Just a minor point. I just upgraded to Mothur version 25. I tried running catchall (the one that was included in the Linux download). Originally, I got the standard error about Mono not being installed, so I installed the proper version of Mono. I tried running it again, but I got a new error that read: “Cannot open assembly '/home/dbaptista/mothur/v25/CatchAllcmdL.exe: no such file or directory. [Error]: the catchall program did not run properly. Please check to make sure it is located in the same folder as your mothur executable.”
I then confirmed catchall was in the same folder as my Mothur executable. I tried a bunch of things that didn’t work, and then realized that the file name of my executable could be the problem. It seems that the catchall program included in the Linux download is spelled: “CatchAllmdL” whereas Mothur version 25 is trying to access a file named: “CatchAllmdL.exe” (as noted in the above error). I changed my filename to match, and it seems to have run fine.
I don’t know if this was a problem in previous versions of Mothur since I just upgraded from v21 and this is the first time I’ve run catchall, but maybe you can modify the name of the download included in the Linux package, or fix the pathway in Mothur? Incidentally, the program downloaded directly from the catchall website for Linux is: “CatchAllmdL_version3.0.exe”, so it also has the capital “C”. Just an observation that might save some headache for Linux users.
For reference, I’m using Linux Ubuntu version 10.04 “Lucid Lynx”. Thanks.
I cannot seem to get past this step, I have done everything you stated in your post. I don’t know where to go from here.
Here is the response I get…
"mothur > catchall()
Using /Volumes/TOSHIBA EXT/Sequences/final.bacteria.an.shared as input file for the shared parameter.
Processing group jvert.01
0.03
Cannot open assembly ‘/Users/jvert/Desktop/Sequence’: No such file or directory.
[ERROR]: the catchall program did not run properly. Please check to make sure it is located in the same folder as your mothur executable."
The weird part is… my assembly is titled “/Users/jvert/Desktop/Sequence” when the actual files are in: "/Users/jvert/Desktop/Sequence Analysis/’
But, it does not seem to pick that up.
Yes, I have already downloaded Mono and I have installed it as correctly as I can tell.
Hey guys …I am trying to use Catchall with my Mac…
And just downloaded the program from the website link : http://www.mothur.org/wiki/Catchall
and I just can’t make it work…Is it something to do with the wine bottler program to run windows in Mac’s??..or something I don’t know…Tried changing the “c”
and the program is with the mothur executable… so really don’t know :roll:
this what I get:
mothur > catchall(shared=16S_juvs_final.an.pick.subsample.shared)
Processing group JUVT0A
0.03
sh: mono: command not found
[ERROR]: the catchall program did not run properly. Please check to make sure it is located in the same folder as your mothur executable.
I am still having issues with catchall. Mono is installed. I moved to the latest release. I’m no longer redirecting my files (I have all of the files in the same folder). And still no luck. Any suggestions?
When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.
Distributed under the GNU General Public License
Type ‘help()’ for information on the commands that are available
unique
[ERROR]: this command doesn’t create a sabund output file.
[ERROR]: Could not open
CatchAll Version 3.1
1 arguments instead of 2 or 3 arguments
[ERROR]: the catchall program did not run properly. Please check to make sure it is located in the same folder as your mothur executable.