Hello,
I use fastq-dump in SRAToolkit to download raw data for RNA-seq analysis
My command line is: fastq-dump --split-files SRR1819888 & (I submit it to the background).
Then I always get error report from ncbi: ncbi_error_report.xml
Inside is :
</repository> <tools> <ascp> <max_rate>"1000m"</max_rate> </ascp> </tools> <vdb> <lib> <paths> <kfg>"/disk3/zhangjunhong/opt/SRA_Toolkit/bin"</kfg> </paths> </lib> </vdb> </config> <remoteaccess available="true"/> <currentprotectedrepository found="false"/> </configuration> <object path="SRR1557039" type="table" fs_type="unexpected"> </object> <software> <vdblibrary vers="2.7.8"/> <build static="f <Er <Error rc=" rc(rccont,rcnamelist,rcinserting,rcstring,rcempty)"="" function="VDBManagerListExternalSchemaModules"/> </build> <tool date="Dec 21 2015" name="fastq-dump" vers="2 <Bin <Binary path=" disk3="" zhangjunhong="" opt="" sra_toolkit="" bin="" fastq-dump"="" type="alias" md5="b8a9729b9fde6a7301467f7154db 40"> <alias resolved="fastq-dump.2"> <alias resolved="fastq-dump.2.5.7"/> </alias> </binary> </tool> </software> <env> </env> </report>
I have done homework and troubleshooting but still I have no ideal with this.
<object path="SRR1557039" type="table" fs_type="unexpected">
Do you have idea about this?
Thanks Shicheng! Sorry for my late response! In fact I've solved this problem by switching to use aspera for downloading SRA data with command like this:
ascp –i ~/asperaweb_id_dsa.openssh –k 1 –T –l 200m anonftp@ftp.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/SRR304/SRR304976/SRR304976.sra ./
And then convert the SRA data to fastq using fastq-dump (SRA-toolkit):
fastq-dump –O output_directory --split-files SRR304976.sra
This works very well. And unfortunately, I still don't know what's wrong with my SRAToolkit.
And even SRAToolkit team admits that many bugs exist. Aspera works better with resuming function.
Anyway, I use SRAToolkit as converter now...