Hey everyone,
I am trying to download some fastqs from SRA. I did this a hundred times using the snakemake wrapper "v1.3.2/bio/sra-tools/fasterq-dump" or the command-line. However, I haven't done it in few month and just wanted to do it again. This time I cannot make it work. Even though, if I just restart the workflow that I used before I just get the output/log: Cannot use '--ngc' as ngc file..
I cannot make sense of it. So for example the very easy command fasterq-dump SRR22816448 outputs ... query unauthorized ..., which is the normal output. However, if I add my ngc file to the command (which should have access) fasterq-dump --ngc prj_XXXXX.ngc SRR22816448, it just states Cannot use '--ngc' as ngc file.. I tried multiple SRRs, multiple ngc files, the command line (sra-tools 3.0.3 installed via conda), the snakemake wrapper, but all fail. Even those that worked before. What's happening here? I am out of answers.
Totally random suggestion but is it possible that your
ngccredentials have expired?No, I don't think so. This one got just approved and when I hit this error I tried some old ones that I do still have access to.
It seems to be related to this https://github.com/ncbi/sra-tools/issues/777. Seems like the SRA doesn't support the conda version anymore. Let's hope the people from
biocondamake a new build soon.Are you getting the error outside of snakemake as well?
Yes, I tried it directly within the command line.
It's years back that I used it but can't you provide the credential file via
vdb-configwhich then internally forwards it to tools such as fasterq-dump?Never did it that way. Can you give a short howto to that?
Besides that it looks like the developers are aware of this. They answered my on Githb: "(...) we will have a new release on May, 9 that has a fix for this issue."
See https://www.ncbi.nlm.nih.gov/sra/docs/sra-dbgap-download-old/
I do not know if this still works in 2023, but you can try. What I personally like is to first get sra files with prefetch which is more stable than fast(erq)-dump and then convert locally to fastq with fastq-dump or parallel-fastq-dump. Essentially,
vdb-configopens a GUI that you can use to provide the credential. hth