Closed GopiGugan closed 1 year ago
INSTALL.md
with R Dependencies
tidyquant
yaml
matrixStats
ape
optparse
phytools
devtools
LambdaSkyline
rpy2
and pyyaml
Traceback (most recent call last):
File "/home/covizu/covizu/batch.py", line 160, in <module>
result, infection_prediction = make_beadplots(by_lineage, args, cb.callback, t0=cb.t0.timestamp())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/covizu/covizu/covizu/utils/batch_utils.py", line 399, in make_beadplots
cne = find_Ne(ctree, 'clabels_file.csv', False)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/covizu/covizu/covizu/utils/batch_utils.py", line 211, in find_Ne
Ne = subprocess.Popen("Rscript " + os.path.dirname(__file__) + "/skyline_est.R -t " +
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib64/python3.11/subprocess.py", line 1024, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "/usr/lib64/python3.11/subprocess.py", line 1816, in _execute_child
errpipe_read, errpipe_write = os.pipe()
^^^^^^^^^
OSError: [Errno 24] Too many open files
We were not closing the temporary files that were being created. Fixed after closing them
Run was successful:
472