[khmer] Not enough disk space?

[C. Titus Brown]

Hi Cedar,

I'll look at it when I get a chance - in the mean time, here's a short term
fix:

try using -f to force bypass this check.

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