Question: merlin output error
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gravatar for User6891
3.6 years ago by
User6891250
Europe
User6891250 wrote:

Hi all,

I’m running Merlin on human SNParray data using the following command:

/home/tools/merlin/merlin-1.1.2/merlin -d familystructureexp1.dat,exp1.dat -p familystructureexp1.ped,exp1.ped -m exp1.map --pairs --npl /home/tools/linkage_iscan/20160418_output_merlin/npl_exp1.txt

the tool is running until a certain point on chromosome 8

Analysing Chromosome 8 Family: 1 - Founders: 6 - Descendants: 10 - Bits: 13 Skipping Marker rs12678174 [BAD INHERITANCE] Skipping Marker rs10503424 [BAD INHERITANCE] Skipping Marker rs11783712 [BAD INHERITANCE] Skipping Marker rs7000539 [BAD INHERITANCE] Skipping Marker rs1907549 [BAD INHERITANCE] Skipping Marker rs279955 [BAD INHERITANCE] Skipping Marker rs2447175 [BAD INHERITANCE] Skipping Marker rs6996149 [BAD INHERITANCE] Skipping Marker rs3829210 [BAD INHERITANCE] merlin: ./libsrc/MathVector.h:73: double& Vector::operator: Assertion `n < dim' failed. MERLIN HAS CRASHED The operating system has decided to terminate Merlin, probably due to a memory access problem. If you set a memory usage limit (--megabytes:9999), Merlin may be able to recover gracefully from out of memory errors. You can reduce Merlin's memory requirements with the --swap option, which uses some of your free disk space as memory. The --smallSwap option uses even less memory and disk space. Alternatively, you could try a --singlepoint analysis, or use one of the options --zero, --one, --two, --three, to find an approximate solution if you are analysing a dense map.

I’ve tried the —megabytes:9999, —swap & —smallSwap option, but I always get the same error.

Did someone encounter the same problem?

merlin • 1.3k views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by User6891250
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