Problem with RAxML writing to working directory under Cygwin

[Ryan]

Hello,

I am using RAxML v. 7.3.2 under Cygwin on a machine running windows 7. When I use -w in the program call, I get the following error message:

The file /results_all/RAxML_info.MZIGS_all1 RAxML wants to open for writing or appending can not be opened [mode: ab], exiting ...

I have used previous program versions on other windows machines and never had this problem.  Analyses run fine without designating a working directory on my current machine.  Is this a bug, or do I need to tweak something in my system settings? 

Thanks,

Ryan

[Simon Berger]

Hello Ryan,

can you please supply the whole commandline? As far as I know, the root directory in cygwin is mapped to a real directory on some windows drive. Can you make sure that '/results_all/' (where ever that really is) exists, and the disk is not full? 
Does the cygwin installation provide a shell/command prompt? If there is one, have you tried to create the output directory from there before running raxml (i.e., 'mkdir /results_all' )?

Simon

[Ryan]

Simon,

Here is the line I use to call the program:

raxmlHPC-PTHREADS-SSE3 -p 1234 -x 123456 -T 4  -f a -s MZIGS_all1.phy -n MZIGS_all1 -w results_all -m GTRGAMMA -o Mac -# 100

I am executing the file from the directory that contains the alignment file, so there is not other path information necessary.  The folder is real, because I can see it in the windows file viewer and by typing "ls -l" at the cygwin command prompt.  I can navigate to it with the cd command, copy files into the folder etc.  I have tried creating the folder with mkdir and it doesn't change anything. There is plenty of room available.

Is there a windows executable for the current version?

Thanks for the quick replies,

Ryan

[Ryan]

Also, giving the path to a file in another folder works (such as -s alignments/RPB1_less.phy).  So it can navigate the file hierarchy fine in that sense.  It's just the working directory.

Ryan

[Alexandros Stamatakis]

when using -w you need to specify the full path, not the relative path,

Alexis

--
Alexandros Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University of Arizona at Tucson

www.exelixis-lab.org

[Simon Berger]

Hello Ryan,

as Alexi said, the root cause is that you do not supply an absolute path (i.e., no leading '/' in the directory). In this case, raxml will automatically insert the '/' in the beginning, which is probably not what you want. Just put the whole path of the current directory (i.e., the output of the pwd command) in front of the output directory and you should be fine. On the cygwin prompt you should be able to do this automatically using something like -w $PWD/results_all

The last official win32 release was 3 months ago, you can download them at https://github.com/sim82/standard-RAxML/tree/win32/binaries . I'll put an update of the win32 binaries on my TODO for next week...

Simon