Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Running a script over a bunch of vcf files #35

Open
MaryGoAround opened this issue Jan 23, 2024 · 0 comments
Open

Running a script over a bunch of vcf files #35

MaryGoAround opened this issue Jan 23, 2024 · 0 comments

Comments

@MaryGoAround
Copy link

MaryGoAround commented Jan 23, 2024

Hi

I am interested in individual-level WGS vcf files in "/mnt/project/Bulk/DRAGEN WGS/Whole genome variant call files (VCFs) (DRAGEN) [500k release]" for a list of participants in eid.txt.
eid.txt

I want to locate these vcf files so I done as below but I get error

usr@LV19Y7325V dnanexus-upload-agent-1.5.33-osx %
 dx ls "/mnt/project/Bulk/DRAGEN WGS/Whole genome variant call files (VCFs) (DRAGEN) [500k release]" VCF/*gz > tempfile.txt ;
zsh: no matches found: VCF/*gz

I tried this command and got error too

usr@LV19Y7325V dnanexus-upload-agent-1.5.33-osx %
 for i in `cat eid.txt`; do dx find data --property eid=$i --folder "/mnt/project/Bulk/DRAGEN WGS/Whole genome variant call files (VCFs) (DRAGEN) [500k release]" ; done
cat: eid.txt: No such file or directory

Or, I tried this

usr@LV19Y7325V ~ % dx ls './*.gz*'                         
dxpy.utils.resolver.ResolutionError: Unable to resolve "*.gz*" to a data object or folder name in '/Bulk/DRAGEN WGS/Whole genome variant call files (VCFs) (DRAGEN) [500k release]'

Please could somebody help me with this?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant