Errors when downloading SRA data using fastq-dump

Question: Errors when downloading SRA data using fastq-dump

4.9 years ago by

qingxiangg • 40

qingxiangg • 40 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 <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.

Do you have idea about this?

sequencing • 1.8k views

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modified 4.9 years ago by Shicheng Guo • 8.5k • written 4.9 years ago by qingxiangg • 40

4.9 years ago by

Shicheng Guo • 8.5k

Shicheng Guo • 8.5k 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 COMMENT • link modified 4.9 years ago • written 4.9 years ago by Shicheng Guo • 8.5k

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 REPLY • link written 4.8 years ago by qingxiangg • 40

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