Open prithikasritharan opened 4 years ago
Hi Prithika,
Thank you for writing. I am currently on paternity leave. Will look into your issue next week, when I am back to work.
Best,
Jonas
Hi Prithika,
This error arises when there is no kmers available to estimate the parameters for the negative binomial genomic kmer count distribution for each sample. These parameters are estimated from kmers that are unique to regions of the genome with no variation. In your case it seems like there is no such kmers, which it likely due to the large number of input variants compared to the size of the genome (1 variant per 6.84 basepair).
Are you using a variant database as input or are these variants predicted directly from your 19 samples? If you are using a database I would recommend filtering some of the variation using for example a frequency treshold. If predicted, is it from aligned assemblies or mapped reads?
Best,
Jonas
Hi Jonas,
Many thanks for getting back to me. I had initially used a large variant database containing variants from 1011 strains (totalling 1,953,710 variants) as input but now I have tried re-running the pipeline using just the variants called from mapped reads for my 19 samples (282,435 variants therefore 1 variant per 43.04 basepairs) but it still seems to be producing the same error.
I will try filtering the frequency threshold to further reduce the number of variants in the input VCF.
Many thanks, Prithika
That is strange. I would have expected it to work using the smaller variant set. Would it be possible for you to share with me the smaller variant set and the reference genome? I think it might be easier for me to debug if I had access to the data.
Hi Jonas,
I re-ran the pipeline from scratch and this seems to have done the trick. I'm currently still running bayestyper genotype
, I have used the smaller variant set and this seems to be running fine as it has bypassed the assertion failure stage.
Many thanks again, Prithika
Glad to hear that it works now. Please let me know if you run into any other issues.
Hi,
I am using Bayestyper to genotype my yeast strains after the clustering step but I'm getting an assertion failure error. I ran
bayestyper genotype
with the --noise-genotyping parameter due to the smaller genome size but it produces the following error:Do you have any suggestions as to what may be causing this error?
Many thanks, Prithika