bio fetch with SRR accession shows HTTP error

[akannan2987]

Hello Albert,

Thanks for this bio package. I wanted to fetch the information for SRR10971381. However when run the command below, I get a HTTP bad reqest error. Would you know why. How should I resolve it?

$ bio fetch SRR10971381
Output
Error for SRR10971381, nuccore, gbwithparts, text: HTTP Error 400: Bad Request

On the other hand bio search SRR10971381 works fine....
akannan@nrnb226 ~/bioinformatics/work/biostar_handbook/covid_analysis
$ bio search SRR10971381
output
[
{
"run_accession": "SRR10971381",
"sample_accession": "SAMN13922059",
"first_public": "2020-02-05",
"country": "China: Wuhan",
"sample_alias": "Human-BALF",
"fastq_bytes": "1160191847;1216048922",
"read_count": "28282964",
"library_name": "1",
"library_strategy": "RNA-Seq",
"library_source": "METATRANSCRIPTOMIC",
"library_layout": "PAIRED",
"instrument_platform": "ILLUMINA",
"instrument_model": "Illumina MiniSeq",
"study_title": "Complete genome of a novel coronavirus associated with severe human respiratory disease in Wuhan, China",
"fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR109/081/SRR10971381/SRR10971381_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR109/081/SRR10971381/SRR10971381_2.fastq.gz"
}
]

Many thanks for your help.

Abhilash Kannan

[Istvan Albert]

the fetch does not quite work yet for fetching SRR numbers (though it is planned to have it work),

but I will put in a fix to notify you of this instead of attempting to access a different resource

to actually fetch you need either use the FTP links returned in the search or the sratools, I have recently written on short post on just how many confusing options are out there:

Tutorial:How to get FASTQ reads from the Short Read Archive (SRA)

• https://www.biostars.org/p/9493498/

[akannan2987]

Dear ialbert, thanks for your reply. Sure I will keep looking for your notification and see if it works at a later time point.
Thanks for sharing this link. It is indeed helpful.