Galaxy FastQC exome processing time
I am attempting to run a FastQC in Galaxy on a paired Fastq exome file (3-4gb .gz each). I launched the VM with 32 CPUs and 120gb of ram. My file has now been running for 22 hours.
I wanted to know if this is a normal time or if there is a setting I can optimize. My end goal after the FastQC analysis is to do a variant calling and the adapters have already been removed from the file from the genetics company.
I had success in Terra in turning the same fastq files into ubam and gvcf (I opened the gvcf in IGV) so I don't believe the fastq files are an issue.
Lastly this is my 2nd attempt as my first attempt with 2 cpus and 32gb of ram ran for 24h and the first pair of outputs still did not process so I cancelled the job and now running it in a new workspace.
Any insight that can be provided would be appreciated.
Comments
1 comment
Hi Nicolas,
Just to confirm, are you running this on one 3-4 GB file, or are you working with multiple files at once? Are the files located in a workspace in Terra? If so would you be able to share this workspace with support by clicking the Share button in your workspace? The Share option is in the three-dots menu at the top-right.
Please provide us with a link to your workspace and the name of the file. We’ll be happy to take a closer look as soon as we can!
Best,
Emily
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