Error when creating BLAT Servers Table

[McCully, Dwayne (NIH/NIAMS) [C]]

Hello Genome Mirror Support,

 

When running the update I got the following error and the update stopped. 

Please advise on what to do next?

 

 

sent 55,599 bytes  received 1,084,157 bytes  207,228.36 bytes/sec

total size is 261,114,875  speedup is 229.10

| Creating or updating the BLAT servers table

ERROR at line 1: Unknown command '\-'.

Cannot write to '-' (Broken pipe).

Exit error 1 occurred on line 1

The UCSC Genome Browser installation script exited with an error.

Please contact us at genome...@soe.ucsc.edu and send us an output log

of the command prefixed with "bash -x", e.g.

bash -x browserSetup.sh install 2>&1 > install.log

 

 

Dwayne McCully

NIAMS, NIH, SITB

Contractor

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and reporting your issues.

Could you run the following command and then send us the output to help debug the issues?

bash -x browserSetup.sh install 2>&1 > install.log

We need the last few lines with the error to debug the issues.

If you have any further questions, please reply to genome...@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 Genome Browser

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[Hoover, David (NIH/CIT) [E]]

Here's what I see when I try to create a docker container:

> 79.27 + checkDownloadUdr
> 79.27 + [[ ! -f /usr/local/bin/udr ]]
> 79.27 + echo2 'Downloading download-tool udr (UDP-based rsync with multiple streams) to /usr/local/bin/udr'
> 79.27 + command echo '|' 'Downloading download-tool udr (UDP-based rsync with multiple streams) to /usr/local/bin/udr'
> 79.27 + echo '|' 'Downloading download-tool udr (UDP-based rsync with multiple streams) to /usr/local/bin/udr'
> 79.27 | Downloading download-tool udr (UDP-based rsync with multiple streams) to /usr/local/bin/udr
> 79.27 + waitKey
> 79.27 + echo
> 79.27
> 79.27 + downloadFile http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/udr
> 79.27 + url=http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/udr
> 79.27 + which wget
> 79.27 + wget -nv http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/udr -O -
> 80.19 2025-02-20 18:03:31 URL:http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/udr [2840528/2840528] -> "-" [1]
> 80.19 + chmod a+x /usr/local/bin/udr
> 80.19 + '[' '!' -f /usr/local/apache/cgiInstallComplete.flag ']'
> 80.19 + '[' -f /usr/local/apache ']'
> 80.19 + '[' -d /usr/local/apache -a linux '!=' OSX ']'
> 80.19 + mysqlDbSetup
> 80.19 + echo2
> 80.19 + command echo '|'
> 80.19 + echo '|'
> 80.19 |
> 80.19 + echo2 Creating Mysql databases customTrash, hgTemp and hgcentral
> 80.19 + command echo '|' Creating Mysql databases customTrash, hgTemp and hgcentral
> 80.19 + echo '|' Creating Mysql databases customTrash, hgTemp and hgcentral
> 80.19 | Creating Mysql databases customTrash, hgTemp and hgcentral
> 80.19 + waitKey
> 80.19 + echo
> 80.19
> 80.19 + mysql -e 'CREATE DATABASE IF NOT EXISTS customTrash;'
> 80.20 + mysql -e 'CREATE DATABASE IF NOT EXISTS hgcentral;'
> 80.21 + mysql -e 'CREATE DATABASE IF NOT EXISTS hgTemp;'
> 80.22 + mysql -e 'CREATE DATABASE IF NOT EXISTS hgFixed;'
> 80.22 + updateBlatServers
> 80.22 + echo2 Creating or updating the BLAT servers table
> 80.22 + command echo '|' Creating or updating the BLAT servers table
> 80.22 + echo '|' Creating or updating the BLAT servers table
> 80.22 | Creating or updating the BLAT servers table
> 80.22 + downloadFile http://hgdownload.soe.ucsc.edu/admin/hgcentral.sql
> 80.22 + url=http://hgdownload.soe.ucsc.edu/admin/hgcentral.sql
> 80.22 + which wget
> 80.22 + mysql hgcentral
> 80.23 + wget -nv http://hgdownload.soe.ucsc.edu/admin/hgcentral.sql -O -
> 80.37 ERROR at line 1: Unknown command '\-'.
> 80.44 Cannot write to ‘-’ (Broken pipe).
> 80.44 + exitHandler 1 1
> 80.44 + '[' 1 == 100 -o 1 == 0 ']'
> 80.44 + echo Exit error 1 occurred on line 1
> 80.44 Exit error 1 occurred on line 1
> 80.44 + echo The UCSC Genome Browser installation script exited with an error.
> 80.44 The UCSC Genome Browser installation script exited with an error.
> 80.44 + echo Please contact us at genome...@soe.ucsc.edu and send us an output log
> 80.44 Please contact us at genome...@soe.ucsc.edu and send us an output log
> 80.44 + echo of the command prefixed with '"bash -x",' e.g.
> 80.44 of the command prefixed with "bash -x", e.g.
> 80.44 + echo 'bash -x browserSetup.sh install 2>&1 > install.log'
> 80.44 bash -x browserSetup.sh install 2>&1 > install.log

On 2/19/2025 1:40 PM, 'Jairo Navarro Gonzalez' via UCSC Genome Browser Mirror-Specific Support wrote:
> Hello,
>
> Thank you for using the UCSC Genome Browser and reporting your issues.
>
> Could you run the following command and then send us the output to help debug the issues?
>
> bash -x browserSetup.sh install 2>&1 > install.log
>
> We need the last few lines with the error to debug the issues.
>

> If you have any further questions, please reply to genome...@soe.ucsc.edu <mailto:genome...@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 <mailto:genom...@soe.ucsc.edu>.

>
> Jairo Navarro
> UCSC Genome Browser
>
>

> On Wed, Feb 19, 2025 at 9:36 AM 'McCully, Dwayne (NIH/NIAMS) [C]' via UCSC Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>> wrote:
>
> Hello Genome Mirror Support,____
>
> __ __
>
> When running the update I got the following error and the update stopped. ____
>
> Please advise on what to do next?____
>
> __ __
>
> __ __
>
> sent 55,599 bytes  received 1,084,157 bytes  207,228.36 bytes/sec____
>
> total size is 261,114,875  speedup is 229.10____
>
> | Creating or updating the BLAT servers table____
>
> ERROR at line 1: Unknown command '\-'.____
>
> Cannot write to '-' (Broken pipe).____
>
> Exit error 1 occurred on line 1____
>
> The UCSC Genome Browser installation script exited with an error.____
>
> Please contact us at genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu> and send us an output log____
>
> of the command prefixed with "bash -x", e.g.____
>
> bash -x browserSetup.sh install 2>&1 > install.log____
>
> __ __
>
> __ __
>
> Dwayne McCully____
>
> NIAMS, NIH, SITB____
>
> Contractor____

>
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>
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>
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.

> To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirro...@soe.ucsc.edu>.
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--
David Hoover, Ph.D.
Computational Biologist
High Performance Computing Services,
Center for Information Technology,
National Institutes of Health
12 South Dr., Rm 2N207
Bethesda, MD 20892, USA
TEL: (+1) 301-435-2986
Email: hoov...@hpc.nih.gov

[Hoover, David (NIH/CIT) [E]]

I think the problem is "wget -nv $1 -O -" is getting truncated with a pipefail error.

[Christopher Lee]

Hi David and Dwayne,

The issue here is that we are generating the sql dump with a newer version of mariadb than what is running on your servers/docker containers and the newer version is including an invalid command on your machines. We are discussing internally how best to move forward and will update here once we have made a decision.

Thanks,

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[McCully, Dwayne (NIH/NIAMS) [C]]

Thank you!!

 

Dwayne

To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAC7r7-JZ54HMtZsHH4mbvrY-c6O1_FJHWXB5VkrCAJe%3DypT8dg%40mail.gmail.com.

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[Christopher Lee]

Hi Everyone,

We have regenerated the table dump, you should be able to re-run your installation scripts as you were before. Let us know if everything is working.

Thanks,

[McCully, Dwayne (NIH/NIAMS) [C]]

Hi Christopher,

 

I have rerun the browserSetup.sh script and it completed successfully. 

 

Thanks to everyone for the assistance!!

 

Dwayne

 

Dwayne McCully

NIAMS, NIH

Contractor