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DReichLab / AdmixTools

Tools test whether admixture occurred and more
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Run error for qpWave #27

Open albeele1 opened 7 years ago

albeele1 commented 7 years ago

(vlog): negative or zero value 0

albeele1 commented 7 years ago

The par file was made following the readme file:

genotypename: input genotype file (in eigenstrat or packedancestrymap r format) snpname: input snp file (in eigenstrat format) indivname: input indiv file (in eigenstrat format) popleft: left population list (1 per line) popright: right population list (1 per line) details: YES

but the example file for the program has two additional lines DIR: ../data
S1: qpdata

Not sure where to generate qpdata--which program will do that?

also I am assuming that DIR: is the path to the data. Is it necessary if you are within the directory with all the files within?

bumblenick commented 7 years ago

Please send me a copy of your parameter file

Nick

Sent from my iPhone

On Jun 30, 2017, at 11:44 AM, albeele1 notifications@github.com wrote:

The par file was made following the readme file:

genotypename: input genotype file (in eigenstrat or packedancestrymap r format) snpname: input snp file (in eigenstrat format) indivname: input indiv file (in eigenstrat format) popleft: left population list (1 per line) popright: right population list (1 per line) details: YES

but the example file for the program has two additional lines DIR: ../data S1: qpdata

Not sure where to generate qpdata--which program will do that?

also I am assuming that DIR: is the path to the data. Is it necessary if you are within the directory with all the files within?

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DinRigtigeFar commented 5 years ago

I also can't find any documentation anywhere as to what S1 is referring to.

francescomontinaro commented 5 years ago

Hi,

I have just encountered the same error: (vlog): negative or zero value 0.

Any suggestion on what could cause it?

Here is the log for the qpWave run:

THE INPUT PARAMETERS

PARAMETER NAME: VALUE

genotypename:input.geno snpname: input.snp indivname: input.ind popleft: leftwTargetBR-08_cont_2.tmp popright: rightBR-08_cont_2.tmp details: YES

qpWave version: 410

read 1073741824 bytes read 1718626600 bytes packed geno read OK end of inpack

left pops: test Anatolia_EBA Russia_EHG

right pops: Russia_AfontovaGora3 Iberia_ElMiron Belgium_GoyetQ116_1_published Iran_Ganj_Dareh_N_published Russia_Kostenki14 Jordan_PPNB Russia_MA1_HG.SG Ethiopia_4500BP.SG Israel_Raqefet_M_Natufian Ust_Ishim_HG_published.DG Czech_Vestonice15 Georgia_Kotias.SG

0 test 1 1 Anatolia_EBA 3 2 Russia_EHG 1 3 Russia_AfontovaGora3 1 4 Iberia_ElMiron 1 5 Belgium_GoyetQ116_1_published 1 6 Iran_Ganj_Dareh_N_published 3 7 Russia_Kostenki14 1 8 Jordan_PPNB 5 9 Russia_MA1_HG.SG 1 10 Ethiopia_4500BP.SG 1 11 Israel_Raqefet_M_Natufian 3 12 Ust_Ishim_HG_published.DG 1 13 Czech_Vestonice15 1 14 Georgia_Kotias.SG 1 jackknife block size: 0.050 snps: 609331 indivs: 25 number of blocks for block jackknife: 711 dof (jackknife): 545.422 numsnps used: 5666 fatalx: (vlog): negative or zero value 0 Aborted

bumblenick commented 5 years ago

A quick response. 1) Please check that you are using the latest version. I thought I had updated recently 2) Using qpWave with just 2 left pops is strange. What are you trying to do? Probably you should just be studying f_4(l_1, l_2, r_1, r_2) with l_i in left R_i in right 3) You have a large number of right populations. Default is to use only snps valid in all pops. Only 5666 such which is too few. allsnps: YES is a possibility but this is not entirely mathematically valid.

Good luck

Nick

On Mon, Jul 22, 2019 at 8:27 AM Francesco Montinaro < notifications@github.com> wrote:

Hi,

I have just encountered the same error: (vlog): negative or zero value 0.

Any suggestion on what could cause it?

Here is the log for the qpWave run: THE INPUT PARAMETERS

PARAMETER NAME: VALUE

genotypename:input.geno snpname: input.snp indivname: input.ind popleft: leftwTargetBR-08_cont_2.tmp popright: rightBR-08_cont_2.tmp details: YES qpWave version: 410

read 1073741824 bytes read 1718626600 bytes packed geno read OK end of inpack

left pops: test Anatolia_EBA Russia_EHG

right pops: Russia_AfontovaGora3 Iberia_ElMiron Belgium_GoyetQ116_1_published Iran_Ganj_Dareh_N_published Russia_Kostenki14 Jordan_PPNB Russia_MA1_HG.SG Ethiopia_4500BP.SG Israel_Raqefet_M_Natufian Ust_Ishim_HG_published.DG Czech_Vestonice15 Georgia_Kotias.SG

0 test 1 1 Anatolia_EBA 3 2 Russia_EHG 1 3 Russia_AfontovaGora3 1 4 Iberia_ElMiron 1 5 Belgium_GoyetQ116_1_published 1 6 Iran_Ganj_Dareh_N_published 3 7 Russia_Kostenki14 1 8 Jordan_PPNB 5 9 Russia_MA1_HG.SG 1 10 Ethiopia_4500BP.SG 1 11 Israel_Raqefet_M_Natufian 3 12 Ust_Ishim_HG_published.DG 1 13 Czech_Vestonice15 1 14 Georgia_Kotias.SG 1 jackknife block size: 0.050 snps: 609331 indivs: 25 number of blocks for block jackknife: 711 dof (jackknife): 545.422 numsnps used: 5666 fatalx: (vlog): negative or zero value 0 Aborted

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bumblenick commented 5 years ago

Apologies. I do see you have a left pop called "test" so you have 3 left pops which is more reasonable. Also try qpAdm to see if you get the same error.

N

On Mon, Jul 22, 2019 at 9:45 AM Nick Patterson nickp@broadinstitute.org wrote:

A quick response. 1) Please check that you are using the latest version. I thought I had updated recently 2) Using qpWave with just 2 left pops is strange. What are you trying to do? Probably you should just be studying f_4(l_1, l_2, r_1, r_2) with l_i in left R_i in right 3) You have a large number of right populations. Default is to use only snps valid in all pops. Only 5666 such which is too few. allsnps: YES is a possibility but this is not entirely mathematically valid.

Good luck

Nick

On Mon, Jul 22, 2019 at 8:27 AM Francesco Montinaro < notifications@github.com> wrote:

Hi,

I have just encountered the same error: (vlog): negative or zero value 0.

Any suggestion on what could cause it?

Here is the log for the qpWave run: THE INPUT PARAMETERS

PARAMETER NAME: VALUE

genotypename:input.geno snpname: input.snp indivname: input.ind popleft: leftwTargetBR-08_cont_2.tmp popright: rightBR-08_cont_2.tmp details: YES qpWave version: 410

read 1073741824 bytes read 1718626600 bytes packed geno read OK end of inpack

left pops: test Anatolia_EBA Russia_EHG

right pops: Russia_AfontovaGora3 Iberia_ElMiron Belgium_GoyetQ116_1_published Iran_Ganj_Dareh_N_published Russia_Kostenki14 Jordan_PPNB Russia_MA1_HG.SG Ethiopia_4500BP.SG Israel_Raqefet_M_Natufian Ust_Ishim_HG_published.DG Czech_Vestonice15 Georgia_Kotias.SG

0 test 1 1 Anatolia_EBA 3 2 Russia_EHG 1 3 Russia_AfontovaGora3 1 4 Iberia_ElMiron 1 5 Belgium_GoyetQ116_1_published 1 6 Iran_Ganj_Dareh_N_published 3 7 Russia_Kostenki14 1 8 Jordan_PPNB 5 9 Russia_MA1_HG.SG 1 10 Ethiopia_4500BP.SG 1 11 Israel_Raqefet_M_Natufian 3 12 Ust_Ishim_HG_published.DG 1 13 Czech_Vestonice15 1 14 Georgia_Kotias.SG 1 jackknife block size: 0.050 snps: 609331 indivs: 25 number of blocks for block jackknife: 711 dof (jackknife): 545.422 numsnps used: 5666 fatalx: (vlog): negative or zero value 0 Aborted

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francescomontinaro commented 5 years ago

Thank you very much,

allsnps:YES fixed the issue, which is mainly due to very small snps remaining. Francesco

On Mon, 22 Jul 2019 at 14:47, bumblenick notifications@github.com wrote:

Apologies. I do see you have a left pop called "test" so you have 3 left pops which is more reasonable. Also try qpAdm to see if you get the same error.

N

On Mon, Jul 22, 2019 at 9:45 AM Nick Patterson nickp@broadinstitute.org wrote:

A quick response. 1) Please check that you are using the latest version. I thought I had updated recently 2) Using qpWave with just 2 left pops is strange. What are you trying to do? Probably you should just be studying f_4(l_1, l_2, r_1, r_2) with l_i in left R_i in right 3) You have a large number of right populations. Default is to use only snps valid in all pops. Only 5666 such which is too few. allsnps: YES is a possibility but this is not entirely mathematically valid.

Good luck

Nick

On Mon, Jul 22, 2019 at 8:27 AM Francesco Montinaro < notifications@github.com> wrote:

Hi,

I have just encountered the same error: (vlog): negative or zero value 0.

Any suggestion on what could cause it?

Here is the log for the qpWave run: THE INPUT PARAMETERS

PARAMETER NAME: VALUE

genotypename:input.geno snpname: input.snp indivname: input.ind popleft: leftwTargetBR-08_cont_2.tmp popright: rightBR-08_cont_2.tmp details: YES qpWave version: 410

read 1073741824 bytes read 1718626600 bytes packed geno read OK end of inpack

left pops: test Anatolia_EBA Russia_EHG

right pops: Russia_AfontovaGora3 Iberia_ElMiron Belgium_GoyetQ116_1_published Iran_Ganj_Dareh_N_published Russia_Kostenki14 Jordan_PPNB Russia_MA1_HG.SG Ethiopia_4500BP.SG Israel_Raqefet_M_Natufian Ust_Ishim_HG_published.DG Czech_Vestonice15 Georgia_Kotias.SG

0 test 1 1 Anatolia_EBA 3 2 Russia_EHG 1 3 Russia_AfontovaGora3 1 4 Iberia_ElMiron 1 5 Belgium_GoyetQ116_1_published 1 6 Iran_Ganj_Dareh_N_published 3 7 Russia_Kostenki14 1 8 Jordan_PPNB 5 9 Russia_MA1_HG.SG 1 10 Ethiopia_4500BP.SG 1 11 Israel_Raqefet_M_Natufian 3 12 Ust_Ishim_HG_published.DG 1 13 Czech_Vestonice15 1 14 Georgia_Kotias.SG 1 jackknife block size: 0.050 snps: 609331 indivs: 25 number of blocks for block jackknife: 711 dof (jackknife): 545.422 numsnps used: 5666 fatalx: (vlog): negative or zero value 0 Aborted

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