Problems with WarpTools ts_aretomo

[Dylan Noone]

Hey all,

I am having some trouble using the inbuilt AreTomo tilt series alignment for warp.

I have tried going through this google group, and saw some similar posts, but not a workaround (unless I missed something).

I am using the following script to run my job on our cluster:

#!/bin/sh

#SBATCH --partition="bubeck"

#SBATCH --job-name=Warp

#SBATCH --output=Out_017_warp_tilt_series_alignment_AreTomo_output_corr.out

#SBATCH --error=17_warp_tilt_series_alignment_AreTomo_corr-%j.err

#SBATCH --nodes=1

#SBATCH --ntasks=1

#SBATCH --cpus-per-task=90

#SBATCH --time=10:00:00

#SBATCH --gres=gpu:a10:1

#SBATCH --exclusive  

# --- In case we already have some conda active – deactivate

 

if command -v conda > /dev/null 2>&1; then

    conda deactivate > /dev/null 2>&1 || true  # ignore any errors

    conda deactivate > /dev/null 2>&1 || true  # ignore any errors

fi

unset _CE_CONDA

unset CONDA_DEFAULT_ENV

unset CONDA_EXE

unset CONDA_PREFIX

unset CONDA_PROMPT_MODIFIER

unset CONDA_PYTHON_EXE

unset CONDA_SHLVL

unset PYTHONPATH

unset LD_PRELOAD

unset LD_LIBRARY_PATH

 

# --- Load Module (this will define the path to the warp python

# --- and conda environment)

. /bbsrc/soft/Modules/init/sh > /dev/null 2>&1

module load warp/2.0.0 > /dev/null 2>&1

 

# --- Define conda environment

# --- This is done by the module using the command:

# ---     /bbsrc/scripts/warp/activate-2.0.0.sh

# --- So, below commented out, but left here for info only

NEEDED="n"

if [ $NEEDED == "y" ]

then

# >>> conda initialize >>>

# !! Contents within this block are managed by 'conda init' !!

__conda_setup="$('/bbsrc/soft/warp/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"

if [ $? -eq 0 ]; then

    eval "$__conda_setup"

else

    if [ -f "/bbsrc/soft/warp/etc/profile.d/conda.sh" ]; then

        . "/bbsrc/soft/warp/etc/profile.d/conda.sh"

    else

        export PATH="/bbsrc/soft/warp/bin:$PATH"

    fi

fi

unset __conda_setup

# <<< conda initialize <<<

fi

# --- Activate environment

conda activate warp

# --- Only see the first GPU

export CUDA_VISIBLE_DEVICES=0

echo "=== CUDA VISIBILITY TEST ==="

echo "CUDA_VISIBLE_DEVICES=$CUDA_VISIBLE_DEVICES"

nvidia-smi

# --- Put programs below - WarpTools, MTools, MCore, ...

module load cuda/12.4

module load /bbsrc/beebylab/modules/aretomo/2

 

WarpTools ts_aretomo \

--settings warp_tiltseries.settings \

--angpix 10 \

--alignz 800 \

--axis_iter 5 \

--min_fov 0 \

--device_list 0 \

--output_processing aretomo_alignz_800

 

However, it seems to skip making anything. I have the following appear in the .err file my script makes (for brevity I just put what it says for one TS):

Failed to process /bbsrc/home/dnoone/nooned/Dylan/warp/aretomo_alignz_800/Position_1_2.tomostar, marked as unselected

Check logs in /bbsrc/home/dnoone/nooned/Dylan/warp/aretomo_alignz_800/logs for more info.

Use the change_selection WarpTool to reactivate this item if required.

Exception details:

System.Exception: Could not find Position_1_2.xf

   at Warp.TiltSeries.ImportAlignments(ProcessingOptionsTomoImportAlignments options) in /home/runner/micromamba/envs/package-build/conda-bld/warp_1757710231489/work/WarpLib/TiltSeries/TiltSeries.ImportAlignments.cs:line 84

   at WarpTools.Commands.AreTomoTiltseries.<>c__DisplayClass0_2.<Run>b__4(WorkerWrapper worker, TiltSeries t) in /home/runner/micromamba/envs/package-build/conda-bld/warp_1757710231489/work/WarpTools/Commands/Tiltseries/AreTomoTiltseries.cs:line 179

   at WarpTools.Commands.BaseCommand.<>c__DisplayClass1_0`1.<IterateOverItems>b__0(WorkerWrapper worker, T[] items) in /home/runner/micromamba/envs/package-build/conda-bld/warp_1757710231489/work/WarpTools/Commands/BaseCommand.cs:line 70

   at WarpTools.Commands.BaseCommand.<>c__DisplayClass2_0`1.<IterateOverItems>g__ProcessItem|2(Int32 index, Int32 threadID, Int32 jsonIndex) in /home/runner/micromamba/envs/package-build/conda-bld/warp_1757710231489/work/WarpTools/Commands/BaseCommand.cs:line 192

 

Then the log files look like this:

2025-10-22 15:05:02.831 Received "TomoStack", with 2 arguments, for GPU #0, 22266 MB free:

2025-10-22 15:05:07.843 Created tilt stack for /bbsrc/home/dnoone/nooned/Dylan/warp/aretomo_alignz_800/Position_1_2.tomostar

2025-10-22 15:05:07.845 Execution took 4.958 seconds

2025-10-22 15:05:07.847

2025-10-22 15:05:07.900 Received "TomoAretomo", with 2 arguments, for GPU #0, 22046 MB free:

2025-10-22 15:05:07.928 Executing AreTomo2 in /bbsrc/home/dnoone/nooned/Dylan/warp/aretomo_alignz_800/tiltstack/Position_1_2 with arguments: -InMrc Position_1_2.st -AngFile Position_1_2.rawtlt -VolZ 0 -OutBin 0 -TiltAxis -175.92 0 -AlignZ 80 -TiltCor 1 -OutImod 1 -DarkTol 0 -OutMrc Position_1_2_aligned.mrc -Gpu 0 -Patch 0 0

2025-10-22 15:05:08.083

2025-10-22 15:05:08.086 -InMrc      Position_1_2.st

2025-10-22 15:05:08.088 -OutMrc     Position_1_2_aligned.mrc

2025-10-22 15:05:08.089 -AlnFile   

2025-10-22 15:05:08.091 -AngFile    Position_1_2.rawtlt

2025-10-22 15:05:08.092 -RoiFile   

2025-10-22 15:05:08.094 -TmpFile   

2025-10-22 15:05:08.096 -LogFile   

2025-10-22 15:05:08.097 -AlignZ     80

2025-10-22 15:05:08.099 -VolZ       0

2025-10-22 15:05:08.100 -OutBin     1.00

2025-10-22 15:05:08.102 -TiltRange  0.00  0.00

2025-10-22 15:05:08.103 -TiltAxis   -175.92  0.00

2025-10-22 15:05:08.105 -Gpu        0

2025-10-22 15:05:08.106 -TiltCor    1.00  0.00

2025-10-22 15:05:08.108 -ReconRange  -90.00  90.00

2025-10-22 15:05:08.109 -PixSize    0.00

2025-10-22 15:05:08.111 -ImgDose    0.00

2025-10-22 15:05:08.112 -Kv         0.00

2025-10-22 15:05:08.114 -Cs         0.00

2025-10-22 15:05:08.115 -AmpContrast  0.07

2025-10-22 15:05:08.117 -ExtPhase   0.00  0.00

2025-10-22 15:05:08.118 -FlipVol    0

2025-10-22 15:05:08.120 -FlipInt    0

2025-10-22 15:05:08.122 -Sart       20  5

2025-10-22 15:05:08.123 -Wbp        0

2025-10-22 15:05:08.125 -Patch      0  0

2025-10-22 15:05:08.126 -TiltScheme  0.00  0.0  0.0

2025-10-22 15:05:08.128 -OutXF      0

2025-10-22 15:05:08.129 -Align      1

2025-10-22 15:05:08.131 -CropVol    0  0

2025-10-22 15:05:08.132 -OutImod    1

2025-10-22 15:05:08.134 -DarkTol    0.00

2025-10-22 15:05:08.136 -Bft        500.0  500.0

2025-10-22 15:05:08.137 -IntpCor    1

2025-10-22 15:05:08.138

2025-10-22 15:05:08.140 Error: GPU 0 is invalid, skip

2025-10-22 15:05:08.142 Executed AreTomo for /bbsrc/home/dnoone/nooned/Dylan/warp/aretomo_alignz_800/Position_1_2.tomostar

2025-10-22 15:05:08.144 Execution took 0.240 seconds

2025-10-22 15:05:08.146

 

Any one have any idea what the issue could be?

[Dylan Noone]

P.S. AreTomo alone works fine with the same options - it's only when I call it via warptools

[Alister Burt]

Hi Dylan,

That AreTomo error saying the GPU is invalid is strange, when doing your wrapped/unwrapped comparison are you running AreTomo from inside the WarpTools conda environment?

In general people have had issues with AT2’s IMOD compatibility so we recommend using the old AreTomo 1.3.4 in the wrapper

https://github.com/czimaginginstitute/AreTomo2/issues/21

As always, you can run your tilt series alignments outside of warp and import results from IMOD style metadata

https://warpem.com/reference/warptools/custom_tilt_series_alignments/

Cheers,

Alister

Sent from mobile - apologies for brevity

On Oct 23, 2025, at 00:40, 'Dylan Noone' via Warp <war...@googlegroups.com> wrote:

P.S. AreTomo alone works fine with the same options - it's only when I call it via warptools

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[Dylan Noone]

Hey Alister,

Thanks for the response.

Indeed what I have done as a work around was run AreTomo outside of warp with the -OutImod 2 flag for the .xf files etc. As such that second link is of extra interest to me:

https://warpem.com/reference/warptools/custom_tilt_series_alignments/

However, when I click on it it leads me to a "not found" page. I have tried different browser, so could I please confirm this is the correct link?

Thank you for you time and guidance thus far.

Best,

Dylan

[Dylan Noone]

To respond to your specific question at the start yes this is when I run AreTomo from within the Warp conda.

[Alister Burt]

Sorry, there’s something misconfigured with the site - change warpem.com to warpem.github.io in the url

Sent from mobile - apologies for brevity

On Oct 23, 2025, at 08:16, 'Dylan Noone' via Warp <war...@googlegroups.com> wrote:

Hey Alister,

To view this discussion visit https://groups.google.com/d/msgid/warp-em/7dff4f14-3871-4642-aa97-84ea68c13b1an%40googlegroups.com.

[Dylan Noone]

Works, thanks!