fastq-dump.2.4.2 failed *.sra

Question

[yiruic]

I tried to use fastq-dump.2.4.2 --split-files *.sra to convert sra file to fastq file. And, half of the data succeed, but half of them showed the error message.

fastq-dump.2.4.2 error: name not found while resolving tree within virtual file system module - failed ERR048042.sra

The ncbi-error report was shown below:

<Report>
 <Run>
  <Date>
   <Start value="Tue Sep 20 2016 1:18:13 AM"/>
   <End value="Tue Sep 20 2016 1:18:13 AM"/>
  </Date>
  <Home name="HOME" value="/home/yrc"/>
  <Cwd>/data2/yrc/work/db</Cwd>
  <CommandLine argc="3">
   <Arg index="0" value="fastq-dump.2.4.2"/>
   <Arg index="1" value="--split-files"/>
   <Arg index="2" value="ERR048042.sra"/>
  </CommandLine>
  <Result rc="RC(rcVFS,rcTree,rcResolving,rcName,rcNotFound)"/>
  <User admin="false"/>
 </Run>
 <Configuration>
  <Files count="0">
  </Files>
  <refseq state="not found"/>
  <krypto state="pwfile: not found"/>
  <sra state="not found"/>
  <Config>
    <APPNAME>fastq-dump</APPNAME>
    <BUILD>RELEASE</BUILD>
    <HOME>/home/yrc</HOME>
    <HOST></HOST>
    <NCBI_HOME>/home/yrc/.ncbi</NCBI_HOME>
    <NCBI_SETTINGS>/home/yrc/.ncbi/user-settings.mkfg</NCBI_SETTINGS>
    <OS>linux</OS>
    <PWD>/data2/yrc/work/db</PWD>
    <USER>yrc</USER>
    <VDB_CONFIG></VDB_CONFIG>
    <VDB_ROOT></VDB_ROOT>
    <kfg>
      <arch>
        <bits>64</bits>
        <name>hillary.clemson.edu</name>
      </arch>
    </kfg>
    <vdb>
      <lib>
        <paths>
          <kfg></kfg>
        </paths>
      </lib>
    </vdb>
  </Config>
  <CurrentProtectedRepository>
   <Error rc="RC(rcKFG = rcLastModule_v1_0,rcNode,rcOpening,rcPath,rcNotFound)" function="KRepositoryMgrCurrentProtectedRepository" (null)="(null)"/>
  </CurrentProtectedRepository>
 </Configuration>
 <Object path="ERR048042.sra" type="database" fs_type="archive" size="434328374">
  <Dependencies>
   <Error rc="RC(rcKFG = rcLastModule_v1_0,rcNode,rcOpening,rcPath,rcNotFound)" function="VDatabaseListDependencies"/>
  </Dependencies>
 </Object>
 <SOFTWARE>
  <VDBLibrary vers="2.6.4"/>
  <Build static="false">
   <Error rc="RC(rcCont,rcNamelist,rcInserting,rcString,rcEmpty)" function="VDBManagerListExternalSchemaModules"/>
  </Build>
  <Tool date="Oct 14 2014" name="fastq-dump.2.4.2" vers="2.4.2">
   <Binary path="/home/yrc/bin/fastq-dump.2.4.2" type="file" md5="f5aff6b2bb23b70b74f4fe99fea2a490"/>
  </Tool>
 </SOFTWARE>
</Report>

Thank you!

Answer 1

[Chris Cole]

I find the .sra file format to be a real pain to work with. I usually download the fastq files directly from ENA e.g. http://www.ebi.ac.uk/ena/data/view/ERR048042

[yiruic]

Yessss. Thank you. That is a good point.

Answer 2

[yiruic]

I figured out, sra toolkit should be updated......