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timflutre / eqtlbma

Package to detect eQTLs jointly in multiple subgroups (e.g. tissues) via Bayesian Model Averaging.
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003486
GNU General Public License v3.0
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eqtlbma test_basic.bash segmentation fault #5

Closed oursu closed 10 years ago

oursu commented 10 years ago

Hi,

I just cloned eqtlbma from github today, and ran the test_basic.bash I got an error saying segmentation fault (below), and I wanted to check whether you have any advice on how to solve this. I made no modification at all in the test files.

Thank you, Oana

Error below: /home/oursu/devtools/eqtlbma3/eqtlbma/tests/test_basic.bash --p2e /home/oursu/devtools/eqtlbma3/eqtlbma/src/eqtlbma_bf --p2R /home/oursu/devtools/eqtlbma3/eqtlbma/tests/functional_tests.R START test_basic.bash 2014-04-26 22:52:05 cmd-line: /home/oursu/devtools/eqtlbma3/eqtlbma/tests/test_basic.bash --p2e /home/oursu/devtools/eqtlbma3/eqtlbma/src/eqtlbma_bf --p2R /home/oursu/devtools/eqtlbma3/eqtlbma/tests/functional_tests.R temp dir: /home/oursu/tmp_test_16332 simulate data and calculate expected results ... analyze data to get observed results ... /home/oursu/devtools/eqtlbma3/eqtlbma/tests/test_basic.bash: line 108: 16354 Segmentation fault (core dumped) $pathToBf --geno list_genotypes.txt --scoord snp_coords.bed.gz --exp list_phenotypes.txt --gcoord gene_coords.bed.gz --cis 5 --out obs_bf --outss --outw --type join --bfs all --gridL grid_phi2_oma2_general.txt.gz --gridS grid_phi2_oma2_with-configs.txt.gz -v 1 &>stdout_bf compare obs vs exp results ... /usr/bin/zdiff: line 68: obs_bf_sumstats_s1.txt.gz: No such file or directory file 'obs_bf_sumstats_s1.txt.gz' has differences with exp

timflutre commented 10 years ago

Hi, can you follow exactly all the commands below (i.e. a clean re-installation), and tell me if it still gives an error?

cd $HOME mkdir -p tmp cd tmp git clone https://github.com/timflutre/eqtlbma.git cd eqtlbma/ autoreconf --install --force --symlink ./configure --prefix=$HOME/tmp/ make make check

All the tests should pass (I just tested on my computer). Note that, after "make", I didn't launch test_basic.bash itself. Instead I launched "make check". This is related to the usage of libtool (but I won't go into the details).

Once you've done that, you can do "make install", and now you can launch test_basic.bash on its own:

make install ./tests/test_basic.bash --p2e ~/tmp/bin/eqtlbma_bf --p2R ~/tmp/eqtlbma/tests/functional_tests.R

And it should also work (I also just tested on my computer).

If you encounter an error, relaunch "test_basic.bash" with option "--noclean". This will perform the test without deleting the files and temporary directory. Then, look at the file "stdout_bf" in the temporary directory: where does the segmentation fault occur?

oursu commented 10 years ago

Thank you very very much. I was able to successfully run your test_basic.bash script!