BOLT-LMM

The BOLT-LMM algorithm computes statistics for testing association between phenotype and genotypes using a linear mixed model

For further information: https://alkesgroup.broadinstitute.org/BOLT-LMM/BOLT-LMM_manual.html

Running on Comet

The existing binaries of BOLT-LMM (as available at: https://alkesgroup.broadinstitute.org/BOLT-LMM/downloads/) do not run without modification. Specifically they are built against versions of GLIBC that appear not to match current versions.

A custom version of BOLT-LMM has been compiled from the latest source with optimisations for the CPU architecture of Comet. You can load this as follows:

$ module load BOLT-LMM

To run BOLT-LMM, call the bolt binary:

$ module load BOLT-LMM
$ bolt
                      +-----------------------------+
                      |                       ___   |
                      |   BOLT-LMM, v2.5     /_ /   |
                      |   June 21, 2025       /_/   |
                      |   Po-Ru Loh            //   |
                      |                        /    |
                      +-----------------------------+

Copyright (C) 2014-2025 Harvard University.
Distributed under the GNU GPLv3 open source license.

Compiled with USE_SSE: fast aligned memory access
Boost version: 1_85

Command line options:

bolt 

ERROR: Use exactly one of the --bfile, --bfilegz, or --fam,bim,bed input formats
Aborting due to error processing command line arguments
For list of arguments, run with -h (--help) option

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