Comments (6)
bumblenick
commented on July 21, 2024
In eigenstrat format the geno file contains lines in which the number of
characters
is the same as the number of samples (individuals)
Here you have a line with 478 characters but 5253 samples.
By the way, I don't recommend eigenstrat format for such large datasets.
Use convertf to make packed format. ADMIXTOOLS will then run much faster
Nick
…On Thu, Jun 7, 2018 at 12:24 PM, geneanalyst ***@***.***> wrote:
I have previously run qpdstat with no problem. Now with a new dataset I
got the following error:
fatalx:
(ineigenstrat) mismatch line length 478 5253
Aborted (core dumped)
And the output file contains this error:
/home/d/ADMIXTOOLS1/qpDstat: parameter file: pardstat1
THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
indivname: MASTER_HiCov27.ind
snpname: MASTER_HiCov27.snp
genotypename: MASTER_HiCov27.geno
popfilename: list_dstat
qpDstat version: 711
(ineigenstrat) bad line 1019420 ::1121212121110211
Any ideas as to what the problem is?
Thanks
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geneanalyst
commented on July 21, 2024
Any idea what may be causing this. I converted from plink map and ped files.
Can I go from plink map, ped, pedind ( pedind is basically a fam file with column 6 a mirror of column 1) to packed format using the following par file:
genotypename: SASIA.ped
snpname: SASIA.map
indivname: SASIA.pedind
outputformat: PACKEDPED
genotypeoutname: SASIA.geno
snpoutname: SASIA.snp
indivoutname: SASIA.ind
familynames: YES
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bumblenick
commented on July 21, 2024
outputformat is in my usage lower case so you should be able to leave out
the outputformat line.
But why is your output then in eigenstrat format?
Possibilities:
1) system trouble (file too big and truncated?)
2) misformat of your PLINK files??
By the way you can run convertf with input files SASIA.geno etc and no
output files. In effect this
tests if your files are well-formed.
Nick
…On Thu, Jun 7, 2018 at 4:19 PM, geneanalyst ***@***.***> wrote:
Any idea what may be causing this. I converted from plink map and ped
files.
Can I go from plink map, ped, pedind ( pedind is basically a fam file with
column 6 a mirror of column 1) to packed format using the following par
file:
genotypename: SASIA.ped
snpname: SASIA.map
indivname: SASIA.pedind
outputformat: PACKEDPED
genotypeoutname: SASIA.geno
snpoutname: SASIA.snp
indivoutname: SASIA.ind
familynames: YES
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geneanalyst
commented on July 21, 2024
I converted using the above par file. Then ran qpdstat. Now I have this error:
/home/d/ADMIXTOOLS1/qpDstat -p pardstat1 > dstat_SIS.txt
fatalx:
bad chrom: rs3094315
Aborted (core dumped)
The .snp file looks fine to me:
1 rs3094315 0.020130 752566 A G
1 rs12124819 0.020242 776546 A G
1 rs28765502 0.022137 832918 T C
1 rs7419119 0.022518 842013 T G
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bumblenick
commented on July 21, 2024
Oh! I think I realized your trouble. outputformat packedped is packed
plink.
The default and what I recommend is packed ancestrymap. and your .snp file
is in PLINK format NOT reichlab format
(see examples).
Rerun with no outputformat set and observe that the snp file now begins
rs3094315 1 ...
that is with columns flipped.
I've thought about making my software look at the file contents to
determine format, but for
now a .snp file must be in Reich lab format.
Nick
…On Thu, Jun 7, 2018 at 6:07 PM, geneanalyst ***@***.***> wrote:
I converted using the above par file. Then ran qpdstat. Now I have this
error:
/home/d/ADMIXTOOLS1/qpDstat -p pardstat1 > dstat_SIS.txt
fatalx:
bad chrom: rs3094315
Aborted (core dumped)
The .snp file looks fine to me:
1 rs3094315 0.020130 752566 A G
1 rs12124819 0.020242 776546 A G
1 rs28765502 0.022137 832918 T C
1 rs7419119 0.022518 842013 T G
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geneanalyst
commented on July 21, 2024
Converted without outputformat set. Problem solved. Thanks.
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