Illegal instruction
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- Dominant language
- 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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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.
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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