Assembly succeeds on VM but not on notebook


Not sure if anyone will be looking at this forum, but wanted to flag a concern.

I’ve been using a VM on Climb, and more recently have been using a notebook server.

Using Flye to assemble metagenomes, I have discovered that I can do it on the VM but not on the notebook. Using the same zipped fastq file, it worked fine on the VM but on the notebook I get ‘ERROR looks like the system ran out of memory’. I tried filtering the fastqs so I was only using 60% of them, but same error.

I have looked in the flye.logs:

  • Notebook server, total RAM 1377GB, available RAM 1370GB 96 threads available (tried using 8, 12, 80 and 96 threads
  • VM, total RAM 105GB, available RAM 104GB 16 threads available (used 12 threads)

This makes me a bit nervous about losing the instances at the end of September - grateful if anyone has an explanation


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