Last updated on 10.Mar 2022

Troubles with ARB?

  1. Customizing ARB
    1. What environment variables is ARB aware of?
    2. Where does ARB save my properties?
  2. Known problems with integrated tools
    1. fig2dev displays an error
  3. Linkage/library problems
    1. Arb complains about a missing libstdc++-libc...
    2. When I try to run arb I get the message ´arb_ntree - no such file or directory.´
  4. ARB says 'Error: Can´t open display: ...'
  5. When I try to save my database in /usr/arb/lib/pts I get an error.
  6. Problems concerning the PT-Server
    1. When I try to work with the PT-Server I get the message 'Could not open socket on Server'
    2. When I try to run probe-design ARB complains it can´t open the server ARB_PT_SERVER0
    3. After some time I can´t start the PT_SERVER any more. I have to reboot the computer.
    4. I am looking for signatures for some algal taxonomic groups.
  7. Problems concerning the ARB Nameserver
    1. While synchronizing species IDs, I get the following error message: ´Error in ARB_name_server: Missing default value for add.field (option has to be -fstart=defaultValue)´
  8. When I want to align a sequence, it gave a fatal error : out of memory (in the message box).
  9. I have attempted to import the new RDP tree into ARB.
  10. I want to print the entire 16S rrna phylogenetic tree but have not been able to print more than the first page.
  1. Customizing ARB

    1. What environment variables is ARB aware of?

      A detailed list is available from the ARB online help.

    2. Where does ARB save my properties?

      They are saved in ~/.arb_prop.
      If you want share your ARB settings with another user or copy them to your second home directory simply copy ~/.arb_prop.

  2. Known problems with integrated tools

    1. fig2dev displays an error
      When printing or exporting to xfig an error message concerning fig2dev has been printed in the arb console window:

      System error occured while running ´fig2dev -L ps -M -m 1.0000 /tmp/arb print user 4626.xfig /tmp/arb :print user 4626.ps´

      Reason: You´ve updated from an older ARB version and there´s a leftover fig2dev binary in /usr/arb/bin which is called instead of the one installed globally on your machine.
      Solution: Delete fig2dev from /usr/arb/bin
      Reason: You don´t have fig2dev installed or your version is outdated.
      Solution: Install (a newer) fig2dev.

  3. Linkage/library problems

    1. Arb complains about a missing libstdc++-libc...
      When I try to run arb I get the message

      arb_ntree: error while loading shared libraries: libstdc++-libc6.2-2.so.3: cannot open shared object file : No such file or directory

      or something similar.

      Reason: On your system another version of libstdc++ is installed than on our system.
      If anybody knows a general solution to solve this library problem, please mail it to . Thanks.
      Solution: Create a link in /usr/lib to the version existing on your system (preferrable a newer version) using

      ln -s yyy xxx

      where xxx should be the name of the missing library arb complains about and yyy should be the name of the version of libstdc++ existing on your installation.
      Solution: For Debian-Linux you need to install the following packages: libc5, xpm4.7, xlib6
      To install them run 'apt-get install libc5 xpm4.7 xlib6'
      Solution: ARB uses Redhat 6.2 libraries. To use ARB you have to install ld.so-1.05-13.i386.rpm and libc-5.3.12-31.i386.rpm (use http://www.rpmfind.net to find them)
      Solution: On Fedora Core 2 systems you need to install the compat-libstdc++-7.3-2.96.126.i386.rpm from Disk #3 of FC2. Symlink to /usr/lib/libstdc++-3-libc6.2-2-2.10.0.so or similar.
      Solution: For Ubuntu 5.10 the following solution has been reported to us:
      I used the synaptic package manager to install the libstdc++2.10-dev library (to eliminated the usually libstdc++-libc6.2-2.so.3 error) and transfig and xfig.
      (I think the symlinking like above was necessary as well -Ralf)

    2. When I try to run arb I get the message ´arb_ntree - no such file or directory.´
      Even if I call /usr/arb/bin/arb_ntree directly, I get the same message and

      ldd /usr/arb/bin/arb_ntree

      outputs similar results.

      Reason: You have a Linux-Distribution based on the new shared C-libraries (i.e. SuSE 6.4 or higher) and use one of our last-century ARB-versions.
      Solution: Start your Linux installation tool (i.e. yast) and install the ShlibS5 library(SuSE).
      Solution: Reported by users: For RedHat7.1: ld.so-1.9.5-13.i386.rpm and libc-5.3.12-31.i386.rpm (these packages are not included in the 7.1 distribution, but they are included in the 6.2 distribution so it should work if you´ve updated from 6.2; these RPMs are also available from http://mirrors.kernel.org/redhat/redhat/redhat-6.2-en/os/i386/RedHat/RPMS/ )
      Solution: Reported by Gregory Devulder: With Mandrake 8.0, three libraries are missing (ld.so, libdl.so.1 and ld-linux.so.1) So, after installing the RPM libc-5.3.12-35mdk.i586.rpm you copy this three libraries into /lib. Then you do

      chmod a+x ld-linux.so.1

      The three libraries can be found on the site http://home.get2net.dk/bt/ftp/ld-linux/.

  4. ARB says 'Error: Can´t open display: ...'
    If I try to login from another computer and start ARB, it says

    ARB:Loading '/data/arb/lib/arb_default/ntree.arb' done
    Error: Can´t open display: ...

    Reason: Your enviroment variable DISPLAY is not set correctly.
    Solution: Start a xterm, type ...

    DISPLAY='IP:0.0'
    export DISPLAY

    ... if you´re using bash or ...

    setenv DISPLAY 'IP:0.0'

    in case of tcsh. Replace 'IP' by the name or ip-address of your current machine.

  5. When I try to save my database in /usr/arb/lib/pts I get an error.

    Reason: This directory is protected from saving databases to, in order to avoid inconsistencies with the PT-Server-databases.
    Solution: Save your databases somewhere else.

  6. Problems concerning the PT-Server

    1. When I try to work with the PT-Server I get the message 'Could not open socket on Server'

      Reason: This is a bug in ARB. It uses wrong ports for communication.
      Solution: Edit /usr/arb/lib/arb_tcp.dat and change the port numbers to different values. Ports 3152 and following worked fine for other people. If not - try other port numbers.
      Goto ARB_NTREE/Etc/Probe functions/PTserver admin/template to edit /usr/arb/lib/arb_tcp.dat

    2. When I try to run probe-design ARB complains it can´t open the server ARB_PT_SERVER0

      Reason: You forgot to create the index file for the pt_server.
      Solution: Load your database, open the ETC/Probe/PT_SERVER admin window, choose your server and press update. Than wait for the process to finish (this may take several hours).
      Reason: The link /usr/arb/lib/pts points to no valid directory.
      Solution: Goto the directory where arb_install is located. Enter 'sh ./arb_install', do not update the old package but enter the correct location for the pt_server files when asked.
      Solution: Consult the section "PT_SERVER What Why and How" in ARB-help

    3. After some time I can´t start the PT_SERVER any more. I have to reboot the computer.

      Reason: You have an old version of ARB.
      Solution: Please download the latest release from the ARB download site and install it.

    4. I am looking for signatures for some algal taxonomic groups.
      I am not sure I understand what the PT_SERVER is. I guess that we have to load rRNA data in /usr/arb/lib/etc? The rrna.arb, 16s_rrna_align.arb etc. are not in the ARB package? Am I right? I wonder how I can load my alignment in this PT_SERVER, so that I can design probes for the groups I am interested in?

      Solution: Load your data and update the pt_server (only your private data will be accessible).
      Solution: Merge your data with Wolfgang Ludwigs database and update the pt_server afterwards.

  7. Problems concerning the ARB Nameserver

    1. While synchronizing species IDs, I get the following error message: ´Error in ARB_name_server: Missing default value for add.field (option has to be -fstart=defaultValue)´

      Reason: You have updated ARB from an older installation and your /usr/arb/lib/arb_tcp.dat is outdated.
      Solution: Edit the file /usr/arb/lib/arb_tcp.dat and fix the nameserver definition for ARB_NAME_SERVER_START: the parameter at the end of the line has to be ´-fstart=1´. Take a look at the default arb_tcp.dat showing a correct definition.

  8. When I want to align a sequence, it gave a fatal error : out of memory (in the message box).
    So extra memory was installed. Also the amount of hard disk has been increased, due to the message (console message :

    alert : arb_naligner[3151]
    out of logical swap space during brk/sbrk
    see swap (im)

    After the installations these problems were not solved. The computer needs a lot of time performing a command.

    Solution: Check your swap ( try the command 'swap -s', or 'free' or 'top' or 'swapon -v', or if failed read the manual pages ( 'man -k swap' or man swap ); There should be at least 150 mbytes swap. It is not to difficult to add new swap to your system, normally it just means creating a file and telling the system that that file should be added as swap. Consult the man pages for more details.
    Solution: Sometimes the aligner V2 needs an extreme amount of memory. If so switch to the new FastAligner in the new ARB_EDIT4 sequence editor, of which a prototype is available since Mai 97.

  9. I have attempted to import the new RDP tree into ARB.
    I have the new RDP alignment and the tree imported in newick format in a database. However, the tree seems to be 'inactive' in ARB, and it is all black ??? What can i do?

    Reason: The labels at the tips of the tree have to match the 'name' field in the database. Otherwise you have a tree consisting of 'zombies'.
    Solution: All you can do is to change all the names in the newick file, which is a lot of work for a big tree.

  10. I want to print the entire 16S rrna phylogenetic tree but have not been able to print more than the first page.

    Reason: The problem with printing multiple pages is, that we use a public domain postscript generator. It sends all pages at once to the printer and let's the printer split the document into multiple pages. Because of limited printer memory, many printers refuse to print more than x pages.
    Solution: Try to reduce the size of the tree being printed. Start with a fully collapsed tree and print it. Open group by group and print to find out the size of the tree your printer can handle (Note: folded groups are not send to the printer). To print the entire tree fold the groups at the bottom and print, than fold all group except some inner groups, ..., finally fold everything except the last groups.
    Solution: Try to install a non postscript printer ( for Linux users only ). ( Use your native printer driver instead ). Linux can do the postscript precessing itself and your PC has much more memory than the printer

If you did not find a solution here please refer to the various manuals regarding ARB installation and usage. If that did not help please feel free to