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Struggling to download using SRA toolkit from an Accession list

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
ascession toolkit sra
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updated by samuel.a.odonnell samuel.a.odonnell • written by SethJ • SethJ

I did, that's why I asked because I couldn't work out how to deal with it.

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written by SethJ • SethJ

You are trying to run fasterq-dump using a Bioproject accession number. If you prefetched the individual SRA accessions, you should be running those accessions through fasterq-dump.

Can you show us the output of head -5 SRR_Acc_List.txt?

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written by GenoMax GenoMax

1 answer

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

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written by samuel.a.odonnell samuel.a.odonnell

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