Does a job using CVMFS take a long time? I implemented CVMFS configuration on my local galaxy with reference to https://galaxyproject.org/admin/reference-data-repo/ Then I executed bwa job for test using hg38, but it is still running after about 6 hours. Smaller one such as dm3 finished but it took about 50 minutes. It seems to be slow for the size of the data. In both cases, input data is the same, paired-end fasq filest about 400MB each and the second run with dm3 finished less than a minute.
I think it’s not a problem of our network because downloading data from other sites, such as UCSC chromosome data, comes out to 2-3MB/s. I would like to know if the galaxy with CVMFS performance is normal, and if there is a setting that would improve performance.