Open ruthchia opened 7 years ago
I am sorry that I completely missed this thread. But in principle, genome-wide data should be run together. Separate running on each genome segment would defy the purpose of information pooling.
But this shows we need to define an upper bound of penalty, instead of allowing inf. Will change the code.
Hi William,
I've also been running in to this issue, with the most recent code. Do you know of any workarounds?
Can you be a little more specific about the problem? i.e. Does it always occur or just happens by chance? It would be also helpful to check the intermediate output files. Specifically, check
pheno.enrich.out
, where pheno is your phenotype namegwas_signals
is emptyqtl_pip
These will help us to determine the stage where the problem occured.
Thanks!
Hi William,
I encountered this issue even when running the examples
. To be specific, I prepared the workspace/
folder as suggested, and ran the command ./bin/enloc HDL_blood.enloc.params
Below are the outputs (the last line indicates the error).
Start enrichment analysis
Impute eQTL data ...
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Perform enrichment analysis by multiple imputation ...
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Read in 1700 loci, 6127680 locus-SNP pairs ...
Loading annotations ...
Read in 1700 loci, 6127680 locus-SNP pairs ...
Loading annotations ...
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Read in 1700 loci, 6127680 locus-SNP pairs ...
Loading annotations ...
Killed
Initializing ...
Starting EM ...
Applying adaptive L2 penalty = 0.628
Iter loglik Intercept annot.1
1 -1691.244 -8.537 0.385
2 1754.912 -9.208 0.807
3 1999.852 -9.601 1.262
4 2055.000 -9.845 1.750
5 2072.175 -10.000 2.261
6 2079.071 -10.100 2.760
7 2082.963 -10.168 3.213
8 2085.898 -10.215 3.597
9 2088.341 -10.250 3.911
10 2090.343 -10.277 4.161
11 2091.915 -10.298 4.357
12 2093.103 -10.315 4.509
13 2093.978 -10.329 4.627
14 2094.611 -10.340 4.718
15 2095.066 -10.349 4.788
16 2095.392 -10.356 4.842
17 2095.628 -10.361 4.884
18 2095.798 -10.366 4.915
19 2095.923 -10.369 4.940
20 2096.014 -10.372 4.959
Illegal division by zero at ./bin/enloc line 470, <FILE> line 1.
I failed to find HDL.enrich.out
, gwas_signals
, qtl_pip
in the workspace/
folder, but I have checked less HDL_blood/mi_est/*.est
, all of which are empty except one file ./HDL_blood/mi_est/HDL.mi.12.est
, which has the following content.
Intercept -10.372 -10.395 -10.348
annot.1 4.959 3.392 6.525
Where should the error be? Thank you very much William. Jiarun
Hi William,
I have run your Enloc on schizophrenia GWAS data with the example gtex_whole_blood.v6.tgz
. Please find the workspace folder in my Google Drive. I simply ran ./bin/enloc SCZ_blood.enloc.params
under the workspace folder as you had suggested. And the output was as follows. (The last line indicates the error)
Start enrichment analysis
Impute eQTL data ...
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Perform enrichment analysis by multiple imputation ...
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Read in 1702 loci, 8286510 locus-SNP pairs ...
Loading annotations ...
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Read in 1702 loci, 8286510 locus-SNP pairs ...
Loading annotations ...
Read in 1702 loci, 8286510 locus-SNP pairs ...
Loading annotations ...
Killed
Initializing ...
Starting EM ...
Applying adaptive L2 penalty = 0.788
Iter loglik Intercept annot.1
1 -2974.383 -8.638 0.264
2 1659.174 -9.005 0.473
3 1758.203 -9.126 0.641
4 1767.504 -9.169 0.785
5 1768.721 -9.185 0.914
6 1768.986 -9.191 1.034
7 1769.133 -9.193 1.150
8 1769.271 -9.194 1.264
9 1769.418 -9.195 1.377
10 1769.577 -9.195 1.491
11 1769.753 -9.196 1.607
12 1769.947 -9.196 1.725
13 1770.162 -9.197 1.845
14 1770.398 -9.197 1.967
15 1770.657 -9.198 2.089
16 1770.937 -9.199 2.210
17 1771.236 -9.199 2.330
18 1771.549 -9.200 2.446
19 1771.870 -9.201 2.557
20 1772.193 -9.202 2.662
21 1772.509 -9.203 2.759
22 1772.812 -9.204 2.849
23 1773.097 -9.205 2.931
24 1773.359 -9.207 3.004
25 1773.596 -9.208 3.069
26 1773.806 -9.208 3.127
27 1773.991 -9.209 3.177
28 1774.152 -9.210 3.221
29 1774.290 -9.211 3.259
30 1774.408 -9.211 3.291
31 1774.508 -9.212 3.319
Illegal division by zero at ./bin/enloc line 470, <FILE> line 1.
Could you reproduce the error? And where should the error be and how might I solve the problem? Thank you very much William. Jiarun
I am not completely certain on the issue. But it seems that you are running enloc in an environment that restricts the usage of multiple CPUs/threads. I suggest you change the use_openmp
option in the parameter file to 0 and re-run your analysis.
Let me know if it solves the problem.
William
Hi William, I ran enloc on my dataset and had an error message " Illegal division by zero..." Snapshot or error message in below:
I know that enloc is installed correctly because of the several datasets that I have, a few was completed and a few failed. Can you please help me figure out the root for this error?
Briefly, I've subsetted by GWAS data according to chr, and the subset only contains 500 SNPs flanking my top SNP in the loci of interest. Would this be a problem for enloc?
Thanks Ruth