installing SATe on a linux cluster

[Kathleen Brown]

Hello,

I am hoping someone is able to help me with the trouble I've been having getting SATe working on a computer cluster. I have been using the Mac version of SATe on my personal machine with no problems, but I have thus far been unable to get the linux version of it to work on the cluster.
It installs with no errors and is locating its dependencies, but it doesn't seem to be able to successfully invoke them. Here are the errors I am getting:

First was this one.

SATe ERROR: SATe is exiting because of an error:
SATe failed because one of the programs it tried to run failed.
The invocation that failed was:
    "/usr/bin/python" "/raid/home/kathleenb/applications/satesrc-v2.2.5-2012Oct16/sate-core/bin/mafft" "--ep" "0.123" "--quiet" "/raid/home/kathleenb/.sate/satejob/tempbq2U0b/init_aln/tempmafft7wfwqu/input.fasta"

A workaround has been posted for this problem in another thread, but when I got past this error I just got a different one:

SATe ERROR: SATe is exiting because of an error:
The invocation:
"/raid/home/kathleenb/applications/satesrc-v2.2.5-2012Oct16/sate-core/bin/fasttreeMP" "-quiet" "-wag" "-gamma" "-log" "/raid/home/kathleenb/.sate/satejob/temp8dt4Xu/init_tree/tempfasttreebm7dhw/log" "/raid/home/kathleenb/.sate/satejob/temp8dt4Xu/init_tree/tempfasttreebm7dhw/input.fasta"
failed

Any insight would be appreciated. I am working with a pretty big data set, so I would love to be able to run these jobs on the cluster. Let me know if you need more information.

Thank you,
Kathleen

[Jamie Oaks]

Hi Kathleen,

Thanks for your post. Regarding the first error you posted, what was your work around? It looks like the mafft invocation is looking for the link to the mafft executable in the correct place ('satesrc-v2.2.5-2012Oct16/sate-core/bin/mafft'). After running 'python setup.py develop' this path should be a symbolic link to 'satesrc-v2.2.5-2012Oct16/sate-core/resources/scripts/mafft'. Can you check these paths to see if 'satesrc-v2.2.5-2012Oct16/sate-core/resources/scripts/mafft' exists and if 'satesrc-v2.2.5-2012Oct16/sate-core/bin/mafft' is a link to it ('ls -l' should show this)? Furthermore, if you could navigate to 'satesrc-v2.2.5-2012Oct16/sate-core/bin' and run 'ls -l *' to check if the setup script successfully created links to the various tools, that might be helpful. You should get something like the following, but with different paths:

####
lrwxrwxrwx 1 jamie jamie   56 Jan  2 19:45 clustalw2 -> /home/jamie/software/dev/sate/sate-tools-linux/clustalw2
lrwxrwxrwx 1 jamie jamie   58 Jan  2 19:45 fakealigner -> /home/jamie/software/dev/sate/sate-tools-linux/fakealigner
lrwxrwxrwx 1 jamie jamie   55 Jan  2 19:45 faketree -> /home/jamie/software/dev/sate/sate-tools-linux/faketree
lrwxrwxrwx 1 jamie jamie   55 Jan  2 19:45 fasttree -> /home/jamie/software/dev/sate/sate-tools-linux/fasttree
lrwxrwxrwx 1 jamie jamie   57 Jan  2 19:45 fasttreeMP -> /home/jamie/software/dev/sate/sate-tools-linux/fasttreeMP
lrwxrwxrwx 1 jamie jamie   63 Jan  2 19:45 mafft -> /home/jamie/software/dev/sate/sate-core/resources/scripts/mafft
lrwxrwxrwx 1 jamie jamie   53 Jan  2 19:45 muscle -> /home/jamie/software/dev/sate/sate-tools-linux/muscle
lrwxrwxrwx 1 jamie jamie   55 Jan  2 19:45 opal.jar -> /home/jamie/software/dev/sate/sate-tools-linux/opal.jar
lrwxrwxrwx 1 jamie jamie   57 Jan  2 19:45 padaligner -> /home/jamie/software/dev/sate/sate-tools-linux/padaligner
lrwxrwxrwx 1 jamie jamie   52 Jan  2 19:45 prank -> /home/jamie/software/dev/sate/sate-tools-linux/prank
lrwxrwxrwx 1 jamie jamie   55 Jan  2 19:45 randtree -> /home/jamie/software/dev/sate/sate-tools-linux/randtree
lrwxrwxrwx 1 jamie jamie   52 Jan  2 19:45 raxml -> /home/jamie/software/dev/sate/sate-tools-linux/raxml
lrwxrwxrwx 1 jamie jamie   53 Jan  2 19:45 raxmlp -> /home/jamie/software/dev/sate/sate-tools-linux/raxmlp

real_bin:
total 16
lrwxrwxrwx 1 jamie jamie 66 Jan  2 19:45 disttbfast -> /home/jamie/software/dev/sate/sate-tools-linux/real_bin/disttbfast
lrwxrwxrwx 1 jamie jamie 63 Jan  2 19:45 dvtditr -> /home/jamie/software/dev/sate/sate-tools-linux/real_bin/dvtditr
lrwxrwxrwx 1 jamie jamie 70 Jan  2 19:45 pairlocalalign -> /home/jamie/software/dev/sate/sate-tools-linux/real_bin/pairlocalalign
lrwxrwxrwx 1 jamie jamie 62 Jan  2 19:45 tbfast -> /home/jamie/software/dev/sate/sate-tools-linux/real_bin/tbfast
####

If you have run setup.py without errors and do not see links here, let me know. If you do see links, check to see if the link targets (the path after '->')  exist.

Assuming you find that the links and their targets do exist, the second error you report is likely due to the fasttree binaries that are distributed with the SATe source (in the 'sate-tools-linux' directory). They are both dynamically linked 32-bit builds (I've recently replaced them with statically linked 32-bit builds on github, but after the 2.2.5 release). We distribute SATe with 32-bit builds to try and maximize compatibility, but there can be problems with the 32-bit multi-threaded version ('fasttreeMP') on 64-bit linux systems. It will run fine on one processor, but often does not when using multiple processors.

The best solution for this problem is to download the 64-bit multi-threaded executable from http://www.microbesonline.org/fasttree/#Install (or download the source from here and compile the multi-threaded version on your cluster). Then, rename the executable as "fasttreeMP" and replace the existing executable in the "sate-tools-linux" directory. Let me know if you have questions about how to do this or if it does not fix the problem.

Sorry for the long response, but hopefully some of it is helpful! I have used SATe on Linux-based clusters, so I'm confident that we can get you up and running!

Jamie

[Nate]

FYI: I had problems with both fasttree and fasttreeMP (I use Centos 5.*) and to download and install precompiled binary for both to fix issues (can't upgrade to glibc2.7 so could find the right version of an .so file). After replaced symbolic links in $SATEDIR/sate-core/bin/ directory with new binaries, it now works fine.

Cheers,
Nate

[Jamie Oaks]

Thanks for the info, Nate. Hopefully, the new statically linked fasttree executables will solve some of these issues. They will be packaged with the source for version 2.2.6, which will be released soon.

Jamie

[Kathleen Brown]

Thank you both for your replies. Sorry it took me a bit to get back to you - shortly after I posted they took the cluster offline for maintenance. I think the first error must have been from a bad link. (The workaround incidentally was placing a python script to make the correct call where SATe was looking for it.) After deleting and reinstalling SATe, the links are showing up as they should and mafft runs as intended. I also replaced fasttreeMP with the 64-bit MT version as you suggested, which appeared to do the trick for the second error. I've run a few jobs and so far so good. Thanks so much!

Kathleen