Question: fastq-dump.2.4.2 failed *.sra
0
gravatar for yiruic
2.0 years ago by
yiruic0
yiruic0 wrote:

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!

tool sra • 1.0k views
ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by yiruic0
0
gravatar for Chris Cole
2.0 years ago by
Chris Cole670
Scotland
Chris Cole670 wrote:

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

ADD COMMENTlink written 2.0 years ago by Chris Cole670

Yessss. Thank you. That is a good point.

ADD REPLYlink written 2.0 years ago by yiruic0
0
gravatar for yiruic
2.0 years ago by
yiruic0
yiruic0 wrote:

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

ADD COMMENTlink written 2.0 years ago by yiruic0
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