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!DOCTYPE html>html langen stylemargin: 0; -moz-box-sizing: border-box; -webkit-box-sizing: border-box; box-sizing: border-box; background: #daede2; padding: 5%;>link relicon typeimage/x-icon hrefbiocircuitree-green.jpeg> head>title>Brian Wentzloff dot com - Using GNU parallel to speed up loops/title>!--if lt IE 9>	script srcscript/html5shiv.js>/script>	!endif-->style>          *,          ::before,          ::after {            border-width: 0;          }        /style>script srchttps://cdn.tailwindcss.com>/script>script>        tailwind.config  {          corePlugins: {            preflight: false,          },        }        /script>		style>			code {				background: rgba(51, 52, 52, 1);				color: rgb(255, 254, 254);				border-radius: 0.375em;				border: solid 1px rgba(210, 215, 217, 0.75);				font-family: Courier New, monospace;				font-size: 0.9em;				margin: 0 0.25em;				padding: 0.25em 0.65em; }			  			  pre {				-webkit-overflow-scrolling: touch;				font-family: Courier New, 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pb-0.825em px-0>								a hrefusing-gnu-parallel.html classbox-border text-#333 no-underline transition-border-color duration-0.2s ease-ease-in-out m-0 p-0 border-b-rgba(0,0,0,0.2) border-b border-solid style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;-moz-transition:border-color 0.2s ease-in-out;-ms-transition:border-color 0.2s ease-in-out;-o-transition:border-color 0.2s ease-in-out;-webkit-transition:border-color 0.2s ease-in-out>Using GNU parallel to speed up loops/a>							/li>						/ul>					/nav>				/div>				div classbox-border relative m-0 p-0 iddesign-selection style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;z-index:100>					h3 classbox-border text-2.25em font-extralight tracking-1px leading-1em m-0 pt-0.5em pb-0.25em px-0 style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;font-family:tablet-gothic-condensed,arial narrow,arial,verdana,sans-serif>Projects:/h3>					nav rolenavigation 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ease-in-out;-ms-transition:border-color 0.2s ease-in-out;-o-transition:border-color 0.2s ease-in-out;-webkit-transition:border-color 0.2s ease-in-out>Somed House/a>							/li>						/ul>					/nav>				/div>			/div>			/aside>		section classbox-border relative m-0 p-5% idzen-intro style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;padding-bottom:0px> 			header rolebanner style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border relative m-0 p-0> 				h1 style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;background:#ea2e49 classbox-border text-white inline-block font-light tracking-2px uppercase mb-1em m-0 px-1em py-0.5em>Bioinformatics/h1>				h2 style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;font-family:tablet-gothic-condensed,arial narrow,arial,verdana,sans-serif classbox-border text-white font-black text-6em tracking-1px leading-1em m-0 p-0>Using GNU parallel to speed up loops/h2>			/header>			div classbox-border relative text-white m-0 p-15%0 idzen-summary rolearticle style-moz-box-sizing:border-box;-webkit-box-sizing:border-box> 				p style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border text-1em leading-1.5em font-light tracking-2px uppercase m-0 px-0 py-0.5em>This was written sometime in 2021 or 2022./p> 				p style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border text-1em leading-1.5em font-light tracking-2px uppercase mt-1em m-0 pt-1.5em px-0 py-0.5em border-t-#ea2e49 border-t border-solid>I want to share a new technique Ive recently learned that has sped up some of my scripts on the HPC significantly. Anywhere that I would normally use a for loop, I am now using the GNU parallel utility instead.1/p> 			/div>			  			div classbox-border relative text-#333 ml--30% m-0 pl-30% pr-5% py-5% idzen-preamble rolearticle style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;background:rgba(255,255,255,0.9)> 				!--h3 style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;font-family:tablet-gothic-condensed,arial narrow,arial,verdana,sans-serif classbox-border text-2.25em font-extralight tracking-1px leading-1em m-0 pt-0.5em pb-0.25em px-0>The Road to Enlightenment/h3--> 				p style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border text-1em font-normal leading-1.5em m-0 px-0 py-0.5em>Here are the results of a pseudo-experiment I ran to quantify its benefit:/p> 				p style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border text-1em font-normal leading-1.5em m-0 px-0 py-0.5em>					I started with a simple loop to run a bwa mem alignment on 5 samples downloaded from NCBI. This is how I have done loops in the past and have seen everyone else mostly use them:/p>pre>code>for samplename in SRR518710 SRR518711 SRR518712 SRR518713 SRR518717dobwa mem arctos.fna.gz ${samplename}_1.fastq ${samplename}_2.fastq > test_${samplename}.mapped.samdone/code>/pre>p style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border text-1em font-normal leading-1.5em m-0 px-0 py-0.5em>/p>This loop will run the `bwa mem` command one at a time until all 5 samples have been processed. It took me an average of 31 minutes, 6 seconds to run this entire script (the SRR files used were intentionally small for testing purposes. CPU efficiency 90%; memory efficiency 14%).2/p> 			/div> 		/section> div classbox-border relative m-0 p-5% idzen-supporting rolemain style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;> div classbox-border relative text-white m-0 p-5% idzen-explanation rolearticle style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;padding-top:0px;> !--h3 style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;font-family:tablet-gothic-condensed,arial narrow,arial,verdana,sans-serif classbox-border text-2.25em font-extralight tracking-1px leading-1em m-0 pt-0.5em pb-0.25em px-0>So What is This About?/h3--> p style-moz-box-sizing:border-box;-webkit-box-sizing:border-box; classbox-border text-1em font-normal leading-1.5em m-0 px-0 py-0.5em stroke-black drop-shadow-0_1.2px_1.2px_rgba(0,0,0,0.8)>A better way to do this would be to have each of the five bwa mem commands running simultaneously instead of one after the other. As we discussed in Bioinformatics Club, one way to do this is by appending an & character to the end of the command. Here is what that looks like:/p> pre style>code>for samplename in SRR518710 SRR518711 SRR518712 SRR518713 SRR518717dobwa mem arctos.fna.gz ${samplename}_1.fastq ${samplename}_2.fastq > test_${samplename}.mapped.sam &done /code>/pre> p style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border text-1em font-normal leading-1.5em m-0 px-0 py-0.5em drop-shadow-0_1.2px_1.2px_rgba(0,0,0,0.8)>This speeds things up significantly. It took an average of 27 minutes, 1.8 seconds to run this script, which is about a 13% decrease in runtime (Memory use was much higher than the first method: 95% CPU efficiency, 66% memory efficiency)./p> /div> !--div classbox-border relative text-white m-0 p-5% idzen-participation rolearticle style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;background:rgba(234,46,73,0.9)> h3 style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;font-family:tablet-gothic-condensed,arial narrow,arial,verdana,sans-serif classbox-border text-2.25em font-extralight tracking-1px leading-1em m-0 pt-0.5em pb-0.25em px-0>Participation/h3> p style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border text-1em font-normal leading-1.5em m-0 px-0 py-0.5em>Strong visual design has always been our focus. You are modifying this page, so strong abbr titleCascading Style Sheets style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border m-0 p-0>CSS/abbr> skills are necessary too, but the example files are commented well enough that even abbr titleCascading Style Sheets style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border m-0 p-0>CSS/abbr> novices can use them as starting points. Please see the a hrefhttps://csszengarden.com/pages/resources/ titleA listing of CSS-related resources style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;-moz-transition:border-color 0.2s ease-in-out;-ms-transition:border-color 0.2s ease-in-out;-o-transition:border-color 0.2s ease-in-out;-webkit-transition:border-color 0.2s ease-in-out classbox-border no-underline transition-border-color duration-0.2s ease-ease-in-out text-white m-0 p-0 border-b-rgba(0,0,0,0.2) border-b border-solid>abbr titleCascading Style Sheets style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border m-0 p-0>CSS/abbr> Resource Guide/a> for advanced tutorials and tips on working with abbr titleCascading Style Sheets style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border m-0 p-0>CSS/abbr>./p> p style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border text-1em font-normal leading-1.5em m-0 px-0 py-0.5em>You may modify the style sheet in any way you wish, but not the abbr titleHyperText Markup Language style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border m-0 p-0>HTML/abbr>. This may seem daunting at first if you’ve never worked this way before, but follow the listed links to learn more, and use the sample files as a guide./p> p style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border text-1em font-normal leading-1.5em m-0 px-0 py-0.5em>Download the sample a hrefhttps://csszengarden.com/examples/index titleThis pages source HTML code, not to be modified. style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;-moz-transition:border-color 0.2s ease-in-out;-ms-transition:border-color 0.2s ease-in-out;-o-transition:border-color 0.2s ease-in-out;-webkit-transition:border-color 0.2s ease-in-out classbox-border no-underline transition-border-color duration-0.2s ease-ease-in-out text-white m-0 p-0 border-b-rgba(0,0,0,0.2) border-b border-solid>HTML/a> and a hrefhttps://csszengarden.com/examples/style.css titleThis pages sample CSS, the file you may modify. style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;-moz-transition:border-color 0.2s ease-in-out;-ms-transition:border-color 0.2s ease-in-out;-o-transition:border-color 0.2s ease-in-out;-webkit-transition:border-color 0.2s ease-in-out classbox-border no-underline transition-border-color duration-0.2s ease-ease-in-out text-white m-0 p-0 border-b-rgba(0,0,0,0.2) border-b border-solid>CSS/a> to work on a copy locally. Once you have completed your masterpiece (and please, don’t submit half-finished work) upload your abbr titleCascading Style Sheets style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border m-0 p-0>CSS/abbr> file to a web server under your control. a hrefhttps://csszengarden.com/pages/submit/ titleUse the contact form to send us your CSS file style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;-moz-transition:border-color 0.2s ease-in-out;-ms-transition:border-color 0.2s ease-in-out;-o-transition:border-color 0.2s ease-in-out;-webkit-transition:border-color 0.2s ease-in-out classbox-border no-underline transition-border-color duration-0.2s ease-ease-in-out text-white m-0 p-0 border-b-rgba(0,0,0,0.2) border-b border-solid>Send us a link/a> to an archive of that file and all associated assets, and if we choose to use it we will download it and place it on our server./p> /div--> div classbox-border relative mt-10% m-0 p-5% idzen-benefits rolearticle style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;background:rgba(255,255,255,0.9);margin-top:0px> !--h3 style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;font-family:tablet-gothic-condensed,arial narrow,arial,verdana,sans-serif classbox-border text-2.25em font-extralight tracking-1px leading-1em m-0 pt-0.5em pb-0.25em px-0>Benefits/h3--> p style-moz-box-sizing:border-box;-webkit-box-sizing:border-box; classbox-border text-1em font-normal leading-1.5em m-0 px-0 py-0.5em;>However, we can make this even faster using the parallel utility. Here is how that looks:/p> pre>code>module load parallelgnuparallel bwa mem arctos.fna.gz {}_1.fastq {}_2.fastq > test_{}.mapped.sam \::: SRR518710 SRR518711 SRR518712 SRR518713 SRR518717/code>/pre> p style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border text-1em font-normal leading-1.5em m-0 px-0 py-0.5em>Using this utility, it took me an average of 24 minutes, 11 seconds to run this script. That is another 10% decrease in runtime (22% decrease in total compared to the first method). Plus, in my opinion, the code ends up a bit cleaner. As an added bonus, memory usage is lower using this method than the second method using & (27% memory efficiency, 94% CPU efficiency)./p> p style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border text-1em font-normal leading-1.5em m-0 px-0 py-0.5em>Here is an article that explains what the parallel utility is doing and why it is so much faster: a hrefhttps://www.biostars.org/p/63816/>https://www.biostars.org/p/63816//a>/p> p rolecontentinfo style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border text-1em leading-1.5em font-light tracking-2px uppercase mt-1em m-0 pt-1.5em px-0 py-0.5em border-t-#ea2e49 border-t border-solid>By a hrefhttp://www.mezzoblue.com/ style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;-moz-transition:border-color 0.2s ease-in-out;-ms-transition:border-color 0.2s ease-in-out;-o-transition:border-color 0.2s ease-in-out;-webkit-transition:border-color 0.2s ease-in-out classbox-border text-#333 no-underline transition-border-color duration-0.2s ease-ease-in-out m-0 p-0 border-b-rgba(0,0,0,0.2) border-b border-solid>Dave Shea/a>. Bandwidth graciously donated by a hrefhttp://www.mediatemple.net/ style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;-moz-transition:border-color 0.2s ease-in-out;-ms-transition:border-color 0.2s ease-in-out;-o-transition:border-color 0.2s ease-in-out;-webkit-transition:border-color 0.2s ease-in-out classbox-border text-#333 no-underline transition-border-color duration-0.2s ease-ease-in-out m-0 p-0 border-b-rgba(0,0,0,0.2) border-b border-solid>mediatemple/a>. Now available: a hrefhttps://www.amazon.com/exec/obidos/ASIN/0321303474/mezzoblue-20/ style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;-moz-transition:border-color 0.2s ease-in-out;-ms-transition:border-color 0.2s ease-in-out;-o-transition:border-color 0.2s ease-in-out;-webkit-transition:border-color 0.2s ease-in-out classbox-border text-#333 no-underline transition-border-color duration-0.2s ease-ease-in-out m-0 p-0 border-b-rgba(0,0,0,0.2) border-b border-solid>Zen Garden, the book/a>./p> /div>!--  div classbox-border relative m-0 p-5% idzen-requirements rolearticle style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;background:rgba(255,255,255,0.9)> h3 style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;font-family:tablet-gothic-condensed,arial narrow,arial,verdana,sans-serif classbox-border text-2.25em font-extralight tracking-1px leading-1em m-0 pt-0.5em pb-0.25em px-0>Requirements/h3> p style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border text-1em font-normal leading-1.5em m-0 px-0 py-0.5em>Where possible, we would like to see mostly abbr titleCascading Style Sheets, levels 1 and 2 style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border m-0 p-0>CSS 1 & 2/abbr> usage. abbr titleCascading Style Sheets, levels 3 and 4 style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border m-0 p-0>CSS 3 & 4/abbr> should be limited to widely-supported elements only, or strong fallbacks should be provided. The CSS Zen Garden is about functional, practical abbr titleCascading Style Sheets style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border m-0 p-0>CSS/abbr> and not the latest bleeding-edge tricks viewable by 2% of the browsing public. The only real requirement we have is that your abbr titleCascading Style Sheets style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border m-0 p-0>CSS/abbr> validates./p> p style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border text-1em font-normal leading-1.5em m-0 px-0 py-0.5em>Luckily, designing this way shows how well various browsers have implemented abbr titleCascading Style Sheets style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border m-0 p-0>CSS/abbr> by now. When sticking to the guidelines you should see fairly consistent results across most modern browsers. Due to the sheer number of user agents on the web these days — especially when you factor in mobile — pixel-perfect layouts may not be possible across every platform. That’s okay, but do test in as many as you can. Your design should work in at least IE9+ and the latest Chrome, Firefox, iOS and Android browsers (run by over 90% of the population)./p> p style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border text-1em font-normal leading-1.5em m-0 px-0 py-0.5em>We ask that you submit original artwork. Please respect copyright laws. Please keep objectionable material to a minimum, and try to incorporate unique and interesting visual themes to your work. We’re well past the point of needing another garden-related design./p> p style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border text-1em font-normal leading-1.5em m-0 px-0 py-0.5em>This is a learning exercise as well as a demonstration. You retain full copyright on your graphics (with limited exceptions, see a hrefhttps://csszengarden.com/pages/submit/guidelines/ style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;-moz-transition:border-color 0.2s ease-in-out;-ms-transition:border-color 0.2s ease-in-out;-o-transition:border-color 0.2s ease-in-out;-webkit-transition:border-color 0.2s ease-in-out classbox-border text-#333 no-underline transition-border-color duration-0.2s ease-ease-in-out m-0 p-0 border-b-rgba(0,0,0,0.2) border-b border-solid>submission guidelines/a>), but we ask you release your abbr titleCascading Style Sheets style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border m-0 p-0>CSS/abbr> under a Creative Commons license identical to the a hrefhttp://creativecommons.org/licenses/by-nc-sa/3.0/ titleView the Zen Gardens license information. style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;-moz-transition:border-color 0.2s ease-in-out;-ms-transition:border-color 0.2s ease-in-out;-o-transition:border-color 0.2s ease-in-out;-webkit-transition:border-color 0.2s ease-in-out classbox-border text-#333 no-underline transition-border-color duration-0.2s ease-ease-in-out m-0 p-0 border-b-rgba(0,0,0,0.2) border-b border-solid>one on this site/a> so that others may learn from your work./p> p rolecontentinfo style-moz-box-sizing:border-box;-webkit-box-sizing:border-box classbox-border text-1em leading-1.5em font-light tracking-2px uppercase mt-1em m-0 pt-1.5em px-0 py-0.5em border-t-#ea2e49 border-t border-solid>By a hrefhttp://www.mezzoblue.com/ style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;-moz-transition:border-color 0.2s ease-in-out;-ms-transition:border-color 0.2s ease-in-out;-o-transition:border-color 0.2s ease-in-out;-webkit-transition:border-color 0.2s ease-in-out classbox-border text-#333 no-underline transition-border-color duration-0.2s ease-ease-in-out m-0 p-0 border-b-rgba(0,0,0,0.2) border-b border-solid>Dave Shea/a>. Bandwidth graciously donated by a hrefhttp://www.mediatemple.net/ style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;-moz-transition:border-color 0.2s ease-in-out;-ms-transition:border-color 0.2s ease-in-out;-o-transition:border-color 0.2s ease-in-out;-webkit-transition:border-color 0.2s ease-in-out classbox-border text-#333 no-underline transition-border-color duration-0.2s ease-ease-in-out m-0 p-0 border-b-rgba(0,0,0,0.2) border-b border-solid>mediatemple/a>. Now available: a hrefhttp://www.amazon.com/exec/obidos/ASIN/0321303474/mezzoblue-20/ style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;-moz-transition:border-color 0.2s ease-in-out;-ms-transition:border-color 0.2s ease-in-out;-o-transition:border-color 0.2s ease-in-out;-webkit-transition:border-color 0.2s ease-in-out classbox-border text-#333 no-underline transition-border-color duration-0.2s ease-ease-in-out m-0 p-0 border-b-rgba(0,0,0,0.2) border-b border-solid>Zen Garden, the book/a>./p> /div> --> footer style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;background:rgba(246,247,146,0.9) classbox-border relative clear-both text-white w-6/12 m-0 px-5% py-1em> a hrefhttps://github.com/bwentzloff titleGithub link to Brian Wentzloffs Github classbox-border text-#333 no-underline transition-border-color duration-0.2s ease-ease-in-out mr-0.5em m-0 p-0 border-b-rgba(0,0,0,0.2) border-b border-solid style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;-moz-transition:border-color 0.2s ease-in-out;-ms-transition:border-color 0.2s ease-in-out;-o-transition:border-color 0.2s ease-in-out;-webkit-transition:border-color 0.2s ease-in-out>GH/a> a hrefhttps://www.linkedin.com/in/brianwentzloff/ titleLink to Brian Wentzloffs LinkedIn classbox-border text-#333 no-underline transition-border-color duration-0.2s ease-ease-in-out mr-0.5em m-0 p-0 border-b-rgba(0,0,0,0.2) border-b border-solid style-moz-box-sizing:border-box;-webkit-box-sizing:border-box;-moz-transition:border-color 0.2s ease-in-out;-ms-transition:border-color 0.2s ease-in-out;-o-transition:border-color 0.2s ease-in-out;-webkit-transition:border-color 0.2s ease-in-out>LI/a> /footer> /div>/div>div classbox-border relative m-0 p-0 rolepresentation style-moz-box-sizing:border-box;-webkit-box-sizing:border-box>/div>div classbox-border relative m-0 p-0 rolepresentation style-moz-box-sizing:border-box;-webkit-box-sizing:border-box>/div>div classbox-border relative m-0 p-0 rolepresentation style-moz-box-sizing:border-box;-webkit-box-sizing:border-box>/div>div classbox-border relative m-0 p-0 rolepresentation style-moz-box-sizing:border-box;-webkit-box-sizing:border-box>/div>div classbox-border relative m-0 p-0 rolepresentation style-moz-box-sizing:border-box;-webkit-box-sizing:border-box>/div>div classbox-border relative m-0 p-0 rolepresentation style-moz-box-sizing:border-box;-webkit-box-sizing:border-box>/div>/body>/html>

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Domain > brianwentzloff.com

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