[biomart-users] errno: 28 "No space left on device"

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Ray
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[biomart-users] 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.

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Re: [biomart-users] errno: 28 "No space left on device"

Syed Haider-5
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


On Wed, 15 May 2019 at 12:30, Ray <[hidden email]> wrote:
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.

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Ray
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Re: [biomart-users] errno: 28 "No space left on device"

Ray
Great! Thanks for your help!

On Wednesday, May 15, 2019 at 7:54:18 PM UTC+8, Syed Haider wrote:
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


On Wed, 15 May 2019 at 12:30, Ray <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="htwL2PBsAAAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">baili...@...> wrote:
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.


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Re: [biomart-users] errno: 28 "No space left on device"

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

On 15 May 2019, at 14:10, Ray <[hidden email]> wrote:

Great! Thanks for your help!

On Wednesday, May 15, 2019 at 7:54:18 PM UTC+8, Syed Haider wrote:
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


On Wed, 15 May 2019 at 12:30, Ray <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="htwL2PBsAAAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;" class="">baili...@...> wrote:
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.



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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

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Re: [biomart-users] errno: 28 "No space left on device"

Thomas Maurel
Dear Ray,

The issue has now been fixed. 

Thanks a lot for your patience.
Kind Regards,
Thomas

On 16 May 2019, at 14:17, Thomas Maurel <[hidden email]> wrote:

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

On 15 May 2019, at 14:10, Ray <[hidden email]> wrote:

Great! Thanks for your help!

On Wednesday, May 15, 2019 at 7:54:18 PM UTC+8, Syed Haider wrote:
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


On Wed, 15 May 2019 at 12:30, Ray <[hidden email]> wrote:
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.



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To view this discussion on the web, visit https://groups.google.com/d/msgid/biomart-users/f166b06a-655e-4cd7-ad3c-dcc2ad4b1520%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--
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


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For more options, visit https://groups.google.com/d/optout.

--
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

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