Fastq-dump paired downloader does not retrieve the SRA files from the accession number, how tio fix?

Question

[dublukkvas1954]

Fastq-dump paired downloader does not retrieve the SRA files from the accession number, how tio fix? This module works on Galaxy cloud instance.

[GenoMax]

Galaxy related questions are best posted over at Galaxy Biostars.

You can grab the fastq files from EBI-ENA if you don't want to wait for a resolution to your original question and upload them to Galaxy.

[dublukkvas1954]

I know, thx, are there alternative Galaxy modules to get SRA files automatically from the accession number and did you face a similar trouble with fastq-dump downloader?

[Tonor]

Try the NCBI SRA toolkit:

https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software

Answer 1

[Shicheng Guo]

Several different bugs have been found for fastq-dump. However, what you should do is make sure the fastq-dump should be most latest version. You need to update the software frequently since old version can not works well after new version come out. It is ridiculous but it is truth. if it still don't work after you use latest version, then give up and use wget or curl to download the fastq or SRA from ftp server. for example:

for i in SRR1648425 SRR1648426 SRR1648427 SRR1648428
do
       wget http://sra-download.ncbi.nlm.nih.gov/srapub/$i
       mv $i $i.sra
       fastq-dump --gzip --split-files $i.sra
done