[khmer] questions about abundance-dist.py

C. Titus Brown ctb at msu.edu
Fri Sep 27 19:36:58 PDT 2013


On Fri, Sep 27, 2013 at 05:00:35PM +0800, cy_jiang wrote:
> Hi all, 
> I tried to use the load-into-counting.py and abundance-dist.py to count the kmer in my dataset, but it seems to stuck at the second step. The following information are present:
> 
> 
> hashtable from R1.kh
> K: 20
> HT sizes: [7500000031, 7500000047, 7500000049, 7500000073]
> outputting to R1.hist
> preparing that....
> 
> 
> my command is : scripts/abundance-dist.py -z R1.kh R1.fa R1.hist
> 
> 
> It has been running like this for more than 6 hours. Does it running normally? Or should I cut it down?

Hi Daniel,

that's very odd and not a bug we've seen before.  We've identified a problem
with loading hash tables, sometimes related to disk space, but here
the script has already loaded in the hash table... If you can try it with
another ht size that might help us debug things (i.e. build a different
hash table with load-into-counting).  Alternatively, try
abundance-dist-single if you just want an answer :)

--titus
-- 
C. Titus Brown, ctb at msu.edu




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