Header Leaderboard Ad


Installing Newbler 2.7 on Ubuntu 12.04, java problem



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

  • #16
    I edited the start up scripts to point in the direction of the new Oracle Java executable, and it seems to initially work.

    The GUI looks to start up, with the picture of the 454 machine and "starting...".... but then dissapears without crashing out in the terminal. So the terminal still indicates the program is running but no GUI.

    Maybe it is due to the Java version, java/jdk1.7.0_21?
    Any ideas?

    Last edited by JackieBadger; 05-10-2013, 03:12 AM.


    • #17
      Originally posted by JackieBadger View Post
      Maybe it is due to the Java version, java/jdk1.7.0_21?
      Any ideas?


      Yes, it is. Do not use Java 7 with the Roche suite, instead go for 6.

      Nevertheless, don't forget to check if there are any limts on your machine,

      ulimit -a
      should help ..
      Last edited by sklages; 05-10-2013, 03:58 AM.


      • #18
        Thanks a lot, guys. Its all up and running now.
        ulimit -a shows no limits on the machine on the machine with the new installation.

        Thanks again


        • #19
          OK so I got the memory crash again on the more powerful machine.

          Here is the ulimit -a output:

          core file size (blocks, -c) 0
          data seg size (kbytes, -d) unlimited
          scheduling priority (-e) 0
          file size (blocks, -f) unlimited
          pending signals (-i) 514997
          max locked memory (kbytes, -l) 64
          max memory size (kbytes, -m) unlimited
          open files (-n) 1024
          pipe size (512 bytes, -p) 8
          POSIX message queues (bytes, -q) 819200
          real-time priority (-r) 0
          stack size (kbytes, -s) 8192
          cpu time (seconds, -t) unlimited
          max user processes (-u) 514997
          virtual memory (kbytes, -v) unlimited
          file locks (-x) unlimited

          My reference file is a genome scaffold consiting of 2,962,365 contigs; 1,555,444,314 bp

          My query sequences consit of 1,151,700 contigs: 390,436,936 bp
          It is after the Index/screening of my query sequences where the compuation runs out of memory.
          On both machines (29GB, and 62GB available respectivly) mapping crashes when it uses a little over 50% of the available RAM

          ANy ideas how to remedy?
          Maybe I should cut my refernce file in half?

          THanks again, guys
          Last edited by JackieBadger; 05-10-2013, 04:27 AM.


          • #20
            Seems gsmapper wants to use more than 64GB RAM .. well, it's a "heavy" reference ...
            Just take a few thousands of the largest contigs (is it a cDNA backbone?) and try again, just to see if the installation itself is OK (it probably is).

            Finally you need to reduce your reference contigs or look for a more powerful machine.

            Just curious, why do you want to map many, many contigs on even more many, many contigs? Maybe you should look for another software to achieve the results you are expecting?

            EDIT: Oh, I haven't noticed your 50% issue. Maybe you should contact your sysadm about that. It is worth a try ;-)
            Last edited by sklages; 05-10-2013, 04:36 AM.


            • #21
              Thanks. WIll do.

              The reference is a genome of a closely related species to the cDNA query sequencs I have (poly A/T trimmed).
              So I want to use the reference to essential construct ESTs and look for SNPs.
              De Novo EST assembly works fine, although it seems intuative to use a reference where possible.


              • #22
                Have you solved your "50% problem"?


                • #23
                  I assumed it was because for a human sized genome I needed a lot more RAM, so we are using some clusters.


                  Latest Articles


                  • seqadmin
                    Improved Targeted Sequencing: A Comprehensive Guide to Amplicon Sequencing
                    by seqadmin

                    Amplicon sequencing is a targeted approach that allows researchers to investigate specific regions of the genome. This technique is routinely used in applications such as variant identification, clinical research, and infectious disease surveillance. The amplicon sequencing process begins by designing primers that flank the regions of interest. The DNA sequences are then amplified through PCR (typically multiplex PCR) to produce amplicons complementary to the targets. RNA targets...
                    Yesterday, 01:49 PM
                  • seqadmin
                    Targeted Sequencing: Choosing Between Hybridization Capture and Amplicon Sequencing
                    by seqadmin

                    Targeted sequencing is an effective way to sequence and analyze specific genomic regions of interest. This method enables researchers to focus their efforts on their desired targets, as opposed to other methods like whole genome sequencing that involve the sequencing of total DNA. Utilizing targeted sequencing is an attractive option for many researchers because it is often faster, more cost-effective, and only generates applicable data. While there are many approaches...
                    03-10-2023, 05:31 AM
                  • seqadmin
                    Expert Advice on Automating Your Library Preparations
                    by seqadmin

                    Using automation to prepare sequencing libraries isn’t a new concept, and most researchers are aware that there are numerous benefits to automating this process. However, many labs are still hesitant to switch to automation and often believe that it’s not suitable for their lab. To combat these concerns, we’ll cover some of the key advantages, review the most important considerations, and get real-world advice from automation experts to remove any lingering anxieties....
                    02-21-2023, 02:14 PM





                  Topics Statistics Last Post
                  Started by seqadmin, 03-17-2023, 12:32 PM
                  0 responses
                  Last Post seqadmin  
                  Started by seqadmin, 03-15-2023, 12:42 PM
                  0 responses
                  Last Post seqadmin  
                  Started by seqadmin, 03-09-2023, 10:17 AM
                  0 responses
                  1 like
                  Last Post seqadmin  
                  Started by seqadmin, 03-03-2023, 12:03 PM
                  0 responses
                  Last Post seqadmin