Question

biomaRt File './ensembl_mart_84/mmusculus_gene_ensembl__translation__main.MYD' not found (Errcode: 13)

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Darya Vanichkina ▴ 130

@darya-vanichkina-6050

Last seen 7.8 years ago

Australia/Centenary Institute Universit…

Hi! I'm getting the following error:

  Query ERROR: caught BioMart::Exception::Database: Error during query execution: File './ensembl_mart_84/mmusculus_gene_ensembl__translation__main.MYD' not found (Errcode: 13)

When running the following commands:

annotation_pfam <- getBM(attributes=c("ensembl_gene_id","pfam"), filters = "ensembl_gene_id", values=annotation$Ensembl.Gene.ID, mart=ensembl)
Error in getBM(attributes = c("ensembl_gene_id", "pfam"), filters = "ensembl_gene_id",  :
  Query ERROR: caught BioMart::Exception::Database: Error during query execution: File './ensembl_mart_84/mmusculus_gene_ensembl__translation__main.MYD' not found (Errcode: 13)

annotation_prosite <- getBM(attributes=c("ensembl_gene_id","prosite"), filters = "ensembl_gene_id", values=annotation$Ensembl.Gene.ID, mart=ensembl)
Error in getBM(attributes = c("ensembl_gene_id", "prosite"), filters = "ensembl_gene_id",  :
  Query ERROR: caught BioMart::Exception::Database: Error during query execution: File './ensembl_mart_84/mmusculus_gene_ensembl__translation__main.MYD' not found (Errcode: 13)

annotation_tigrfam <- getBM(attributes=c("ensembl_gene_id","tigrfam"), filters = "ensembl_gene_id", values=annotation$Ensembl.Gene.ID, mart=ensembl)

Error in getBM(attributes = c("ensembl_gene_id", "tigrfam"), filters = "ensembl_gene_id",  :
  Query ERROR: caught BioMart::Exception::Database: Error during query execution: File './ensembl_mart_84/mmusculus_gene_ensembl__translation__main.MYD' not found (Errcode: 13)

annotation$ensembl_gene_id is the column of the count table that I obtained by using featureCounts to the latest gencode annotations. Why is this error occurring?

biomart • 1.9k views

ADD COMMENT • link 8.6 years ago Darya Vanichkina ▴ 130

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Hi Darya,

At the moment I'm unable to reproduce this error. Can you edit your post to include the output from sessionInfo() and the code you use to define the mart. I guess that's something like:

ensembl = useMart("ensembl", dataset = "mmusculus_gene_ensembl")

Then I can check I'm using the same versions of the package and database as you are.

ADD REPLY • link 8.6 years ago Mike Smith ★ 6.6k

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Dear Darya,

I've just tried a similar query on our main website and mirrors and I am unable to reproduce this error as well:

1) useast

ensembl = useMart(dataset = "mmusculus_gene_ensembl", host='useast.ensembl.org', biomart = "ENSEMBL_MART_ENSEMBL")

annotation_pfam <- getBM(attributes=c(“ensembl_gene_id","pfam"), filters="ensembl_gene_id", values="ENSMUSG00000017167", mart = ensembl)

annotation_pfam

    ensembl_gene_id    pfam

1 ENSMUSG00000017167 PF00754

2 ENSMUSG00000017167 PF02210


2) asia

ensembl = useMart(dataset = "mmusculus_gene_ensembl", host='asia.ensembl.org', biomart = "ENSEMBL_MART_ENSEMBL")

annotation_pfam <- getBM(attributes=c(“ensembl_gene_id”,"pfam"), filters="ensembl_gene_id", values="ENSMUSG00000017167", mart = ensembl)

annotation_pfam

    ensembl_gene_id    pfam

1 ENSMUSG00000017167 PF00754

2 ENSMUSG00000017167 PF02210


3) live website 

ensembl = useMart(dataset = "mmusculus_gene_ensembl", host='www.ensembl.org', biomart = "ENSEMBL_MART_ENSEMBL")

annotation_pfam <- getBM(attributes=c(“ensembl_gene_id”,"pfam"), filters="ensembl_gene_id", values="ENSMUSG00000017167", mart = ensembl)

annotation_pfam

    ensembl_gene_id    pfam

1 ENSMUSG00000017167 PF00754

2 ENSMUSG00000017167 PF02210


4) uswest

ensembl = useMart(dataset = "mmusculus_gene_ensembl", host='uswest.ensembl.org', biomart = "ENSEMBL_MART_ENSEMBL")

annotation_pfam <- getBM(attributes=c(“ensembl_gene_id”,"pfam"), filters="ensembl_gene_id", values="ENSMUSG00000017167", mart = ensembl)

annotation_pfam

    ensembl_gene_id    pfam

1 ENSMUSG00000017167 PF00754

2 ENSMUSG00000017167 PF02210

We believe it was a transient error and we are investigating what happened.

In the meantime could you please confirm which host you were using for your query?

Thank you,

Regards,

Thomas

ADD REPLY • link 8.6 years ago Thomas Maurel ▴ 800

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ensembl=useMart(host="www.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl")