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popgenmethods / smcpp

SMC++ infers population history from whole-genome sequence data.
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job in sleep state while running smc++ cv #143

Closed conniecl closed 4 years ago

conniecl commented 4 years ago

Hi, @terhorst When I use smc++ cv to estimate the Ne of one population with 10,20,30,40,50,60,70,80 samples (vcf file without imputation), something weird happened. About six month ago, I run the smc++ cv with the input contain 20 samples, it works well. I get the final best model json file. But while rerun the same input, I cannot get the result, the command seems under a sleep state for abut 3 days. And what I get only a json file under fold0 dictionary.

Here is my standard error file:

19827 smcpp.analysis.base INFO theta: 0.000100
19829 smcpp.analysis.base INFO rho: 0.000100
19829 smcpp.data_filter INFO Loading data...
26113 smcpp.data_filter INFO 1.19 Gb of data
26117 smcpp.data_filter INFO 1 population
26220 smcpp.estimation_tools WARNING Long runs of homozygosity in contig 20_ind/1.smc.gz:
[ 67432  53355  71764  66114  54269  54398  58942  61469  54202  65939  54763  51873  57650  60263 156023  51673  50378
  60363 164687  50523  66151  65852  73276  50764  52480  51833  50153  66970  57173  50298  72701  52083  61650  81081
 106522  99719  50082 116758 157475  54932  55557  50335  73703 127284  56305  61937  54455  80320  82157  65200  76341
  99124  87717  59616  75754 170744  60870  50692  51790  54257  59690  53605  63749 113241  56031 300723 204149 130416
  57472  89404  72180  76611  57467  51172 119662  58441  75297  53105 130170  82804  67787 215631  89584] (base pairs)
26299 smcpp.estimation_tools WARNING Long runs of homozygosity in contig 20_ind/3.smc.gz:
[ 68651  56188  61871  56721  89119  57007  52843  66315  51933  52636  56011  64023  50878  81558  80994  53730  50165
  62439  70377  75990  75756 350472  83533  59880  61965  51619  50097  53096  55370  50985  51589  72312  61268  53120
 163967  51877  60231  52524  54998 105031 103277 121146 146411 197788  80632  82967  50709  51161  51390  50130  51723
  58069  60289  97850  77898  60196  58295  61223  54252] (base pairs)
26381 smcpp.estimation_tools WARNING Long runs of homozygosity in contig 20_ind/2.smc.gz:
[114326  56153 206779  60865  65676  81282 111735  53244  51075  59405  56869  55417  54576 127718  51608  59036  61087
  61757  83781  51714  52379  58299  72952  63323 170621  79069 388218  98393  52829  53060  53146  51148  70284  53253
  52770  52292  89563 102573  54115  93754  62181  75276 100864  68372  60408  52247 108773  57077  98316  52272  69756
  83181  61970  84991  56734  55596  50161  51626  61665  56099  56671  58401  72840  56437  52512 104230  82582  62434
  57288 424934 138148  97779 169947  56241  50820 104458] (base pairs)
26464 smcpp.estimation_tools WARNING Long runs of homozygosity in contig 20_ind/4.smc.gz:
[ 54603 528645  65407 187049  74246  70048  92184  59490  88586  52616  77185  52416  50508  78567  51060  50150  97826
  67074  92237 100881 134746  90625  55946  50923 302382  61911  79699 131162 106083  61681  56974  68674  54242  91906
  68845  51607 100043 134913 201565  54775  71422  57675  62155 131622  54166  80431 107182  63575  57654  50767  56388
 107498  50619 487859  55470  65913  53114 135161] (base pairs)
26507 smcpp.estimation_tools WARNING Long runs of homozygosity in contig 20_ind/10.smc.gz:
[ 56389  82586  99336  56978  72434  92998  51308  51175  80441  53305  58596  57675 103440 105989  77971  67385  58493
  85556  50122  53036  52447  53653 113160 188166  76825  76810  64648  55853  54229  78973 164585  91096  58328  66401
  54087  51952  55311  70633  64757  51493  64550  55165  58932  72948  63072  52782  53291  59071  58681  52261  50021
  60193] (base pairs)
71143 smcpp.optimize.plugins.progress_printer INFO Starting EM algorithm...
71143 smcpp.optimize.plugins.progress_printer INFO EM iteration 1 of 1...
71143 smcpp.analysis.base INFO Running E-step
144260 smcpp.analysis.base INFO E-step completed
144314 smcpp.optimize.plugins.loglikelihood_monitor INFO Loglik: -139260495.288210
176555 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model:

  100000 ++----------------+---------+------+-----+----+---+--+--+--+----++
         +                                                  Pop. 1 ****** +
         +                                                                +
         +                                                                +
         B********************************                                +
         +                               *                                +
         |                               *                                |
   10000 ++                              B*****************              +B
         +                                                *               +
         +                                                B****************
         +                                                                +
         +                                                                +
         +                                                                +
         +                                                          +     |
    1000 ++----------------+---------+------+-----+----+---+--+--+--+----++
       10000                                                      100000
                                    Generations

176564 smcpp.optimize.plugins.progress_printer INFO Current model:

 2.80  1.90  1.29  1.84
16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45 16.45  6.68  6.68  6.68  6.68  6.68  6.68  6.68  6.68  6.68  6.68  6.68  6.68  6.68  6.68  6.68  6.68  6.68  6.68  6.68  6.68  6.68  6.68  6.68  6.68  6.68  6.68  3.64  3.64  3.64  3.64  3.64  3.64  3.64  3.64  3.64  3.64  3.64  3.64  3.64  3.64  3.64  3.64  3.64  3.64  3.64  3.64  3.64  3.64  3.64  3.64  3.64
176565 smcpp.data_filter INFO Loading data...

and my standard output file:

RUNNING THE L-BFGS-B CODE

           * * *

Machine precision = 2.220D-16
 N =            4     M =           10

At X0         0 variables are exactly at the bounds

At iterate    0    f=  1.37795D+08    |proj g|=  3.00000D+00

At iterate    1    f=  1.35327D+08    |proj g|=  3.67045D+00

At iterate    2    f=  1.35276D+08    |proj g|=  3.62739D+00

At iterate    3    f=  1.35106D+08    |proj g|=  4.05508D+00

At iterate    4    f=  1.35079D+08    |proj g|=  3.94967D+00

At iterate    5    f=  1.35076D+08    |proj g|=  3.95700D+00

At iterate    6    f=  1.35076D+08    |proj g|=  3.96068D+00

At iterate    7    f=  1.35076D+08    |proj g|=  3.96062D+00

At iterate    8    f=  1.35076D+08    |proj g|=  3.07415D+00

At iterate    9    f=  1.35076D+08    |proj g|=  3.07435D+00

At iterate   10    f=  1.35076D+08    |proj g|=  3.07232D+00

At iterate   11    f=  1.35076D+08    |proj g|=  3.07514D+00

At iterate   12    f=  1.35075D+08    |proj g|=  3.21603D+00

At iterate   13    f=  1.35075D+08    |proj g|=  3.47342D+00

At iterate   14    f=  1.35075D+08    |proj g|=  3.61939D+00

At iterate   15    f=  1.35075D+08    |proj g|=  3.61571D+00

At iterate   16    f=  1.35075D+08    |proj g|=  3.96006D+00

At iterate   17    f=  1.35075D+08    |proj g|=  3.95981D+00

At iterate   18    f=  1.35075D+08    |proj g|=  3.95983D+00

           * * *

Tit   = total number of iterations
Tnf   = total number of function evaluations
Tnint = total number of segments explored during Cauchy searches
Skip  = number of BFGS updates skipped
Nact  = number of active bounds at final generalized Cauchy point
Projg = norm of the final projected gradient
F     = final function value

           * * *

   N    Tit     Tnf  Tnint  Skip  Nact     Projg        F
    4     18     20     21     0     0   3.960D+00   1.351D+08
  F =   135075265.97224012

CONVERGENCE: REL_REDUCTION_OF_F_<=_FACTR*EPSMCH

 Cauchy                time 0.000E+00 seconds.
 Subspace minimization time 0.000E+00 seconds.
 Line search           time 0.000E+00 seconds.

 Total User time 0.000E+00 seconds.

and here is my job state: 图片

Sincerely hope can get your advise, and thanks in advance.

terhorst commented 4 years ago

Can you interrupt the program via Ctrl-C to get a stack trace?

terhorst commented 4 years ago

Closing for lack of activity.