[khmer] Not enough disk space?
C. Titus Brown
ctbrown at ucdavis.edu
Wed Jul 15 19:17:49 PDT 2015
Hi Cedar,
while your question helped us rethink some of our space checking code,
I'm still at a loss as to why this was happening to you! If you are
interested in tracking it down, we can send you some commands to try,
but hopefully the '-f' is sufficient.
You can read about some of our followup attempts here:
https://github.com/dib-lab/khmer/pull/1170
best,
--titus
On Wed, Jul 08, 2015 at 06:55:19PM -0700, Cedar McKay wrote:
> I feel like I must be doing something silly, but I can???t figure it out.
>
> My working directory is a 600GB ssd raid0 mounted at /mnt, but khmer is complaining that there isn???t enough disk space, reporting that only 3.5 GB is available, which happens to be exactly what is available on my system partition.
>
> Terminal output below, anyone see something silly I???m doing? Thanks in advance for your help!
>
>
>
> root at node001:/mnt# df -h
> Filesystem Size Used Avail Use% Mounted on
> /dev/xvda1 7.8G 4.1G 3.3G 56% /
> [snip]
> /dev/md0 591G 245G 316G 44% /mnt
>
> root at node001:/mnt# normalize-by-median.py -N 4 -x 28e9 -C 20 -k 25 -s ./ETNP_free.kh ./ETNP_free.fasta.gz
>
> || This is the script 'normalize-by-median.py' in khmer.
> || You are running khmer version 1.4.1
> || You are also using screed version 0.8
> ||
> || If you use this script in a publication, please cite EACH of the following:
> ||
> || * MR Crusoe et al., 2014. http://dx.doi.org/10.6084/m9.figshare.979190
> || * CT Brown et al., arXiv:1203.4802 [q-bio.GN]
> ||
> || Please see http://khmer.readthedocs.org/en/latest/citations.html for details.
>
>
> PARAMETERS:
> - kmer size = 25 (-k)
> - n tables = 4 (-N)
> - min tablesize = 2.8e+10 (-x)
>
> Estimated memory usage is 1.1e+11 bytes (n_tables x min_tablesize)
> --------
> ERROR: Not enough free space on disk for saved table files; Need at least 108.53429248 GB more.
> Table size: 112.0 GB
> Free space: 3.5 GB
>
>
>
>
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--
C. Titus Brown, ctbrown at ucdavis.edu
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