Hi,

I have 40 whole genome sequencing .bam files each one about to 1 TB. Lab manager has downloaded them from Cambridge university to her hard derive. In the other hand my computer in office is windows OS so I have to use linux OS in our Compute Cluster in university to analyze my data. For that I have to drag and drop each .bam file to my scratch in Compute Cluster that each file takes about 2 days for transferring and after finishing I am seeing .bam file becomes crashed. Now, it is about a month I have been given this data but I am still struggling with transferring them. If one of you were in my place what  would you do?

I thought to ask lab manager to download these .bam files directly to Compute Cluster (but she has not done yet)
I thought to ask IT service to install linux on my computer although I guess I would need cluster computing again (

I really don't know what to do

Any consultant please?

That sounds like some big amount of data and therefore it will take time. I do not think that there is any workaround for transferring them to the HPC `scratch` as a desktop computer is simply not powerful enough to handle these amounts of data. For transferring data from A to B I use `rsync` which will keep the transferred file hidden until the transfer has been finished successfully. I prefer the following command:

    rsync -axv --numeric-ids --progress -e "ssh -T -o Compression=no -x" *.bam user@path_to_hpc(...):/scratch/your_username/folder...

This will take time but `--progress` will give you a rough estimation for each file. Check if it might not be faster to directly download to the HPC. Talk to the people involved. Depending on how fast that drive is where the data are currently stored, a new download directly to `scratch` might save you quite some time.