Hi! I downloaded the standalone source code, database, and LD files. The source code seems to be installed correctly since the --help flag works. When I start running a plotting command, the software stalls on the "Extracting region of interest" part. I have python 2.7, R, and plink installed in a conda environment. It doesn't seem like an LD cache is being generated. My file has a pval_nominal and rsID column. I have tried with only a 10 variants and 5000 variants with no change. I also tried decreasing the plotting region with no changes. Has anyone encountered this issue? I feel like it is an installation or LD problem.
Here is my command:
../src/locuszoom/bin/locuszoom --metal file.txt --pvalcol pval_nominal --markercol rsID --refsnp rs2509967 --flank 500kb --plotonly --pop EUR --build hg38 --source 1000G_Nov2014 drawMarkerNames=TRUE showGenes=TRUE showPartialGenes=TRUE showRecomb=FALSE theme=publication geneFontSize=1 width=10 height=7 legend='auto' --prefix test