runtime stats for Disco running on QC community from Shakya et al., 2013

[ctb]

command:

./runDisco.sh -d podar -inP SRR606249.pe.qc.fq.gz -n 16

    resources_used.cput = 287:29:07
    resources_used.energy_used = 0
    resources_used.mem = 35525268kb
    resources_used.vmem = 35977764kb
    resources_used.walltime = 38:07:51

[ctb]

Assembly                    disco-quality-assembly500
# contigs (>= 0 bp)         34512                    
# contigs (>= 1000 bp)      19333                    
# contigs (>= 5000 bp)      6635                     
# contigs (>= 10000 bp)     3928                     
# contigs (>= 25000 bp)     1878                     
# contigs (>= 50000 bp)     888                      
Total length (>= 0 bp)      206611207                
Total length (>= 1000 bp)   196426844                
Total length (>= 5000 bp)   169391211                
Total length (>= 10000 bp)  150559296                
Total length (>= 25000 bp)  118437193                
Total length (>= 50000 bp)  83655083                 
# contigs                   34512                    
Largest contig              459070                   
Total length                206611207                
GC (%)                      51.23                    
N50                         34686                    
N75                         8579                     
L50                         1363                     
L75                         4404                     
# N's per 100 kbp           0.69 

[ctb]

(This is length filtered for contigs >= 500 bp)

[abiswas-odu]

I need to check on this. Just got back from leave. Will see if any unintended checkin made it into the master. The computation performance looks like single thread for this dataset. I will verify...

[ctb]

do we need to set OMP_NUM_THREADS?