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<p class="MsoNormal" style="text-align:left;direction:ltr;unicode-bidi:embed"><span style="font-size:18.0pt;font-family:"Helvetica","sans-serif";color:black">Hello,<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align:left;direction:ltr;unicode-bidi:embed"><span style="font-size:18.0pt;font-family:"Helvetica","sans-serif";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-align:left;direction:ltr;unicode-bidi:embed"><span style="font-size:18.0pt;font-family:"Helvetica","sans-serif";color:black">I have a metagenome of about 2.5G reads. I used the khmer pipeline with dignorm c=20, filtering and
partitioning. After the partitioning step I received 345 groups and a very big knot (123 GB). When using the knot release pipeline a received 8352 pmaps. I'm correctly in find-knots.py using -x 70e9 -N 4. After running a month in this step, only 1450 pmaps
have been processed...is it possible that this stage would take so long? <o:p></o:p></span></p>
<p class="MsoNormal" style="text-align:left;direction:ltr;unicode-bidi:embed"><span style="font-size:18.0pt;font-family:"Helvetica","sans-serif";color:black">Can I split this stage to different computers (run the loop over the</span>
<span style="font-size:18.0pt;font-family:"Helvetica","sans-serif";color:black">pmap_files parallel) ?<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align:left;direction:ltr;unicode-bidi:embed"><span style="font-size:18.0pt;font-family:"Helvetica","sans-serif";color:black">Can you please shed some light as to what could be the cause for this and should I maybe do the partitioning
in a different way ? <o:p></o:p></span></p>
<p class="MsoNormal" style="text-align:left;direction:ltr;unicode-bidi:embed"><span style="font-size:18.0pt;font-family:"Helvetica","sans-serif";color:black">I tried lowering the coverage to c=10 in the dignorm step but got 20% less data which I think is rather
a lot.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align:left;direction:ltr;unicode-bidi:embed"><span style="font-size:18.0pt;font-family:"Helvetica","sans-serif";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-align:left;direction:ltr;unicode-bidi:embed"><span style="font-size:18.0pt;font-family:"Helvetica","sans-serif";color:black">Thank you very much!<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align:left;direction:ltr;unicode-bidi:embed"><span style="font-size:18.0pt;font-family:"Helvetica","sans-serif";color:black">Adi<o:p></o:p></span></p>
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