Describe the bug Hello and thank you for the awesome package.

[BUG] aspera about pysradb HOT 3 CLOSED

NomiCentarix commented on September 21, 2024

[BUG] aspera

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Comments (3)

saketkc commented on September 21, 2024

Thanks, this issue seems to be coming from a library version mismatch from your python installation. I would recommend using conda/bioconda to create a separate enivronment for pysradb.

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NomiCentarix commented on September 21, 2024

ok I fixed the above problem but still don't get the fastq file, only empty folders, with the following code:

from pysradb.sraweb import SRAweb
SRA_OUR_DIR = "/data/NCBI_data/"
db = SRAweb()
gse_to_srp = db.gse_to_srp("GSE226189")
print("gse_to_srp shape:", gse_to_srp.shape)
display(gse_to_srp.head(2))

metadata = db.sra_metadata(gse_to_srp["study_accession"].to_list(), detailed=True)
print(metadata.shape)
display(metadata.head(2))

db.download(df=metadata.head(1), 
            url_col="ena_fastq_http_1",
            use_ascp=True,
            #threads=8,
            skip_confirmation=True,#don't ask for permmision to download
            out_dir=SRA_OUR_DIR)

OS: AWS EC2, Ubuntu 22.04.2 LTS
anaconda3 Python 3.11.5

when the url_col is the default I do get the .sra files.
The link in column "ena_fastq_http_1" seems fine
(http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR236/077/SRR23630177/SRR23630177_1.fastq.gz)

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NomiCentarix commented on September 21, 2024

Hi
Is my new comment can be seen after issue was closed?

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