In github issue 210 this comes up. @hrwang was kind enough to send me a dataset that brings up this error. Now we stand a chance of doing something about it! As in
napoli:~/iwrk/opensource/code/genetics/gemma/tmp/issue210$ ../../bin/gemma -bfile 20 -k BS_kinship.sXX.txt -lmm 1 -c Covariate_PC3.txt -n 1 -o outname GEMMA 0.99.0-pre1 (2021-08-11) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 Reading Files ... ## number of total individuals = 727 ## number of analyzed individuals = 57 ## number of covariates = 4 ## number of phenotypes = 1 ## number of total SNPs/var = 215451 ## number of analyzed SNPs = 72731 Start Eigen-Decomposition... pve estimate =0.956403 se(pve) =0.255427 GSL ERROR: function value is not finite in newton.c at line 88 errno 9
Next I ran with the debug switch and it stops with the slightly more informative
../../bin/gemma -bfile 20 -k BS_kinship.sXX.txt -lmm 1 -c Covariate_PC3.txt -n 1 -o outname -debug GEMMA 0.99.0-pre1 (2021-08-11) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL random generator type: mt19937; seed = 25479 (option -1); first value = 191757793 Reading Files ... ## number of total individuals = 727 ## number of analyzed individuals = 57 ## number of covariates = 4 ## number of phenotypes = 1 ## number of total SNPs/var = 215451 ## number of analyzed SNPs = 72731 Start Eigen-Decomposition... pve estimate =0.956403 se(pve) =0.255427 ERROR: Enforce failed for Trying to take the log of 0.000000 in src/mathfunc.cpp at line 118 in safe_log
Next step is rebuilding gemma with debug info `make debug` and rerun in the debugger. A backtrace of
gdb --args ../../bin/gemma -bfile 20 -k BS_kinship.sXX.txt -lmm 1 -c Covariate_PC3.txt -n 1 -o outname -debug
shows
#2 0x000000000047dcb0 in safe_log (d=d@entry=0) at src/mathfunc.cpp:118
#3 0x00000000004707ea in LogRL_f (l=l@entry=1.0000000000000001e-05, params=params@entry=0x7fffffffcc20)
at src/lmm.cpp:851
#4 0x0000000000471b05 in CalcLambda (func_name=func_name@entry=82 'R', params=...,
l_min=l_min@entry=1.0000000000000001e-05, l_max=100000, n_region=10,
lambda=@0x7fffffffccc8: 3.2054654756518093, logf=@0x7fffffffcca0: 0.83040722111380116)
at src/lmm.cpp:1970
#5 0x0000000000475cac in LMM::AnalyzePlink (this=this@entry=0x7fffffffd1a0, U=U@entry=0x4fcc80,
eval=eval@entry=0x52dff0, UtW=UtW@entry=0x4fccc0, Uty=Uty@entry=0x7fffffffd140, W=W@entry=0x4fe140,
y=<optimized out>, gwasnps=...) at src/lmm.cpp:1860
#6 0x00000000004359f5 in GEMMA::BatchRun (this=this@entry=0x7fffffffe720, cPar=...)
at src/gemma.cpp:2798
#7 0x000000000047bed0 in main (argc=14, argv=0x7fffffffe888) at src/main.cpp:86
In this case a SNP for some reason balks. Another run, after disabling the log check renders
#0 0x00007ffff5e1deca in raise ()
from /gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/lib/libpthread.so.0
#1 0x00000000004245ba in gemma_gsl_error_handler (reason=<optimized out>, file=<optimized out>,
line=88, gsl_errno=<optimized out>) at src/gemma.cpp:75
#2 0x00007ffff7e59f6d in newton_iterate ()
from /gnu/store/qsr7pw4cbka4qhxm3h0bkwwl7h08qfmw-profile/lib/libgsl.so.25
#3 0x0000000000471cba in CalcLambda (func_name=func_name@entry=82 'R', params=...,
l_min=l_min@entry=1.0000000000000001e-05, l_max=100000, n_region=<optimized out>,
lambda=@0x7fffffffccc8: 1.0000000000000001e-05, logf=@0x7fffffffcca0: 507.88508012472289)
at src/lmm.cpp:2040
points out that in line 2040 `gsl_root_fdfsolver_iterate` is not happy executing a Newton root solver. What is interesting is that, in this case, the gemma_gsl_error_handler is called and stops processing. We now have three ways to stop GEMMA from the same error!
The original version bails out inside GSL:
GSL ERROR: function value is not finite in newton.c at line 88 errno 9 #0 0x00007ffff5e1deca in raise () from /gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/lib/libpthread.so.0 #1 0x00007ffff7e59f6d in newton_iterate () from /gnu/store/qsr7pw4cbka4qhxm3h0bkwwl7h08qfmw-profile/lib/libgsl.so.25 #2 0x000000000047a9c5 in CalcLambda(char, FUNC_PARAM&, double, double, unsigned long, double&, double&) [clone .constprop.671] ()
@hrwang had a good suggestion to make sure that the output for the SNP is made invalid and to continue processing. Disabling the error handler let GEMMA continue. I added a check for the status flag to make sure output was set to invalid (nan). In the test set 178 out of 72732 SNPs failed.