python -m robustlink corr_atac output is all NA

[Linshiqi-Git]

Hi, when I used my scATAC-seq and scRNA-seq data to calculate the spearman correlation of enhancer-gene pairs, I found that the results were all NA. However, no error is reported during the operation. Could you please help me find out the reason for this? I am trying to calculate the correlation of all peaks and genes within 1mb of the gene start site.

My output
link_rna_atac_ka30_knn30
STEP3...
02/26/2024 01:39:58 AM Processed_data_RNA-all_full-counts-and-downsampled-CPM_obs-gene_var-cell,Processed_data_ATAC_processed-count-data_obs-gene_var-cell,link_rna_atac_ka30_knn30,0,spearmanr,True,1001
/home/linshq/.local/lib/python3.9/site-packages/anndata/init.py:51: FutureWarning: anndata.read is deprecated, use anndata.read_h5ad instead. ad.read will be removed in mid 2024.
warnings.warn(
02/26/2024 01:43:58 AM (15531, 1) (15531, 8724) (15531,) (8724,)
02/26/2024 01:44:02 AM (15531, 0)(15531, 1)(26747, 15531)_(6072620, 0)
02/26/2024 01:44:02 AM cluster_r10
02/26/2024 01:44:02 AM Number of metacells: 96
02/26/2024 01:46:36 AM (26747, 96) (6072620, 96)
spearmanr chosen!

My code
`echo "STEP1..."
/p300s/biosoft/app/python/python3.9/bin/python3.9 -m robustlink scfusion
-i ${data_dir}
-id ${fusiondata_atac} ${fusiondata_rna}
-fd ${fusiondata_atac}
-im "atac" "rna"
-o ${out_dir}
-tag ${study_tag}
--ka_smooth $ka
--knn $knn
-s ${subsample_frac}
-sn ${subsample_times}

echo "STEP2..."
/p300s/biosoft/app/python/python3.9/bin/python3.9 -m robustlink metacell
-i "${data_dir}/${fusiondata_rna}"
-o ${out_dir}
-tag ${study_tag}
-sn ${subsample_times}
-r ${resolutions}

echo "STEP3..."
for (( i=0; i<${subsample_times}; i++ )); do
/p300s/biosoft/app/python/python3.9/bin/python3.9 -m robustlink corr_atac
--tolink "${data_dir}/$tolink"
--countdata_gene "${data_dir}/${countdata_gene}"
--countdata_enh "${data_dir}/${countdata_enh}"
--scfusion_dir ${scfusion_dir}
--fusiondata_rna ${fusiondata_rna}
--fusiondata_mc ${fusiondata_atac}
-tag ${study_tag}
-isub $i
--corr_type ${corr_type}
-o ${out_dir}
-n ${num_metacell_limit}
-f
done
`