Subtom is a pipeline for subvolume alignment and averaging of electron cryo-tomography data. It uses the TOM toolbox (aquisition and analysis of electron tomography).

• Subtom Main Site: Documentation
• Subtom Download Site: GitHub

• Module Name: subtom (see the modules page for more information)
• Scripts can found in ${SUBTOM_SCRIPTS}

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn4224 are ready for job

[user@cn4224 ~]$ cd /data/${USER}
[user@cn4224 ~]$ mkdir SUBTOM_SCRIPTS
[user@cn4224 ~]$ module load subtom
[user@cn4224 ~]$ cd SUBTOM_SCRIPTS
[user@cn4224 ~]$ cp ${SUBTOM_SCRIPTS}/subtom_average.sh .

At this step you need to (1) modify subtom_average.sh to include the path to your datasets and (2) assign run_local="1"

[user@cn4224 ~]$ chmod u+x subtom_average.sh
[user@cn4224 ~]$ ./subtom_average.sh
Options sourced!

STARTING Averaging - Iteration: 1

STATUS Update: Averaging - Iteration: 1

	0 parallel sums out of 1

biowulf.nih.gov

ERROR Update: Averaging - Iteration: 1

LOG Update: Averaging - Iteration: 1

Summing Batch 1: [####################################### ] - 97% - 840 particles 0:00:50 | 0:00:52
Summing Batch 1: [####################################### ] - 97% - 844 particles 0:00:50 | 0:00:52
Summing Batch 1: [####################################### ] - 97% - 848 particles 0:00:50 | 0:00:52
Summing Batch 1: [####################################### ] - 98% - 852 particles 0:00:51 | 0:00:52
Summing Batch 1: [####################################### ] - 98% - 856 particles 0:00:51 | 0:00:52
Summing Batch 1: [########################################] - 99% - 860 particles 0:00:51 | 0:00:52
Summing Batch 1: [########################################] - 99% - 864 particles 0:00:51 | 0:00:52
Summing Batch 1: [########################################] - 100% - 868 particles 0:00:52 | 0:00:52
Summing Batch 1: [########################################] - 100% - 870 particles 0:00:52 | 0:00:52

STATUS Update: Averaging - Iteration: 1

	1 parallel sums out of 1

FINISHED Averaging - Iteration: 1

Create a batch input file (e.g. subtom.sh) similar to the following.

#! /bin/bash

set -e

module load subtom

/data/$USER/SUBTOM_SCRIPTS/subtom_average.sh

Submit these jobs using the Slurm sbatch command.

Create a swarmfile for the first step of the pipeline (e.g. subtom.swarm). For example:

/data/$USER/SUBTOM_SCRIPTS/subtom_average1.sh
/data/$USER/SUBTOM_SCRIPTS/subtom_average2.sh
/data/$USER/SUBTOM_SCRIPTS/subtom_average3.sh
/data/$USER/SUBTOM_SCRIPTS/subtom_average4.sh
/data/$USER/SUBTOM_SCRIPTS/subtom_average5.sh

Submit this job using the swarm command.

swarm -f subtom.swarm [-g #] --module subtom