failed to readlink

[arunpras]

Hi.

I am trying to set up coronalite for running my ABI paired end reads.

I dont have PBS scheduler and so i tried using the standalone command as given in the documentation using the cut command.

However it gives me a "Failed to readlink(/proc/10065/exe):No such file or directory" error.

Have any of you faced this error and if so how to get around it.

I am running corona lite on my imac with 4GB RAM and 2.66GHZ core2 duo.

Thanks in advance
Arun

[arunpras]

The error occurs in the mapreads command.

[westerman]

Suggestion #1: Run Linux. CoronaLite is heavily Linux oriented. Even when it does not have to be (see below after the stars).

I presume you are running OS-X. I think that OS-X does not have a /proc file system. See an older article: http://osxbook.com/book/bonus/ancient/procfs/ The code in question is trying to create a temporary file from the information it finds in /proc.

If this is true (I don't have my Mac handy), then you will need to modify mapreads.cxx around line 1030 to make the program Mac-compatible. Or at least not Linux-oriented. Why the programmers couldn't use the standard library call (tmpfile) to create a temporary file instead of rolling their own code I do not understand. But this is so typical of the corona lite programs.

If you can't modify a program in C++ and can't find anyone to do it for you then see suggestion #1 above.

******************

My favorite CoronaLite "linux-ism" (which I may have mentioned before) occurs in one of their Perl programs. The code in question:

-----

my $jlist = `seq 0 $numPanelGroups`;
$jlist =~ s/\n/ /g;

-----

For those unfamiliar with the "seq" command all it does is generate a list of numbers. Handy if you are in the shell. Not as handy if you aren't in the shell. The above code makes a system call to generate that list of numbers and then transforms the new-line delimited list into a space-delimited one. A really dumb way to do it, especially inside of Perl. I re-wrote the code to:

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my @jlist = (0..$numPanelGroups);
my $jlist = join ' ', @jlist;

-----

The may be better ways to do it within Perl but at least my code is all inside Perl and does not rely on external Linux commands.

[arunpras]

Thank you

thanks westerman.

I am installing corona lite into my linux system. Hopefully that should solve the issue.

I will let you know how this goes.

Arun

[kmcarr]

my $jlist = `seq 0 $numPanelGroups`;
$jlist =~ s/\n/ /g;

Wow! If they insist on using the seq command they could at least "man seq" first and learn that

my $jlist = `seq -s " " 0 $numPanelGroups`;

would format the string as space-delimited directly, no need for the substitution line.

[ondovb]

You can avoid the "readlink" error on OS X by passing "P=<mapreads directory>" to mapreads. It's just using proc to get the path of the executable, because it assumes the "map" program will be in the same directory if you don't specify a path for it.

I still get a segfault when using multiple threads. Also, this doesn't fix any other problems with OS X in the CoronaLite pipeline...and if you just wanted to do alignment, you could use a Mac-friendly tool. So this is probably a useless tip.