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DReichLab / AdmixTools

Tools test whether admixture occurred and more
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Some issue about the software #52

Open HuangMin0702 opened 5 years ago

HuangMin0702 commented 5 years ago

I meet some problem when I used qpDstat. Some of my genotype data: 292229222299999999999999999999999999999999999999101919999999999999 999229229999299999292999292929992199090092222929222929222229922229 999229229991299999222229291209991222222222222229222222222222222229 999229229992229229222299222229992229222221111019222222222222222222 999229229992229229222222222229992229222222222229222220191112222222 SNP data: scaffold_0:25599 0 0 25599 C T scaffold_0:26840 0 0 26840 C T scaffold_0:27901 0 0 27901 C A scaffold_0:27953 0 0 27953 T A scaffold_0:27992 0 0 27992 G A individual data: GSA1 U GSA GSA2 U GSA GSA3 U GSA GSA4 U GSA GSA5 U GSA GSA6 U GSA GSA7 U GSA GSA8 U GSA GSA9 U GSA Besides, my genotype data have 786 scaffolds. When I run the commond qpDstat -p Dsta_par, it tells some problems: qpDstat: parameter file: Dsta_par

THE INPUT PARAMETERS

PARAMETER NAME: VALUE

genotypename: 66inds_SNP.eigenstratgeno snpname: 66inds_SNP.snp indivname: 66inds_SNP.ind popfilename: list_pop1

qpDstat version: 755

warning: bad chrom: scaffold_0:14883 0 0 14883 C T warning: bad chrom: scaffold_0:15074 0 0 15074 G T warning: bad chrom: scaffold_0:15222 0 0 15222 C T warning: bad chrom: scaffold_0:25526 0 0 25526 C T warning: bad chrom: scaffold_0:25579 0 0 25579 C T warning: bad chrom: scaffold_0:25599 0 0 25599 C T warning: bad chrom: scaffold_0:26840 0 0 26840 C T warning: bad chrom: scaffold_0:27901 0 0 27901 C A warning: bad chrom: scaffold_0:27953 0 0 27953 T A warning: bad chrom: scaffold_0:27992 0 0 27992 G A Segmentation fault (core dumped)

Please tell me what's wrong with my data? Thank you very much.

bumblenick commented 5 years ago

Please check your formats carefully (Try with just 20 scaffolds to see if the code runs) Your snp file looks to me as though you have chromosome number 0 in effect. That is wrong.

Nick

On Tue, Jun 18, 2019 at 11:57 PM HuangMin0702 notifications@github.com wrote:

I meet some problem when I used qpDstat. Some of my genotype data: 292229222299999999999999999999999999999999999999101919999999999999 999229229999299999292999292929992199090092222929222929222229922229 999229229991299999222229291209991222222222222229222222222222222229 999229229992229229222299222229992229222221111019222222222222222222 999229229992229229222222222229992229222222222229222220191112222222 SNP data: scaffold_0:25599 0 0 25599 C T scaffold_0:26840 0 0 26840 C T scaffold_0:27901 0 0 27901 C A scaffold_0:27953 0 0 27953 T A scaffold_0:27992 0 0 27992 G A individual data: GSA1 U GSA GSA2 U GSA GSA3 U GSA GSA4 U GSA GSA5 U GSA GSA6 U GSA GSA7 U GSA GSA8 U GSA GSA9 U GSA Besides, my genotype data have 786 scaffolds. When I run the commond qpDstat -p Dsta_par, it tells some problems: qpDstat: parameter file: Dsta_par THE INPUT PARAMETERS

PARAMETER NAME: VALUE

genotypename: 66inds_SNP.eigenstratgeno snpname: 66inds_SNP.snp indivname: 66inds_SNP.ind popfilename: list_pop1 qpDstat version: 755

warning: bad chrom: scaffold_0:14883 0 0 14883 C T warning: bad chrom: scaffold_0:15074 0 0 15074 G T warning: bad chrom: scaffold_0:15222 0 0 15222 C T warning: bad chrom: scaffold_0:25526 0 0 25526 C T warning: bad chrom: scaffold_0:25579 0 0 25579 C T warning: bad chrom: scaffold_0:25599 0 0 25599 C T warning: bad chrom: scaffold_0:26840 0 0 26840 C T warning: bad chrom: scaffold_0:27901 0 0 27901 C A warning: bad chrom: scaffold_0:27953 0 0 27953 T A warning: bad chrom: scaffold_0:27992 0 0 27992 G A Segmentation fault (core dumped)

Please tell me what's wrong with my data? Thank you very much.

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HuangMin0702 commented 5 years ago

Hi Nich, I have fonund the reason about the error. But I found anthoer problem. The scaffolds can’t more than 100. I attempt to changed source code qpDstat.c. Howover I’m still failure Best wishes, Min

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发件人: bumblenick notifications@github.com 发送时间: Wednesday, June 19, 2019 7:46:06 PM 收件人: DReichLab/AdmixTools 抄送: HuangMin0702; Author 主题: Re: [DReichLab/AdmixTools] Some issue about the software (#52)

Please check your formats carefully (Try with just 20 scaffolds to see if the code runs) Your snp file looks to me as though you have chromosome number 0 in effect. That is wrong.

Nick

On Tue, Jun 18, 2019 at 11:57 PM HuangMin0702 notifications@github.com wrote:

I meet some problem when I used qpDstat. Some of my genotype data: 292229222299999999999999999999999999999999999999101919999999999999 999229229999299999292999292929992199090092222929222929222229922229 999229229991299999222229291209991222222222222229222222222222222229 999229229992229229222299222229992229222221111019222222222222222222 999229229992229229222222222229992229222222222229222220191112222222 SNP data: scaffold_0:25599 0 0 25599 C T scaffold_0:26840 0 0 26840 C T scaffold_0:27901 0 0 27901 C A scaffold_0:27953 0 0 27953 T A scaffold_0:27992 0 0 27992 G A individual data: GSA1 U GSA GSA2 U GSA GSA3 U GSA GSA4 U GSA GSA5 U GSA GSA6 U GSA GSA7 U GSA GSA8 U GSA GSA9 U GSA Besides, my genotype data have 786 scaffolds. When I run the commond qpDstat -p Dsta_par, it tells some problems: qpDstat: parameter file: Dsta_par THE INPUT PARAMETERS

PARAMETER NAME: VALUE

genotypename: 66inds_SNP.eigenstratgeno snpname: 66inds_SNP.snp indivname: 66inds_SNP.ind popfilename: list_pop1 qpDstat version: 755

warning: bad chrom: scaffold_0:14883 0 0 14883 C T warning: bad chrom: scaffold_0:15074 0 0 15074 G T warning: bad chrom: scaffold_0:15222 0 0 15222 C T warning: bad chrom: scaffold_0:25526 0 0 25526 C T warning: bad chrom: scaffold_0:25579 0 0 25579 C T warning: bad chrom: scaffold_0:25599 0 0 25599 C T warning: bad chrom: scaffold_0:26840 0 0 26840 C T warning: bad chrom: scaffold_0:27901 0 0 27901 C A warning: bad chrom: scaffold_0:27953 0 0 27953 T A warning: bad chrom: scaffold_0:27992 0 0 27992 G A Segmentation fault (core dumped)

Please tell me what's wrong with my data? Thank you very much.

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