Rerunning GSL guppy analyses

Guppy gives its outputs using the original file names, so I had to change them to make sure the PCAs have informative labels:

hollybik@edhar:~/GSL_analyses/concat_files$ cp ~/phylosift_v1.0.0_01/PS_temp/2051774008_NA_RozPt_all_assembled.fna.gz/treeDir/concat.updated.1.jplace GSL_concat_NA_RozPt_allassembled.jplace
hollybik@edhar:~/GSL_analyses/concat_files$ cp ~/phylosift_v1.0.0_01/PS_temp/2058419001_SA_AntIs_all_assembled.fna.gz/treeDir/concat.updated.1.jplace GSL_concat_SA_AntIs_allassembled.jplace
hollybik@edhar:~/GSL_analyses/concat_files$ cp ~/phylosift_v1.0.0_01/PS_temp/2058419003_NA_Stram_all_assembled.fna.gz/treeDir/concat.updated.1.jplace GSL_concat_NA_Stram_allassembled.jplace
hollybik@edhar:~/GSL_analyses/concat_files$ cp ~/phylosift_v1.0.0_01/PS_temp/2077657010_SA_Stram_all_assembled.fna.gz/treeDir/concat.updated.1.jplace GSL_concat_SA_Stram_allassembled.jplace

And then reran all the guppy analyses:

./guppy pca –out-dir ~/GSL_analyses/guppy/ ~/GSL_analyses/concat_files/GSL_concat_NA_RozPt_allassembled.jplace ~/GSL_analyses/concat_files/GSL_concat_NA_Stram_allassembled.jplace ~/GSL_analyses/concat_files/GSL_concat_SA_AntIs_allassembled.jplace ~/GSL_analyses/concat_files/GSL_concat_SA_Stram_allassembled.jplace –prefix GSL_concat_guppyPCA

 

./guppy squash –out-dir ~/GSL_analyses/guppy/ ~/GSL_analyses/concat_files/GSL_concat_NA_RozPt_allassembled.jplace ~/GSL_analyses/concat_files/GSL_concat_NA_Stram_allassembled.jplace ~/GSL_analyses/concat_files/GSL_concat_SA_AntIs_allassembled.jplace ~/GSL_analyses/concat_files/GSL_concat_SA_Stram_allassembled.jplace –prefix GSL_concat_guppySquash

 

./guppy kr –out-dir ~/GSL_analyses/guppy/ ~/GSL_analyses/concat_files/GSL_concat_NA_RozPt_allassembled.jplace ~/GSL_analyses/concat_files/GSL_concat_NA_Stram_allassembled.jplace ~/GSL_analyses/concat_files/GSL_concat_SA_AntIs_allassembled.jplace ~/GSL_analyses/concat_files/GSL_concat_SA_Stram_allassembled.jplace -o GSL_concat_guppyKRdist

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