MERLIN: skipped due to megabytes problem

Question

[349151519]

So sorry to be a bother. I am analyzing a big autosomal dominant pedigree diagnosed with Fahr's disease using the GREAT 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. I tried to add --megabytes option with 600000 but still failed. Would you please be so kind to help me with this problem? Thank you!

Sincerely, Yi-Heng Zeng Fujian Medical University, China

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 --megabytes 600000

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**

[ealopera]

I am having the same issue. it looks like Merlin is not reading the --megabytes command at all

[ealopera]

Coming back to this. Merlin is not suited to work above 32000 megabytes. there's no update that allows this. However what you can do is split the family into smaller bits ( ~20 is the recommended by one of the creators)

[349151519]

Thank you so much for replying. I reduced my pedigree size and it worked. : )

[349151519]

Thank you so much for replying. I reduced my pedigree size and it worked. : )

[S. Roa]

Hi! Excuse me, I'm using Merlin for haplotyping and got the same problem... How did you do that? (reduce the pedigree) I have a complex pedigree with 40 founders and 39 no founders, and 50 snp's Thank you for your answer!