error with makeTxDbFromBiomart
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4.4 years ago
bright602 ▴ 50

Hi, I was trying to build the txdb file using the makeTxDbFromBiomart, however, I came across with an error.

The command I typed was :

dicty_txdb <-  makeTxDbFromBiomart(biomart="protists_mart",
+                                      dataset="ddiscoideum_eg_gene",
+                                      host="protists.ensembl.org")


The error message shows:

Download and preprocess the 'transcripts' data frame ... Error in getBM(attributes, filters = bm_filters, values = bm_values, ...) :
Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database protists_mart_38: DBI connect('database=protists_mart_38;host=hh-mysql-eg-mart-web.ebi.ac.uk;port=4599','ensro',...) failed: Can't connect to MySQL server on 'hh-mysql-eg-mart-web.ebi.ac.uk' (111) at /nfs/public/release/ensweb/live/eg_mart/www_91/protists/lib/BioMart/Configuration/DBLocation.pm line 98.


Could you give me some suggestions?

Thanks, Simon

R • 1.3k views
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Are you working behind a firewall? It is possible that the port mentioned 4599 for MySQL is blocked by your firewall.

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Hi, I tried to connect with different networks and it is still having the same error.

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Any luck now? I have had issues connecting to the biomaRt server since around August of 2017. I have to continually retry the connection. It is as if the server has too many requests and is waiting for free slots.