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DReichLab / AdmixTools

Tools test whether admixture occurred and more
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qpadm with single sample - is it possible to run? #86

Closed eshab5 closed 3 years ago

eshab5 commented 3 years ago

Hello Dr.Patterson,

I am trying to run qpadm on a single ancient sample (that is pseudohaploid). I am using that as my target.

My .par file looks like this: genotypename: file.geno snpname: file.snp indivname: file.ind popleft: left.pops popright: right.pops allsnps: YES details: YES inbreed : YES oldallsnpsmode: NO

My left and right population files, have one population per line

When I submit this par file for the run, I am getting:

fatalx: pop: SampleA has sample size 1 and inbreed set sh: line 1: 96340 Aborted qpfstats -p /tmp/ppp.96308 > /tmp/fslog.96308 /var/spool/torque/mom_priv/jobs/31750267.cri16sc001.SC: line 16: 96308 Segmentation fault

Therefore, I wanted to kindly know if it is possible to run qpadm on a single sample taken as a target?

Thanking You, Esha

bumblenick commented 3 years ago

Dear Esha qpAdm only uses f4 stats; Code inbreed: NO (although this is kinda a lie) and all should be well.

Nick

Nick

On Fri, Nov 12, 2021 at 1:20 PM Esha Bandyopadhyay @.***> wrote:

Hello Dr.Patterson,

I am trying to run qpadm on a single ancient sample (that is pseudohaploid). I am using that as my target.

My .par file looks like this: genotypename: file.geno snpname: file.snp indivname: file.ind popleft: left.pops popright: right.pops allsnps: YES details: YES inbreed : YES oldallsnpsmode: NO

My left and right population files, have one population per line

When I submit this par file for the run, I am getting:

fatalx: pop: SampleA has sample size 1 and inbreed set sh: line 1: 96340 Aborted qpfstats -p /tmp/ppp.96308 > /tmp/fslog.96308 /var/spool/torque/mom_priv/jobs/31750267.cri16sc001.SC: line 16: 96308 Segmentation fault

Therefore, I wanted to kindly know if it is possible to run qpadm on a single sample taken as a target?

Thanking You, Esha

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eshab5 commented 3 years ago

Dear Dr.Patterson,

It worked! Thank you so much.

Sincerely, Esha