Repeatmasker Crashes Before End Of Run With "Can'T Fork..."

Question

[User 9996]

I've been trying to run RepeatMasker but it keeps crashing with the error "Can't fork...". In the RepeatMasker script source code, this is here:

FORK: {
    if ( $pid = fork ) {
      $flag = 1;
      waitpid( $pid, 0 );                     #Waits for child to finish...
      my ( $status ) = $?;
      if ( WIFSTOPPED( $status ) ) {
        my ( $signal ) = WSTOPSIG( $status );
        print "\nforksys:  Program terminated by a signal $signal.\n";
        print "The executing command was:  $cmd\n";
        return 1;
      }
      if ( WIFEXITED( $status ) ) {
        my ( $temp ) = WEXITSTATUS( $status );
        return $temp;
      }
      if ( WIFSIGNALED( $status ) ) {
        my ( $signal ) = WTERMSIG( $status );
        print "\nforksys:  Program terminated by a signal $signal.\n";
        print "The executing command was:  $cmd\n";
        return 1;
      }
    }
    elsif ( defined $pid ) {
      exec( "$cmd" ) or die "Exec $cmd failed\n";
    }
    elsif ( $! =~ /No more process/o ) {
      print "$!\n";
      sleep 5;
      redo FORK;
    }
    else {
      die "Can't fork...\n";
    }
  }
}

any idea what parameter could be causing this or how it can be debugged? I ran RM with 6 processors and sensitive search but am now changing it to the "qq" option ("quick and dirty search") and giving it only 1 processor, to see if that helps in case it's a weird threading thing that happens. any thoughts on this?? thank you.

[David Quigley]

Couldn't say why, but you're running into a problem when RepeatMasker tries to spawn a new process. That's an unusual problem to have, thus the perfunctory error message. Update your question after trying with a single execution thread.