mothur

Merge.taxsummary crash

Hi all,

When I am merging tax summary files with Merge.taxsummary my instance of mothur crashes (segmentation fault 11). However, the command only crashes when I have the “simple” flag enabled upon generating the initial tax summary files. There is no crash if the default flags are kept.

  • Jake

Hi Jake,
Thanks for reporting this issue. The merge.taxsummary command was not designed to work with the simple format. I added the addition of a format parameter for merge.taxsummary to our list of feature requests. You can follow the progress here, https://github.com/mothur/mothur/issues/659. As a workaround you can combine the taxonomy files before summarizing. Here’s how:

mothur > merge.files(input=taxonomyFile1-taxonomyFile2…-taxonomyFileN, output=complete.taxonomy) - combine the taxonomy files
mothur > summary.tax(taxonomy=complete.taxonomy, output=simple) - summarize complete taxonomy in simple format

Kindly,
Sarah

Excellent! That’s a fine workaround for the time being. Thanks for your help!

  • Jake

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