Batch Submission of pytom-match-pick from AreTomo3 Output

This script automates batch submission of pytom-match-pick jobs on an HPC cluster (SLURM) by reading metadata directly from AreTomo3 outputs. It:

• Extracts tilt angles from IMOD/<prefix>_st.tlt
• Reads defocus (average of defocus1/defocus2 in Å, converted to μm) from <prefix>_CTF.txt
• Computes per-tilt exposure by cumulatively summing --dose in acquisition order (<prefix>_Imod/<prefix>_order_list.csv)
• Generates one SLURM submission script per tomogram

and will run on all tomograms/<prefix>.mrc files by default unless specified --include or --exclude

--dry-run will generate the bash scripts without submitting them, allowing for quick sanity checks or manual execution.

---

Usage

./batch_pytom_aretomo3.py \
  -i /path/to/aretomo3/output \  # required
  -d submission \                # default: submission
  -t /path/to/template.mrc \    # required
  -m /path/to/mask.mrc \        # required
  -g 0 \                         # required, GPU IDs
  --voxel-size-angstrom 7.64 \  # required
  --dose 2 \                     # required, e-/Ų per tilt
  [--include Position_*] [--exclude Position_5] \  # optional wildcard filtering
  [--angular-search 10] [--particle-diameter 140] \ # either or required
  -s 2 2 1 \                    # optional
  --per-tilt-weighting \       # optional
  --non-spherical-mask \       # optional
  --tomogram-ctf-model phase-flip \ # optional
  -r \                          # optional
  --rng-seed 69 \               # default: 69
  [--dry-run]                    # optional

Flag Summary

Core flags

Flag	Description	Default
-i, --aretomo-dir	AreTomo3 output directory	—
-t, --template	Template MRC for matching	—
-m, --mask	Mask MRC for matching	—
-g, --gpu-ids	GPU IDs (e.g. 0 or 0 1)	—
--voxel-size-angstrom	Voxel size in Å	—
--dose	Electron dose per tilt (e‑/Ų)	—
-d, --output-dir	Top-level folder for outputs	submission
--include / --exclude	Wildcard patterns for prefix filtering	all / none
--particle-diameter	Particle diameter in Å (Crowther sampling)	none
--angular-search	Override angular search (float max or .txt)	none
--dry-run	Generate scripts without submitting	off

Input Options

Flag	Description	Default
-s, --volume-split	Split volume into X Y Z blocks	none
--search-x START END	Search range along x-axis	none
--search-y START END	Search range along y-axis	none
--search-z START END	Search range along z-axis	none
--non-spherical-mask	Enable non-spherical mask support	off
--tomogram-ctf-model	CTF model used (e.g. phase-flip)	none
-r, --random-phase-correction	STOPGAP-style random-phase correction	off
--half-precision	Use float16 output	off
--rng-seed	RNG seed for phase correction	69
--per-tilt-weighting	Enable per-tilt CTF weighting	off
--low-pass LOW_PASS	Low-pass filter cutoff in Å	none
--high-pass HIGH_PASS	High-pass filter cutoff in Å	none
--phase-shift PHASE_SHIFT	Phase shift in degrees	0.0
--defocus-handedness	Defocus gradient handedness (-1,0,1)	none
--spectral-whitening	Enable spectral whitening	off
--relion5-tomograms-star	Path to RELION5 tomograms.star override	none

Written by default!

Flag	Description	Default
--amplitude-contrast	Amplitude contrast fraction	0.07
--spherical-aberration	Spherical aberration (mm)	2.7
--voltage	Voltage (kV)	300

SLURM Settings

Flag	Description	Default
--partition	SLURM partition	emgpu
--ntasks	SLURM ntasks	1
--nodes	SLURM nodes	1
--ntasks-per-node	SLURM tasks per node	1
--cpus-per-task	SLURM CPUs per task	4
--gres	SLURM GPU resource (e.g. gpu:1)	gpu:1
--mem	SLURM memory (GB)	128
--qos	SLURM Quality of Service	emgpu
--time	SLURM time limit	05:00:00
--mail-type	SLURM mail notifications	none

---

Example Output

After running, you’ll get one folder per tomogram under submission/:

submission/
├─ Position_1/
│  ├─ Position_1.tlt
│  ├─ Position_1_defocus.txt
│  ├─ Position_1_exposure.txt
│  └─ submit_Position_1.sh
├─ Position_2/
└─ Position_3/

Sample submit_Position_1.sh:

#!/bin/bash -l
#SBATCH -o pytom.out%j
#SBATCH -D ./
#SBATCH -J pytom_1
#SBATCH --partition=emgpu
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=4
#SBATCH --gres=gpu:1
#SBATCH --mail-type=none
#SBATCH --mem=128G
#SBATCH --qos=emgpu
#SBATCH --time=05:00:00

ml purge
ml pytom-match-pick

pytom_match_template.py \
  -v ../Position_1_Vol.mrc \
  -a submission/Position_1/Position_1.tlt \
  --dose-accumulation submission/Position_1/Position_1_exposure.txt \
  --defocus submission/Position_1/Position_1_defocus.txt \
  -t /path/to/template.mrc \
  -d submission/Position_1 \
  -m /path/to/mask.mrc \
  --angular-search 10 \
  -s 2 2 1 \
  --voxel-size-angstrom 7.64 \
  -r \
  --rng-seed 69 \
  -g 0 \
  --amplitude-contrast 0.07 \
  --spherical-aberration 2.7 \
  --voltage 300 \
  --per-tilt-weighting \
  --tomogram-ctf-model phase-flip \
  --non-spherical-mask

Full Help Output

Run ./batch_pytom_aretomo3.py -h to see all flags and defaults. Feel free to open an issue or submit a PR for further customization!