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OndrejSladky / fmsi

FMSI is an exact f-masked-superstrings-based index for membership queries and set operations on k-mer sets.
MIT License
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Memory usage/requirements should be better documented #30

Closed karel-brinda closed 6 days ago

karel-brinda commented 2 weeks ago

There should be two clearly separated pieces of info:

  1. Memory for index running (this is already sh there)

  2. Memory needed for index construction (e.g., for HG) – just a rough idea to know eg what machine to choose on a cluster - high mem vs standard, etc.

karel-brinda commented 2 weeks ago

These are my values from the human genome, k=31, index construction:

experiment  run   real_s  real_s_py   user_s  sys_s  percent_cpu  max_ram_kb  fs_inputs  fs_outputs  exit_code  command
None        None  975.17  975.179138  955.58  15.56  99%          46845014    0          1396768     0          fmsi index -p masked_superstring.mones.fa