error during demo when generating visualisations in the CNV step

[alextidd]

Hi,
I was running HiScanner with the demo data (https://github.com/parklab/hiscanner_demo). Here is what I ran:

module load ISG/conda
conda activate hiscanner
hiscanner init
hiscanner validate
hiscanner run --step snp
hiscanner run --step phase
hiscanner run --step ado
hiscanner run --step normalize
hiscanner run --step segment
hiscanner run --step cnv

I got this error in the CNV step:

INFO     Running cnv step...
INFO     Starting CNV calling pipeline
INFO     Using standard (RDR + BAF) mode
INFO     Saving final calls to /nfs/casm/team268im/at31/bin/repos/hiscanner_demo/hiscanner_out/final_calls
INFO     Processing cell SRR6204923_Lymphocyte-068
INFO     Processing cell SRR6204878_Lymphocyte-015
INFO     Processing cell SRR6204925_Lymphocyte-066
INFO     Reading segments for SRR6204878_Lymphocyte-015 (lambda=1024)
INFO     Reading segments for SRR6204923_Lymphocyte-068 (lambda=1024)
INFO     Annotating segments
INFO     Annotating segments
INFO     Finding allelic balanced clusters
INFO     Reading segments for SRR6204925_Lymphocyte-066 (lambda=1024)
INFO     Finding allelic balanced clusters
INFO     Annotating segments
INFO     Finding allelic balanced clusters
INFO     Inferring ploidy
INFO     Inferring ploidy
INFO     Inferring ploidy
INFO     Inferred ploidy: 2.002386909927674
INFO     Merging segments
INFO     Inferred ploidy: 1.9923240518785057
INFO     Merging segments
INFO     Inferred ploidy: 2.002539398771822
INFO     Merging segments
INFO     Generating visualizations
ERROR    Error in CNV calling pipeline: Can only use .str accessor with string values!
ERROR    Error running pipeline: Can only use .str accessor with string values!

All other steps completed successfully. Any idea what I am doing wrong here?
Thanks very much!

[yifnzhao]

Hi Alex, thanks for trying HiScanner. I suspect that the CN_total column got lost somehow in the segment merging step, but I could not reproduce the error. Could you upload the output in final_calls/ folder from your demo run so I could investigate this further?

[taejoohw]

Hi all,

I had the same issue. I solved it after correcting it as follows:

/pipeline/cnv.py line 149, adding ".astype(str)"

cell_data['CHROM'] = cell_data['CHROM'].str.replace('chr', '').astype(int) > cell_data['CHROM'] = cell_data['CHROM'].astype(str).str.replace('chr', '').astype(int)

I hope this helps.