mdbarnesUCSD

Hi @gafishbein, Could you please let us know what versions of SigProfiler packages you have installed in your environment? Also, can you please confirm that running from a new directory...

Thank you for providing this, we are looking into this issue and will update here.

Hi @gafishbein, I believe the issue was due to sigProfilerPlotting and was present in v.1.3.21. Could you please update to sigProfilerPlotting v1.3.22, which should now resolve this issue. Please reach...

Please re-open this thread if you are still encountering this issue, thanks!

We moved forward with support for inputs for SV VCFs versions 4.1, 4.2, and 4.3. In a future release we hope to add support for VCF versions 4.4 and 4.5.

Hi @ywhnet, Please review if either of the proposed solutions in these tickets helps resolve your issue: - https://github.com/AlexandrovLab/SigProfilerExtractor/issues/240 - https://github.com/AlexandrovLab/SigProfilerExtractor/issues/227 Thanks!

Please re-open if still encounter this issue after reviewing the other tickets. Thanks!

Hi @xiaoyaojianghuzai, Your input matrix has 96 rows and 2 columns, but your extraction is from signatures 1 to 25. This does not work and you need a larger input...

Hi @xiaoyaojianghuzai, The maximum_signatures needs to be a value less than the number of samples that you have. I would suggest start with matrix inputs rather than VCFs. You can...

Please generate your matrices separately and provide those as inputs to SigProfilerExtractor. The matrix generation step should not take anywhere near 10 days. How many mutations are you working with?...