Possible BLAT issue on RHEL 7 / Apache 2.4.6
Jacob Albretsen
We are trying to get a Genome Browser in Cloud instance working
internally. Our setup is as follows:
- Red Hat Enterprise Linux 7.3 with SELinux disabled
- Apache: 2.4.6-45.el7
- Installed using the browserSetup.sh script.
Note, I made minior changes to the install script. It was designed to
look for the old SysV scripts, however RHEL / CentOS 7 uses systemd as
its init process. I modified a number of lines to make use of that. I
can send you a diff if you need one or would like ideas on how to
improve the script.
Everything is working great as far as we can tell with the exception of
hgBlat. When we run a query sequence 250bp or below, the results work.
With a query sequence larger than 250bp, the result times out. I looked
at the Apache error logs and found this message (IP and hostnames removed):
[Wed Apr 26 13:53:53.423026 2017] [core:error] [pid 1683] (70007)The
timeout specified has expired: [client <<REMOVED IP>>:59972] AH00574:
ap_content_length_filte
r: apr_bucket_read() failed, referer: http://<<REMOVED
HOSTNAME>>/cgi-bin/hgBlat
From experience and research into Apache, I added the following line to
the 001-browser.conf file:
Timeout 600
This fixed the timeout error, however now there is a string length error.
[Fri Apr 28 13:13:56.260513 2017] [cgi:error] [pid 16709] [client
10.31.1.50:45778] AH01215: [Fri Apr 28 13:13:56 201] [hgBlat] [client <<
REMOVED IP>>] [hgsid=59_7Au4bN43WLoLqUmO5DxFV] [/cgi-bin/hgBlat]
Couldn't read string length, referer: http://<<REMOVED
HOSTNAME>>/cgi-bin/hgBlat
This appears to be a message from hgBlat. Running a Google search on
the message returns the Genome Browser source code.
Any help you could give us to fix this issue so we can run larger
sequences would be much appreciated.
Thanks!
--
Jacob Albretsen
jalb...@myriad.com
Myriad Genetics
Linux System Engineer
Jairo Navarro Gonzalez
Hello Jacob,
Thank you for using the UCSC Genome Browser and reporting your BLAT issues.
Our engineers have shared that this seems to be an issue some users have when talking to our servers since we are using Jumbo frames. To help troubleshoot, could you answer the following questions:
1. Is this is a local bare metal server, a VM, or a commercial cloud service like AWS?
2. What command-line options did you give to browserSetup.sh when installing?
3. Does this curl command work without errors?
4. What does tracepath say?
I look forward to your reply. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Jairo Navarro
UCSC Genomics Institute
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Jacob Albretsen
Hello Jacob,
Thank you for using the UCSC Genome Browser and reporting your BLAT issues.
Our engineers have shared that this seems to be an issue some users have when talking to our servers since we are using Jumbo frames. To help troubleshoot, could you answer the following questions:
1. Is this is a local bare metal server, a VM, or a commercial cloud service like AWS?
2. What command-line options did you give to browserSetup.sh when installing?
browserSetup.sh install browserSetup.sh minimal hg19 hg38 browserSetup.sh addTools
3. Does this curl command work without errors?
4. What does tracepath say?
1: gateway.myriad.com 1.776ms
1: gateway.myriad.com 0.489ms
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Too many hops: pmtu 1500
Resume: pmtu 1500
Cath Tyner
Thank you for providing additional details in your last response. Can you please try running gfClient, to test the blat connection? Please respond to th
https://genome.ucsc.edu/goldenpath/help/blatSpec.html#gfClientUsage
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Cath Tyner
I meant to include this related mailing list question, which includes an example of using gfServer/Client
You can also search our support archives for more information.
Jacob Albretsen
Cath,
Sorry it's taken a while to get back to you.
I was able to use hg19.2bit to create a gfServer. Note I had to download the nearly 800M file to do so.
From here I was able to do several queries using gfClient and get results, including ones larger than 250bp. Example (paste is wrapped, but you get the idea):
# /usr/local/bin/blat/gfClient localhost 17779 . testQuery333.fa
output333.psl
Output is in output333.psl
# cat output333.psl
psLayout version 3
match mis- rep. N's Q gap Q gap T gap T
gap strand Q Q Q Q T
T T T block blockSizes qStarts
tStarts
match match count bases count
bases name size start end name
size start end count
---------------------------------------------------------------------------------------------------------------------------------------------------------------
333 0 0 0 0 0 0 0 - BARD1_11_333bp
333 0 333 chr2 243199373 215593399 215593732
1 333, 0, 215593399,
Does this indicate that the issue may very well be network restrictions?
Thanks!
- Jake
Chris Villarreal
Dear Jacob,
Apologies for the delayed response and for sending an incorrect example of the gfServer test. The gfServer test was meant for the UCSC server, not localhost. Could you please send us the output of the following commands:
twoBitToFa "http://hgdownload.soe.ucsc.edu/gbdb/hg38/hg38.2bit:chrM" in.fa
gfClient blat1a.cse.ucsc.edu 17779 seqDir in.fa out.psl
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
-Chris V
UCSC Genome Browser
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/508f42e0-f4a8-5ecd-beb3-17c58e85ad8d%40myriad.com.