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stschiff / msmc

Implementation of the multiple sequential markovian coalescent
GNU General Public License v3.0
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error running msmc #36

Closed JPingAMMS closed 5 years ago

JPingAMMS commented 6 years ago

running 8 haplotypes for estimating Ne. And what I get is,

read 260864 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr10.txt
read 255964 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr11.txt
read 244425 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr12.txt
read 197484 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr13.txt
read 171440 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr14.txt
read 149298 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr15.txt
read 155058 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr16.txt
read 129607 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr17.txt
read 150660 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr18.txt
read 101668 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr19.txt
read 435286 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr2.txt
read 116107 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr20.txt
read 73866 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr21.txt
read 66201 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr22.txt
read 372724 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr3.txt
read 374496 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr4.txt
read 334388 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr5.txt
read 320806 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr6.txt
read 294493 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr7.txt
read 288326 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr8.txt
read 220013 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr9.txt
estimating scaled mutation rate: 0.000342567
error in parsing command line: object.Exception@model/triple_index_marginal.d(72): 5 140079892583040
----------------
??:? pure @safe void std.exception.bailOut!(Exception).bailOut(immutable(char)[], ulong, const(char[])) [0x57c550]
??:? pure @safe bool std.exception.enforce!(Exception, bool).enforce(bool, lazy const(char)[], immutable(char)[], ulong) [0x63a641]
??:? ulong model.triple_index_marginal.MarginalTripleIndex.computeNrSubpops(const(ulong[])) [0x5d03d9]
??:? void msmc.parseCommandLine(immutable(char)[][]) [0x5e47dc]
??:? _Dmain [0x5e3f67]
??:? _D2rt6dmain211_d_run_mainUiPPaPUAAaZiZ6runAllMFZ9__lambda1MFZv [0x630383]
??:? void rt.dmain2._d_run_main(int, char**, extern (C) int function(char[][])*).tryExec(scope void delegate()) [0x6302ab]
??:? void rt.dmain2._d_run_main(int, char**, extern (C) int function(char[][])*).runAll() [0x630328]
??:? void rt.dmain2._d_run_main(int, char**, extern (C) int function(char[][])*).tryExec(scope void delegate()) [0x6302ab]
??:? _d_run_main [0x630217]
??:? main [0x5f39d7]
??:? __libc_start_main [0xe44e3fa4]

The cmd line was,

msmc -R -o 02.MSMC.Ne.pl.out/03.Out/HAN.ne.8haps \
  -i 50 -t 10 -p '1*2+15*1+1*2' \
  02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr1.txt \
  02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr10.txt \
  02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr11.txt \
  02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr12.txt \
  02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr13.txt \
  02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr14.txt \
  02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr15.txt \
  02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr16.txt \
  02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr17.txt \
  02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr18.txt \
  02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr19.txt \
  02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr2.txt \
  02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr20.txt \
  02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr21.txt \
  02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr22.txt \
  02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr3.txt \
  02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr4.txt \
  02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr5.txt \
  02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr6.txt \
  02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr7.txt \
  02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr8.txt \
  02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr9.txt

Thanks in advance.

stschiff commented 6 years ago

Hmm. Looks like overfitting. I have now built in an option to artificially constrain the coalescence rates, see release 1.1.0, with options --loBoundLambda and --hiBoundLambda. Lambda is the scaled coalescence rate, with typical values around 1000 or so (it's on average around 2/theta, where theta is the heterozygosity), so you could try setting a lower bound of 10, and an upper bound of 1e6 or so. Please try that and if it doesn't resolve the issue, please email me the input data, so I can have a look.

stschiff commented 6 years ago

Please try MSMC2 (www.github.com/stschiff/msmc2 http://www.github.com/stschiff/msmc2) for now, it’s the better tool anyway, and I’m trying to find out what causes these weird errors in MSMC in the mean time.

Best, Stephan

On 2 Jul 2018, at 14:26, Jie Ping notifications@github.com wrote:

running 8 haplotypes for estimating Ne. And what I get is,

read 260864 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr10.txt read 255964 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr11.txt read 244425 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr12.txt read 197484 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr13.txt read 171440 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr14.txt read 149298 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr15.txt read 155058 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr16.txt read 129607 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr17.txt read 150660 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr18.txt read 101668 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr19.txt read 435286 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr2.txt read 116107 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr20.txt read 73866 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr21.txt read 66201 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr22.txt read 372724 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr3.txt read 374496 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr4.txt read 334388 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr5.txt read 320806 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr6.txt read 294493 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr7.txt read 288326 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr8.txt read 220013 SNPs from file 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr9.txt estimating scaled mutation rate: 0.000342567 error in parsing command line: object.Exception@model/triple_index_marginal.d(72): 5 140079892583040

??:? pure @safe void std.exception.bailOut!(Exception).bailOut(immutable(char)[], ulong, const(char[])) [0x57c550] ??:? pure @safe bool std.exception.enforce!(Exception, bool).enforce(bool, lazy const(char)[], immutable(char)[], ulong) [0x63a641] ??:? ulong model.triple_index_marginal.MarginalTripleIndex.computeNrSubpops(const(ulong[])) [0x5d03d9] ??:? void msmc.parseCommandLine(immutable(char)[][]) [0x5e47dc] ??:? _Dmain [0x5e3f67] ??:? _D2rt6dmain211_d_run_mainUiPPaPUAAaZiZ6runAllMFZ9lambda1MFZv [0x630383] ??:? void rt.dmain2._d_run_main(int, char, extern (C) int function(char[][])*).tryExec(scope void delegate()) [0x6302ab] ??:? void rt.dmain2._d_run_main(int, char*, extern (C) int function(char[][])).runAll() [0x630328] ??:? void rt.dmain2._d_run_main(int, char, extern (C) int function(char[][])*).tryExec(scope void delegate()) [0x6302ab] ??:? _d_run_main [0x630217] ??:? main [0x5f39d7] ??:? libc_start_main [0xe44e3fa4] The cmd line was,

msmc -R -o 02.MSMC.Ne.pl.out/03.Out/HAN.ne.8haps \ -i 50 -t 10 -p '12+151+1*2' \ 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr1.txt \ 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr10.txt \ 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr11.txt \ 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr12.txt \ 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr13.txt \ 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr14.txt \ 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr15.txt \ 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr16.txt \ 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr17.txt \ 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr18.txt \ 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr19.txt \ 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr2.txt \ 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr20.txt \ 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr21.txt \ 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr22.txt \ 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr3.txt \ 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr4.txt \ 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr5.txt \ 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr6.txt \ 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr7.txt \ 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr8.txt \ 02.MSMC.Ne.pl.out/02.Combine/HAN/HAN.chr9.txt Thanks in advance.

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