Issue in UCSC database access

[LinduniR]

Hi,
I tried to get output files for example data using $ GenEpi -g example -p example -o ./ command. But, I got an error:
pymysql.err.OperationalError: (2003, "Can't connect to MySQL server on 'genome-mysql.cse.ucsc.edu' (timed out)")

I searched for "genome-mysql.cse.ucsc.edu'. But, it is not available.

So, It would be really appreciated if you can give any suggestion to overcome this problem.

Thank you in advance.

[Chester75321]

Hi, May I ask that did you use GenEpi through a campus network? Sometimes, the error raises because the firewall of the campus network would block the connection of the UCSC genome database. Switching to another network may help. Otherwise, could you please try the following commands on your terminal? mysql --user=genome --host=genome-mysql.cse.ucsc.edu mysql --user=genome --host=genome-mysql.*soe.*ucsc.edu I found that UCSC updated their domain of the database. I can update GenEpi for you if the new connection string work. Thanks a lot. Chester LinduniR <notifications@github.com> 於 2020年5月24日 週日 下午5:47寫道：

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Hi, I tried to get output files for example data using $ GenEpi -g example -p example -o ./ command. But, I got an error: pymysql.err.OperationalError: (2003, "Can't connect to MySQL server on ' genome-mysql.cse.ucsc.edu' (timed out)") I searched for "genome-mysql.cse.ucsc.edu'. But, it is not available. So, It would be really appreciated if you can give any suggestion to overcome this problem. Thank you in advance. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#4>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADUJNCYVPV3TS6ROONZPHRDRTDULNANCNFSM4NI2DFZA> .

[LinduniR]

Hi Chester, Sorry for late reply. I'm using HPC system provided by the campus for my analysis. HPC support at QUT suggested me to download gene information from UCSC and create UCSCGenomeDatabase.txt file outside HPC environment. And use UCSCGenomeDatabase.txt file for further analysis using HPC. I think I can run the command $ GenEpi -g example -p example -o ./ as I have to skip the first step. To do what HPC support in my campus suggested, after creating UCSCGenomeDatabase.txt file, I have to run script for each step mentioned in GenEpi package, manually with Python. Am I correct? Is there any other way to do that? Thank you in advance. Kind Regards, Linduni

________________________________ From: Chester <notifications@github.com> Sent: Tuesday, May 26, 2020 2:00 PM To: Chester75321/GenEpi <GenEpi@noreply.github.com> Cc: Linduni Rodrigo <undugodage.rodrigo@hdr.qut.edu.au>; Author <author@noreply.github.com> Subject: Re: [Chester75321/GenEpi] Issue in UCSC database access (#4) Hi, May I ask that did you use GenEpi through a campus network? Sometimes, the error raises because the firewall of the campus network would block the connection of the UCSC genome database. Switching to another network may help. Otherwise, could you please try the following commands on your terminal? mysql --user=genome --host=genome-mysql.cse.ucsc.edu mysql --user=genome --host=genome-mysql.*soe.*ucsc.edu I found that UCSC updated their domain of the database. I can update GenEpi for you if the new connection string work. Thanks a lot. Chester LinduniR <notifications@github.com> 於 2020年5月24日 週日 下午5:47寫道：

Hi, I tried to get output files for example data using $ GenEpi -g example -p example -o ./ command. But, I got an error: pymysql.err.OperationalError: (2003, "Can't connect to MySQL server on ' genome-mysql.cse.ucsc.edu' (timed out)") I searched for "genome-mysql.cse.ucsc.edu'. But, it is not available. So, It would be really appreciated if you can give any suggestion to overcome this problem. Thank you in advance. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#4><https://urldefense.com/v3/__https://github.com/Chester75321/GenEpi/issues/4*3E__;JQ!!NVzLfOphnbDXSw!UpCnfYup5n5bdt-MilPyyhX5QJR8d51IH4EnpMFaZdkag0CiyJllXgMWZ7vow7HXfVKoJpWmw2iccw$>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADUJNCYVPV3TS6ROONZPHRDRTDULNANCNFSM4NI2DFZA><https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ADUJNCYVPV3TS6ROONZPHRDRTDULNANCNFSM4NI2DFZA*3E__;JQ!!NVzLfOphnbDXSw!UpCnfYup5n5bdt-MilPyyhX5QJR8d51IH4EnpMFaZdkag0CiyJllXgMWZ7vow7HXfVKoJpVBqUBQRA$> .

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[Chester75321]

Hi Linduni, The command $ GenEpi -g example -p example -o ./ is only for a quick test, which only takes few minutes on any common laptop to obtain the result. I thought it could be run on a laptop directly outside the HPC environment. For your real data, using the HPC system is a good choice, but you don't have run script for each step manually with Python. You could use the optional argument -s (self-defined genome regions) to provide the genome database for GenEpi and skip the step for downloading the UCSC database. The command would be like this: $ GenEpi -g path_to/your.gen -p path_to/your.csv - s path_to/UCSCGenomeDatabase.txt -o ./ (please see: https://genepi.readthedocs.io/en/latest/example.html#self-defined-genome-region). The default genome build of the UCSCGenomeDatabase.txt is hg19, which could be download from here: https://github.com/Chester75321/GenEpi/tree/master/genepi. If you're using other genome builds, please let me know. I could download them for you. Moreover, I released a new version of GenEpi (v.2.0.10), including an update for the host of the UCSC database. Maybe it could solve the problem from the campus network. Please give it a try if you like. Thanks a lot. Best, Chester LinduniR <notifications@github.com> 於 2020年6月2日 週二 上午9:15寫道：

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Hi Chester, Sorry for late reply. I'm using HPC system provided by the campus for my analysis. HPC support at QUT suggested me to download gene information from UCSC and create UCSCGenomeDatabase.txt file outside HPC environment. And use UCSCGenomeDatabase.txt file for further analysis using HPC. I think I can run the command $ GenEpi -g example -p example -o ./ as I have to skip the first step. To do what HPC support in my campus suggested, after creating UCSCGenomeDatabase.txt file, I have to run script for each step mentioned in GenEpi package, manually with Python. Am I correct? Is there any other way to do that? Thank you in advance. Kind Regards, Linduni ________________________________ From: Chester ***@***.***> Sent: Tuesday, May 26, 2020 2:00 PM To: Chester75321/GenEpi ***@***.***> Cc: Linduni Rodrigo ***@***.***>; Author < ***@***.***> Subject: Re: [Chester75321/GenEpi] Issue in UCSC database access (#4) Hi, May I ask that did you use GenEpi through a campus network? Sometimes, the error raises because the firewall of the campus network would block the connection of the UCSC genome database. Switching to another network may help. Otherwise, could you please try the following commands on your terminal? mysql --user=genome --host=genome-mysql.cse.ucsc.edu mysql --user=genome --host=genome-mysql.*soe.*ucsc.edu I found that UCSC updated their domain of the database. I can update GenEpi for you if the new connection string work. Thanks a lot. Chester LinduniR ***@***.***> 於 2020年5月24日 週日 下午5:47寫道： > Hi, > I tried to get output files for example data using $ GenEpi -g example -p > example -o ./ command. But, I got an error: > pymysql.err.OperationalError: (2003, "Can't connect to MySQL server on ' > genome-mysql.cse.ucsc.edu' (timed out)") > > I searched for "genome-mysql.cse.ucsc.edu'. But, it is not available. > > So, It would be really appreciated if you can give any suggestion to > overcome this problem. > > Thank you in advance. > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#4>< https://urldefense.com/v3/__https://github.com/Chester75321/GenEpi/issues/4*3E__;JQ!!NVzLfOphnbDXSw!UpCnfYup5n5bdt-MilPyyhX5QJR8d51IH4EnpMFaZdkag0CiyJllXgMWZ7vow7HXfVKoJpWmw2iccw$>, or unsubscribe > < https://github.com/notifications/unsubscribe-auth/ADUJNCYVPV3TS6ROONZPHRDRTDULNANCNFSM4NI2DFZA >< https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ADUJNCYVPV3TS6ROONZPHRDRTDULNANCNFSM4NI2DFZA*3E__;JQ!!NVzLfOphnbDXSw!UpCnfYup5n5bdt-MilPyyhX5QJR8d51IH4EnpMFaZdkag0CiyJllXgMWZ7vow7HXfVKoJpVBqUBQRA$> > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub< https://urldefense.com/v3/__https://github.com/Chester75321/GenEpi/issues/4*issuecomment-633795146__;Iw!!NVzLfOphnbDXSw!UpCnfYup5n5bdt-MilPyyhX5QJR8d51IH4EnpMFaZdkag0CiyJllXgMWZ7vow7HXfVKoJpVosYjkZA$>, or unsubscribe< https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/APU2PHPWV7YXN3UJUIT7VLLRTM5EJANCNFSM4NI2DFZA__;!!NVzLfOphnbDXSw!UpCnfYup5n5bdt-MilPyyhX5QJR8d51IH4EnpMFaZdkag0CiyJllXgMWZ7vow7HXfVKoJpXTCdcIwg$>. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADUJNC3WKQUQSHPGOL34BETRURHCNANCNFSM4NI2DFZA> .