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add computer maintenance nb
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kubu4 committed Dec 22, 2023
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95 changes: 49 additions & 46 deletions docs/index.xml
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<guid>https://robertslab.github.io/sams-notebook/posts/2023/2023-12-18-Samples-Submitted---Gadus-macrocephalus-liver-tissues-to-Azenta-for-RNA-seq/index.html</guid>
<pubDate>Mon, 18 Dec 2023 08:00:00 GMT</pubDate>
</item>
<item>
<title>Computer Management - Replace Failing HDDs on Gannet Expansion Unit (Synology RX1217)</title>
<dc:creator>Sam White</dc:creator>
<link>https://robertslab.github.io/sams-notebook/posts/2023/2023-12-10-Computer-Management---Replace-Failing-HDDs-on-Gannet-Expansion-Unit-(Synology-RX1217)/index.html</link>
<description><![CDATA[




<p>Started receiving alerts from Gannet (Synology RS3618XS) that three drives were failing and in a “critical state” in the expansion unit (Rynology RX1217) in late November 2023. Ordered three replacement drives (Seagate Iron Wolf Pro; 16TB) and they finally arrived. I swapped two of the drives, following the Synology Storage Manager wizard, but had to wait for the drives to go through various checks before I could install the third (will do this this weekend).</p>
<p>However, when trying to investigate the drive failures using Seagate’s SeaTools, both drives passed the “generic short test”. However, neither drive could complete the “generic long test.” No errors were generated, just that the “generic long test” failed. When I registered the drives with Seagate, Seagate indicated that the drives’ warranties ended on 11/27/2023! These were brand new drives purchased in July 2023! The warranty should be significantly longer than 5 months.</p>
<p>Will reach out to the vendor via Amazon to see what can be done about this…</p>



]]></description>
<category>HDD</category>
<category>Synology</category>
<category>Gannet</category>
<category>Seagate</category>
<category>RX1217</category>
<category>Computer Management</category>
<guid>https://robertslab.github.io/sams-notebook/posts/2023/2023-12-10-Computer-Management---Replace-Failing-HDDs-on-Gannet-Expansion-Unit-(Synology-RX1217)/index.html</guid>
<pubDate>Sun, 10 Dec 2023 08:00:00 GMT</pubDate>
</item>
<item>
<title>Data Investigation - Mysterious Case of Excessive Exons in CEABIGR</title>
<dc:creator>Sam White</dc:creator>
Expand Down Expand Up @@ -1792,7 +1817,14 @@ font-style: inherit;">print</span>(exon.count.ncbi.gff)</span></code></pre></div


<section id="section" class="level2">
<h2 class="anchored" data-anchor-id="section">20231218</h2>
<h2 class="anchored" data-anchor-id="section">2023129</h2>
<ul>
<li><p>Read Ch.3 of “Race After Technology: The New Jim Code”</p></li>
<li><p>Helped get Lindasy Alma set up for qPCRs and usage of the PCR Workstation in FTR 213.</p></li>
</ul>
</section>
<section id="section-1" class="level2">
<h2 class="anchored" data-anchor-id="section-1">20231218</h2>
<section id="in-lab" class="level3">
<h3 class="anchored" data-anchor-id="in-lab">In lab</h3>
<ul>
Expand All @@ -1801,8 +1833,8 @@ font-style: inherit;">print</span>(exon.count.ncbi.gff)</span></code></pre></div
</ul>
</section>
</section>
<section id="section-1" class="level2">
<h2 class="anchored" data-anchor-id="section-1">20231215</h2>
<section id="section-2" class="level2">
<h2 class="anchored" data-anchor-id="section-2">20231215</h2>
<section id="coral-e5-github-repo" class="level3">
<h3 class="anchored" data-anchor-id="coral-e5-github-repo"><a href="https://github.com/urol-e5/deep-dive">Coral E5</a> (GitHub repo)</h3>
<ul>
Expand All @@ -1816,17 +1848,17 @@ font-style: inherit;">print</span>(exon.count.ncbi.gff)</span></code></pre></div
</ul>
</section>
</section>
<section id="section-2" class="level2">
<h2 class="anchored" data-anchor-id="section-2">20231214</h2>
<section id="section-3" class="level2">
<h2 class="anchored" data-anchor-id="section-3">20231214</h2>
<section id="hackweek" class="level3">
<h3 class="anchored" data-anchor-id="hackweek">Hackweek</h3>
<ul>
<li>Helped with Hisat2/Stringtie stuff.</li>
</ul>
</section>
</section>
<section id="section-3" class="level2">
<h2 class="anchored" data-anchor-id="section-3">20231213</h2>
<section id="section-4" class="level2">
<h2 class="anchored" data-anchor-id="section-4">20231213</h2>
<section id="hackweek-1" class="level3">
<h3 class="anchored" data-anchor-id="hackweek-1">Hackweek</h3>
<ul>
Expand All @@ -1835,17 +1867,17 @@ font-style: inherit;">print</span>(exon.count.ncbi.gff)</span></code></pre></div
</ul>
</section>
</section>
<section id="section-4" class="level2">
<h2 class="anchored" data-anchor-id="section-4">20231211</h2>
<section id="section-5" class="level2">
<h2 class="anchored" data-anchor-id="section-5">20231211</h2>
<section id="hackweek-2" class="level3">
<h3 class="anchored" data-anchor-id="hackweek-2">Hackweek</h3>
<ul>
<li>Worked on broken URLs in notebook and lab website.</li>
</ul>
</section>
</section>
<section id="section-5" class="level2">
<h2 class="anchored" data-anchor-id="section-5">20231206</h2>
<section id="section-6" class="level2">
<h2 class="anchored" data-anchor-id="section-6">20231206</h2>
<section id="ceabigr-github-repo-1" class="level3">
<h3 class="anchored" data-anchor-id="ceabigr-github-repo-1"><a href="https://github.com/sr320/ceabigr">CEABIGR</a> (GitHub repo)</h3>
<ul>
Expand All @@ -1859,8 +1891,8 @@ font-style: inherit;">print</span>(exon.count.ncbi.gff)</span></code></pre></div
</ul>
</section>
</section>
<section id="section-6" class="level2">
<h2 class="anchored" data-anchor-id="section-6">20231205</h2>
<section id="section-7" class="level2">
<h2 class="anchored" data-anchor-id="section-7">20231205</h2>
<p><a href="https://github.com/sr320/ceabigr">CEABIGR</a> (GitHub repo)</p>
<ul>
<li>Started to investigate weird exon count issues identified last week.</li>
Expand All @@ -1870,15 +1902,15 @@ font-style: inherit;">print</span>(exon.count.ncbi.gff)</span></code></pre></div
<li>It was decided to have everyone begin writing their methods in the manuscript.</li>
</ul>
</section>
<section id="section-7" class="level2">
<h2 class="anchored" data-anchor-id="section-7">20231204</h2>
<section id="section-8" class="level2">
<h2 class="anchored" data-anchor-id="section-8">20231204</h2>
<p><a href="https://github.com/urol-e5/deep-dive">Coral E5</a> (GitHub repo)</p>
<ul>
<li>Updated multiple README files</li>
</ul>
</section>
<section id="section-8" class="level2">
<h2 class="anchored" data-anchor-id="section-8">20231201</h2>
<section id="section-9" class="level2">
<h2 class="anchored" data-anchor-id="section-9">20231201</h2>
<p>-<a href="https://github.com/urol-e5/deep-dive">Coral E5</a> (GitHub repo) Meeting</p>
<ul>
<li><p>Revisit trimming.</p>
Expand Down Expand Up @@ -12286,34 +12318,5 @@ font-style: inherit;">&gt;&gt;</span> system_path.log</span></code></pre></div>
<guid>https://robertslab.github.io/sams-notebook/posts/2023/2023-07-26-Read-Extractions---M.magister-MEGAN-Arthropoda-and-Unassigned-Reads-to-FastA/index.html</guid>
<pubDate>Wed, 26 Jul 2023 13:50:00 GMT</pubDate>
</item>
<item>
<title>RNA Quantification - C.gigas PolyIC</title>
<dc:creator>Sam White</dc:creator>
<link>https://robertslab.github.io/sams-notebook/posts/2023/2023-07-21-RNA-Quantification---C.gigas-PolyIC/index.html</link>
<description><![CDATA[




<p>Steven <a href="https://github.com/RobertsLab/resources/issues/1675">asked me to generate cDNA</a> (GitHub Issue) from <a href="http://en.wikipedia.org/wiki/Pacific_oyster"><em>Crassostrea gigas</em> (Pacific oyster)</a> RNA, as part of Matt George’s polyIC project. Before starting reverse transcription, I felt it would be best to quantify the RNA using the Qubit 3.0 using the Broad Range Assay. Steven and I discussed which samples to use earlier this week.</p>
<p>Used 1uL of each sample.</p>
<p>See Results section below for sample/tube labels.</p>
<hr>
<section id="results" class="level1">
<h1>RESULTS</h1>
<ul>
<li><a href="https://docs.google.com/spreadsheets/d/16No1oXbb9foftO--AYqzoJY2jbyLrqUS8AZpjYkU7KU/edit#gid=1874673482">20230721-qubit-cgig-polyIC-RNA</a> (Google Sheet)</li>
</ul>
<p>All samples had ample amount of RNA. Will proceed with reverse transcription.</p>


</section>

]]></description>
<category>2023</category>
<category>Miscellaneous</category>
<guid>https://robertslab.github.io/sams-notebook/posts/2023/2023-07-21-RNA-Quantification---C.gigas-PolyIC/index.html</guid>
<pubDate>Fri, 21 Jul 2023 19:29:00 GMT</pubDate>
</item>
</channel>
</rss>
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</url>
<url>
<loc>https://robertslab.github.io/sams-notebook/posts/2023/2023-12-01-Daily-Bits---December-2023/index.html</loc>
<lastmod>2023-12-19T15:55:36.478Z</lastmod>
<lastmod>2023-12-19T22:12:50.853Z</lastmod>
</url>
<url>
<loc>https://robertslab.github.io/sams-notebook/posts/2023/2023-01-03-Daily-Bits---January-2023/index.html</loc>
Expand Down Expand Up @@ -5970,10 +5970,14 @@
</url>
<url>
<loc>https://robertslab.github.io/sams-notebook/index.html</loc>
<lastmod>2023-12-19T15:59:11.186Z</lastmod>
<lastmod>2023-12-22T00:32:11.509Z</lastmod>
</url>
<url>
<loc>https://robertslab.github.io/sams-notebook/posts/2023/2023-12-18-Samples-Submitted---Gadus-macrocephalus-liver-tissues-to-Azenta-for-RNA-seq/index.html</loc>
<lastmod>2023-12-19T14:30:18.067Z</lastmod>
</url>
<url>
<loc>https://robertslab.github.io/sams-notebook/posts/2023/2023-12-10-Computer-Management---Replace-Failing-HDDs-on-Gannet-Expansion-Unit-(Synology-RX1217)/index.html</loc>
<lastmod>2023-12-22T00:26:03.269Z</lastmod>
</url>
</urlset>
22 changes: 22 additions & 0 deletions ...er-Management---Replace-Failing-HDDs-on-Gannet-Expansion-Unit-(Synology-RX1217)/index.qmd
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---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
title: Computer Management - Replace Failing HDDs on Gannet Expansion Unit (Synology RX1217)
date: '2023-12-10'
draft: false
engine: knitr
categories:
- HDD
- Synology
- Gannet
- Seagate
- RX1217
- Computer Management
---
Started receiving alerts from Gannet (Synology RS3618XS) that three drives were failing and in a "critical state" in the expansion unit (Rynology RX1217) in late November 2023. Ordered three replacement drives (Seagate Iron Wolf Pro; 16TB) and they finally arrived. I swapped two of the drives, following the Synology Storage Manager wizard, but had to wait for the drives to go through various checks before I could install the third (will do this this weekend).

However, when trying to investigate the drive failures using Seagate's SeaTools, both drives passed the "generic short test". However, neither drive could complete the "generic long test." No errors were generated, just that the "generic long test" failed. When I registered the drives with Seagate, Seagate indicated that the drives' warranties ended on 11/27/2023! These were brand new drives purchased in July 2023! The warranty should be significantly longer than 5 months.

Will reach out to the vendor via Amazon to see what can be done about this...

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