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