[khmer] Duration of do-partition.py (very long !)

[Alexis Groppi]

Hi Titus,

After digital normalization and filter-below-abund, upon your advice I 
performed do.partition.py on 2 sets of data (approx 2.5 millions of 
reads (75 nt)) :

/khmer-BETA/scripts/do-partition.py -k 20 -x 1e9 
/ag/khmer/Sample_174/174r1_prinseq_good_bFr8.fasta.keep.below.graphbase 
/ag/khmer/Sample_174/174r1_prinseq_good_bFr8.fasta.keep.below
and
/khmer-BETA/scripts/do-partition.py -k 20 -x 1e9 
/ag/khmer/Sample_174/174r2_prinseq_good_1lIQ.fasta.keep.below.graphbase 
/ag/khmer/Sample_174/174r2_prinseq_good_1lIQ.fasta.keep.below

For the first one I got a 
174r1_prinseq_good_bFr8.fasta.keep.below.graphbase.info with the 
information : 33 subsets total
Thereafter 33 files .pmap from 0.pmap to 32.pmap regurlarly were created 
and finally I got unique file 
174r1_prinseq_good_bFr8.fasta.keep.below.part (all the .pmap files were 
deleted)
This treatment lasted approx 56 hours.

For the second set (174r2), do-partition.py is started since 32 hours 
but I only got the 
174r2_prinseq_good_1lIQ.fasta.keep.below.graphbase.info with the 
information : 35 subsets total
And nothing more...

Is this duration "normal" ?
(The parameters for the threads are by default (4 threads))
33 subsets and only one file at the end ?
Should I stop do-partition.py on the second set and re run it with more 
threads ?

Thanks for your help

Alexis



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