Error while downloading fastq files from SRA
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12 months ago
pisiposo84 ▴ 50

I would like to download the fastq file associated to this SRA entry SRR6755970 I would use sra toolkit as follow

fasterq-dump SRR6755970

but I am getting error messages like

> 2020-03-17T15:29:15 fasterq-dump.2.10.4 err: name not found while
> resolving query within virtual file system module - failed to resolve
> accession 'CM000667.1' - Cannot resolve accession ( 404 )
> 2020-03-17T15:29:16 fasterq-dump.2.10.4 err: name not found while
> resolving query within virtual file system module - failed to resolve
> accession 'CM000681.1' - Cannot resolve accession ( 404 )
> 2020-03-17T15:29:21 fasterq-dump.2.10.4 err: name not found while
> resolving query within virtual file system module - failed to resolve
> accession 'CM000681.1' - Cannot resolve accession ( 404 )
> 2020-03-17T15:29:27 fasterq-dump.2.10.4 err: name not found while
> resolving query within virtual file system module - failed to resolve
> accession 'CM000681.1' - Cannot resolve accession ( 404 )
> ^Cfasterq-dump (PID 21865) was killed (signal 2)

it works for other data like SRR6755975, SRR6755976... no idea what is causing the issue, suggestions?

RNA-Seq • 1.3k views
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Get fastq files from EBI-ENA.

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One generally loads SRA files first with prefetch and then converts them on your machine to fastq with fastq-dump or fasterq-dump, covered in Fast download of FASTQ files from the European Nucleotide Archive (ENA). This also contains download from ENA that genomax mentioned.

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12 months ago
wm ▴ 490

As above answers, use prefetch to download sra files.

Besides, in your example, the file (SRR6755970, 23GB) is larger than default maximum allowed (20GB). you could change it to a larger number.

$ prefetch --max-size 24G SRR6755970
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