Error in parse_final_snp

[palmfern]

Error when generating the final cell_snp_Aallele.npz cell_snp_Ballele.npz and unique_snp_ids.npy.

The parse_final_snp.log file:

/CalicoST//utils/get_snp_matrix.py:97: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perf
orm elementwise comparison
phased_AD = np.where( (df_snp.GT.values == "0|1").reshape(-1,1), AD.A, (DP-AD).A )
Traceback (most recent call last):
File "/CalicoST//utils/get_snp_matrix.py", line 183, in
cell_snp_Aallele, cell_snp_Ballele, unique_snp_ids = cell_by_gene_lefthap_counts(args.cellsnplite_result_dir, args.eagle_out_dir, barcode_list)
File "CalicoST//utils/get_snp_matrix.py", line 97, in cell_by_gene_lefthap_counts
phased_AD = np.where( (df_snp.GT.values == "0|1").reshape(-1,1), AD.A, (DP-AD).A )
AttributeError: 'bool' object has no attribute 'reshape'

[Congm12]

Hi,

This looks like an edge case of file parsing. Can you check and make sure that the phasing outputs <output_snpinfo>/phasing/chr*.phased.vcf.gz contain nonempty and more than a single record of phasing results beyond the file header?

If you don't need the phasing output files, you can rerun snakemake command with --keep-incomplete option to retain partial results.

snakemake --cores <number threads> --configfile config.yaml --snakefile calicost.smk --keep-incomplete all

[palmfern]

After checking the data, it seems that this error happens when no or only 1 heterozygous SNP in the vcf files.