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chrchang / plink-ng

A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Development is now focused on building out support for multiallelic, phased, and dosage data in PLINK 2.0.
https://www.cog-genomics.org/plink/2.0/
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Can't run anny PLINK command on Ubuntu 22.04 #256

Closed MatusBuci closed 9 months ago

MatusBuci commented 9 months ago

Hey all, Recently I have installed PLINK 1.9 on my Ubuntu 22.04 laptop and every time I've tried any command both on terminal and RStudio I've received the following message listed below. I have been working with PLINK on Windows for some time and I'm new to Linux. Can you explain to me please what might be the cause of this problem and give me some advice on how to solve it ? Thanks.

system("plink") PLINK v1.90p 64-bit (13 Feb 2023) www.cog-genomics.org/plink/1.9/ (C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3

plink <input flag(s)...> [command flag(s)...] [other flag(s)...] plink --help [flag name(s)...]

Commands include --make-bed, --recode, --flip-scan, --merge-list, --write-snplist, --list-duplicate-vars, --freqx, --missing, --test-mishap, --hardy, --mendel, --ibc, --impute-sex, --indep-pairphase, --r2, --show-tags, --blocks, --distance, --genome, --homozyg, --make-rel, --make-grm-gz, --rel-cutoff, --cluster, --pca, --neighbour, --ibs-test, --regress-distance, --model, --bd, --gxe, --logistic, --dosage, --lasso, --test-missing, --make-perm-pheno, --unrelated-heritability, --tdt, --dfam, --qfam, --tucc, --annotate, --clump, --gene-report, --meta-analysis, --epistasis, --fast-epistasis, and --score.

"plink --help | more" describes all functions (warning: long).

system("plink --bfile plink --goat --recode vcf --out plink_example") PLINK v1.90p 64-bit (13 Feb 2023) www.cog-genomics.org/plink/1.9/ (C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 Error: Failed to open plink_example.log. Try changing the --out parameter.

chrchang commented 9 months ago

Basic usage questions like this should be posted in the plink2-users Google group (https://groups.google.com/g/plink2-users ), not here.