Align tilt-series additional arguments

[FlorianBeckOle]

Describe your problem get an error when setting additional arguments in Align tilt-series AreTomo job. Did not work for any add option. I tried -Wbp 1

Environment:

• OS: sel15
• MPI runtime: impi/2018.4
• RELION version: relion5.0-beta-3
• Memory: 768GB
• GPU: NVIDIA L40S

Dataset: -2 tomograms with 60 tilts

Job options:

• Type of job: Align Tilt Series Aretomo
• Number of MPI processes: -
• Number of threads: -
• Full command which relion_python_tomo_align_tilt_series AreTomo --sample-thickness-nanometers 250 --do-tilt-angle-offset-correction --gpu 0 --gpu 1 --gpu 2 --gpu 3 --tilt-series-star-file External/job004/tiltseries_filtered.star --output-directory AlignTiltSeries/job009/ -Wbp 1 --pipeline_control AlignTiltSeries/job009/

Error message: Currently Loaded Modulefiles: 1) intel/18.0.5(default) 3) IMOD/4.11.1(default) 5) RELION/5.0-beta-3NC
2) impi/2018.4(default) 4) ARETOMO/1.3.4
Usage: -c AreTomo [OPTIONS] Try '-c AreTomo --help' for help. ╭─ Error ──────────────────────────────────────────────────────────────────────╮ │ No such option: -W │ ╰──────────────────────────────────────────────────────────────────────────────╯ srun: error: hpcl9303: task 0: Exited with exit code 2 srun: Terminating StepId=559534.0

[EuanPyle]

Hi, This is not a RELION bug: This will not work as RELION is not directly running AreTomo through the GUI so AreTomo commands will not work through additonal arguments. You could try going into AlignTiltSeries/jobXYZ/external/TS_XYZ and re-running AreTomo in there (without alignment!) to generate your tomogram in WBP

[FlorianBeckOle]

Hi, This is not a RELION bug: This will not work as RELION is not directly running AreTomo through the GUI so AreTomo commands will not work through additonal arguments. You could try going into AlignTiltSeries/jobXYZ/external/TS_XYZ and re-running AreTomo in there (without alignment!) to generate your tomogram in WBP

Thanks for the answer. Do you think of adding the additional arguments feature ?

[EuanPyle]

it's probably not a priority to do that right now, as it is possible to run your request outside RELION but within the workflow

(ie. go into AlignTiltSeries/jobXYZ/external/TS_XYZ and run: AreTomo3 -InMrc [the_tilt_series.mrc] -OutMrc [whatever.mrc] -Align 0 -VolZ [ThicknessOfTomo] -Wbp

[EuanPyle]

Although of course, you could make a feature request by posting onto CCPEM mailing list. I'm not so much involved with feature additions anymore