UtaHar
commented
5 years ago Hi again,
for your information, when testing the pipeline on a server and allocating more CPUs, the summarise function did work. I hope this helps,
Uta
Closed UtaHar closed 5 years ago
UtaHar
commented
5 years ago Hi again,
for your information, when testing the pipeline on a server and allocating more CPUs, the summarise function did work. I hope this helps,
Uta
Dear BraCeR team,
I built a bracer singularity image from the docker to run it on a HPC. However, the summarise command on the test_data fails. Any idea from the error message, what happend?
Singularity bracer.simg:~> bracer summarise /data/results
DB_FILE> changeo_input_H.tab GROUP_FUNC> indexJunctions GROUP_ARGS> {'mode': 'gene', 'fields': None, 'action': 'set'} CLONE_FUNC> distanceClones CLONE_ARGS> {'seq_field': 'JUNCTION', 'sym': 'avg', 'model': 'hh_s5f', 'linkage': 'single', 'distance': 0.2, 'norm': 'len'} NPROC> 4
PROGRESS> Grouping sequences PROGRESS> 12:53:18 (2) 0.0 min
PROGRESS> Assigning clones PROGRESS> 12:53:18 [####################] 100% (2) 0.0 min
OUTPUT> changeo_input_H_clone-pass.tab CLONES> 1 RECORDS> 2 PASS> 2 FAIL> 0 END> DefineClones
DB_FILE> changeo_input_L.tab GROUP_FUNC> indexJunctions GROUP_ARGS> {'mode': 'gene', 'fields': None, 'action': 'set'} CLONE_FUNC> distanceClones CLONE_ARGS> {'sym': 'avg', 'linkage': 'single', 'distance': 0.2, 'norm': 'len', 'seq_field': 'JUNCTION', 'model': 'hh_s5f'} NPROC> 4
PROGRESS> Grouping sequences PROGRESS> 12:53:19 (3) 0.0 min
PROGRESS> Assigning clones PROGRESS> 12:53:19 [####################] 100% (3) 0.0 min
OUTPUT> changeo_input_L_clone-pass.tab CLONES> 2 RECORDS> 3 PASS> 3 FAIL> 0 END> DefineClones
Traceback (most recent call last): File "/usr/local/bin/bracer", line 11, in
load_entry_point('bracer==0.1', 'console_scripts', 'bracer')()
File "/usr/local/lib/python3.5/dist-packages/bracer-0.1-py3.5.egg/bracerlib/launcher.py", line 43, in launch
Task().run()
File "/usr/local/lib/python3.5/dist-packages/bracer-0.1-py3.5.egg/bracerlib/tasks.py", line 863, in run
self.plot_length_distributions(self.loci, length_filename_root, cells)
File "/usr/local/lib/python3.5/dist-packages/bracer-0.1-py3.5.egg/bracerlib/tasks.py", line 1186, in plot_length_distributions
sns.distplot(lns)
File "/usr/local/lib/python3.5/dist-packages/seaborn/distributions.py", line 224, in distplot
kdeplot(a, vertical=vertical, ax=ax, color=kde_color, kde_kws)
File "/usr/local/lib/python3.5/dist-packages/seaborn/distributions.py", line 657, in kdeplot
cumulative=cumulative, kwargs)
File "/usr/local/lib/python3.5/dist-packages/seaborn/distributions.py", line 284, in _univariate_kdeplot
x, y = _scipy_univariate_kde(data, bw, gridsize, cut, clip)
File "/usr/local/lib/python3.5/dist-packages/seaborn/distributions.py", line 356, in _scipy_univariate_kde
kde = stats.gaussian_kde(data, bw_method=bw)
File "/usr/local/lib/python3.5/dist-packages/scipy/stats/kde.py", line 172, in init
self.set_bandwidth(bw_method=bw_method)
File "/usr/local/lib/python3.5/dist-packages/scipy/stats/kde.py", line 499, in set_bandwidth
self._compute_covariance()
File "/usr/local/lib/python3.5/dist-packages/scipy/stats/kde.py", line 510, in _compute_covariance
self._data_inv_cov = linalg.inv(self._data_covariance)
File "/usr/local/lib/python3.5/dist-packages/scipy/linalg/basic.py", line 819, in inv
raise LinAlgError("singular matrix")
numpy.linalg.linalg.LinAlgError: singular matrix
Thanks for your help! Uta