genomicfeatures rsqlite database or disk is full
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Jake ▴ 90
@jake-7236
Last seen 9 months ago
United States

 

 

Hi,

I am having problems with loading and making TxDb objects. Both of the commands shown below give me an rsqlite database or disk full error. I believe everything is up to date. These files work fine on my desktop, but are not working on my server for some reason.

 exons <- exonsBy(gencode, by=c('gene'))

Error in sqliteFetch(rs, n = -1) : 

  rsqlite_query_fetch: failed: database or disk is full

> gencodeVM4 <- makeTranscriptDbFromGFF(file='gencode.vM4.annotation.gtf', format='gtf')

extracting transcript information

Estimating transcript ranges.

Extracting gene IDs

Processing splicing information for gtf file.

Deducing exon rank from relative coordinates provided

Prepare the 'metadata' data frame ... metadata: OK

Now generating chrominfo from available sequence names. No chromosome length information is available.

Error in sqliteSendQuery(con, statement, bind.data) : 

  rsqlite_query_send: could not execute: database or disk is full

Here is the sessionInfo

> sessionInfo()

R version 3.1.2 (2014-10-31)

Platform: x86_64-unknown-linux-gnu (64-bit)


locale:

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              

 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    

 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   

 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 

 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       


attached base packages:

[1] stats4    parallel  stats     graphics  grDevices utils     datasets 

[8] methods   base     


other attached packages:

 [1] RSQLite_1.0.0          DBI_0.3.1              GenomicFeatures_1.18.3

 [4] AnnotationDbi_1.28.1   Biobase_2.26.0         GenomicRanges_1.18.4  

 [7] GenomeInfoDb_1.2.4     IRanges_2.0.1          S4Vectors_0.4.0       

[10] BiocGenerics_0.12.1   


loaded via a namespace (and not attached):

 [1] base64enc_0.1-2         BatchJobs_1.5           BBmisc_1.9             

 [4] BiocParallel_1.0.3      biomaRt_2.22.0          Biostrings_2.34.1      

 [7] bitops_1.0-6            brew_1.0-6              checkmate_1.5.1        

[10] codetools_0.2-11        digest_0.6.8            fail_1.2               

[13] foreach_1.4.2           GenomicAlignments_1.2.2 iterators_1.0.7        

[16] RCurl_1.95-4.5          Rsamtools_1.18.3        rtracklayer_1.26.2     

[19] sendmailR_1.2-1         stringr_0.6.2           tools_3.1.2            

[22] XML_3.98-1.1            XVector_0.6.0           zlibbioc_1.12.0
genomicfeatures • 2.6k views
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Have you checked to see if the disk is full?

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Yeah there is plenty of space on the disk.

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Could you please tell us where you got that "gencode.vM4.annotation.gtf" file from so we can try to reproduce this?

 Marc

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http://www.gencodegenes.org/mouse_releases/current.html 

It is the comprehensive gene annotation GTF

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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 5.2 years ago
United States

OK I have tried a few times to replicate this.  But with no success so far.  Running the latest version of R (release) I can run the commands here (using the file mentioned above):

library(GenomicFeatures)
gencodeVM4 <- makeTranscriptDbFromGFF(file='../gencode.vM4.annotation.gtf', format='gtf')

With the following sessionInfo():

 

sessionInfo()
R version 3.1.3 Patched (2015-03-16 r68019)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
[1] GenomicFeatures_1.18.3 AnnotationDbi_1.28.2   Biobase_2.26.0        
[4] GenomicRanges_1.18.4   GenomeInfoDb_1.2.4     IRanges_2.0.1         
[7] S4Vectors_0.4.0        BiocGenerics_0.12.1    BiocInstaller_1.16.2  

loaded via a namespace (and not attached):
 [1] base64enc_0.1-2         BatchJobs_1.5           BBmisc_1.9             
 [4] BiocParallel_1.0.3      biomaRt_2.22.0          Biostrings_2.34.1      
 [7] bitops_1.0-6            brew_1.0-6              checkmate_1.5.1        
[10] codetools_0.2-11        DBI_0.3.1               digest_0.6.8           
[13] fail_1.2                foreach_1.4.2           GenomicAlignments_1.2.2
[16] iterators_1.0.7         RCurl_1.95-4.5          Rsamtools_1.18.3       
[19] RSQLite_1.0.0           rtracklayer_1.26.2      sendmailR_1.2-1        
[22] stringr_0.6.2           tools_3.1.3             XML_3.98-1.1           
[25] XVector_0.6.0           zlibbioc_1.12.0        

 

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Googling the error a little bit produces this which suggests that your sqlite database could be corrupted. Could you start over with a new one? See also this.

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Hmm.  But the code that was presented was not code that would have saved a SQLite DB to disc (IOW it should only exist in memory). 
 

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I suppose it's possible for an in-memory database to get corrupted as well. So I'm wondering if the problem happens consistently or just happened once. Jake, can you let us know?

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After updating to R 3.2.0 and Bioconductor 3.1, this issue went away and everything works fine now.

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