Smartpca memory error

[LucasP78]

I am running smartpca with 81 million mutations, 2504 samples, .snp, .ind, and .eigenstratgeno input files, and fastmode enabled.
I use the following command to run it:

smartpca -p filepath/parameter_file

After 20 hours, smartpca fails and I get the following error message in my log file:

*** Error in `smartpca': free(): invalid size: 0x00002bbd4662b010 ***
======= Backtrace: =========
...
======= Memory map: ========
...
number of samples used: 2504 number of snps used: 81255192

I am not sure what could be causing this error. Any help is appreciated!

[bumblenick]

I don't know the cause of the problem but 1) Use packedancestryformat NOT eigenstrat 2) Very unlikely that you need more than 1M snps -- majorly downsample Nick

…

On Fri, Apr 7, 2023 at 11:46 AM LucasP78 ***@***.***> wrote: I am running smartpca with 81 million mutations, 2504 samples, .snp, .ind, and .eigenstratgeno input files, and fastmode enabled. I use the following command to run it: *smartpca -p filepath/parameter_file* After 20 hours, smartpca fails and I get the following error message in my log file: **** Error in `smartpca': free(): invalid size: 0x00002bbd4662b010 *** ======= Backtrace: ========= ... ======= Memory map: ======== ... number of samples used: 2504 number of snps used: 81255192* I am not sure what could be causing this error. Any help is appreciated! — Reply to this email directly, view it on GitHub <#87>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEE77B6G6BIJL44HXMD2F2DXAAZGFANCNFSM6AAAAAAWWV5UCA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[LucasP78]

Thank you!