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matsen / pplacer

Phylogenetic placement and downstream analysis
http://matsen.fredhutch.org/pplacer/
GNU General Public License v3.0
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merging with guppy #335

Closed Jangus2111 closed 10 years ago

Jangus2111 commented 10 years ago

I have a question about the merge command in guppy. If this is not the correct place for this question, please direct me to the right place.

I have about 100 metagenomes that were first run through phylosift. I want to analyze the 16s placements with epca. For my larger metagenomes, there are multiple .jplace files with each corresponding to a different "chuck" of the phylosift run. I wrote a script that will merge all the .jplace files for a particular metagenome and output the merged .jplace files to another directory. Everything works fine, but there is one curious aspect of the output that I noticed. Some metagenomes only have 1 .jplace file and when merge is run on these their resulting file size is much bigger. This is odd because I would expect that if there is only 1 file to merge it would just output the input file with no change in file size.

Thanks,

Angus

cmccoy commented 10 years ago

Hi Angus -

Generally, pplacer-users is the right place for questions like this.

I tried running guppy merge with a single input on a few .jplace files, but didn't notice any size differences. Would you be able to send me an example and the command you ran?

cmccoy commented 10 years ago

Resolved offline