Run error for qpWave about admixtools HOT 7 OPEN

On Jun 30, 2017, at 11:44 AM, albeele1 ***@***.***> 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? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

On Mon, Jul 22, 2019 at 8:27 AM Francesco Montinaro < ***@***.***> 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 — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#27?email_source=notifications&email_token=AEE77B4TM4N3WQ7ZPZ7AKZLQAWRTLA5CNFSM4DRLM2LKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2PYGSI#issuecomment-513770313>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEE77BZ6RWYSAGIMEQKYSPTQAWRTLANCNFSM4DRLM2LA> .

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 < ***@***.***> 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 > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#27?email_source=notifications&email_token=AEE77B4TM4N3WQ7ZPZ7AKZLQAWRTLA5CNFSM4DRLM2LKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2PYGSI#issuecomment-513770313>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AEE77BZ6RWYSAGIMEQKYSPTQAWRTLANCNFSM4DRLM2LA> > . >

On Mon, 22 Jul 2019 at 14:47, bumblenick ***@***.***> 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 ***@***.***> 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 < > ***@***.***> 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 >> >> — >> You are receiving this because you commented. >> Reply to this email directly, view it on GitHub >> < #27?email_source=notifications&email_token=AEE77B4TM4N3WQ7ZPZ7AKZLQAWRTLA5CNFSM4DRLM2LKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2PYGSI#issuecomment-513770313 >, >> or mute the thread >> < https://github.com/notifications/unsubscribe-auth/AEE77BZ6RWYSAGIMEQKYSPTQAWRTLANCNFSM4DRLM2LA > >> . >> > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#27?email_source=notifications&email_token=ADZQPMBNKZDASH6PX3BCWKLQAW27HA5CNFSM4DRLM2LKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2P7B6Y#issuecomment-513798395>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADZQPMHCWGJFYKZGAGKBE3DQAW27HANCNFSM4DRLM2LA> .