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dincarnato / RNAFramework

RNA structure probing and post-transcriptional modifications mapping high-throughput data analysis
http://www.rnaframework.com
GNU General Public License v3.0
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Connection to UCSC genome database failed - rf-index #73

Open aharden012 opened 2 weeks ago

aharden012 commented 2 weeks ago

Hello - I am relatively new to bioinformatics in general, so apologies if this is simply me missing something.

I had previously run the rf-index command with no issue, which is why getting this error now is confusing me.

When running: $ rf-index -g hg19 -a refGene -b2 I get the output: [+] Connecting to UCSC genome database (genome-mysql.cse.ucsc.edu:3306)...

[!] Error: Connection to UCSC genome database failed. Please check the genome assembly and try again.

I am able to manually access the genome database, but for some reason the rf-index command cannot. As far as I know, nothing has changed on my end.

Any help would be greatly appreciated. And please let me know if I need to provide more information!

dincarnato commented 2 weeks ago

Hi @aharden012,

I tried and the command works smoothly on my end. Are you using this from two different machines? Is it possible that, for some reason, your University network is blocking MySQL connections (port 3306)?

Best, Danny

dincarnato commented 2 weeks ago

For instance, can you show me the output of the following command: telnet genome-mysql.cse.ucsc.edu 3306