Question: Is there a way to download FASTq files from SRR IDs?
0
gravatar for Paul
13 months ago by
Paul60
India
Paul60 wrote:

I have a bunch of SRR IDs and need to download Fastq files for the same.

I tried downloading SRAtoolkit for the same by doing

apt-get install sra-toolkit
export PATH=$PATH:$PWD/sratoolkit.2.8.2-1-ubuntu64/bin
which fastq-dump
/User/sratoolkit.2.8.2-1-ubuntu64/bin/fastq-dump
fastq-dump --stdout SRR390728 | head -n 8

Shows an error like

 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -29184 ( SSL - An invalid SSL record was received )
 fastq-dump.2.8.2 err: item not found while constructing within virtual database module - the path 'SRR390728' cannot be opened as database or table

What should I do? Is there any other way to download read files rather than using fastq-dump?

Since I have multiple SRR IDs, is there any other method I can download all the Fastq files in a go?

fastq eutility sra • 1.7k views
ADD COMMENTlink modified 11 months ago by Biostar ♦♦ 20 • written 13 months ago by Paul60
5

Save yourself the trouble and get the fastq's from EBI-ENA.

ADD REPLYlink written 13 months ago by genomax56k

In case it is not mirrored there, use the prefetch tool to download SRAs via Aspera (100Mb/s) and then run fastq-dump on that file. Fastq-dump as a download tool is unusably slow, error prone and a hugh PITA ( like the entire SRA format ).

ADD REPLYlink written 13 months ago by ATpoint7.5k

Thank you @genomax EBI-ENA. worked well in my case :)

ADD REPLYlink modified 13 months ago • written 13 months ago by Paul60
1

are you working behind a proxy ?

ADD REPLYlink written 13 months ago by Pierre Lindenbaum112k
1

You are installing sra-toolkit system-wide with apt, but are using a downloaded binary. I guess your system is missing some shared library, or with an incompatible version. What is your OS, which version? Try using your system-installed fastq-dump:

/usr/bin/fastq-dump --stdout SRR390728 | head -n 8

I just tested my apt-get installed fastq-dump and it works:

$ fastq-dump  --version

fastq-dump : 2.8.1

$ which fastq-dump 
/usr/bin/fastq-dump

$ fastq-dump --stdout SRR390728 | head -n 8
@SRR390728.1 1 length=72
CATTCTTCACGTAGTTCTCGAGCCTTGGTTTTCAGCGATGGAGAATGACTTTGACAAGCTGAGAGAAGNTNC
+SRR390728.1 1 length=72
;;;;;;;;;;;;;;;;;;;;;;;;;;;9;;665142;;;;;;;;;;;;;;;;;;;;;;;;;;;;;96&&&&(
@SRR390728.2 2 length=72
AAGTAGGTCTCGTCTGTGTTTTCTACGAGCTTGTGTTCCAGCTGACCCACTCCCTGGGTGGGGGGACTGGGT
+SRR390728.2 2 length=72
;;;;;;;;;;;;;;;;;4;;;;3;393.1+4&&5&&;;;;;;;;;;;;;;;;;;;;;<9;<;;;;;464262
ADD REPLYlink written 13 months ago by h.mon19k
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