Question: Errors when downloading SRA data using fastq-dump
0
gravatar for qingxiangg
23 months ago by
qingxiangg30
qingxiangg30 wrote:

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 &lt;Er &lt;Error rc=" rc(rccont,rcnamelist,rcinserting,rcstring,rcempty)"="" function="VDBManagerListExternalSchemaModules"/> </build> <tool date="Dec 21 2015" name="fastq-dump" vers="2 &lt;Bin &lt;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?

sequencing • 928 views
ADD COMMENTlink modified 23 months ago by Shicheng Guo4.6k • written 23 months ago by qingxiangg30
1
gravatar for Shicheng Guo
23 months ago by
Shicheng Guo4.6k
Shicheng Guo4.6k wrote:

I tried 1 minutes ago with your command: fastq-dump --split-files SRR1819888 &

And everything works fine. You can try to

1, Install lastest fastq-dump (fastq-dump : 2.5.5 works well)

2, check firewall

3, show your OS

Try again and provide more informations so that others can help you.

ADD COMMENTlink modified 23 months ago • written 23 months ago by Shicheng Guo4.6k

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...

ADD REPLYlink written 22 months ago by qingxiangg30
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