Test Results

Page Contents

Four sample genomes were tested with MGEScan-LTR and MGEScan-nonLTR programs.

  • Test genome sequences:
  • Test Environment:
    Cloud instances of FutureSystems at Indiana University (http://futuresystems.org).
  • Hardware Spec:
    • Intel Xeon X5550 2.66GHz
    • 8 vCPUs
    • 16 GB DDR3 1333 MHz
    • 160GB 7200RPM SATA
  • Operating System:
    • Ubuntu 14.04 LTS

Test Genome Sequences

_images/mgescan-test-results.png

D. melanogaster (dm3)

Evaluation

Elapsed time for MGEScan (dm3)
Program Total nonLTR LTR Options
MGEScan1.3.1 3 hrs 40 mins (13,220 secs) 55 mins (3,320 secs) 2 hrs 45 mins (9,900 secs) HMMER2, no MPI
MGEScan2 2 hrs 35 mins (9,304 secs) 19 mins (1,170 secs) 2 hrs 35 mins (9,304 secs) HMMER3.1b1, no MPI
MGEScan2 with MPI 1 hr 48 mins (6,502 secs) 15 mins (929 secs) 1 hr 48 mins (6,502 secs) HMMER3.1b1, MPI with 4 processors

Extra Files

C. intestinalis (KH)

Evaluation

Elapsed time for C. intestinalis
Program Total nonLTR LTR Options
MGEScan1.3.1 5 hours 18 minutes 36 seconds 34 minutes 47 seconds 4 hours 43 minutes 49 seconds HMMER 2.3.2, no MPI
MGEScan2 4 hours 5 minutes 27 seconds 9 minutes 23 seconds 4 hours 5 minutes 27 seconds HMMER 3.1b1, no MPI
MGEScan2 with MPI 1 hour 22 minutes 37 seconds 3 minutes 2 seconds 1 hour 22 minutes 37 seconds HMMER 3.1b1, MPI with 4 processors

D. pulex (GCA_000187875.1)

Evaluation

Elapsed time for MGEScan (dpulex)
Program Total nonLTR LTR Options
MGEScan1.3.1 4 hrs 5mins (14,697 secs) 1hr 8mins (4,127 secs) 2 hrs 57 mins (10,570 secs) HMMER 2.3.2, no MPI
MGEScan2 2 hrs 36 mins (9,414 secs) 46 mins (2,780 secs) 2 hrs 36 mins (9,414 secs) HMMER 3.1b1, no MPI
MGEScan2 with MPI 1hr 3mins (3,823 secs) 15 mins (878 secs) 1 hr 3mins (3,823 secs) HMMER 3.1b1, MPI with 4 processors

Test Results with Previous MGEScan 1.3.1