running msmc without final result

[rxw125]

hi,Stephan, i just started to use msmc . installed the software v1.1.0, found and downloaded the test data from msmc2. but i have been troubled with some problems with simple command at the begining. My questions are as follows:

(1) without final result

cmd：

~/msmc-master/build/msmc -R -o EUR_AFR_msmc_output EUR_AFR.chr1.multihetsep.txt

log：
read 589382 SNPs from file EUR_AFR.chr1.multihetsep.txt
estimating scaled mutation rate: 0.000451928
Version: 1.1.0
input files: ["EUR_AFR.chr1.multihetsep.txt"]
maxIterations: 20
mutationRate: 0.000451928
recombinationRate: 0.000112982
subpopLabels: [0, 0, 0, 0, 0, 0, 0, 0]
timeSegmentPattern: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2]
nrThreads: 80
nrTtotSegments: 40
verbose: false
outFilePrefix: EUR_AFR_msmc_output
naiveImplementation: false
hmmStrideWidth: 1000
fixedPopSize: false
fixedRecombination: true
unboundedCrossCoal: false
initialLambdaVec: []
loBoundLambda: 0
hiBoundLambda: inf
directedEmissions: false
skipAmbiguous: false
indices: [0, 1, 2, 3, 4, 5, 6, 7]
logging information written to EUR_AFR_msmc_output.log
loop information written to EUR_AFR_msmc_output.loop.txt
final results written to EUR_AFR_msmc_output.final.txt
[1/1] estimating total branchlengths

but there is no EUR_AFR_msmc_output.final.txt file and the EUR_AFR_msmc_output.loop.txt is blank

I test my own data and come across the same problem

（2） OutOfMemoryError

i found the defaults of nrTreads was too large and there is one chr（maybe small numbers of SNPs lead to the previous problem）,I executed the command as follows :

~/msmc-master/build/msmc -p 10*1 -o EUR_AFR_msmc_output EUR_AFR.chr1.multihetsep.txt -t 2 

log:
read 589382 SNPs from file EUR_AFR.chr1.multihetsep.txt
estimating scaled mutation rate: 0.000451928
Version: 1.1.0
input files: ["EUR_AFR.chr1.multihetsep.txt"]
maxIterations: 20
mutationRate: 0.000451928
recombinationRate: 0.000112982
subpopLabels: [0, 0, 0, 0, 0, 0, 0, 0]
timeSegmentPattern: [9220752, 0, 169013428, 1, 140234331517568, 0, 0, 0, 9220752, 0]
nrThreads: 2
nrTtotSegments: 140234518972501
verbose: false
outFilePrefix: EUR_AFR_msmc_output
naiveImplementation: false
hmmStrideWidth: 1000
fixedPopSize: false
fixedRecombination: false
unboundedCrossCoal: false
initialLambdaVec: []
loBoundLambda: 0
hiBoundLambda: 10
directedEmissions: false
skipAmbiguous: false
indices: [0, 1, 2, 3, 4, 5, 6, 7]
logging information written to EUR_AFR_msmc_output.log
loop information written to EUR_AFR_msmc_output.loop.txt
final results written to EUR_AFR_msmc_output.final.txt
core.exception.OutOfMemoryError@src/core/exception.d(700): Memory allocation failed

I also changed my parameters several times, but all return the same erro OutOfMemoryError. Could you give me some suggestions?

Thank you in advance.

[stschiff]

Running on 8 haplotypes with Cross-Coalescence rate is like the heaviest you can run with MSMC. MSMC2 is a bit better in that respect. Try running on four haplotypes first, so e.g. by adding -I 0,1,4,5.