<p>I wanted to know the HGT genes in a Metabacillus strain and I noticed that several papers use HGTector for this purpose. I installed HGTector through conda and tried to download the database for Bacillota using the example codes given on the hgtector github page -</p>
<pre><code>hgtector database -c bacteria -o db1 -t 1239
</code></pre>
<p>The code for Bacillota is 1239. It took an awfully long time (approx. 13h) for the download to end and several warning messages were displayed saying so and so files could not be downloaded. When I checked &quot;db1&quot; only 1000 or so files were there, signifying that the download was incomplete as there are 9112 files under Bacillota. I am not sure if the problem is with my code or because there is not enough disk space or something else. Following are my system and Wifi details :</p>
<pre><code>Lenovo Ideapad, 16GB memory
12th Gen i5 - 1235U x 12 Processor
1 TB Disk capacity
OS = Ubuntu 22.04.3 LTS
Wifi speed = 32Mb/s
</code></pre>
<p>I have posted this on github about 4 days ago but no response yet. If  my disk space is not enough could anyone suggest any other tool to study horizontally transferred genes? I have scanned the web but did not find anything satisfactory.</p>
<p>I ran <code>df -h</code> and it shows ~700 GB of free disk space even after the download of 1000 files which should be around 2 GB.</p>
<p>I've tried again at 'family' level with similar results. I don't think I can use HGTector for now. What do you think of RecentHGT? This is the paper for it - <a href="https://www.frontiersin.org/articles/10.3389/fmicb.2018.00973/full" rel="nofollow noreferrer">link</a></p>
<p>Thank you</p>

CC BY-SA 4.0
2023-10-18T18:06:58.733Z
Have you tried running the download in a different way? Like, can you download the db directly and not through the tool? [They provide links on the github for prebuilt databases](http://www.htslib.org/).
Maximilian Press
CC BY-SA 4.0
2023-10-20T04:38:12.097Z
Yes I did, but I think the disk space is not enough. My system does not show any error related to this but either way, the download stops midway with not so meaningful  warning messages. So I just gave up.
K_081
<genome><bacteria><ecology>
How to use HGTECTOR tool for identifying HGT genes in a bacterial genome?
# How to use HGTECTOR tool for identifying HGT genes in a bacterial genome?

(Asked by: username_0 on 2023-10-15)

I wanted to know the HGT genes in a Metabacillus strain and I noticed that several papers use HGTector for this purpose. I installed HGTector through conda and tried to download the database for Bacillota using the example codes given on the hgtector github page -
hgtector database -c bacteria -o db1 -t 1239

The code for Bacillota is 1239. It took an awfully long time (approx. 13h) for the download to end and several warning messages were displayed saying so and so files could not be downloaded. When I checked "db1" only 1000 or so files were there, signifying that the download was incomplete as there are 9112 files under Bacillota. I am not sure if the problem is with my code or because there is not enough disk space or something else. Following are my system and Wifi details :
Lenovo Ideapad, 16GB memory
12th Gen i5 - 1235U x 12 Processor
1 TB Disk capacity
OS = Ubuntu 22.04.3 LTS
Wifi speed = 32Mb/s

I have posted this on github about 4 days ago but no response yet. If  my disk space is not enough could anyone suggest any other tool to study horizontally transferred genes? I have scanned the web but did not find anything satisfactory.
I ran df -h and it shows ~700 GB of free disk space even after the download of 1000 files which should be around 2 GB.
I've tried again at 'family' level with similar results. I don't think I can use HGTector for now. What do you think of RecentHGT? This is the paper for it - link
Thank you

**Tags:** genome, bacteria, ecology
> **Comments:**
> **username_1**: Have you tried running the download in a different way? Like, can you download the db directly and not through the tool? [They provide links on the github for prebuilt databases](http://www.htslib.org/).  
> **username_0**: Yes I did, but I think the disk space is not enough. My system does not show any error related to this but either way, the download stops midway with not so meaningful  warning messages. So I just gave up.  

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## 0 answers

