Question: SNPTEST in mac
0
gravatar for ccolmenares
2.5 years ago by
ccolmenares0 wrote:

Hi everyone. I've received impute2 files in gz format and I want to running in SNPTEST

I use the next command

./snptest -data /Users/claudiacolmenares/Desktop/PA_gwas_chr_4_python_filtered.impute2.gz.gen /Users/claudiacolmenares/Desktop/PA_gwas_chr_4_python_filtered.impute2.gz.sample  -summary_stats_only -o /example/ex.out

And this is the error message

Welcome to SNPTEST v2.5.2 (revision 675f81d8832d51b2d556fd962912b2ca96cfa6c6)
© University of Oxford 2008-2015
https://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html
Read LICENCE file for conditions of use.

==============

Data Files : 
 -gen files : /Users/claudiacolmenares/Desktop/PA_gwas_chr_4_python_filtered.impute2.gz.gen 
 -sample files : /Users/claudiacolmenares/Desktop/PA_gwas_chr_4_python_filtered.impute2.gz.sample 

Tests : 
 (no tests specified)
 -method none

reading sample exclusion lists

Inspecting data (this may take some time)...
!! Error detected in source "/Users/claudiacolmenares/Desktop/PA_gwas_chr_4_python_filtered.impute2.gz.sample".
!! Quitting.
libc++abi.dylib: terminating with uncaught exception of type genfile::ResourceNotOpenedError: genfile::ResourceNotOpenedError
Abort trap: 6

I also tried this command

./snptest -data /Users/claudiacolmenares/Desktop/PA_gwas_chr_4_python_filtered.impute2.gz.gen -summary_stats_only -o /example/ex.out

But I have this error message

ERROR: -data must be supplied an even number of values.

Any suggestions to solve this??? Thanks!!

snp • 978 views
ADD COMMENTlink modified 2.5 years ago by RamRS30k • written 2.5 years ago by ccolmenares0

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time. Formatting bar

ADD REPLYlink written 2.5 years ago by RamRS30k

thanks!! I will do it the next time!

ADD REPLYlink written 2.5 years ago by ccolmenares0
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