"? No covariance is fitted to this data" issue

[phillevn]

Hi,
I am running fGWAS for a longitudinal study and I have an issue that I don't know what happened. The number of sample is around 10,000 and the there are 4 observation time points. I got the following error.

obj.phe_EA <- fg.load.phenotype( file.phe.long_EA, file.phe.cov_EA, file.phe.time_EA, file.plot.pdf="/ddn/home2/r2725/projects/jeannette/data/curve.fitting_EA.pdf")
No curve or new curve type is specified, curve fitting is being performed.
Searching curve type ......

• [ 1 / 10 ] try curve: Logistic
• [ 2 / 10 ] try curve: Bi-Logistic
• [ 3 / 10 ] try curve: ABRK
• [ 4 / 10 ] try curve: Pharmacology
• [ 5 / 10 ] try curve: Exponential
• [ 6 / 10 ] try curve: Bi-Exponential
• [ 7 / 10 ] try curve: Power
• [ 8 / 10 ] try curve: Legendre2
• [ 9 / 10 ] try curve: Legendre3
• [ 10 / 10 ] try curve: Legendre4
  Curve Fitting Summary:
  type parm AIC AICc BIC SSE MSE RMSE R2
  1 Logistic 3 8799.088 5.400554 8815.891 162339.75 22.38243 4.731007 -0.1617916
  2 Bi-Logistic 6 8794.128 5.398092 8827.733 161452.51 22.26010 4.718061 -0.1554420
  3 ABRK 4 7405.987 4.704008 7428.391 80813.23 11.14204 3.337970 0.4216566
  4 Pharmacology 3 8799.688 5.400854 8816.491 162388.43 22.38914 4.731716 -0.1621400
  5 Exponential 2 8797.698 5.399855 8808.900 162389.27 22.38926 4.731729 -0.1621460
  6 Bi-Exponential 4 8800.852 5.401441 8823.256 162320.58 22.37978 4.730728 -0.1616544
  7 Power 2 8797.565 5.399788 8808.767 162378.44 22.38776 4.731571 -0.1620685
  8 Legendre2 3 8799.634 5.400827 8816.437 162384.06 22.38854 4.731653 -0.1621087
  9 Legendre3 4 8801.350 5.401690 8823.753 162360.95 22.38535 4.731316 -0.1619433
  10 Legendre4 5 8802.187 5.402114 8830.191 162266.58 22.37234 4.729941 -0.1612679
  Curve Type==> ABRK <==
  Parameter range estimation ......
  Searching covariance matrix .......
  *[ 1 / 13 ]: try covariance matrix: AR1
  *[ 1 / 13 ]: try covariance matrix: SAD1
  *[ 1 / 13 ]: try covariance matrix: ARMA(1,1)
  *[ 1 / 13 ]: try covariance matrix: ARH1
  *[ 1 / 13 ]: try covariance matrix: CS
  *[ 1 / 13 ]: try covariance matrix: CSH
  *[ 1 / 13 ]: try covariance matrix: VS
  *[ 1 / 13 ]: try covariance matrix: SI
  *[ 1 / 13 ]: try covariance matrix: FA1
  *[ 1 / 13 ]: try covariance matrix: FAH1
  *[ 1 / 13 ]: try covariance matrix: TOEP
  *[ 1 / 13 ]: try covariance matrix: TOEPH
  *[ 1 / 13 ]: try covariance matrix: HF
  Error in fg_dat_est(ret, curve.type, covariance.type, file.plot.pdf, options) :
  ? No covariance is fitted to this data.
  Calls: fg.load.phenotype -> fg_load_phenotype -> fg_dat_est
  In addition: There were 42 warnings (use warnings() to see them)
  Execution halted

I am wondering if you can help me to find a way to solve that issue? Thank you very much.

[xiahui625649]

Your file.phe.cov_EA may not be defined.

[phillevn]

Thanks for looking at the error. The problem is very strange. If I choose to get "Power" function for the curve. I can get it run fine. That means it is not about missing data file. Also, if I reduce the number of covariances, it has the same error even it ran fine for the full set. What are the possible causes of the issues if you can tell?