[BioC] why 3UTR sequences cannot be obtained any more?

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Fri Jul 3 11:40:02 CEST 2009

Maura, it's not unknown for the biomart database to be down when the data is being upgraded. Go to the ensembl biomart webpage and e mail the helpdesk.

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch on behalf of mauede at alice.it
Sent: Fri 03/07/2009 10:22 AM
To: Bioconductor  List; Martin  Morgan
Subject: [BioC] why 3UTR sequences cannot be obtained any more?
Two days ago I managed to write a crude script (attached), to get 3'UTR sequences, that worked fine. 
Since then I have been working on improving and refining my script and been unable to get 3UTR sequence any more.
Right now I ran the script  that worked two days  ago  (attached) and realized it does not work any longer .... I am shocked .....

I keep getting the following error message:

Error in getBM(c(seqType, type), filters = type, values = id, mart = mart,  :
  Query ERROR: caught BioMart::Exception: non-BioMart die(): DBD::mysql::st execute failed: File './sequence_mart_54/hsapiens_genomic_sequence__dna_chunks__main.MYD' not found (Errcode: 27) at /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Dataset/GenomicSequence/DNAAdaptor.pm line 209.

I even tried to simplify it further asking for fewer and fewer attributes (data) but inevitably it stumbles upon requesting 3utr sequences
even if  I can prove it worked a couple of days ago as I have the email I sent out to the Bioconductor scientists that helped me out at finding the right query attributes and filters combination. My email, dated July 22009, showed some of the extracted 3'utr sequences.
Now I am unable at reproducing the same result running the same script. How come ?

I would appreciate some feedback. 
If the database system is under maintenance or being updated or changed... it's fine.I'd just like to know. 
At the very least I'd like to understand the cause of the failure which I cannot get from the printed error message.

Thank you in advance for your attention.

e tutti i telefonini TIM!
Vai su 

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