Segal Lab Executables : Troubleshooting and Frequently Asked Questions


  1. How do I know if the executable is compatible to my machine?
  2. Can I run the executable on a Mac?
  3. I get an error like: cat: tmp_84638.clu: No such file or directory
  4. I get an error like: sh: line 1: 19764 Segmentation fault

How do I know if the executable is compatible to my machine?


There are several things to check, all of them can be done using the uname command.

ParameterCommandSupported values
Operating systemuname -oLinux operating system
Architectureuname -mi686 (32 bit machine)
Kernel versionuname -r2.4.21-37 or newer



Can I run the executable on a Mac?


You can not. We hope to publish a Mac version of our executables soon...


I get an error like: cat: tmp_84638.clu: No such file or directory


This error means that the main C++ executable failed. This might happen because a shared library required is not available on your machine. To see the shared library dependencies of the C++ executable go to the directory where you unpacked the executable and type:
ldd bin/map_learn_static
ldd shows the shared libraries our executable requires. These 3 shared libraries might not be found:
  • libxerces-c.so.27
  • libgslcblas.so.0
  • libgsl.so.0

We supply these shared libraries in the tar and the executable links with them at runtime. The other shared libraries are standard ones, and if any of them is not found then there's either a problem with your $LD_LIBRARY_PATH environment variable, or the library was not installed properly (or not installed at all). Solving this problem is out of our scope, since these are standard Linux/GNU/C++ libraries.

If ldd finds all the required shared libraries and the error persists you need to get a more informative error. In order to do this define an environment variable named SEGAL_LAB_DEBUG with the value 1 (setenv SEGAL_LAB_DEBUG 1), and then run the executable (from the same terminal in which you defined the SEGAL_LAB_DEBUG variable). This should help you see the actual error. If it seems like something related to our executable and not to your specific environment then please email Eran Segal with the error details. If defining SEGAL_LAB_DEBUG has no effect then you need to download the updated version of the executable.


I get an error like: sh: line 1: 19764 Segmentation fault


This error usually means that your input fasta file is in Windows format (line ends with "\r\n"). The executable expects a valid linux file, where each line should end with "\n" (also known as DOS format).
There are many ways to convert a file from Windows to DOS format, here are some options:
  • dos2unix <file name>
  • awk '{ sub("\r$", ""); print }' <file name> > <new file name>