DReichLab / DReichLab/EIG

Illegal instruction

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C
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Description

Hello, I have been trying to run smartpca and I keep getting this error:

/home/bamorim/EIG/bin/smartpca -p smartpca.params.txt

THE INPUT PARAMETERS

##PARAMETER NAME: VALUE
genotypename: /home/bamorim/DEMI/PCA/DEMI_HumanOrigins.Khwe.ped
snpname: /home/bamorim/DEMI/PCA/DEMI_HumanOrigins.Khwe.map
indivname: /home/bamorim/DEMI/PCA/DEMI_HumanOrigins.Khwe.ped
evecoutname: /home/bamorim/DEMI/PCA/DEMI_HumanOrigins.Khwe.pca.evec.txt
evaloutname: /home/bamorim/DEMI/PCA/DEMI_HumanOrigins.Khwe.pca.eval.txt
lsqproject: YES

smartpca version: 18140

norm used

lsqproject used
genetic distance set from physical distance
genotype file processed
snps deleted (nodata): 0. deletesnpoutname: for detailsnumber of samples used: 85 number of snps used: 478950
number of pops for axes: 1
Using 23 threads, and partial sum lookup algorithm.
snp AX-50064432 ignored . allelecnt: 0 missing: 1
snp AX-50069775 ignored . allelecnt: 0 missing: 0
snp AX-50070472 ignored . allelecnt: 0 missing: 0
snp AX-50071782 ignored . allelecnt: 0 missing: 0
snp AX-50074365 ignored . allelecnt: 0 missing: 0
snp AX-50075476 ignored . allelecnt: 0 missing: 4
snp AX-50120905 ignored . allelecnt: 0 missing: 0
snp AX-50142355 ignored . allelecnt: 0 missing: 0
snp AX-50149625 ignored . allelecnt: 0 missing: 0
snp AX-50201779 ignored . allelecnt: 0 missing: 0
total number of snps killed in pass: 3942 used: 475008
Illegal instruction

I have tried running this analysis with both .ped/.map and eigenstrat that I converted using convertf and I keep getting the same illegal instruction error. I also get this error if I use all my dataset (853 individuals) and when I specify poplistname. Do you know what I could be doing wrong?

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First steps

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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the reported smartpca command with the supplied smartpca.params.txt, first using the .ped/.map inputs and then the convertf-generated eigenstrat data. Check where execution stops after SNP processing and compare the behavior across the 85- and 853-individual datasets and with poplistname. Done means identifying whether the failure is tied to the executable runtime or to a particular input or parameter combination, with a reproducible case documented.

Written by the indexing model from the issue text.

Assessment

Tech stack
c
Domain
bioinformatics
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
28/100

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