PMBio/GNetLMM

partial results are overwritten

Opened this issue · 3 comments

matthiasheinig commented

The tutorial for running the initial scan says: "The partial results from the previous step are stored in assoc0file.startSnp__._.matrix" Actually, this is not the case and all batch processes write to the same file specified with --assoc0file

brakitsch commented

Hi Matthias,

thanks a lot for trying out our software. I am really sorry that you are running into problems (again).

I am not sure if I understand completely why the files are overwritten. While it is true that the filename is specified with --assoc0file, the filenames are startSnp dependent: $ASSOC0FILE.startSnp_$i. I just tried it again on my computer and it generates the files:

lmm.startSnp_0..matrix
lmm.startSnp_10000..matrix
...
lmm.startSnp_*.matrix

which are then merged in the next step. In which file are your results written?

Best,
Barbara

P.S.: we also generalized the phenotype file reader such that any delimiter works.

matthiasheinig commented

Hi Barbara,

the files are all written to assoc0file without adding the suffix. Have you done any updates in the meantime? I am rerunning now and appending the suffix to the assoc0file argument myself..

Best,
Matthias

Am 18.05.2016 um 21:13 schrieb brakitsch notifications@github.com:

Hi Matthias,

thanks a lot for trying out our software. I am really sorry that you are running into problems (again).

I am not sure if I understand completely why the files are overwritten. While it is true that the filename is specified with --assoc0file, the filenames are startSnp dependent: $ASSOC0FILE.startSnp_$i. I just tried it again on my computer and it generates the files:

lmm.startSnp_0..matrix
lmm.startSnp_10000..matrix
...
lmm.startSnp_*.matrix

which are then merged in the next step. In which file are your results written?

Best,
Barbara

P.S.: we also generalized the phenotype file reader such that any delimiter works.

—
You are receiving this because you authored the thread.
Reply to this email directly or view it on GitHub

brakitsch commented

Hi Matthias,

you were right and my description was indeed confusing. I added the suffixes by hand in the example usagel/ demo script and assumed in the tutorial that the user did this as well. I modified the code such that the suffixes are now automatically added in all steps.

Please let me know if you have any further problems.

Best,
Barbara