run_test2.sh does not successfully complete

marbl / metAMOS

A metagenomic and isolate assembly and analysis pipeline built with AMOS

http://marbl.github.io/metAMOS

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run_test2.sh does not successfully complete #111

Closed treangen closed 10 years ago

treangen commented 10 years ago

Phylosift/pplacer runs for several hours and never terminates on run_test2.sh. Works fine on reads, but not when run_test2 asm is used as input.

Working on fix but this test is deprecated and will be removed. Users should use instead test_phylosift as the proper test for verifying Phylosift was installed properly and is working.

koadman commented 10 years ago

this is probably a pplacer memory usage issue. contigs containing several of the concat markers can require 25-30GB for phylogenetic placement.

treangen commented 10 years ago

Thanks Aaron! good to know. closing issue, user can resolve by increasing available memory.