Bug in plink --merge-list using one ped/map file per sample about plink-ng HOT 13 CLOSED

For my example above PLINK v1.07 works as expected here. Here is the concordance rate for the same 6 samples after merging the ped files using v1.07:

SC112442_PB100119_F03.OldPlink.log:695230 concordant, for a concordance rate of 1.
SC112445_PB100119_E09.OldPlink.log:695106 concordant, for a concordance rate of 1.
SC197867_PB100119_D10.OldPlink.log:694912 concordant, for a concordance rate of 1.
SC198277_PB100119_E10.OldPlink.log:694855 concordant, for a concordance rate of 1.
SC198278_PB100119_F10.OldPlink.log:695217 concordant, for a concordance rate of 1.
SC198302_PB100119_H01.OldPlink.log:695791 concordant, for a concordance rate of 1.

from plink-ng.

Yes, please send the files to me at chrchang523 at gmail. This sounds like a .ped-specific bug that wasn't noticed till now because --merge-list is normally used on .bed files, but fixing it would be a very high priority.

from plink-ng.

(or post the files to Dropbox and send me a link, etc.)

from plink-ng.

Thanks!
I emailed you the files.

from plink-ng.

Hmm, I don't see an email.

from plink-ng.

I resent from my gmail in case my NIH account didn't want to send the attachment. Let me know if you received it.

from plink-ng.

Got it this time, thanks.

from plink-ng.

Great. Thanks for working on this!

from plink-ng.

Should be fixed by 21ab4fa; let me know if you still see any problems.

from plink-ng.

Thanks for fixing this so quickly! I'll test the new release when I get a chance and close this issue if everything looks good.

Eric

from plink-ng.

This bug looks fixed to me too. Thanks again!

I have an additional question about the .ped --merge-list, though. It seems like this command takes a good bit of RAM. On our system it has max memory of about 127GB per job. And this is consistent whether we're merging 5 ped files or 5000. Is this expected?

Eric

from plink-ng.

plink 1.9 defaults to reserving half of available RAM as workspace memory, but you can change this with --memory [# of MB you want plink to use]. Unless you have very long variant IDs, 4-16 GB is usually enough.

from plink-ng.

Thanks! That explains the memory usage since I'm running on 260GB nodes. I'll close this issue since you fixed the bug in the new release. Thanks again for fixing this issue and releasing a new version in less than a day!

Eric

from plink-ng.