Hello, 1) are the plink files for the WGS going to be available soon? 2) I need help to run batch jobs on SAK
I am running the Swiss Army Knife using the GUI. I need to convert a list of files from vcf to plink so I am running the analysis in batch. This is the command I am using:
for file in ukb23352_c21_*vcf.gz; do plink --vcf $file --make-bed --allow-no-vars --extract range /mnt/project/Bulk/Whole genome sequences/Whole genome GraphTyper joint call pVCF/Plink_files/ Markers_recode_Positions.txt. --out ${file%_*}; done'
I get this error:
Error: --extract accepts at most 2 parameters.
For more information, try "plink --help <flag name>" or "plink --help | more".
I tried to point to the file in different ways, but I would get the following error:
Error: Failed to open Markers_recode_Positions.txt.
I need to be able to use that file to extract the SNPs from, but I don?t seem to be able to add it as input file when batch is on (I tried adding it together with the files I need to run the analysis on, but still, it doesn?t get found).
If I don?t use the batch parameter, I am able to add the file, and it can be used in the for loop, without adding the path, as I can include it as a input. However, if I don?t run batch jobs the whole analysis takes too long.
Thanks so much
Comments
4 comments
hi Marianna, I asked our BioInformatician about your SAK question, and he suggests:
This /mnt/project/Bulk/Whole genome sequences/Whole genome GraphTyper joint call pVCF/Plink_files/ Markers_recode_Positions.txt need to be in changed to " /mnt/project/Bulk/Whole genome sequences/Whole genome GraphTyper joint call pVCF/Plink_files/ Markers_recode_Positions.txt"
Hope that helps!
Thanks.
I tried using the quotes, but I got the second error: : Failed to open Markers_recode_Positions.txt.
But to be clear, is there a space between ' " ' and '/mnt' ? I tried without space and it did not work.
However, I will try and give it another go in case I missed something anyway.
There should be no space. Did you try this in UI or CLI? It might be escape character issue. Try this in UI might be easier.
Yes, I have used the user interface.
I need to run a batch job on each "ukb.....vcf.gz" file for a chromosome. I can easily upload these files and run a vcf-plink conversion on each of them, in batch.
However, a part of this analysis would be to simultaneously extract only the SNPs of interest according to Markers_recode_Positions.txt. So I do not need to run a batch job for Markers_recode_Positions.txt, but it needs to be accessible for the analyses on the other input files. I could not find a way to select it as input file to be used this way...
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