kingfisher-download
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wwood
Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.
Hi I would like to try Kingfisher package with a bunch of ENA and SRA files. I installed aspera connect and kingfisher. When I run it I get following error...
I got error below. How could I do that? ``` python ena-fast-download.py ERR962744 03/12/2021 02:27:29 PM INFO: Using aspera ssh key file: $HOME/.aspera/connect/etc/asperaweb_id_dsa.openssh 03/12/2021 02:27:29 PM INFO: Querying ENA for...
Since there are data deposited in [GSA](https://ngdc.cncb.ac.cn/gsa/browse/CRA002276) but not in SRA/ENA, it would be useful to add the option to download from GSA. I was able to use Aspera for...
https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&page_size=10&acc=SRR13615821&display=metadata  I ran kingfisher and it pulled 3 fastq files for 1 record. A single ended and 2 paired end files. ``` (base) [jespinoz@exp-15-28 split_reads]$ kingfisher --version 0.3.1 ID=SRR13615821...
> SRA data are available either with full base quality scores (SRA Normalized Format), or with simplified quality scores (SRA Lite), depending on user preference. Both formats can be streamed...
At `kingfisher get --run-identifiers-list` condition, if one term error, the software will exit. Can you add a parameter to control ignore this error, and continue downloading other terms?