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mlebeur / merlin

MERLIN performs common pedigree analyses. Input files describe relationships between individuals in your dataset, store marker genotypes, disease status and quantitative traits and provide information on marker locations and allele frequencies. MERLIN supports input files in either QTDT or LINKAGE format. Although the two formats are very similar, in the discussion below we will focus on QTDT format.
https://csg.sph.umich.edu/abecasis/Merlin/tour/linkage.html
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Ask for help: Merlin megabytes problem! #1

Open fjmuzengyiheng opened 3 years ago

fjmuzengyiheng commented 3 years ago

Hi, so sorry to be a bother. I am analyzing a big autosomal dominant pedigree using Merlin (parametric linkage analysis). I filtered and extracted markers from chr8 (644 SNPs in total) and prepared input files that Merlin requires. But it crashed with "megabytes" problem and Merlin skipped analyzing!

Here is my command: merlin -d cxj-chr8-7.dat -p cxj-chr8-7.ped -m cxj-chr8-7.map --model cxj-chr8-7.model --grid 1 --markerNames --pdf --tabulate --bits 60

Here is the error log: Estimating allele frequencies... [using all genotypes] ................................................... Done estimating frequencies for 654 markers

Analysis models will be retrieved from file [cxj-chr8-7.model]... Input: VERY_RARE_DISEASE 0.0001 0.0001,1.0000,1.000 Dominant_Model Validated: Loaded model 'Dominant_Model' Table processed. 1 models recognized

Family: 1 - Founders: 13 - Descendants: 32 - Bits: 51 SKIPPED: At least -24139 megabytes needed

Have you ever met this problem? Thank you.

Sincerely, Yi-Heng Zeng Fujian Medical University, China

mlebeur commented 3 years ago

Hi,

Have you look at the part of the README :

CONTROLLING RESOURCE USAGE

You can instruct Merlin not to tackle big pedigrees through the --bits and --megabytes options. In any case, Merlin will try to gracefully skip pedigrees when it runs out of memory. Note that on some 32-bit systems attempting to allocate blocks of > 2048MB will result in a crash. To avoid this problem, set --megabytes:2048 in the command line when analysing large pedigrees.

Best,

Manuel