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

Simulating Euk Reads + GSL analyses

Using the artsim program to simulate some more data from Euk genomes. Command for PE reads:

./art_illumina -i /Users/hollybik/Dropbox/U
C\ Davis\ Projects/PhyloSift/Euk\ NCBI\ Test\ data/C_elegans_genome.fasta -p -l
100 -f 2 -m 200 -s 10 -o /Users/hollybik/Dropbox/UC\ Davis\ Projects/PhyloSift
/Euk\ NCBI\ Test\ data/artsim_euks/artsim_2x

./art_illumina -i /Users/hollybik/Dropbox/U
C\ Davis\ Projects/PhyloSift/Euk\ NCBI\ Test\ data/C_elegans_mito_genome.fasta
-p -l 100 -f 2 -m 200 -s 10 -o /Users/hollybik/Dropbox/UC\ Davis\ Projects/Phyl
oSift/Euk\ NCBI\ Test\ data/artsim_euks/artsim_2x_C_elegans_mt_genome_sim

./art_illumina -i /Users/hollybik/Dropbox/U
C\ Davis\ Projects/PhyloSift/Euk\ NCBI\ Test\ data/Saccharomyces_cerevisiae_gen
ome.fasta -p -l 100 -f 2 -m 200 -s 10 -o /Users/hollybik/Dropbox/UC\ Davis\ Pro
jects/PhyloSift/Euk\ NCBI\ Test\ data/artsim_euks/artsim_2x_Saccharomyces_genom
e_sim

./art_illumina -i /Users/hollybik/Dropbox/U
C\ Davis\ Projects/PhyloSift/Euk\ NCBI\ Test\ data/Saccharomyces_cerevisiae_mt_
genome.fasta -p -l 100 -f 2 -m 200 -s 10 -o /Users/hollybik/Dropbox/UC\ Davis\
Projects/PhyloSift/Euk\ NCBI\ Test\ data/artsim_euks/artsim_2x_Saccharomyces_mt
_genome_sim

  • -p is for paired end simulation
  • -l is for read length
  • -f is for fold coverage
  • -m is the mean size of DNA fragments for PE simulations
  • -s is the standard deviation of DNA frament size for PE simulations

Running artsim data on phylosift_v1.0.0_01

./phylosift all –paired /User
s/hollybik/Dropbox/UC\ Davis\ Projects/PhyloSift/Euk\ NCBI\ Test\ data/artsim_e
uks/artsim_2x_C_elegans_genome_sim1.fq /Users/hollybik/Dropbox/UC\ Davis\ Proje
cts/PhyloSift/Euk\ NCBI\ Test\ data/artsim_euks/artsim_2x_C_elegans_genome_sim2
.fq –debug

./phylosift all –paired /Users/ho
llybik/Dropbox/UC\ Davis\ Projects/PhyloSift/Euk\ NCBI\ Test\ data/artsim_euks/arts
im_2x_Saccharomyces_genome_sim1.fq /Users/hollybik/Dropbox/UC\ Davis\ Projects/Phyl
oSift/Euk\ NCBI\ Test\ data/artsim_euks/artsim_2x_Saccharomyces_genome_sim2.fq –de
bug

./phylosift all –paired /Users/ho
llybik/Dropbox/UC\ Davis\ Projects/PhyloSift/Euk\ NCBI\ Test\ data/artsim_euks/arts
im_2x_Saccharomyces_mt_genome_sim1.fq /Users/hollybik/Dropbox/UC\ Davis\ Projects/P
hyloSift/Euk\ NCBI\ Test\ data/artsim_euks/artsim_2x_Saccharomyces_mt_genome_sim2.f
q –debug

./phylosift all –paired /Users/ho
llybik/Dropbox/UC\ Davis\ Projects/PhyloSift/Euk\ NCBI\ Test\ data/artsim_euks/arts
im_2x_C_elegans_mt_genome_sim1.fq /Users/hollybik/Dropbox/UC\ Davis\ Projects/Phylo
Sift/Euk\ NCBI\ Test\ data/artsim_euks/artsim_2x_C_elegans_mt_genome_sim2.fq –debu
g

GSL Data – running Guppy analyses on the finished PhyloSift runs

./guppy pca –out-dir ~/GSL_analyses/guppy
/ ~/phylosift_v1.0.0_01/PS_temp/2051774008_NA_RozPt_all_assembled.fna.gz/treeDir/con
cat.updated.1.jplace ~/phylosift_v1.0.0_01/PS_temp/2058419001_SA_AntIs_all_assembled
.fna.gz/treeDir/concat.updated.1.jplace ~/phylosift_v1.0.0_01/PS_temp/2058419003_NA_
Stram_all_assembled.fna.gz/treeDir/concat.updated.1.jplace ~/phylosift_v1.0.0_01/PS_
temp/2077657010_SA_Stram_all_assembled.fna.gz/treeDir/concat.updated.1.jplace –pref
ix GSL_concat_guppyPCA

./guppy squash –out-dir ~/GSL_analyses/guppy/ ~/phylosift_v1.0.0_01/PS_temp/2051774008_NA_RozPt_all_assembled.fna.gz/treeDir/concat.updated.1.jplace ~/phylosift_v1.0.0_01/PS_temp/2058419001_SA_AntIs_all_assembled.fna.gz/treeDir/concat.updated.1.jplace ~/phylosift_v1.0.0_01/PS_temp/2058419003_NA_Stram_all_assembled.fna.gz/treeDir/concat.updated.1.jplace ~/phylosift_v1.0.0_01/PS_temp/2077657010_SA_Stram_all_assembled.fna.gz/treeDir/concat.updated.1.jplace –prefix GSL_concat_guppySquash

./guppy kr –out-dir ~/GSL_analyses/guppy/
~/phylosift_v1.0.0_01/PS_temp/2051774008_NA_RozPt_all_assembled.fna.gz/treeDir/conc
at.updated.1.jplace ~/phylosift_v1.0.0_01/PS_temp/2058419001_SA_AntIs_all_assembled.
fna.gz/treeDir/concat.updated.1.jplace ~/phylosift_v1.0.0_01/PS_temp/2058419003_NA_S
tram_all_assembled.fna.gz/treeDir/concat.updated.1.jplace ~/phylosift_v1.0.0_01/PS_t
emp/2077657010_SA_Stram_all_assembled.fna.gz/treeDir/concat.updated.1.jplace -o GSL_
concat_guppyKRdist