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Illumina / Cyrius

A tool to genotype CYP2D6 with WGS data
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RuntimeWarning: divide by zero encountered in true_divide #7

Closed PavitaKae closed 3 years ago

PavitaKae commented 3 years ago

my command = python3 star_caller.py --manifest manifest.txt --genome 38 --prefix test --outDir result --threads 8 INFO:root:Processing sample HSxx at 2020-12-14 15:39:01.967956 xx/Cyrius/depth_calling/bin_count.py:84: RuntimeWarning: divide by zero encountered in true_divide y_counts = y_counts / np.median(y_counts) xx/Cyrius/depth_calling/bin_count.py:84: RuntimeWarning: invalid value encountered in true_divide y_counts = y_counts / np.median(y_counts) xx/envs/cyr_env/lib/python3.7/site-packages/numpy/core/fromnumeric.py:3373: RuntimeWarning: Mean of empty slice. out=out, **kwargs) xx/envs/cyr_env/lib/python3.7/site-packages/numpy/core/_methods.py:170: RuntimeWarning: invalid value encountered in double_scalars ret = ret.dtype.type(ret / rcount) INFO:root:Processing sample HSxx at 2020-12-14 15:39:02.742290

result tsp file = Sample Genotype Filter HSxx None None json file = {"HSxx": {"Coverage_MAD": NaN, "Median_depth": 0.0, "Total_CN": null, "Spacer_CN": null, "Total_CN_raw": null, "Spacer_CN_raw": null, "Variants_called": null, "CNV_group": null, "Genotype": null, "Filter": null, "Raw_star_allele": null, "Call_info": null, "Exon9_CN": null, "CNV_consensus": null, "d67_snp_call": null, "d67_snp_raw": null, "Variant_raw_count": null}, "HS01002_mini": {"Coverage_MAD": NaN, "Median_depth": 0.0, "Total_CN": null, "Spacer_CN": null, "Total_CN_raw": null, "Spacer_CN_raw": null, "Variants_called": null, "CNV_group": null, "Genotype": null, "Filter": null, "Raw_star_allele": null, "Call_info": null, "Exon9_CN": null, "CNV_consensus": null, "d67_snp_call": null, "d67_snp_raw": null, "Variant_raw_count": null}} Why i cannot get result of genotype?

xiao-chen-xc commented 3 years ago

Hi @PavitaKae, a few things to check would be: -Are you using a WGS bam (the whole bam, not a bamlet)? -Does the genome build, i.e. 38, in your command line match the reference genome of your bam file? -Is your input bam file a local one or a remote one, like one stored in Amazon s3?

PavitaKae commented 3 years ago

ok, i got it. I wrong in bam file, i cut only CYP2D6 region for calculated. when I change to WGS bam, result look ok. How to check WGS bam? it must be all chromosome?

Thank you

xiao-chen-xc commented 3 years ago

You can check with the people or the paper from whom/which you got the data. A WGS bam should have even coverage across most of the genome.

PavitaKae commented 3 years ago

I found region in data folder, i check this and I got result already. Thank you