Open msfuentealba opened 1 year ago
Hi @msfuentealba,
The issue is most likely the use of the 2.9.1 version of fastq-dump/sra-toolkit in that container. I've got an updated version (uses sra-toolkit 3.0.x), but I need to test it out before pushing it to the public repo.
I'll try to do that in the next couple of days.
Hi @msfuentealba
I've updated the pump docker image to be 1.1.3 which now uses SRAtoolkit 3.0.2 for both prefetch and fastq-dump, so hopefully should fix this error.
Please give the new image a try and let me know.
Thanks, Chris
Hi all,
I'm trying to run the monorail-external with SRA input but I'm getting the following error. Any ideas? Thanks
I'm running the command
/bin/bash ../monorail-external-master/singularity/run_recount_pump.sh ../recount-pump_1.1.1.sif SRR21355139 SRP394927 grcm38 20 ../monorail-external-master/
Other datasets work fine.