113 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 02-03-2025, 09:07 AM
              0 responses
              89 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 01-31-2025, 08:31 AM
              0 responses
              49 views
              0 likes
              Last Post seqadmin  
              Working...
              X