ExaML

Project home page:  https://github.com/stamatak/ExaML

The software is installed on Oscar, here is the steps to run the software. 

# Step 1: Convert the input file into binary format to make it faster for ExaML to read later on
parser -s $EXAMLDATA/49 -m DNA -n 49.unpartitioned
# So we are transforming an unpartitioned phylip file with 49 DNA sequences into a binary file.

# If we want to partition the data, we will have to pass a standard RAxML partition file to the parser, e.g:
Note that, every time you change the partition scheme, you will have to re-generate a binary alignment file that encodes the partitioning scheme!
parser -s  $EXAMLDATA/49 -q $EXAMLDATA/49.model -m DNA -n 49.partitioned

# These two commands will generate four output files
-rw-r-----  1 ldong ccvstaff  34K Oct  1 13:01 49.unpartitioned.binary
-rw-r-----  1 ldong ccvstaff  141 Oct  1 13:01 RAxML_info.49.unpartitioned
-rw-r-----  1 ldong ccvstaff  35K Oct  1 13:01 49.partitioned.binary
-rw-r-----  1 ldong ccvstaff  139 Oct  1 13:01 RAxML_info.49.partitioned

# Step 2: Prepare the qsub script
# copy the example qsub script to local folder:
cp $EXAMLDATA/ExaML_script.qsub .

# Edit the script to fit your need. For now, you only need to change the email address to your own email. 
# When you work on your own data, all the parts highlighted in red should be changed accordingly. 
# Specifically, "debug" needs to change "dq', because the debug queue only allow walltime less than 40 minutes. 
# For a list of all options of the "examl" command, please run command "examl -h".
# Here I use linux editor "vi" for editing the script. Here is the introduction to the editor: http://www.cs.colostate.edu/helpdocs/vi.html
# Certainly, you can use any text editor. 
vi ExaML_script.qsub

#!/bin/bash
#PBS -N ExaML.test
#PBS -l nodes=2:ppn=8
#PBS -q debug 
#PBS -l walltime=20:00
#PBS -j oe
#PBS -M xxx@brown.edu

module load examl/1.0.0

NPROCS=`wc -l < $PBS_NODEFILE`

cd $PBS_O_WORKDIR

mpirun -np $NPROCS  -machinefile $PBS_NODEFILE examl -s 49.unpartitioned.binary -t  $EXAMLDATA/49.tree -m GAMMA -n T1
mpirun -np $NPROCS  -machinefile $PBS_NODEFILE examl  -s 49.partitioned.binary -t  $EXAMLDATA/49.tree -m GAMMA -n T2

# Step 3: Submit the mpirun job through qsub
# After change the email address, save the script by Esc, then :, then wq, then enter.
# Submit the mpi job to debug queue on Oscar
qsub ExaML_script.qsub

# Check the status by showq command:
showq -u $USER

# Step 4: Review the results
# After the job finishes (you should get an email notice), here is the file list:
ls -l
-rw-r-----  1 ldong ccvstaff  34K Oct  1 13:01 49.unpartitioned.binary
-rw-r-----  1 ldong ccvstaff  141 Oct  1 13:01 RAxML_info.49.unpartitioned
-rw-r-----  1 ldong ccvstaff  35K Oct  1 13:01 49.partitioned.binary
-rw-r-----  1 ldong ccvstaff  139 Oct  1 13:01 RAxML_info.49.partitioned
-rw-r-----  1 ldong ccvstaff  436 Oct  1 16:38 ExaML_script.qsub
-rw-r-----  1 ldong ccvstaff  91K Oct  1 16:39 ExaML_binaryCheckpoint.T1_0
-rw-r-----  1 ldong ccvstaff  91K Oct  1 16:39 ExaML_binaryCheckpoint.T1_1
-rw-r-----  1 ldong ccvstaff  91K Oct  1 16:39 ExaML_binaryCheckpoint.T1_2
-rw-r-----  1 ldong ccvstaff  91K Oct  1 16:39 ExaML_binaryCheckpoint.T1_3
-rw-r-----  1 ldong ccvstaff  91K Oct  1 16:39 ExaML_binaryCheckpoint.T1_4
-rw-r-----  1 ldong ccvstaff  91K Oct  1 16:39 ExaML_binaryCheckpoint.T1_5
-rw-r-----  1 ldong ccvstaff  91K Oct  1 16:39 ExaML_binaryCheckpoint.T1_6
-rw-r-----  1 ldong ccvstaff  91K Oct  1 16:39 ExaML_binaryCheckpoint.T1_7
-rw-r-----  1 ldong ccvstaff  91K Oct  1 16:39 ExaML_binaryCheckpoint.T1_8
-rw-r-----  1 ldong ccvstaff  91K Oct  1 16:39 ExaML_binaryCheckpoint.T1_9
-rw-r-----  1 ldong ccvstaff  91K Oct  1 16:39 ExaML_binaryCheckpoint.T1_10
-rw-r-----  1 ldong ccvstaff  91K Oct  1 16:39 ExaML_binaryCheckpoint.T1_11
-rw-r-----  1 ldong ccvstaff  91K Oct  1 16:39 ExaML_binaryCheckpoint.T1_12
-rw-r-----  1 ldong ccvstaff  299 Oct  1 16:39 ExaML_log.T1
-rw-r-----  1 ldong ccvstaff 2.6K Oct  1 16:39 ExaML_result.T1
-rw-r-----  1 ldong ccvstaff 2.4K Oct  1 16:39 ExaML_info.T1
-rw-r-----  1 ldong ccvstaff  95K Oct  1 16:39 ExaML_binaryCheckpoint.T2_0
-rw-r-----  1 ldong ccvstaff  95K Oct  1 16:39 ExaML_binaryCheckpoint.T2_1
-rw-r-----  1 ldong ccvstaff  95K Oct  1 16:39 ExaML_binaryCheckpoint.T2_2
-rw-r-----  1 ldong ccvstaff  95K Oct  1 16:39 ExaML_binaryCheckpoint.T2_3
-rw-r-----  1 ldong ccvstaff  95K Oct  1 16:39 ExaML_binaryCheckpoint.T2_4
-rw-r-----  1 ldong ccvstaff  95K Oct  1 16:39 ExaML_binaryCheckpoint.T2_5
-rw-r-----  1 ldong ccvstaff  95K Oct  1 16:39 ExaML_binaryCheckpoint.T2_6
-rw-r-----  1 ldong ccvstaff  95K Oct  1 16:39 ExaML_binaryCheckpoint.T2_7
-rw-r-----  1 ldong ccvstaff  95K Oct  1 16:39 ExaML_binaryCheckpoint.T2_8
-rw-r-----  1 ldong ccvstaff  95K Oct  1 16:39 ExaML_binaryCheckpoint.T2_9
-rw-r-----  1 ldong ccvstaff  95K Oct  1 16:39 ExaML_binaryCheckpoint.T2_10
-rw-r-----  1 ldong ccvstaff  253 Oct  1 16:39 ExaML_log.T2
-rw-r-----  1 ldong ccvstaff 2.6K Oct  1 16:39 ExaML_result.T2
-rw-r-----  1 ldong ccvstaff 2.5K Oct  1 16:39 ExaML_info.T2
-rw-------  1 ldong ccvstaff 7.1K Oct  1 16:40 ExaML.test.o5330077

# The qsub output file can be reviewed by less command:
less ExaML.test.o5330077

Let me know if you have any question to use the software.

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