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Entering edit mode
11 months ago
Lior • 0

Hey all, I wrote a script in python that gets the SRR ids from a SRP id and then downloads all FASTQ files for every SRR. How can it only work on some SRRs?

For example, SRP000124 provides these:

SRR954969
SRR001030


and downloads the FASTQ files as it should. But, SRP234963 which provides much more SRRs:

SRR10600874
SRR10600875
.
.
.
SRR10600943
SRR10600944


Nothing crashes, it just gets stuck after executing the fasterq-dump command and waits forever.

The actual command is "fasterq-dump " + srr_id + ' --split-3' + ' -O /output/'

Any information you can provide for me will be much appreciated, as you can tell this is my first project in this subject.

Thanks!

python SRP SRR SRATOOLKIT fasterq-dump • 455 views