I am attempting to run a FastQC on a paired FastQ exome file.
I was wondering what was the expected runtime because my first attempt on a VM off terra with 2 cpus and 32gb of ram i left for past 24h with it not being complete. The fastq files were not compressed.
I have created a new VM with 32 cpus and 120gb of ram. This time i loaded the files as compressed .gz and each file is roughly 3-4gb. I understand that with more cpus both files are being processed at once.
What is the normal time for an exome fastqc analysis to take? My end goal is to do variant calling on my exome data i received. The adapters have already been removed from the file from the genetics company.
Are the jobs queued (gray) or yellow (executing)?
The jobs says running and i would say yellow/peach colour). It has now been 21h45 minutes.
Thanks. That does mean the job is running. It is usually best to let executing jobs finish. If you quit out, the job logs will not be as complete (success or fail). Those usually have clues about what is going on.
In general, have you run other work on your new server? If not, there could be a configuration problem. The Terra people would be able to help more about that. See Terra - Galaxy Community Hub
These specific files we have ran through successfully in Terra to obtain a uBam and gvcf but we have not had any success in running with galaxy to get to a variant analysis.
Thank you for your answers, i will reach out to the Terra galaxy hub.