Hi all,
I have been running the fine mapping tool FOCUS for my data (https://github.com/bogdanlab/focus). Using the default p value, I have been able to fine map all chromosomes except for chromosome 6. It is getting stuck at region 6:30798168 - 6:31570931. From reading the Wiki, I know that the HLA region is not fine mapped by default, but I cannot think of another reason why the program is getting stuck on chromosome 6. Any troubleshooting advice would be very appreciated as it has been stuck on this chromosome for a few days.
#Focus finemap code
focus finemap sumstats.gz 1000G.EUR.QC.6 focus.db --chr 6 --out sumstats.chr6
Additionally, when using any p value less stringent than the default (i.e. a p<0.001 or p<0.01), chromosome 1 comes out with a .tsv file of zero output and an operational error is cited. I seem to have unlimited memory, CPU time and sqlite3 is the most updated version, so I am not sure how I can remedy this. Is this a common problem (as chromosome 1 is the largest in terms of base pairs to run/fine map)?
Thank you very much in advance!
MacKenzie
