errno: 28 "No space left on device"

[Ray]

When I was using the getSequence to get about 1,2000 sequences, it shows the following error:

Error in getBM(c(seqType, type), filters = c(type, "upstream_flank"),  : 
  Query ERROR: caught BioMart::Exception::Database: Error during query execution: Disk full (/mnt/mysqltmp/#sql_73d3_0.MAI); waiting for someone to free some space... (errno: 28 "No space left on device")

here is my code 

seq=getSequence(id=gene2ensemble$Ensembl_gene_identifier,type='ensembl_gene_id',seqType = 'coding_gene_flank',upstream = 200,mart = ensembl)

the id are a list of ensemble ids.

Please help me solve this problem.

Thanks in advance.

[Syed Haider]

Hi Ray,

Seems like large query leading to exhausting MySQL tmp directory size. I have cc'ed Ensembl team who might be able to help/clear/extend the space. Or perhaps worth breaking down your query in batches i.e send Ensembl IDs in batches of 100 at a time and collate results on client (your) side.

Best wishes,

Syed

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[Ray]

Great! Thanks for your help!

[Thomas Maurel]

Dear Ray,

Thanks a lot for letting us know. I have reported this to our Web team which will look into this as soon as possible.

Apologies for any inconvenience caused,

Kind Regards,

Thomas

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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

[Thomas Maurel]

Dear Ray,

The issue has now been fixed. 

Thanks a lot for your patience.

Kind Regards,

Thomas

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