Question: Fastq-dump crashing with core dump?
gravatar for alan
4.5 years ago by
United States
alan80 wrote:

I've got a bunch of SRR files that I need to convert into fastqs.  I'm running a command like this one:


~/bin/sratoolkit.2.5.1-centos_linux64/bin/fastq-dump -v -v --split-3 --outdir /<OUTPATH>/ /<SOMEPATH>/SRR988439.sra.ncbi_enc


And a bunch of the time, it's crashing with a core dump and generating an ncbi_error_report.xml.

Here's the only segment there that seems to show an error, but I can't figure what's going on.  

  <VDBLibrary vers="2.7.2"/>
  <Build static="false">
   <Error rc="RC(rcCont,rcNamelist,rcInserting,rcString,rcEmpty)" function="VDBManagerListExternalSchemaModules"/>
  <Tool date="May 28 2015" name="/home/<SOMEUSER>/ncbi/sratoolkit.2.5.1-centos_linux64/bin/fastq-dump" vers="2.5.1">
   <Binary path="/home/<SOMEUSER>/ncbi/sratoolkit.2.5.1-centos_linux64/bin/fastq-dump" type="alias" md5="1a8642e8d30d6c6cfd75cccc383cc70b">
    <Alias resolved="fastq-dump.2">
     <Alias resolved="fastq-dump.2.5.1"/>


I would also note that I have had this same error with an earlier version of the SRA toolkit.   (2.3.5)

sra dump fastq sra software error • 1.7k views
ADD COMMENTlink modified 4.4 years ago by Biostar ♦♦ 20 • written 4.5 years ago by alan80

What do you get when you type this in your home folder:

which fastq-dump
ADD REPLYlink written 4.5 years ago by RamRS25k

fastq-dump isn't on my path.

ADD REPLYlink written 4.5 years ago by alan80

Just checking.

ADD REPLYlink written 4.5 years ago by RamRS25k
gravatar for genomax
4.5 years ago by
United States
genomax75k wrote:

That is an encrypted SRA file. You will need to decrypt it using

This procedure will probably work:

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by genomax75k

But why would it take hours to fail?  why would it generate multi-gigabyte partial (?) fastqs that look fine except for possible truncation?

The SRA (short-read-archive) data distributed through the dbGaP are encrypted but there is no need to decrypt them. The NCBI SRA toolkit can work directly on encrypted SRA data without decryption. Decrypted SRA data is in a binary format that is not human readable and can only be processed by the SRA toolkit anyway.

ADD REPLYlink modified 4 weeks ago by RamRS25k • written 4.5 years ago by alan80

That guide is a bit vague. You do have the dbGaP repository key for your account since that seems to be required? Perhaps someone who has direct working experience with these type of files will be able to help.

ADD REPLYlink written 4.5 years ago by genomax75k
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