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MultiVI: no integration_col_categorical argument #293

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wlason opened this issue Jul 16, 2024 · 0 comments
Open

MultiVI: no integration_col_categorical argument #293

wlason opened this issue Jul 16, 2024 · 0 comments
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@wlason
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wlason commented Jul 16, 2024

When running panpipes with atac,rna,prot, I get the follwing error from MultiVI:

OSError: Job 1204848 has non-zero exitStatus 2: hasExited=True, wasAborted=FalsehasSignal=False, terminatedSignal='' \
statement = python [dir]/panpipes/panpipes/python_scripts/batch_correct_multivi.py
--scaled_anndata [dir]/panpipes/2_preprocess/multiome.h5mu --output_csv batch_correction/umap_multimodal_multivi.csv --figdir figures/ --scvi_seed 1492 --integration_col_categorical sample_id --integration_col_continuous
--neighbors_method scanpy --neighbors_metric euclidean --neighbors_n_pcs 30 --neighbors_k 30 > logs/4_multimodal_multivi.log \

usage: batch_correct_multivi.py [-h] [--scaled_anndata SCALED_ANNDATA] \
[--output_csv OUTPUT_CSV] \
[--integration_col_categorical INTEGRATION_COL_CATEGORICAL] \
[--integration_col_continuous INTEGRATION_COL_CONTINUOUS] \
[--figdir FIGDIR] \
[--neighbors_n_pcs NEIGHBORS_N_PCS] \
[--neighbors_method NEIGHBORS_METHOD] \
[--neighbors_k NEIGHBORS_K] \
[--neighbors_metric NEIGHBORS_METRIC] \
[--scvi_seed SCVI_SEED] \
batch_correct_multivi.py: error: argument --integration_col_continuous: expected one argument \

the integration_col_continuous is not present in the yaml for integration workflow, I wonder if it might have been missed from the ruffus/yaml but is in the python script?

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