I haven't worked with the SRA run selector in a while. Sorry if I'm missing something obvious. If it makes. a difference, I installed SRA toolkit using brew. It seems to work fine, and is able to successfully download the test data it asked for on github.
My goal is to re-align the dataset with the BioProject ID PRJNA945471. I downloaded the total asscession list (SRR_Acc_List.txt) from the SRA Run Selector and moved it to the folder I want it to download the data to. I am having errors with both the prefetch, and the fasterq-dump. Help at any point in the progress would be appreciated, I don't want to have to run fasterq-dump on every sample individually.
When I tried to just prefetch the ascession list, it didn't work, giving me the error
prefetch SRR_Acc_List.txt
2026-08-04T14:38:16 prefetch.3.4.1: 1) Resolving 'SRR_Acc_List.txt'... 'SRR_Acc_List.txt' is a local non-kart file
I managed to prefetch it using
prefetch PRJNA945471
When I tried to run using the BioProjectID I got the below error (although the first part was repeated a bunch).
fasterq-dump PRJNA945471
2026-08-04T14:46:25 fasterq-dump.3.4.1 int: string unexpected while executing query within virtual file system module - multiple response SRR URLs for the same service 's3'
2026-08-04T14:46:27 fasterq-dump.3.4.1 err: the input data is missing the QUALITY-column
fasterq-dump quit with error code 3
When I tried running it using the accession list it once again complained about the lack of quality.
fasterq-dump SRR_Acc_List.txt
2026-08-04T15:02:02 fasterq-dump.3.4.1 err: the input data is missing the QUALITY-column
fasterq-dump quit with error code 3
2 answers
I think the issue is that you cannot feed fasterq-dump a file containing a list of accessions.
You might want to try something like below to loop over your list and prefetch then download
while read acc; do
prefetch "$acc"
fasterq-dump "$acc"
done < SRR_Acc_List.txt
I would just check what is actually in your SRR_Acc_List.txt file first
One thing neither answer above mentions: it's suspicious that PRJNA945471 and SRR_Acc_List.txt gave you the exact same "missing QUALITY-column" error, even though neither is a valid run accession. That's a strong sign sra-tools cached something under one of those literal strings from an earlier failed attempt, and fasterq-dump is now reading that stale/incomplete cache instead of actually resolving a real accession.
Before running samuel's loop, it's worth clearing whatever got cached under those names: check ~/ncbi/public/sra/ (or wherever your vdb-config points) for anything named PRJNA945471 or SRR_Acc_List and remove it, then retry. Otherwise you may hit the same error again even with valid SRR accessions if the cache path collides.
Also worth knowing for next time: prefetch can take a kart file (the "Cart File" download from SRA Run Selector, not the plain accession list .txt) as a single argument — that's the "list" format it actually understands. The plain accession list only works one line at a time, which is why the loop is the right fix here.
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Check the manual
I did, that's why I asked because I couldn't work out how to deal with it.
You are trying to run
fasterq-dumpusing a Bioproject accession number. If you prefetched the individual SRA accessions, you should be running those accessions throughfasterq-dump.Can you show us the output of
head -5 SRR_Acc_List.txt?You can try the nf-core/fetchngs workflow or loop over the accession list.