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


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!



Prepare the 'metadata' data frame ... metadata: OK
Error in sqliteSendQuery(con, statement, : 
  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)

[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     


rnaseq genomicfeatures deseq2 • 929 views
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Xiaokuan Wei230


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.


ADD REPLYlink written 4.4 years ago by Hervé Pagès ♦♦ 14k


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?


ADD REPLYlink written 4.4 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 4.4 years ago by Martin Morgan ♦♦ 24k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 276 users visited in the last hour