How to avoid progress bars?

[Francesco Fantauzzi]

Can I direct plink to suppress progress bars? I am calling plink from within an R Markdown script (using bash) and progress bars clutter the output like here below.

plink --bfile bio.1 --indep-pairwise 200 25 0.4 ## PLINK v1.90b7.2 64-bit (11 Dec 2023) www.cog-genomics.org/plink/1.9/ ## (C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 ## Logging to plink.log. ## Options in effect: ## --bfile bio.1 ## --indep-pairwise 200 25 0.4 ## ## 31998 MB RAM detected; reserving 15999 MB for main workspace. ## 83534 variants loaded from .bim file. ## 89 people (89 males, 0 females) loaded from .fam. ## 89 phenotype values loaded from .fam. ## Using 1 thread (no multithreaded calculations invoked). ## Before main variant filters, 89 founders and 0 nonfounders present. ## Calculating allele frequencies... 0% 1% 2% 3% 4% 5% 6% 7% 8% 9% 10% 11% 12% 13% 14% 15% 16% 17% 18% 19% 20% 21% 22% 23% 24% 25% 26% 27% 28% 29% 30% 31% 32% 33% 34% 35% 36% 37% 38% 39% 40% 41% 42% 43% 44% 45% 46% 47% 48% 49% 50% 51% 52% 53% 54% 55% 56% 57% 58% 59% 60% 61% 62% 63% 64% 65% 66% 67% 68% 69% 70% 71% 72% 73% 74% 75% 76% 77% 78% 79% 80% 81% 82% 83% 84% 85% 86% 87% 88% 89% 90% 91% 92% 93% 94% 95% 96% 97% 98% 99% done. ## Total genotyping rate is 0.994567. ## 83534 variants and 89 people pass filters and QC. ## Among remaining phenotypes, 43 are cases and 46 are controls. ## 1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%87%88%89%90%91%92%93%94%95%96%97%98%99%Pruned 2920 variants from chromosome 1, leaving 3842. ## 1%2%3%4%5%6%7%8%9%10%11%12%13%14%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%89%90%91%92%93%94%95%96%97%98%99%Pruned 3516 variants from chromosome 2, leaving 4151. ## 1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%Pruned 2340 variants from chromosome 3, leaving 3185. ## 1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%90%91%92%93%94%95%96%97%98%99%Pruned 2017 variants from chromosome 4, leaving 2901. ## 0%1%1%2%2%3%3%4%4%5%5%6%6%7%7%8%8%9%9%10%10%11%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%Pruned 2107 variants from chromosome 5, leaving 2901. ## 1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%93%94%95%96%97%98%99%Pruned 2532 variants from chromosome 6, leaving 3160. ## 1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%48%49%50%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%Pruned 1458 variants from chromosome 7, leaving 2268. ## 1%2%3%4%5%6%7%8%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%84%85%86%87%88%89%90%91%92%93%93%94%95%96%97%98%99%Pruned 3071 variants from chromosome 8, leaving 3047. ## 1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%63%64%65%66%67%68%69%70%71%72%73%74%75%76%76%77%78%79%80%81%82%83%84%85%86%87%88%89%89%90%91%92%93%94%95%96%97%98%99%Pruned 2112 variants from chromosome 9, leaving 2694. ## 1%2%2%3%4%5%5%6%7%8%8%9%10%11%11%12%13%14%14%15%16%17%17%18%19%20%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%Pruned 1762 variants from chromosome 10, leaving 2409. ## 1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%91%92%93%94%95%96%97%98%99%Pruned 1629 variants from chromosome 11, leaving 2203. ## 1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%98%99%Pruned 1228 variants from chromosome 12, leaving 2156. ## 1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%Pruned 1351 variants from chromosome 13, leaving 1815. ## 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%Pruned 1024 variants from chromosome 14, leaving 1511. ## 1%2%3%4%5%6%7%8%9%10%12%13%14%15%16%17%18%19%20%21%23%24%25%26%27%28%29%30%31%32%34%35%36%37%38%39%40%41%42%43%45%46%47%48%49%50%51%52%53%54%55%57%58%59%60%61%62%63%64%65%66%68%69%70%71%72%73%74%75%76%77%79%80%81%82%83%84%85%86%87%88%90%91%92%93%94%95%96%97%98%99%Pruned 904 variants from chromosome 15, leaving 1373. ## 1%2%3%4%5%6%8%9%10%11%12%13%15%16%17%18%19%20%22%23%24%25%26%27%29%30%31%32%33%34%36%37%38%39%40%41%43%44%45%46%47%48%50%51%52%53%54%55%57%58%59%60%61%62%64%65%66%67%68%69%71%72%73%74%75%76%78%79%80%81%82%83%85%86%87%88%89%90%92%93%94%95%96%97%99%Pruned 810 variants from chromosome 16, leaving 1336. ## 1%2%3%4%5%7%8%9%10%11%12%14%15%16%17%18%20%21%22%23%24%25%27%28%29%30%31%32%34%35%36%37%38%40%41%42%43%44%45%47%48%49%50%51%52%54%55%56%57%58%60%61%62%63%64%65%67%68%69%70%71%72%74%75%76%77%78%80%81%82%83%84%85%87%88%89%90%91%92%94%95%96%97%98%Pruned 825 variants from chromosome 17, leaving 1299. ## 1%2%2%3%4%5%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%73%74%75%76%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%Pruned 1592 variants from chromosome 18, leaving 1753. ## 1%3%5%6%8%10%11%13%15%17%18%20%22%23%25%27%28%30%32%34%35%37%39%40%42%44%45%47%49%51%52%54%56%57%59%61%63%64%66%68%69%71%73%74%76%78%80%81%83%85%86%88%90%91%93%95%97%98%Pruned 501 variants from chromosome 19, leaving 967. ## 1%2%4%5%7%8%10%11%13%14%16%17%19%20%22%23%25%26%28%29%31%32%34%35%37%38%40%41%43%44%46%47%48%50%51%53%54%56%57%59%60%62%63%65%66%68%69%71%72%74%75%77%78%80%81%83%84%86%87%89%90%92%93%95%96%97%99%Pruned 576 variants from chromosome 20, leaving 1108. ## 1%3%4%6%7%9%10%12%13%15%16%18%19%21%22%24%25%27%28%30%31%33%34%36%37%39%40%42%43%45%47%48%50%51%53%54%56%57%59%60%62%63%65%66%68%69%71%72%74%75%77%78%80%81%83%84%86%87%89%91%92%94%95%97%98%Pruned 695 variants from chromosome 21, leaving 953. ## 1%3%4%6%8%9%11%13%14%16%17%19%21%22%24%26%27%29%31%32%34%35%37%39%40%42%44%45%47%48%50%52%53%55%57%58%60%62%63%65%66%68%70%71%73%75%76%78%79%81%83%84%86%88%89%91%93%94%96%97%99%Pruned 661 variants from chromosome 22, leaving 871. ## Pruning complete. 35631 of 83534 variants removed. ## Writing...Marker lists written to plink.prune.in and plink.prune.out .