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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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Plink hangs #60

Closed Linnm00 closed 5 years ago

Linnm00 commented 6 years ago

(I am new to using plink and not formally trained in bioinformatics), first time trying to use plink it was connecting to web for a long time without anything happening, so i tried --noweb. Without realizing my error I am now stuck. Plink hangs and I can not write any commands, please advise! See below where it gets stuck

/Users/linnmaristorengen/plink_mac/plink ; exit; PLINK v1.90b5.2 64-bit (9 Jan 2018) www.cog-genomics.org/plink/1.9/ (C) 2005-2018 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, --tdt, --qfam, --annotate, --clump, --gene-report, --meta-analysis, --epistasis, --fast-epistasis, and --score.

'plink --help | more' describes all functions (warning: long). logout Saving session... ...copying shared history... ...saving history...truncating history files... ...completed.

[Process executed]

kanyhub commented 2 years ago

HI, I got the same problem. Did anyone figure out what happened here?

chrchang commented 2 years ago

plink is a command-line program. If you don't know what that means, you should spend at least a day learning the basics of using command-line programs before trying to use plink again.