Unable to unzip GATK
I'm using a Ubuntu 24.04 system and trying to get gatk for variant analysis. However, I could not unzip the gatk file. The error message reads:
There was an error while extracting "gatk-4.6.0.0.zip". empty archive
I'd appreciate any advice on how I can work around this.
REQUIRED for all errors and issues:
a) GATK version used: GATK-4.6.0.0
b) Exact command used: N/A
c) Entire program log: N/A
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Hi Giang Tran
Looks like your download was not complete therefore you have an invalid archive.
Can you use wget or curl to download the file in the following link?
https://github.com/broadinstitute/gatk/releases/download/4.6.0.0/gatk-4.6.0.0.zip
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Hey, thank you for the answer! Unfortunately, our current internet connection keeps giving us a hard time downloading through wget. Our current solution is to download gatk from a better internet connection into a portal hard drive and then to transfer it into our Ubuntu machine. The downloads seemed complete but we could not unzip it as mentioned. I would appreciate any advice you can give us given this circumstance.
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Hi Giang Tran
Here is the md5sum of our zip file. You can check your downloaded file to see if the downloaded or copied file is complete and uncorrupt.
cbaeef58af8c338d8d7ad44624cfcc03 gatk-4.6.0.0.zip
I hope this helps.
Regards.
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Hi Gökalp Çelik,Thanks for the answer. Here is what I got from md5sum:$ md5sum gatk-4.6.0.0.zip9eab60f444eecb44e88faebf047003
06 gatk-4.6.0.0.zip Does this mean that the file is corrupted? If so, what would be a good workaround since wget seems to fail every time for me. -
Hi again.
Yes your file seems incorrect and possible corrupt of incomplete. Unfortunately there is no simple workaround for a slow connection. You may need to consult your IT department to provide a solution for your compute environment.
Regards.
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