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weizhouUMICH / SAIGE

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Error creating sparseGRM using 200k WES #427

Open ajlee21 opened 1 year ago

ajlee21 commented 1 year ago

I am trying to run SAIGE on UKB 200k WES data using just 2 chromosomes (chr 21 and chr 22). I am following the steps provided in the tutorial: https://saigegit.github.io/SAIGE-doc/docs/UK_Biobank_WES_analysis.html

docker run -v <local file path>:/test wzhou88/saige:1.1.9 createSparseGRM.R      \
    --plinkFile=../test/ukb_cal_chr21_22_merged_pruned \
    --nThreads=72  \
    --outputPrefix=${test_saige}       \
    --numRandomMarkerforSparseKin=5000      \
    --relatednessCutoff=0.05

I'm getting the following error message:

Error in .sparse2g(x) : negative length vectors are not allowed
Calls: createSparseGRM ... sum -> sum -> callGeneric -> eval -> eval -> .sparse2g
Execution halted

I'm using cloud instance with 140GB of memory and 72 CPUs, which I selected based on the tutorial since they mentioned they used an instance with 35GB of RAM and 72 CPUs to analyze 450K WES data.

I appreciate any insight and help you can provide. Thank you