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It is unlikely that you are currently on an idev node as copying the files while on an idev node causes problems as discussed. Remember the hostname command and showq -u can be used to check if you are on one of the login nodes or one of the compute nodes. If you need more information or help re-launching a new idev node, please see this tutorial. You should request at least 60 minutes on the idev session to make sure the commands have time to finish running. |
Recall that we installed samtools and bcftools in our GVA-SNV conda environment. Make sure you have activated your GVA-SNV environment and you have access to samtools and bcftools version 1.15.1
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If you are not seeing the correct versions, there is either a problem activating or creating your environment. Either try to activate the environment again, go back to the SNV tutorial, or ask for help before continuing. |
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Based on the discussion above, we are selecting the first solution and providing details of how this command should be run. As As this command will generate very little output and take ~45 ~30 minutes to complete, you are once again reminded that the output file from this option is available $BI/gva_course/GVA.multi-sample.vcf if you want to work with it without having to wait on the analysis to run personally.
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