subtom_average

Calculates the average from a given MOTL file in parallel on the cluster or locally.

This subtomogram averaging script uses five MATLAB compiled scripts below:

Options

Directories

scratch_dir

Absolute path to the folder with the input to be processed. Other paths are relative to this one.

local_dir

Absolute path to the folder on a group share, if the scratch directory is cleaned and deleted regularly this can set a local directory to which the important results will be copied. If this is not needed it can be skipped with the option skip_local_copy below.

mcr_cache_dir

Absolute path to MCR directory for the processing.

exec_dir

Directory for executables

Variables

sum_exec

Parallel Summing executable

avg_exec

Weighted Averaging executable

Memory Options

mem_free

The amount of memory the job requires for alignment. This variable determines whether a number of CPUs will be requested to be dedicated for each job. At 24G, one half of the CPUs on a node will be dedicated for each of the processes (12 CPUs). At 48G, all of the CPUs on the node will be dedicated for each of the processes (24 CPUs).

mem_max

The upper bound on the amount of memory the alignment job is allowed to use. If any of the processes request or require more memory than this, the queue will kill the process. This is more of an option for safety of the cluster to prevent the user from crashing the cluster requesting too much memory.

Other Cluster Options

job_name

The job name prefix that will be used for the cluster submission scripts, log files, and error logs for the processing. Be careful that this name is unique because previous submission scripts, logs, and error logs with the same job name prefix will be overwritten in the case of a name collision.

array_max

The maximum number of jobs per cluster submission script. Cluster submission scripts work using the array feature common to queuing systems, and this value is the maximum array size used in a script. If the user requests more batches of processing than this value, then the submission scripts will be split into files of up to array_max jobs.

max_jobs

The maximum number of jobs for alignment. If the number of batches / exceeds this value the script will immediately quit.

run_local

If the user wants to skip the cluster and run the job locally, this value should be set to 1.

skip_local_copy

Set this option to 1 to skip the copying of data to local_dir.

Subtomogram Averaging Workflow Options

Parallelization Options

iteration

The index of the reference to generate : input will be all_motl_fn_prefix_iteration.em (define as integer)

num_avg_batch

The number of batches to split the parallel subtomogram averaging job into.

File Options

all_motl_fn_prefix

Relative path and name of the concatenated motivelist of all particles (e.g. allmotl_iter.em , the variable will be written as a string e.g. all_motl_fn_prefix=’sub-directory/allmotl’)

ref_fn_prefix

Relative path and name of the reference volumes (e.g. ref_iter.em , the variable will be written as a string e.g. ref_fn_prefix=’sub-directory/ref’)

ptcl_fn_prefix

Relative path and name of the subtomograms (e.g. part_n.em , the variable will be written as a string e.g. ptcl_fn_prefix=’sub-directory/part’)

weight_fn_prefix

Relative path and name of the weight file.

weight_sum_fn_prefix

Relative path and name of the partial weight files.

Averaging Options

tomo_row

Which row in the motl file contains the correct tomogram number. Usually row 5 and 7 both correspond to the correct value and can be used interchangeably, but there are instances when 5 contains a sequential ordered value starting from 1, while 7 contains the correct corresponding tomogram.

iclass

Particles with that number in position 20 of motivelist will be added to new average (define as integer e.g. iclass=1). NOTES: Class 1 is ALWAYS added. Negative classes and class 2 are never added.

Example

scratch_dir="${PWD}"

local_dir=""

mcr_cache_dir="${scratch_dir}/mcr"

exec_dir="/net/dstore2/teraraid/dmorado/software/subTOM/bin"

sum_exec="${exec_dir}/alignment/subtom_parallel_sums"

avg_exec="${exec_dir}/alignment/subtom_weighted_average"

mem_free=1G

mem_max=64G

job_name=subTOM

array_max=1000

max_jobs=4000

run_local=0

skip_local_copy=1

iteration=1

num_avg_batch=1

all_motl_fn_prefix="combinedmotl/allmotl"

ref_fn_prefix="ref/ref"

ptcl_fn_prefix="subtomograms/subtomo"

weight_fn_prefix="otherinputs/ampspec"

weight_sum_fn_prefix="otherinputs/wei"

tomo_row=7

iclass=0