[wgs-assembler-users] number of overlapper jobs

[Quan, X. <x....@im...>]

Hi

I am running assemblying for a large genome. I forgot to set the ovlRefBlockSize to a larger number (currently it is the default number 2000000). Now the overlapInCore is running for more than three days and not finished yet. There are more than 4000 jobs have been finished without error. Below is the output statistics for one of the job
"HASH LOADING STOPPED: strings       5420544 out of      5420544 max.
HASH LOADING STOPPED: length      700000034 out of    700000034 max.
HASH LOADING STOPPED: entries     242755113 out of    264241152 max (load 68.90).
### realloc  Extra_Ref_Space  max_extra_ref_ct = 386385931
String_Ct = 5420544  Extra_String_Ct = 13533  Extra_String_Subcount = 21
Read 12224632 kmers to mark to skip
 Kmer hits without olaps = 6269530
    Kmer hits with olaps = 2108710
  Multiple overlaps/pair = 0
 Total overlaps produced = 2107177
      Contained overlaps = 0
       Dovetail overlaps = 0
"

According to the ovljob file, there are  038952 jobs. Is this number the real job number to run? Is it worth I kill the process and restart the overlapper with larger ovlRefBlockSize number?

Thanks!

Dr. Xueping Quan
Research Associate in BioInformatics
Imperial College London
Tel: +44(0)207 594 17 80
email:x....@im...
Personal:http://www3.imperial.ac.uk/people/x.quan
Group:  www3.imperial.ac.uk/savolainenlab<https://exchange.imperial.ac.uk/ecp/Customize/www3.imperial.ac.uk/savolainenlab>