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?
Dr. Xueping Quan
Research Associate in BioInformatics
Imperial College London
Tel: +44(0)207 594 17 80