<p>I'm trying to run <a href="https://genome-blog.soe.ucsc.edu/blog/2017/03/17/how-portable-is-your-track-hub-use-hubcheck-to-find-out/" rel="nofollow noreferrer">hubCheck utility</a>* from inside Kubernetes Pod but for some reason I get this Network error:</p>
<pre><code># I ran hubCheck hubCheck from inside the pod
$ ./hubCheck -noTracks -verbose=2 ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.0/genome_browser_hub/hub.txt
### kent source version 431 ###
Found 2 problems:
Couldn't open ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.0/genome_browser_hub/hub.txt
TCP non-blocking connect() to ftp.ebi.ac.uk IP 193.62.193.138 timed-out in select() after 10000 milliseconds - Cancelling!
</code></pre>
<p>However, when I run <code>hubCheck</code> locally it works fine.</p>
<pre><code>$ ./hubCheck -noTracks -verbose=2 ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.0/genome_browser_hub/hub.txt
### kent source version 430 ###
1 tracks in sacCer3
1 tracks in mm10
1 tracks in ce10
1 tracks in galGal4
1 tracks in ci2
1 tracks in danRer7
1 tracks in dm6
1 tracks in hg38
</code></pre>
<p>The first thing I checked is if the pod has access to the internet, which was the case as you can see below, I can use curl to download <code>hubCheck</code>:</p>
<pre><code># curl -o tools/hubCheck http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/hubCheck
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 33.2M  100 33.2M    0     0  10.0M      0  0:00:03  0:00:03 --:--:-- 10.0M
</code></pre>
<p>I thought this may be caused by a firewall limiting the access to external URL, but I don't think it's the case because other URLs like the one below is working fine both outside and inside K8s:</p>
<pre><code>$ ./hubCheck -noTracks -verbose=2 http://younglab.wi.mit.edu/mESC_ChIAPET_hub/hub.txt
### kent source version 431 ###
4 tracks in mm9
</code></pre>
<p>Any help on this would be greatly appreciated!</p>
<hr />
<ul>
<li>hub Check is a database which facilitates online UCSC Genome Browser display</li>
</ul>

CC BY-SA 4.0
2022-06-14T12:38:56.883Z
There are not many Kubernetes users here, but you never know. This question is perhaps better answered via UCSC's online support
M__
CC BY-SA 4.0
2022-06-14T13:16:01.623Z
@M__, Thank you, I think I'll do that, I asked on SO but the question didn't get enough attention
Bilal
<networks><ucsc>
Running hubCheck utility from inside K8s's Pod
# Running hubCheck utility from inside K8s's Pod

(Asked by: username_0 on 2022-06-14)

I'm trying to run hubCheck utility* from inside Kubernetes Pod but for some reason I get this Network error:
# I ran hubCheck hubCheck from inside the pod
$ ./hubCheck -noTracks -verbose=2 ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.0/genome_browser_hub/hub.txt
### kent source version 431 ###
Found 2 problems:
Couldn't open ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.0/genome_browser_hub/hub.txt
TCP non-blocking connect() to ftp.ebi.ac.uk IP 193.62.193.138 timed-out in select() after 10000 milliseconds - Cancelling!

However, when I run hubCheck locally it works fine.
$ ./hubCheck -noTracks -verbose=2 ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.0/genome_browser_hub/hub.txt
### kent source version 430 ###
1 tracks in sacCer3
1 tracks in mm10
1 tracks in ce10
1 tracks in galGal4
1 tracks in ci2
1 tracks in danRer7
1 tracks in dm6
1 tracks in hg38

The first thing I checked is if the pod has access to the internet, which was the case as you can see below, I can use curl to download hubCheck:
# curl -o tools/hubCheck http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/hubCheck
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 33.2M  100 33.2M    0     0  10.0M      0  0:00:03  0:00:03 --:--:-- 10.0M

I thought this may be caused by a firewall limiting the access to external URL, but I don't think it's the case because other URLs like the one below is working fine both outside and inside K8s:
$ ./hubCheck -noTracks -verbose=2 http://younglab.wi.mit.edu/mESC_ChIAPET_hub/hub.txt
### kent source version 431 ###
4 tracks in mm9

Any help on this would be greatly appreciated!


hub Check is a database which facilitates online UCSC Genome Browser display

**Tags:** networks, ucsc
> **Comments:**
> **username_1**: There are not many Kubernetes users here, but you never know. This question is perhaps better answered via UCSC's online support  
> **username_0**: @M__, Thank you, I think I'll do that, I asked on SO but the question didn't get enough attention  

---

## 0 answers

