In [15]:

    

# Set up for the Jupyter notebook
base = "/project/flatiron2/analysis_SHOGUN/data/references"
name = "rep82"
fna = "{}/{}/{}.fna".format(base, name, name)
tax = "{}/{}/{}.tax".format(base, name, name)


    

In [16]:

    

%%capture capt_reg
%time !/export/scratch/ben/bin/utree-build_gg {fna} {tax} {base}/{name}/{name}.ubt 48 16


    

In [14]:

    

%time !/export/scratch/ben/bin/utree-compress {base}/{name}/{name}.ubt {base}/{name}/{name}.ctr


    

    




Invalid input filename
CPU times: user 12 ms, sys: 4 ms, total: 16 ms
Wall time: 166 ms

In [13]:

    

!echo {base}/{name}/{name}.ctr


    

    




/project/flatiron2/analysis_SHOGUN/data/references/rep82_dusted/rep82_dusted.ctr

In [ ]:

    

name = "rep82_dusted"


    

In [ ]:

    

%%capture capt_dust
%time !/export/scratch/ben/bin/utree-build_gg {fna} {tax} {base}/{name}/{name}.ubt 48 16


    

In [ ]:

    

%time !/export/scratch/ben/bin/utree-compress {base}/{name}/{name}.ubt {base}/{name}/{name}.ctr


    

In [11]:

    

capt_reg.show()


    

    




Using up to 48 threads.
Tree initialized.
Setting overlap to 16
Parsed map. 1948897 bytes, 12976 lines.
Done with sequence parse: 1262899870 k-mers made
Refining tree...
CPU times: user 14.8 s, sys: 1.72 s, total: 16.5 s
Wall time: 52min 54s

In [12]:

    

capt_dust.show()


    

    




Using up to 48 threads.
Tree initialized.
Setting overlap to 16
Parsed map. 1948897 bytes, 12976 lines.
Done with sequence parse: 1262899870 k-mers made
Refining tree...
CPU times: user 32.5 s, sys: 3.66 s, total: 36.2 s
Wall time: 1h 23min 46s

In [ ]:

    

print()