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.
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!
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