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Question: GenomicFeatures error: rsqlite_query_send: could not execute1: database or disk is full
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gravatar for Xiaokuan Wei
2.4 years ago by
Xiaokuan Wei230
United States
Xiaokuan Wei230 wrote:

Guys,

I tried to use "GenomicFeatures" to create trxDb. But I kept hitting the same error as below. Actually, I have plenty of disk space and I really don't know how to solve this issue. Thank you for your any help!

 

 

hse<-makeTxDbFromGFF("/genome/human/hg19_ensemble.gtf",format="gtf")
Prepare the 'metadata' data frame ... metadata: OK
Error in sqliteSendQuery(con, statement, bind.data) : 
  rsqlite_query_send: could not execute1: database or disk is full

 

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)

locale:
[1] C

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

other attached packages:
[1] GenomicFeatures_1.20.1 AnnotationDbi_1.30.1   Biobase_2.28.0        
[4] GenomicRanges_1.20.5   GenomeInfoDb_1.4.1     IRanges_2.2.5         
[7] S4Vectors_0.6.1        BiocGenerics_0.14.0   

loaded via a namespace (and not attached):
 [1] XML_3.98-1.3            Rsamtools_1.20.4        Biostrings_2.36.1      
 [4] GenomicAlignments_1.4.1 bitops_1.0-6            futile.options_1.0.0   
 [7] DBI_0.3.1               RSQLite_1.0.0           zlibbioc_1.14.0        
[10] XVector_0.8.0           futile.logger_1.4.1     lambda.r_1.1.7         
[13] BiocParallel_1.2.7      tools_3.2.1             biomaRt_2.24.0         
[16] RCurl_1.95-4.7          rtracklayer_1.28.6     

 

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Xiaokuan Wei230
1

Hi,

Could it be that you are running out of RAM? makeTxDbFromGFF() and all the functions in the makeTxDb* family create the SQLite db in memory, not on disk. Note that the error message you get, which is coming from the SQLite C code itself and relayed by the RSQLite package, is misleading.

H.

ADD REPLYlink written 2.4 years ago by Hervé Pagès ♦♦ 13k

Herve,

Thank you for your answer and I am sorry that I cannot reply to you earlier. Actually, I don't think it's a memory issue as our server on cluster has a lot of memory. Also, I have to do this step to create trxDB using my laptop since I cannot do it using the server. It works fine without any problem.

So, I am wondering if the server misses some parts of components which lead to broken SQLite db issue?

-X

ADD REPLYlink written 2.4 years ago by Xiaokuan Wei230

Are there complicated file permissions differences between the R process you're running under and the file system, or perhaps the file system is not local and involves some implicit authentication step? Maybe writing to /tmp would work?

ADD REPLYlink written 2.4 years ago by Martin Morgan ♦♦ 20k
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