Difference between revisions of "Phylogenetics: Bioinformatics Cluster"
(→Editing garli.conf with pico) |
(→Preparing the gogarli SGE script) |
||
Line 352: | Line 352: | ||
=== Preparing the gogarli SGE script === | === Preparing the gogarli SGE script === | ||
+ | |||
+ | Now return to your home directory (using the cd command) and create a gogarli script that will be fed to qsub to start the analysis. Use either pico or cat to create the file with this text: | ||
+ | #$ -o junk.txt -j y | ||
+ | cd $HOME/garlirun | ||
+ | Garli.94 garli.conf | ||
+ | This file will look very similar to the gopaup script you created in part A. The only difference is that the data and control file are in the directory garlirun (not pauprun), the name of the program is Garli.94 (this means Garli version 0.94), and GARLI expects the name of the control file (garli.conf) on the command line instead of the name of the data file (rbcl50.nex). Remember that the name of the data file was specified inside the control file. | ||
+ | |||
+ | === Running GARLI === | ||
+ | |||
+ | Run GARLI by issuing the qsub command: | ||
+ | qsub gogarli | ||
+ | |||
+ | Check progress every few minutes using the qstat command. This run will take 15 or 20 minutes. If you get bored, you can cd into the garlirun directory and use this command to see the tail end of the log file that GARLI creates automatically: | ||
+ | tail 50taxa.log00.log | ||
+ | The tail command is like the cat command except that it only shows you the last few lines of the file (which often is just what you need). | ||
+ | |||
+ | === Mailing the tree to yourself === | ||
+ | |||
+ | After GARLI has finished, you should download the tree file (50taxa.best.tre) using the PSFTP get command, but here is another handy trick: you can email the tree to yourself using this command (issue this from within the garlirun directory where the tree file is located): | ||
+ | mail paul.lewis@uconn.edu < 50taxa.best.tre | ||
+ | This command will send mail to paul.lewis@uconn.edu, and the body of the email message will come from the file 50taxa.best.tre! | ||
=== Running GARLI === | === Running GARLI === |
Revision as of 21:26, 18 February 2007
![]() |
This article is still under construction. Expect it to change frequently until this notice is removed. |
![]() |
EEB 349: Phylogenetics |
The goal of this lab exercise is to show you how to use the Bioinformatics Facility computer cluster to run PAUP* and GARLI. |
Contents
- 1 Part A: Using the UConn Bioinformatics Facility cluster
- 1.1 Obtaining the necessary communications software
- 1.2 Logging in for the first time
- 1.3 Learning enough UNIX to get around
- 1.3.1 ls command: finding out what is in the present working directory
- 1.3.2 pwd command: finding out what directory you are in
- 1.3.3 mkdir command: creating a new directory
- 1.3.4 cd command: leaving the nest and returning home again
- 1.3.5 Creating the gopaup file using the cat command
- 1.3.6 Creating run.nex using the pico editor
- 1.4 Using PSFTP to upload the algae.nex data file
- 1.5 A few more UNIX commands
- 1.6 Starting a PAUP* analysis
- 1.7 Tips and tricks
- 2 Part B: Starting a GARLI run on the cluster
Part A: Using the UConn Bioinformatics Facility cluster
The Bioinformatics Facility is part of the UConn Biotechnology Center, which is located behind the Up-N-Atom Cafe in the lower level of the Biology/Physics building. Jeff Lary maintains a 17-node Apple Xserve G5 Cluster that can be used by UConn graduate students and faculty to conduct bioinformatics-related research (sequence analysis, biological database searches, phylogenetics, molecular evolution). You have each been given accounts on the cluster, and today you will learn how to start analyses remotely (i.e. from this computer lab), check on their status, and download the results when your analysis is finished.
Obtaining the necessary communications software
You will be using a couple of simple (and free) programs to communicate with the head node of the cluster. Visit the PuTTY web site, scroll down to the section labeled "Binaries" and save putty.exe and psftp.exe on your desktop.
PuTTY
The program PuTTY will allow you to communicate with the cluster using a protocol known as SSH (Secure Shell) that encrypts everything sent over the internet. You will use PuTTY to send commands to the cluster and see the output generated. In the old days, a protocol known as Telnet was used for this purpose, but it is no longer used because it did not encrypt anything, making it easy for someone with access to the network to see your username and password in plain text.
PSFTP
The other program you will use is called PSFTP. It allows you to transfer files back and forth using SFTP (Secure File Transfer Protocol). It replaces the old protocol (FTP) that, like Telnet, sent usernames and passwords unencrypted across the network.
Programs vs. protocols
SSH and SFTP are protocols, not programs. PuTTY and PSFTP are programs that implement the SSH and SFTP protocols, respectively. In a little while from now, you may be thinking "I liked FTP much better than SFTP!" because you probably used user-friendly, graphical FTP programs in the past. If you think this, then you are confusing protocols with programs that implement them. There are much fancier, easy-to-use programs for using SSH and SFTP than PuTTY and PSFTP, but these will serve us well today. One nice thing is that these programs are so small that you can just download them whenever and whereever you happen to need them. If you find yourself wanting a fancier SFTP client, check out FileZilla (on Windows) or Fugu (for Macs).
Logging in for the first time
On the whiteboard you will find your login id (user name) and password.
Double-click the PuTTY icon on your desktop to start the program. In the Host Name (or IP address) box, type bbcxsrv1.biotech.uconn.edu. Now type Bioinformatics cluster into the Saved Sessions box and press the Save button. This will save having to type the computer's name each time you want to connect. Now click the Open button to start a session. The first time you connect, you will get a PuTTY Security Alert. Just press the Yes button to close this dialog.
Now you should see the following prompt:
login as:
Type in your username and press Enter. Now you should see the password prompt:
Password:
Type in your password and press Enter. If all goes well, you should see something like this:
Welcome to Darwin! [bbcxsrv1:~] plewis%
except that your username should appear instead of mine (plewis).
The first thing you should do is change your password. Type
passwd
and press the Enter key, then follow the directions to change your password. If you have trouble thinking up passwords that are acceptable, check out the Java Password Generator web site. It generates passwords that are not really words but sound like they are, so they are easier to remember than completely random passwords.
Learning enough UNIX to get around
I'm presuming that you do not know a lot of UNIX commands, but even if you are already a UNIX guru, please complete this section anyway because otherwise you will fail to create some files you will need later.
The cluster comprises MacIntosh G5 computers running MacOSX, but MacOSX is essentially a UNIX operating system with a very nice user interface. But today you will not be using the nice user interface! Instead, you will be communicating using the UNIX command console, so the first step is to learn a few important UNIX commands. You can use these commands on any MacIntosh running MacOSX by opening the Terminal application, which you can find in the Applications/Utilities folder on your hard drive.
ls command: finding out what is in the present working directory
The ls command lists the files in the present working directory. Try typing just
ls
If you need more details about files than you see here, type
ls -la
instead. This version provides information about file permissions, ownership, size, and last modification date.
pwd command: finding out what directory you are in
Typing
pwd
shows you the full path of the present working directory. The path shown should end with your username, indicating that you are currently in your home directory.
mkdir command: creating a new directory
Typing the following command will create a new directory named pauprun in your home directory:
mkdir pauprun
Use the ls command now to make sure a directory of that name was indeed created.
cd command: leaving the nest and returning home again
The cd command lets you change the present working directory. To move into the newly-created pauprun directory, type
cd pauprun
You can always go back to your home directory (no matter how lost you get!) by typing just cd by itself
cd
Creating the gopaup file using the cat command
The cat command was designed for concatenating files, but I most often use it for viewing and creating files. To create a new file named gopaup, type the following (be sure to leave a space between each item, just as you see it below) and then press the Enter key
cat - > gopaup
Note that you no longer see the unix prompt, and the system appears to be hung. This is ok! The text you typed is admittedly somewhat cryptic:
- The hyphen (-) after the word cat means "use text typed from the console"
- The greater-than symbol (>) means "redirect the output to a file"
- The gopaup part is the name of the file to which the output will be redirected
The cat command is now waiting for you to type something. Type the following and, when finished, press the Ctrl-d key combination to tell cat that you are done:
#$ -o junk.txt -j y cd $HOME/pauprun paup -n run.nex
If you make mistakes while typing, don't fear! You can fix them later using the pico editor. Use the cat command again to view the contents of the file you just created:
cat gopaup
Basically, cat just spews out the contents of whatever you give it to work with. If you give it a file name, it spews out the contents of the file. If you give it a hyphen, it reads text you type until you press Ctrl-d, then it spews that text out again. In your case, when you used the hyphen, you also told it to redirect its output to the file gopaup, so that's why you did not see what it spewed.
Creating run.nex using the pico editor
Another way to create a new file, or edit one that already exists, is to use the pico editor. Most people like using pico better than cat for creating new files: the only advantage cat has over pico is that it is guaranteed to be present on every UNIX computer, whereas pico is only present on some. You will now use pico to create a run.nex file containing a paup block. You will later execute this file in PAUP* to perform an analysis.
First use the pwd command to see where you are, then use cd to go into the pauprun directory if you are not already there. Type
pico run.nex
This will open the pico editor, and it should say [ New File ] at the bottom of the window to indicate that the run.nex file does not already exist. Note the menu of the commands along the bottom two rows. Each of these commands is invoked using the Ctrl key with the letter indicated. Thus, ^X Exit indicates that you can use the Ctrl key in combination with the letter X to exit pico.
For now, type the following into the editor:
#nexus begin paup; log file=algae.output.txt start replace flush; execute algae.nex; set criterion=likelihood autoclose; lset nst=2 basefreq=estimate tratio=estimate rates=gamma shape=estimate; hsearch swap=none start=stepwise addseq=random nrep=1; lset basefreq=previous tratio=previous shape=previous; hsearch swap=tbr start=1; savetrees file=algae.ml.tre brlens; log stop; quit; end;
Once you have entered everything, use ^X to exit. Pico will ask if you want to save the modified buffer, at which point you should press the Y key to answer yes. Pico will now ask you whether you want to use the file name run.nex; this time just press Enter to accept. Pico should now exit and you can use cat to look at the contents of the file you just created:
cat run.nex
Using PSFTP to upload the algae.nex data file
Locate the file algae.nex that we used in the previous lab. If you have deleted it, you will need to download and save it again.
Make sure that algae.nex is in the same place as the PSFTP program, then start PSFTP by double-clicking it.
PSFTP should say something like this:
psftp: no hostname specified; use "open host.name" to connect
To open a connection to the cluster, type
open bbcxsrv1.biotech.uconn.edu
then supply your username and password when prompted.
To upload algae.nex to the cluster, type
put algae.nex
If you do not see any error messages, then you can assume that the transfer worked. Type
quit
to exit the PSFTP program.
A few more UNIX commands
You have now transfered a large file (algae.nex) to the cluster, but it is not in the right place. The algae.nex file should be in your home directory, whereas the run.nex file is in the pauprun directory. The run.nex file contains this line
execute algae.nex
which means that algae.nex should also be located in the pauprun directory. Use the following commands to ensure that (1) you are in your home directory, and (2) algae.nex is also in your home directory:
cd $HOME ls algae.*
Note the use of a wildcard character (*) in the ls command. This will show you only files that begin with the letters algae followed by a period and any number of other non-whitespace characters.
mv command: moving or renaming a file
Now use the mv command to move algae.nex to the directory pauprun:
mv algae.nex pauprun
The mv command takes two arguments. The first argument is the name of the directory or file you want to move, whereas the second argument is the destination. The destination could be either a directory (which is true in this case) or a file name. If the directory pauprun did not already exist, mv would have interpreted this as a request to rename algae.nex to the file name pauprun! So, be aware that mv can rename files as well as move them.
cp command: copying a file
The cp command copies files. It leaves the original file in place and makes a copy elsehwere. You could have used this command to get a copy of algae.nex into the directory pauprun:
cp algae.nex pauprun
This would have left the original in your home directory, and made a duplicate of this file in the directory pauprun.
rm command: cleaning up
The rm command removes files. If you had used the cp command to copy algae.nex into the pauprun directory, you could remove the original file using these commands:
cd rm algae.nex
The first cd command just ensures that the copy you are removing will be the one in your home directory (typing cd by itself acts the same as typing cd $HOME). If it bothers you that the system always asks your permission before deleting a file, you can force the issue using the -f option (but just keep in mind that this is more dangerous):
rm -f algae.nex
To delete an entire directory (don't try this now!), you can add the -r flag, which means to recursively apply the remove command to everything in every subdirectory:
rm -rf pauprun
The above command would remove everything in the pauprun directory (without asking!), and then remove the pauprun directory itself. I want to stress that this is a particularly dangerous command, so make sure you are not weary or distracted when you use it! Unlike the Windows or Mac graphical user interface, files deleted using rm are not moved first to the Recycle Bin or Trash, they are just gone. There is no undo for the rm command.
Starting a PAUP* analysis
If you've been following the directions in sequence, you now have two files (algae.nex and run.nex) in your $HOME/pauprun directory on the cluster, whereas the gopaup file should be in $HOME. Use the cd command to make sure you are in your home directory, then the cat command to look at the contents of the gopaup file you created earlier. You should see this:
#$ -o junk.txt -j y cd $HOME/pauprun paup -n run.nex
This file will be used by software called the Sun Grid Engine (SGE for short) to start your run. SGE provides a command called qsub that you will use to submit your analysis. SGE will then look for a node (i.e. machine) in the cluster that is currently not being used (or is being used to a lesser extent than other nodes) and will start your analysis on that node. This saves you the effort of looking amongst all 17 nodes in the cluster for one that is not busy.
Here is an explanation of each of the lines in gopaup:
- Lines beginning with the two characters #$ are interpreted as commands by SGE itself. In this case, the command tells SGE to send any output from the program to a file named junk.txt and the -j y part says to append any error output to this as well (the j stands for join and the y for yes)
- The second line is simply a cd command that changes the present working directory to the pauprun directory you created earlier. This will ensure that anything saved by PAUP* ends up in this directory rather than in your home directory. Note that $HOME is like a macro that will be expanded to the full path to your home directory.
- The third and last line simply starts up PAUP* and executes the run.nex file. The -n flag tells PAUP* that no human is going to be listening or answering questions, so it should just use default answers to any questions it needs to ask during the run.
Submitting a job using qsub
Now you are ready to start the analysis. Make sure you are in your home directory, then type
qsub gopaup
Checking status using qstat
You can see if your run is still going using the qstat command:
qstat
If it is running, you will see an entry containing gopaup and the state will be r, for running. Here is what it looked like for me (I've omitted the rightmost part):
job-ID prior name user state submit/start at queue ----------------------------------------------------------------------------------------------- 5540 0.55500 gopaup plewis r 02/18/2007 13:38:47 all.q@node003.cluster.private 5535 0.55500 bskinkultr jockusch r 02/16/2007 16:18:49 all.q@node006.cluster.private 5525 0.55500 mb.sh plapierre r 02/15/2007 10:46:17 all.q@node010.cluster.private 5433 0.55500 mb.sh plapierre r 02/08/2007 18:40:50 all.q@node012.cluster.private 5539 0.55500 bskinkultr jockusch r 02/18/2007 12:22:55 all.q@node015.cluster.private
My run is listed first, and is currently running on node 3 of the cluster.
Killing a job using qdel
Sometimes it is clear that an analysis is not going to do what you wanted it to. Suppose that just after you press the Enter key to start an analysis, you realize that you forgot to put in a savetrees command in your paup block (so in the end you will not be able to see the results of the search). In such situations, you really want to just kill the job, fix the problem, and then start it up again. Use the qdel command for this. Note that in the output of the qstat command above, my run had a job-ID equal to 5540. I could kill the job like this:
qdel 5540
SGE will say that it has scheduled the job for deletion, but in practice it kills it almost instantaneously in my experience. Be sure to delete any output files that have already been created before starting your run over again.
While PAUP* is running
While PAUP* is running, you can use cat to look at the log file:
cd pauprun cat algae.output.txt
Using PSFTP to download the resulting treefile
When PAUP* finishes, qstat will no longer list your process. At this point, you need to use PSFTP to get the log and tree files that were saved back to your local computer. Start up PSFTP and type
open bbcxsrv1.biotech.uconn.edu
Note that both the log file (algae.output.txt) and the tree file (algae.ml.tre) are in the pauprun directory. PSFTP dropped you in your home directory, but you can tell PSFTP to change to the pauprun directory in the same way you tell UNIX that you want to change directories:
cd pauprun
You can likewise type ls in PSFTP to get a listing of files. Do this now to make sure you see the two files you want to download. Now, use the get command to download the files:
get algae.ml.tre get algae.output.txt
Finally, close PSFTP using any of the following commands: quit, exit, bye.
Why both junk.txt and algae.output.txt?
In your home directory, SGE saved the output that PAUP* normally sends to the console to a file named junk.txt (we specified that it should do this in the gopaup file). I had you name this file junk.txt because you will not need this file after the run: the log command in your paup block ends up saving the same output in the file algae.output.txt. Why did we tell PAUP* to start a log file if SGE was going to save the output anyway? The main reason is that you can view the log file during the run, but you cannot view junk.txt until the run is finished. There will come a day when you have a PAUP* run that has been going for several days and want to know whether it is 10% or 90% finished. At this point you will appreciate being able to view the output file!
Delete junk.txt using the rm command
Because you do not need junk.txt, delete it using the rm command:
cd rm -f junk.txt
You also no longer need the log and tree files because you downloaded them to your local computer using PSFTP:
cd pauprun rm -f algae.ml.tre rm -r algae.output.txt
It is a good idea to delete files you no longer need for two reasons:
- you will later wonder whether you downloaded those files to your local machine and will have to spend time making sure you actually have saved the results locally
- our cluster only has so much disk space, and thus it is just not possible for everyone to keep every file they ever created
Tips and tricks
Here are some miscellaneous tips and tricks to make your life easier while using PuTTY to communicate with the cluster.
Command completion using the tab key
You can often get away with only typing the first few letters of a filename; try pressing the Tab key after the first few letters and PuTTY will try to complete the thought. For example, cd into the pauprun directory, then type
cat alg<TAB>
If algae.nex is the only file in the directory in which the first three letters are alg, then PuTTY will type in the rest of the file name for you.
Wildcards
I've already mentioned this tip, but it bears repeating. When using most UNIX commands that accept filenames (e.g. ls, rm, mv, cp), you can place an asterisk inside the filename to stand in for any number of letters. So
ls algae*
will produce output like this
algae.ml.tre algae.nex algae.output.txt
Man pages
If you want to learn more options for any of the UNIX commands, you can use the man command to see the manual for that command. For example, here's how to see the manual describing the ls command:
man ls
It is important to know how to escape from a man page! The way to get out is to type the letter q. You can page down using Ctrl-f, page up through a man page using Ctrl-b, go to the end using Shift-g and return to the very beginning using 1,Shift-g (that is, type a 1, release it, then type Shift-g). You can also move line by line in a man page using the down and up arrows, and page by page using the PgUp and PgDn keys.
Part B: Starting a GARLI run on the cluster
GARLI is a program written by Derrick Zwickl for estimating the phylogeny using maximum likelihood, and is currently one of the best programs to use if you have a large problem (i.e. many taxa). I used GARLI to estimate the 738-taxon green plant phylogeny on the poster outside my office door in less than 5 hours. Another excellent ML program for large problems is RAxML, written by Alexandros Stamatakis.
GARLI does not give you much choice in the way of search strategy or substitution model. It uses the GTR+I+G model (General Time Reversible substitution model, with invariable sites and discrete gamma rate heterogeneity), and uses a genetic algorithm search strategy. The genetic algorithm (or GA, for short) search strategy is like other heuristic search strategies in that it cannot guarantee that the optimal tree will be found. Thus, as will all heuristic searches, it is a good idea to run GARLI several times (using different pseudorandom number seeds) to see if there is any variation in the estimated tree.
Today you will run GARLI on the cluster for a dataset with 50 taxa. This is not a particularly large problem, but then you only have an hour or so to get this done!
Preparing the GARLI control file
Like many non-interactive programs, GARLI uses a control file to specify the settings it will use during a run. Here is the control file distributed with GARLI:
[general] datafname = rana.phy streefname = random ofprefix = ranaGarli randseed = -1 megsclamemory = 500 availablememory = 512 logevery = 10 saveevery = 100 refinestart = 1 outputeachbettertopology = 1 enforcetermconditions = 1 genthreshfortopoterm = 20000 scorethreshforterm = .05 significanttopochange = 0.05 outputphyliptree = 0 outputmostlyuselessfiles = 0 dontinferproportioninvariant = 0 [master] nindivs = 4 holdover = 1 selectionintensity = .5 holdoverpenalty = 0 stopgen = 5000000 stoptime = 5000000 startoptprec = .5 minoptprec = .01 numberofprecreductions = 40 topoweight = 1.0 modweight = .05 brlenweight = .2 randnniweight = .2 randsprweight = .3 limsprweight = .5 intervallength = 100 intervalstostore = 5 limsprrange = 6 meanbrlenmuts = 5 gammashapebrlen = 1000 gammashapemodel = 1000 bootstrapreps = 0 inferinternalstateprobs = 0
Most of these settings are fine, but you will need to change a few of them before running GARLI.
Using curl to download the file
The first step is to get this file onto the cluster where you can use pico to edit it. You have already learned several ways to create a file on the cluster:
- cat - > filename ... Ctrl-d
- pico filename
Now you will learn a third way: using the curl program. Curl is useful when you know that a file exists on the internet at some URL. Curl stands for "Copy URL" - it allows you to copy a file at a particular address (URL) on the internet to your present working directory. I have placed a copy of the garli.conf file above at the following URL:
http://hydrodictyon.eeb.uconn.edu/eeb349/garli.conf
You can view it in a web browser if you wish. Here is how to get this file copied from that web address to your home directory on the cluster. I assume you have already logged into the cluster using PuTTY:
curl http://hydrodictyon.eeb.uconn.edu/eeb349/garli.conf > garli.conf
Curl acts a lot like cat: it basically spews the file to the console, so if you want to save it to a file, you need to redirect the output of curl to a file, which is what the > garli.conf part on the end is about.
Editing garli.conf with pico
Now fire up pico and edit this file:
pico garli.conf
You will only need to change two lines. Change this line
datafname = rana.phy
so that it looks like this instead
datafname = rbcl50.nex
Then change this line
ofprefix = ranaGarli
so that it looks like this instead
ofprefix = 50taxa
The ofprefix is used by GARLI to begin the name of all output files. I usually use something different than the data file name here. If you eventually want to delete all of the various files that GARLI creates, you can just say
rm -f 50taxa*
If, however, you specify ofprefix = rbcl50, then the command
rm -f rbcl50*
would not only wipe out the files GARLI created, but would also delete the data file!
Once you have finished changing those two lines, exit pico using Ctrl-x, then create a directory named garlirun and move garli.conf into that directory.
Download the data file using curl
I have placed the data file (rbcl50.nex) at the following address:
http://hydrodictyon.eeb.uconn.edu/eeb349/rbcl50.nex
so you can use curl to download this file to the garlirun directory as follows:
cd $HOME/garlirun curl http://hydrodictyon.eeb.uconn.edu/eeb349/rbcl50.nex
Preparing the gogarli SGE script
Now return to your home directory (using the cd command) and create a gogarli script that will be fed to qsub to start the analysis. Use either pico or cat to create the file with this text:
#$ -o junk.txt -j y cd $HOME/garlirun Garli.94 garli.conf
This file will look very similar to the gopaup script you created in part A. The only difference is that the data and control file are in the directory garlirun (not pauprun), the name of the program is Garli.94 (this means Garli version 0.94), and GARLI expects the name of the control file (garli.conf) on the command line instead of the name of the data file (rbcl50.nex). Remember that the name of the data file was specified inside the control file.
Running GARLI
Run GARLI by issuing the qsub command:
qsub gogarli
Check progress every few minutes using the qstat command. This run will take 15 or 20 minutes. If you get bored, you can cd into the garlirun directory and use this command to see the tail end of the log file that GARLI creates automatically:
tail 50taxa.log00.log
The tail command is like the cat command except that it only shows you the last few lines of the file (which often is just what you need).
Mailing the tree to yourself
After GARLI has finished, you should download the tree file (50taxa.best.tre) using the PSFTP get command, but here is another handy trick: you can email the tree to yourself using this command (issue this from within the garlirun directory where the tree file is located):
mail paul.lewis@uconn.edu < 50taxa.best.tre
This command will send mail to paul.lewis@uconn.edu, and the body of the email message will come from the file 50taxa.best.tre!