Closed SCDealy closed 9 months ago
NOTE: the sra-tools bug below sounds like it might be the problem (it's the same version: 2.11.0), but the response to the bug was "Download the latest toolkit." with no explanation.
https://github.com/ncbi/sra-tools/issues/663
FWIW.
I'm running into the same issue with fetchngs v. 1.10. Latest sra-tools version as of now is 3.0.6.
Could be worth updating the nf-core sratools modules to a newer version.
FYI, I was having the same issue but just updated to the newly released 1.11.0 and it seems to have fixed the problem for me (thanks nf-core!)
Yep, this should have been fixed with https://github.com/nf-core/fetchngs/commit/a9e5646e60a24f59346392d7acc657f8efcd29e0
Description of the bug
fetchngs successfully handles sra files, but when prefetch gets an sralite file, fasterq-dump can't see it. After fetchngs runs I checked the working directory for the failed SRA file and found it in a sub-directory that was given the SRA accession as its name. Of all the SRA files I tried to process, this is the only one that was downloaded as an sralite file.
I am new to NextFlow (first time using it), so I am still figuring out how things work, but it appears that fasterq-dump doesn't know to look for an sralite file in the sub-directory so it doesn't find it.
Command used and terminal output
Relevant files
SRR_Acc_List.txt nextflow.log
System information