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

[ialbert]

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.