is a local non-kart file

prefetch was handed a plain accession list, which it does not accept

why

prefetch takes either a single accession, or a kart file โ€” the \"Cart File\" download from the SRA Run Selector. The plain SRR_Acc_List.txt is a different format and is not read as a list.

what to do

Loop over it one line at a time: while read acc; do prefetch \"$acc\"; fasterq-dump \"$acc\"; done < SRR_Acc_List.txt โ€” and check the file's contents first, since a stray header line gets treated as an accession too.

traced ยท SRA toolkit case, Sep 2026
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