When I run bfast match (version 0.7.0a), the program often "hangs" while reading the index (as evidenced by the last line of output to stderr):
If I look at the process with "top" it is still active. Generally, loading an index file takes 5-8 minutes (from the timing info provided from bfast); but, often times I've had it take up to 15 hours! This most often happens when I submit the processes to our PBS cluster. When I run them 'locally' (but on the same machines/disks that are in the PBS cluster), I don't have this issue (though the sample size is much smaller than when I submit to the cluster, since I'm submitting 20+ bfast match commands at the same time). I realize this could be a consequence of high disk/network usage (the index files and FASTQ files are located on a shared NFS GPFS filesystem on high performance dedicated fileservers), but I thought I would see if anyone else sees this issue.
An example command line call:
Thanks!
Reading index from /path/to/NFSfilesystem/hg19.fasta.nt.2.1.bif.
An example command line call:
Code:
bfast match -A 0 -t -n 16 -f /path/to/NFSfilesystem/hg19.fasta -r /path/to/NFSfilesystem/Sample.fastq.gz -i 4 -z -T /localdisk/scratch/ > /path/to/NFSfilesystem/D1BUKACXX_MN02_002_4.bmf
Comment