parklab / pasdqc Goto Github PK

hello
I am using a Mac El Capitan, and cant run it to the end

I first tried samples aligned to hg19 with "chr" included with the chromosome number, and it seems not to recognise this
eg
Processing: 1
Executing: samtools view -q 30 -L /usr/local/lib/python3.6/site-packages/PaSDqc/db/grch37.chr1.map.bed /Volumes/Toshiba4Tb/single_cell_data/67_10.picoplex.qs.oct18/67_10.SN.qiascout.picoplex.merged.bam 1 | cut -f 3,4 | uniq > /Volumes/Toshiba4Tb/single_cell_data/67_10.picoplex.qs.oct18/cov/67_10.SN.qiascout.picoplex.merged.chr1.map.pos
[main_samview] region "1" specifies an unknown reference name. Continue anyway.

I realigned data to hg19 without "chr", and seems to work, but only up to a point.

I then downloaded one of your SRA low coverage files, and get the exact same problem:

PaSDqc QC -i /Volumes/Toshiba4Tb/walsh.bam -d /Volumes/Toshiba4Tb/ -c db/categorical_spectra_0.1x.txt

......
Executing: samtools view -uh -q 30 /Volumes/Toshiba4Tb/walsh.bam 22 | samtools depth -b PaSDqc/cov/walsh.chr22.map.pos - > PaSDqc/cov/walsh.chr22.map.pos.cov; rm PaSDqc/cov/walsh.chr22.map.pos
[main_samview] random alignment retrieval only works for indexed BAM or CRAM files.
PaSDqc/psd/walsh.chroms.spec
/usr/local/lib/python3.6/site-packages/PaSDqc/PSDTools.py:34: FutureWarning:

read_table is deprecated, use read_csv instead, passing sep='\t'.

PaSDqc/psd/SRS379201.walsh.chroms.spec
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/usr/local/Cellar/python/3.6.5/Frameworks/Python.framework/Versions/3.6/lib/python3.6/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/usr/local/bin/PaSDqc", line 102, in _build_and_save
psd = PaSDqc.PSDTools.SamplePSD.build_from_dir(str(dir_in), sample=sample, clean=clean, build=build)
File "/usr/local/lib/python3.6/site-packages/PaSDqc/PSDTools.py", line 268, in build_from_dir
df = cls._build_dataframe(file_list, build)
File "/usr/local/lib/python3.6/site-packages/PaSDqc/PSDTools.py", line 313, in _build_dataframe
psd_list = [ChromPSD(str(f)) for f in f_list]
File "/usr/local/lib/python3.6/site-packages/PaSDqc/PSDTools.py", line 313, in
psd_list = [ChromPSD(str(f)) for f in f_list]
File "/usr/local/lib/python3.6/site-packages/PaSDqc/PSDTools.py", line 35, in init
self.chrom = str(self.df.chrom.iloc[0])
File "/usr/local/lib/python3.6/site-packages/pandas/core/indexing.py", line 1500, in getitem
return self._getitem_axis(maybe_callable, axis=axis)
File "/usr/local/lib/python3.6/site-packages/pandas/core/indexing.py", line 2230, in _getitem_axis
self._validate_integer(key, axis)
File "/usr/local/lib/python3.6/site-packages/pandas/core/indexing.py", line 2139, in _validate_integer
raise IndexError("single positional indexer is out-of-bounds")
IndexError: single positional indexer is out-of-bounds
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/usr/local/bin/PaSDqc", line 265, in
args.func(args)
File "/usr/local/bin/PaSDqc", line 210, in QC
PSD(args)
File "/usr/local/bin/PaSDqc", line 95, in PSD
[p.get() for p in res]
File "/usr/local/bin/PaSDqc", line 95, in
[p.get() for p in res]
File "/usr/local/Cellar/python/3.6.5/Frameworks/Python.framework/Versions/3.6/lib/python3.6/multiprocessing/pool.py", line 644, in get
raise self._value
IndexError: single positional indexer is out-of-bounds

So I guess there is something wrong in my Python setup? If you have any suggestions, I will be grateful

thanks
christos

$ make
python setup.py sdist
running sdist
running egg_info
creating PaSDqc.egg-info
writing requirements to PaSDqc.egg-info/requires.txt
writing PaSDqc.egg-info/PKG-INFO
writing top-level names to PaSDqc.egg-info/top_level.txt
writing dependency_links to PaSDqc.egg-info/dependency_links.txt
writing manifest file 'PaSDqc.egg-info/SOURCES.txt'
reading manifest file 'PaSDqc.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'PaSDqc.egg-info/SOURCES.txt'
running check
creating PaSDqc-1.1.0
creating PaSDqc-1.1.0/PaSDqc
creating PaSDqc-1.1.0/PaSDqc.egg-info
creating PaSDqc-1.1.0/PaSDqc/db
creating PaSDqc-1.1.0/scripts
copying files to PaSDqc-1.1.0...
copying MANIFEST.in -> PaSDqc-1.1.0
copying README.md -> PaSDqc-1.1.0
copying setup.py -> PaSDqc-1.1.0
copying PaSDqc/PSDTools.py -> PaSDqc-1.1.0/PaSDqc
copying PaSDqc/init.py -> PaSDqc-1.1.0/PaSDqc
copying PaSDqc/amplicon.py -> PaSDqc-1.1.0/PaSDqc
copying PaSDqc/extra_tools.py -> PaSDqc-1.1.0/PaSDqc
copying PaSDqc/mappable_positions.py -> PaSDqc-1.1.0/PaSDqc
copying PaSDqc/plotly_tools.py -> PaSDqc-1.1.0/PaSDqc
copying PaSDqc/report_writer.py -> PaSDqc-1.1.0/PaSDqc
copying PaSDqc/simulate.py -> PaSDqc-1.1.0/PaSDqc
copying PaSDqc.egg-info/PKG-INFO -> PaSDqc-1.1.0/PaSDqc.egg-info
copying PaSDqc.egg-info/SOURCES.txt -> PaSDqc-1.1.0/PaSDqc.egg-info
copying PaSDqc.egg-info/dependency_links.txt -> PaSDqc-1.1.0/PaSDqc.egg-info
copying PaSDqc.egg-info/requires.txt -> PaSDqc-1.1.0/PaSDqc.egg-info
copying PaSDqc.egg-info/top_level.txt -> PaSDqc-1.1.0/PaSDqc.egg-info
copying PaSDqc/db/bulk_1x.smooth3.spec -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/categorical_spectra_0.1x.txt -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/categorical_spectra_1x.txt -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.centromeres.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chr1.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chr10.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chr11.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chr12.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chr13.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chr14.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chr15.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chr16.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chr17.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chr18.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chr19.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chr2.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chr20.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chr21.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chr22.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chr3.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chr4.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chr5.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chr6.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chr7.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chr8.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chr9.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chrM.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chrX.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chrY.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/grch37.chrom.sizes -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.centromeres.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chr1.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chr10.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chr11.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chr12.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chr13.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chr14.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chr15.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chr16.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chr17.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chr18.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chr19.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chr2.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chr20.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chr21.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chr22.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chr3.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chr4.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chr5.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chr6.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chr7.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chr8.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chr9.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chrM.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chrX.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying PaSDqc/db/hg19.chrY.map.bed -> PaSDqc-1.1.0/PaSDqc/db
copying scripts/PaSDqc -> PaSDqc-1.1.0/scripts
Writing PaSDqc-1.1.0/setup.cfg
creating dist
Creating tar archive
removing 'PaSDqc-1.1.0' (and everything under it)
pip install dist/*tar.gz
Processing ./dist/PaSDqc-1.1.0.tar.gz
Requirement already satisfied (use --upgrade to upgrade): PaSDqc==1.1.0 from file:///haplox/users/wenger/pipe/single_cell_wgs/bin/PaSDqc/dist/PaSDqc-1.1.0.tar.gz in /haplox/users/wenger/pipe/single_cell_wgs/bin/PaSDqc
Requirement already satisfied: seaborn in /home/wenger/.local/lib/python3.5/site-packages (from PaSDqc==1.1.0)
Collecting astropy (from PaSDqc==1.1.0)
Retrying (Retry(total=4, connect=None, read=None, redirect=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.requests.packages.urllib3.connection.VerifiedHTTPSConnection object at 0x2b69220dd860>, 'Connection to pypi.python.org timed out. (connect timeout=15)')': /simple/astropy/
Retrying (Retry(total=3, connect=None, read=None, redirect=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.requests.packages.urllib3.connection.VerifiedHTTPSConnection object at 0x2b69220ddc88>, 'Connection to pypi.python.org timed out. (connect timeout=15)')': /simple/astropy/
Retrying (Retry(total=2, connect=None, read=None, redirect=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.requests.packages.urllib3.connection.VerifiedHTTPSConnection object at 0x2b69220ddf28>, 'Connection to pypi.python.org timed out. (connect timeout=15)')': /simple/astropy/
Retrying (Retry(total=1, connect=None, read=None, redirect=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.requests.packages.urllib3.connection.VerifiedHTTPSConnection object at 0x2b69220ddbe0>, 'Connection to pypi.python.org timed out. (connect timeout=15)')': /simple/astropy/
Retrying (Retry(total=0, connect=None, read=None, redirect=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.requests.packages.urllib3.connection.VerifiedHTTPSConnection object at 0x2b69220ddba8>, 'Connection to pypi.python.org timed out. (connect timeout=15)')': /simple/astropy/
Could not find a version that satisfies the requirement astropy (from PaSDqc==1.1.0) (from versions: )
No matching distribution found for astropy (from PaSDqc==1.1.0)
make: *** [dist] Error 1

Hi,

I am getting the following error when trying to run the code below:

Wangetal.BC1
bzip2/1.0.6 loaded
zlib/1.2.11 loaded
ncurses/6.1 loaded
libreadline/7.0 loaded
tcl/8.6.8 loaded
sqlite/3.24.0 loaded
expat/2.2.6 loaded
libpng/1.6.37 loaded
freetype/2.9.1 loaded
fontconfig/2.13.1 loaded
libgpg-error/1.32 loaded
libgcrypt/1.8.3 loaded
libxslt/1.1.32 loaded
x11/20180604 loaded
tk/8.6.8 loaded
coreutils/8.30 loaded
gmp/6.1.2 loaded
libffi/3.2.1 loaded
openssl/1.1.0i loaded
python/3.6.8 loaded
setuptools/40.4.3-python-3.6.8 loaded
py/1.7.0-python-3.6.8 loaded
pytest/4.0.0-python-3.6.8 loaded
openpgm/5.2.122 loaded
util-linux/2.32 loaded
libsodium/1.0.16 loaded
zeromq/4.2.5 loaded
pyzmq/17.1.0-python-3.6.8-zmq4 loaded
pip/18.1-python-3.6.8 loaded
requests/2.19.1-python-3.6.8 loaded
ipython/7.2.0-python-3.6.8 loaded
numpy/1.15.2-python-3.6.8 loaded
pandas/0.23.4-python-3.6.8 loaded
scipy/1.1.0-python-3.6.8 loaded
kiwisolver/1.0.1-python-3.6.8 loaded
sip/4.19.13-python-3.6.8 loaded
xz/5.2.4 loaded
libxml2/2.9.7 loaded
gettext/0.19.8.1 loaded
pcre/8.42 loaded
libxslt/1.1.32 unloaded
libxml2/2.9.7 unloaded
icu/63.1 loaded
libxml2/2.9.7-icu-63.1 loaded
libxslt/1.1.32-icu-63.1 loaded
dbus/1.13.6 loaded
glib/2.58.2 loaded
nettle/3.4 loaded
libdrm/2.4.94 loaded
llvm/6.0.1 loaded
mesa/18.3.6 loaded
libglu/9.0.0 loaded
perl/5.28.0 loaded
intltool/0.51.0-perl-5.28.0 loaded
python/3.6.8 unloaded
python/3.7.0 loaded
glib/2.58.2 unloaded
libxslt/1.1.32-icu-63.1 unloaded
libxslt/1.1.32 loaded
glib/2.58.0 loaded
gobject-introspection/1.58.0 loaded
at-spi2-core/2.30.0 loaded
pixman/0.34.0 loaded
cairo/1.14.12 loaded
harfbuzz/1.9.0 loaded
nasm/2.13.03 loaded
x264/20180923 loaded
opus/1.3 loaded
libpng/1.6.37 unloaded
libpng/1.6.35 loaded
libtiff/4.0.9 loaded
libjpeg-turbo/2.0.0 loaded
giflib/5.1.4 loaded
libwebp/1.0.0 loaded
ffmpeg/4.1 loaded
gstreamer/1.14.3 loaded
gst-plugins-base/1.14.3 loaded
littlecms/2.9 loaded
nss/3.41-nspr-4.20 loaded
qt5/5.11.2 loaded
pyqt5/5.11.3-python-3.6.8 loaded
texlive/2018 loaded
python/3.7.0 unloaded
python/3.6.8 loaded
matplotlib/2.2.3-python-3.6.8 loaded
szip/2.1.1 loaded
hdf5/1.10.3 loaded
h5py/2.8.0-python-3.6.8 loaded
libyaml/0.2.1 loaded
pyyaml/3.13-python-3.6.8 loaded
qhull/2015.2 loaded
pillow/5.3.0-python-3.6.8 loaded
cython/0.28.5-python-3.6.8 loaded
scikit-image/0.14.1-python-3.6.8 loaded
astropy/3.2.1-python-3.6.8 loaded
plotly/3.10.0-python-3.6.8 loaded
statsmodels/0.9.0-python-3.6.8 loaded
seaborn/0.9.0-python-3.6.8 loaded
gcccore/6.4.0 unloaded
bzip2/1.0.6 unloaded
zlib/1.2.11 unloaded
zlib/1.2.11 loaded
ncurses/6.1 unloaded
ncurses/6.1 loaded
libreadline/7.0 unloaded
libreadline/7.0 loaded
tcl/8.6.8 unloaded
sqlite/3.24.0 unloaded
expat/2.2.6 unloaded
libpng/1.6.35 unloaded
freetype/2.9.1 unloaded
fontconfig/2.13.1 unloaded
libgpg-error/1.32 unloaded
libgcrypt/1.8.3 unloaded
x11/20180604 unloaded
tk/8.6.8 unloaded
coreutils/8.30 unloaded
gmp/6.1.2 unloaded
libffi/3.2.1 unloaded
openssl/1.1.0i unloaded
openssl/1.1.0i loaded
setuptools/40.4.3-python-3.6.8 unloaded
py/1.7.0-python-3.6.8 unloaded
pytest/4.0.0-python-3.6.8 unloaded
openpgm/5.2.122 unloaded
util-linux/2.32 unloaded
libsodium/1.0.16 unloaded
zeromq/4.2.5 unloaded
pyzmq/17.1.0-python-3.6.8-zmq4 unloaded
pip/18.1-python-3.6.8 unloaded
requests/2.19.1-python-3.6.8 unloaded
ipython/7.2.0-python-3.6.8 unloaded
numpy/1.15.2-python-3.6.8 unloaded
pandas/0.23.4-python-3.6.8 unloaded
scipy/1.1.0-python-3.6.8 unloaded
kiwisolver/1.0.1-python-3.6.8 unloaded
sip/4.19.13-python-3.6.8 unloaded
xz/5.2.4 unloaded
libxml2/2.9.7-icu-63.1 unloaded
gettext/0.19.8.1 unloaded
gettext/0.19.8.1 loaded
pcre/8.42 unloaded
icu/63.1 unloaded
dbus/1.13.6 unloaded
nettle/3.4 unloaded
libdrm/2.4.94 unloaded
llvm/6.0.1 unloaded
mesa/18.3.6 unloaded
libglu/9.0.0 unloaded
perl/5.28.0 unloaded
intltool/0.51.0-perl-5.28.0 unloaded
libxslt/1.1.32 unloaded
glib/2.58.0 unloaded
python/3.6.8 unloaded
gobject-introspection/1.58.0 unloaded
at-spi2-core/2.30.0 unloaded
pixman/0.34.0 unloaded
cairo/1.14.12 unloaded
harfbuzz/1.9.0 unloaded
nasm/2.13.03 unloaded
x264/20180923 unloaded
opus/1.3 unloaded
libtiff/4.0.9 unloaded
libjpeg-turbo/2.0.0 unloaded
giflib/5.1.4 unloaded
libwebp/1.0.0 unloaded
ffmpeg/4.1 unloaded
gstreamer/1.14.3 unloaded
gst-plugins-base/1.14.3 unloaded
littlecms/2.9 unloaded
nss/3.41-nspr-4.20 unloaded
qt5/5.11.2 unloaded
pyqt5/5.11.3-python-3.6.8 unloaded
matplotlib/2.2.3-python-3.6.8 unloaded
szip/2.1.1 unloaded
hdf5/1.10.3 unloaded
h5py/2.8.0-python-3.6.8 unloaded
libyaml/0.2.1 unloaded
pyyaml/3.13-python-3.6.8 unloaded
qhull/2015.2 unloaded
pillow/5.3.0-python-3.6.8 unloaded
cython/0.28.5-python-3.6.8 unloaded
scikit-image/0.14.1-python-3.6.8 unloaded
astropy/3.2.1-python-3.6.8 unloaded
plotly/3.10.0-python-3.6.8 unloaded
statsmodels/0.9.0-python-3.6.8 unloaded
seaborn/0.9.0-python-3.6.8 unloaded
gcccore/6.4.0 loaded
zlib/1.2.11 unloaded
zlib/1.2.11 loaded
ncurses/6.1 unloaded
ncurses/6.1 loaded
libreadline/7.0 unloaded
libreadline/7.0 loaded
openssl/1.1.0i unloaded
openssl/1.1.0i loaded
gettext/0.19.8.1 unloaded
xz/5.2.4 loaded
libxml2/2.9.7 loaded
gettext/0.19.8.1 loaded
bzip2/1.0.6 loaded
tcl/8.6.8 loaded
sqlite/3.24.0 loaded
expat/2.2.6 loaded
libpng/1.6.37 loaded
freetype/2.9.1 loaded
fontconfig/2.13.1 loaded
libgpg-error/1.32 loaded
libgcrypt/1.8.3 loaded
libxslt/1.1.32 loaded
x11/20180604 loaded
tk/8.6.8 loaded
coreutils/8.30 loaded
gmp/6.1.2 loaded
libffi/3.2.1 loaded
python/3.6.8 loaded
setuptools/40.4.3-python-3.6.8 loaded
py/1.7.0-python-3.6.8 loaded
pytest/4.0.0-python-3.6.8 loaded
openpgm/5.2.122 loaded
util-linux/2.32 loaded
libsodium/1.0.16 loaded
zeromq/4.2.5 loaded
pyzmq/17.1.0-python-3.6.8-zmq4 loaded
pip/18.1-python-3.6.8 loaded
requests/2.19.1-python-3.6.8 loaded
ipython/7.2.0-python-3.6.8 loaded
numpy/1.15.2-python-3.6.8 loaded
pandas/0.23.4-python-3.6.8 loaded
scipy/1.1.0-python-3.6.8 loaded
kiwisolver/1.0.1-python-3.6.8 loaded
sip/4.19.13-python-3.6.8 loaded
pcre/8.42 loaded
icu/63.1 loaded
dbus/1.13.6 loaded
nettle/3.4 loaded
libdrm/2.4.94 loaded
llvm/6.0.1 loaded
mesa/18.3.6 loaded
libglu/9.0.0 loaded
perl/5.28.0 loaded
intltool/0.51.0-perl-5.28.0 loaded
glib/2.58.0 loaded
python/3.6.8 unloaded
python/3.7.0 loaded
gobject-introspection/1.58.0 loaded
at-spi2-core/2.30.0 loaded
pixman/0.34.0 loaded
cairo/1.14.12 loaded
harfbuzz/1.9.0 loaded
nasm/2.13.03 loaded
x264/20180923 loaded
opus/1.3 loaded
libtiff/4.0.9 loaded
libjpeg-turbo/2.0.0 loaded
giflib/5.1.4 loaded
libpng/1.6.37 unloaded
libpng/1.6.35 loaded
libwebp/1.0.0 loaded
ffmpeg/4.1 loaded
gstreamer/1.14.3 loaded
gst-plugins-base/1.14.3 loaded
littlecms/2.9 loaded
nss/3.41-nspr-4.20 loaded
glib/2.58.0 unloaded
libxslt/1.1.32 unloaded
libxml2/2.9.7 unloaded
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libxslt/1.1.32-icu-63.1 loaded
glib/2.58.2 loaded
qt5/5.11.2 loaded
python/3.7.0 unloaded
python/3.6.8 loaded
pyqt5/5.11.3-python-3.6.8 loaded
matplotlib/2.2.3-python-3.6.8 loaded
szip/2.1.1 loaded
hdf5/1.10.3 loaded
h5py/2.8.0-python-3.6.8 loaded
libyaml/0.2.1 loaded
pyyaml/3.13-python-3.6.8 loaded
qhull/2015.2 loaded
pillow/5.3.0-python-3.6.8 loaded
cython/0.28.5-python-3.6.8 loaded
scikit-image/0.14.1-python-3.6.8 loaded
astropy/3.2.1-python-3.6.8 loaded
plotly/3.10.0-python-3.6.8 loaded
statsmodels/0.9.0-python-3.6.8 loaded
seaborn/0.9.0-python-3.6.8 loaded
libxslt/1.1.32-icu-63.1 unloaded
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libxslt/1.1.32 unloaded
glib/2.58.2 unloaded
libxslt/1.1.32 loaded
glib/2.58.0 loaded
samtools/1.9 loaded
Processing: 1
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr1.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 1 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr1.map.pos
Processing: 1
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr1.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 1 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr1.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 1 | samtools depth -b PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr1.map.pos - > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr1.map.pos.cov
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 1 | samtools depth -b PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr1.map.pos - > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr1.map.pos.cov
Processing: 2
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr2.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 2 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr2.map.pos
Processing: 2
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr2.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 2 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr2.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 2 | samtools depth -b PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr2.map.pos - > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr2.map.pos.cov
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 2 | samtools depth -b PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr2.map.pos - > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr2.map.pos.cov
Processing: 3
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr3.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 3 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr3.map.pos
Processing: 3
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr3.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 3 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr3.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 3 | samtools depth -b PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr3.map.pos - > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr3.map.pos.cov
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 3 | samtools depth -b PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr3.map.pos - > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr3.map.pos.cov

Processing: 4
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr4.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 4 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr4.map.pos
Processing: 4
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr4.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 4 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr4.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 4 | samtools depth -b PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr4.map.pos - > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr4.map.pos.cov
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 4 | samtools depth -b PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr4.map.pos - > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr4.map.pos.cov
Processing: 5
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr5.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 5 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr5.map.pos
Processing: 5
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr5.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 5 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr5.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 5 | samtools depth -b PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr5.map.pos - > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr5.map.pos.cov
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 5 | samtools depth -b PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr5.map.pos - > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr5.map.pos.cov
Processing: 6
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr6.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 6 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr6.map.pos
Processing: 6
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr6.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 6 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr6.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 6 | samtools depth -b PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr6.map.pos - > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr6.map.pos.cov
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 6 | samtools depth -b PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr6.map.pos - > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr6.map.pos.cov
Processing: 7
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr7.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 7 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr7.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 7 | samtools depth -b PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr7.map.pos - > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr7.map.pos.cov
Processing: 7
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr7.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 7 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr7.map.pos
Processing: 8
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr8.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 8 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr8.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 7 | samtools depth -b PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr7.map.pos - > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr7.map.pos.cov
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 8 | samtools depth -b PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr8.map.pos - > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr8.map.pos.cov
Processing: 8
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr8.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 8 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr8.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 8 | samtools depth -b PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr8.map.pos - > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr8.map.pos.cov
Processing: 9
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr9.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 9 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr9.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 9 | samtools depth -b PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr9.map.pos - > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr9.map.pos.cov
Processing: 9
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr9.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 9 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr9.map.pos
Processing: 10
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr10.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 10 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr10.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 9 | samtools depth -b PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr9.map.pos - > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr9.map.pos.cov
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 10 | samtools depth -b PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr10.map.pos - > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr10.map.pos.cov
Processing: 10
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr10.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 10 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr10.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 10 | samtools depth -b PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr10.map.pos - > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr10.map.pos.cov
Processing: 11
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr11.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 11 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr11.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 11 | samtools depth -b PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr11.map.pos - > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr11.map.pos.cov
Processing: 11
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr11.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 11 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr11.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 11 | samtools depth -b PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr11.map.pos - > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr11.map.pos.cov
Processing: 12
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr12.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 12 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr12.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 12 | samtools depth -b PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr12.map.pos - > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr12.map.pos.cov
Processing: 12
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr12.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 12 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr12.map.pos
Processing: 13
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr13.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 13 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr13.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 12 | samtools depth -b PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr12.map.pos - > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr12.map.pos.cov
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 13 | samtools depth -b PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr13.map.pos - > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr13.map.pos.cov
Processing: 14
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr14.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 14 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr14.map.pos
Processing: 13
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr13.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 13 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr13.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 14 | samtools depth -b PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr14.map.pos - > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr14.map.pos.cov
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 13 | samtools depth -b PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr13.map.pos - > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr13.map.pos.cov
Processing: 15
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr15.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 15 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr15.map.pos
Processing: 14
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr14.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 14 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr14.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 15 | samtools depth -b PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr15.map.pos - > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr15.map.pos.cov
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 14 | samtools depth -b PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr14.map.pos - > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr14.map.pos.cov
Processing: 16
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr16.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 16 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr16.map.pos
Processing: 15
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr15.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 15 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr15.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 15 | samtools depth -b PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr15.map.pos - > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr15.map.pos.cov
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 16 | samtools depth -b PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr16.map.pos - > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr16.map.pos.cov
Processing: 16
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr16.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 16 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr16.map.pos
Processing: 17
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr17.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 17 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr17.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 16 | samtools depth -b PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr16.map.pos - > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr16.map.pos.cov
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 17 | samtools depth -b PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr17.map.pos - > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr17.map.pos.cov
Processing: 17
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr17.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 17 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr17.map.pos
Processing: 18
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr18.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 18 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr18.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 18 | samtools depth -b PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr18.map.pos - > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr18.map.pos.cov
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 17 | samtools depth -b PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr17.map.pos - > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr17.map.pos.cov
Processing: 19
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr19.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 19 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr19.map.pos
Processing: 18
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr18.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 18 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr18.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 19 | samtools depth -b PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr19.map.pos - > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr19.map.pos.cov
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 18 | samtools depth -b PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr18.map.pos - > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr18.map.pos.cov
Processing: 19
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr19.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 19 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr19.map.pos
Processing: 20
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr20.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 20 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr20.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 19 | samtools depth -b PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr19.map.pos - > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr19.map.pos.cov
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 20 | samtools depth -b PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr20.map.pos - > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr20.map.pos.cov
Processing: 21
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr21.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 21 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr21.map.pos
Processing: 20
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr20.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 20 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr20.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 21 | samtools depth -b PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr21.map.pos - > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr21.map.pos.cov
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 20 | samtools depth -b PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr20.map.pos - > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr20.map.pos.cov
Processing: 22
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr22.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 22 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr22.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkTumor.1X.filtered.bam 22 | samtools depth -b PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr22.map.pos - > PaSDqc/cov/Wangetal.BulkTumor.1X.filtered.chr22.map.pos.cov
Processing: 21
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr21.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 21 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr21.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 21 | samtools depth -b PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr21.map.pos - > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr21.map.pos.cov
Processing: 22
Executing: samtools view -q 30 -L /mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/db/grch37.chr22.map.bed /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 22 | cut -f 3,4 | uniq > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr22.map.pos
Executing: samtools view -uh -q 30 /mnt/netapp2/posadalab2/uvibetpf/SCCoverageUniformity/RESULTS/PaSDqcTama/Wangetal.BulkNormal.1X.filtered.bam 22 | samtools depth -b PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr22.map.pos - > PaSDqc/cov/Wangetal.BulkNormal.1X.filtered.chr22.map.pos.cov
PaSDqc/psd/Wangetal.BulkTumor.1X.filtered.chroms.spec
PaSDqc/psd/Wangetal.BulkNormal.1X.filtered.chroms.spec
1.p arm
WARNING: AstropyDeprecationWarning: Importing LombScargle from astropy.stats has been deprecated and will no longer be supported in future. Please import this class from the astropy.timeseries module instead [astropy.stats.lombscargle]
1.p arm
WARNING: AstropyDeprecationWarning: Importing LombScargle from astropy.stats has been deprecated and will no longer be supported in future. Please import this class from the astropy.timeseries module instead [astropy.stats.lombscargle]
1.q arm
1.q arm
10.p arm
10.p arm
10.q arm
10.q arm
11.p arm
11.p arm
11.q arm
11.q arm
12.p arm
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2.p arm
19.q arm
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2.q arm
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20.p arm
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22.p arm
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3.p arm
22.p arm
22.q arm
3.p arm
3.q arm
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4.p arm
4.q arm
4.p arm
4.q arm
5.p arm
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6.p arm
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6.p arm
7.p arm
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9.p arm
8.q arm
9.q arm
/mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/PSDTools.py:324: FutureWarning:

from_items is deprecated. Please use DataFrame.from_dict(dict(items), ...) instead. DataFrame.from_dict(OrderedDict(items)) may be used to preserve the key order.

PaSDqc/psd/Wangetal.BulkTumor.1X.filtered.chroms.spec
9.p arm
9.q arm
/mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/PSDTools.py:324: FutureWarning:

from_items is deprecated. Please use DataFrame.from_dict(dict(items), ...) instead. DataFrame.from_dict(OrderedDict(items)) may be used to preserve the key order.

PaSDqc/psd/Wangetal.BulkNormal.1X.filtered.chroms.spec
Reading data from PaSDqc
Fitting chromosome and sample curves
/mnt/netapp1/Optcesga_FT2_RHEL7/easybuild-cesga/software/Compiler/gcccore/6.4.0/pandas/0.23.4-python-3.6.8/lib/python3.6/site-packages/pandas-0.23.4-py3.6-linux-x86_64.egg/pandas/core/series.py:3727: FutureWarning:

from_csv is deprecated. Please use read_csv(...) instead. Note that some of the default arguments are different, so please refer to the documentation for from_csv when changing your function calls

/mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/extra_tools.py:54: FutureWarning:

Method .as_matrix will be removed in a future version. Use .values instead.

Calculating chromosome properties
/mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/PSDTools.py:451: RuntimeWarning:

invalid value encountered in greater

/mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/PSDTools.py:453: RuntimeWarning:

invalid value encountered in less

Traceback (most recent call last):
File "/mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc//scripts/PaSDqc", line 265, in
args.func(args)
File "/mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc//scripts/PaSDqc", line 211, in QC
report(args)
File "/mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc//scripts/PaSDqc", line 127, in report
[psd.calc_chrom_props(chroms) for psd in psd_list]
File "/mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc//scripts/PaSDqc", line 127, in
[psd.calc_chrom_props(chroms) for psd in psd_list]
File "/mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/PSDTools.py", line 420, in calc_chrom_props
median, mean, lower, upper = self.ampl.amplicon_range(chrom_popt, method=method)
File "/mnt/lustre/scratch/home/uvi/be/tpf/APPS/PASDQC/PaSDqc/PaSDqc/amplicon.py", line 252, in amplicon_range
x = dist.rvs(size=100000)
File "/mnt/netapp1/Optcesga_FT2_RHEL7/easybuild-cesga/software/Compiler/gcccore/6.4.0/scipy/1.1.0-python-3.6.8/lib/python3.6/site-packages/scipy-1.1.0-py3.6-linux-x86_64.egg/scipy/stats/_distn_infrastructure.py", line 470, in rvs
return self.dist.rvs(*self.args, **kwds)
File "/mnt/netapp1/Optcesga_FT2_RHEL7/easybuild-cesga/software/Compiler/gcccore/6.4.0/scipy/1.1.0-python-3.6.8/lib/python3.6/site-packages/scipy-1.1.0-py3.6-linux-x86_64.egg/scipy/stats/_distn_infrastructure.py", line 940, in rvs
raise ValueError("Domain error in arguments.")
ValueError: Domain error in arguments.

Here is the code:

PaSDqc QC \
        -d $WORKDIR/PaSDqcTama/ \
        -n 4 \
        -c /mnt/netapp1/posadalab/APPS/PaSDqc-1.1.0-source/PaSDqc/db/categorical_spectra_1x.txt \
        -q 30 \
        -r ${CONFIG} \
        --noclean

Do you have an idea of what could be going on here?

Thanks in advance,

Tamara

Hi,

I am getting the following error when running the program.

This is the command:
PaSDqc QC \ -d test/ \ -c PaSDqc-1.1.0-source/PaSDqc/db/categorical_spectra_0.1x.txt \ -q 30 \ -r TEST

This is the std error
`
Processing: 1
Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr1.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 1 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr1.map.pos
Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 1 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr1.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr1.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr1.map.pos
Processing: 2
Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr2.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 2 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr2.map.pos
Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 2 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr2.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr2.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr2.map.pos
Processing: 3
Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr3.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 3 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr3.map.pos
Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 3 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr3.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr3.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr3.map.pos
Processing: 4
Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr4.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 4 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr4.map.pos
Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 4 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr4.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr4.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr4.map.pos
Processing: 5
Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr5.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 5 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr5.map.pos
Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 5 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr5.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr5.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr5.map.pos
Processing: 6
Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr6.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 6 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr6.map.pos
Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 6 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr6.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr6.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr6.map.pos
Processing: 7
Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr7.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 7 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr7.map.pos
Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 7 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr7.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr7.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr7.map.pos
Processing: 8
Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr8.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 8 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr8.map.pos
Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 8 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr8.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr8.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr8.map.pos
Processing: 9
Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr9.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 9 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr9.map.pos
Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 9 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr9.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr9.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr9.map.pos
Processing: 10
Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr10.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 10 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr10.map.pos
Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 10 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr10.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr10.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr10.map.pos
Processing: 11
Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr11.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 11 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr11.map.pos
Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 11 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr11.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr11.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr11.map.pos
Processing: 12
Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr12.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 12 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr12.map.pos
Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 12 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr12.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr12.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr12.map.pos
Processing: 13
Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr13.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 13 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr13.map.pos
Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 13 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr13.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr13.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr13.map.pos
Processing: 14
Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr14.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 14 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr14.map.pos
Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 14 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr14.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr14.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr14.map.pos
Processing: 15
Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr15.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 15 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr15.map.pos
Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 15 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr15.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr15.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr15.map.pos
Processing: 16
Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr16.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 16 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr16.map.pos
Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 16 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr16.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr16.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr16.map.pos
Processing: 17
Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr17.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 17 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr17.map.pos
Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 17 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr17.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr17.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr17.map.pos
Processing: 18
Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr18.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 18 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr18.map.pos
Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 18 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr18.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr18.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr18.map.pos
Processing: 19
Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr19.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 19 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr19.map.pos
Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 19 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr19.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr19.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr19.map.pos
Processing: 20
Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr20.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 20 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr20.map.pos
Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 20 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr20.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr20.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr20.map.pos
Processing: 21
Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr21.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 21 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr21.map.pos
Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 21 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr21.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr21.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr21.map.pos
Processing: 22
Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr22.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 22 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr22.map.pos
Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 22 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr22.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr22.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr22.map.pos
PaSDqc/psd/TP-ML-F3-IP.dedup.ps.chroms.spec
1.p arm
/home/uvi/be/.local/lib/python3.5/site-packages/astropy/stats/lombscargle/implementations/fast_impl.py:93: RuntimeWarning:

divide by zero encountered in true_divide

/home/uvi/be/.local/lib/python3.5/site-packages/astropy/stats/lombscargle/implementations/fast_impl.py:93: RuntimeWarning:

invalid value encountered in true_divide

/home/uvi/be/.local/lib/python3.5/site-packages/astropy/stats/lombscargle/implementations/fast_impl.py:104: RuntimeWarning:

invalid value encountered in true_divide

/home/uvi/be/.local/lib/python3.5/site-packages/astropy/stats/lombscargle/implementations/fast_impl.py:122: RuntimeWarning:

invalid value encountered in true_divide

/home/uvi/be/.local/lib/python3.5/site-packages/numpy/lib/function_base.py:4035: RuntimeWarning:

Invalid value encountered in median for 3226 results

1.q arm
/home/uvi/be/.local/lib/python3.5/site-packages/numpy/lib/function_base.py:4035: RuntimeWarning:

Invalid value encountered in median for 1 results

10.p arm
10.q arm
11.p arm
11.q arm
/home/uvi/be/.local/lib/python3.5/site-packages/numpy/lib/function_base.py:4035: RuntimeWarning:

Invalid value encountered in median for 6986 results

12.p arm
12.q arm
13.p arm
13.q arm
14.p arm
14.q arm
/home/uvi/be/.local/lib/python3.5/site-packages/numpy/lib/function_base.py:4035: RuntimeWarning:

Invalid value encountered in median for 7999 results

15.p arm
15.q arm
16.p arm
/home/uvi/be/.local/lib/python3.5/site-packages/numpy/lib/function_base.py:4035: RuntimeWarning:

Invalid value encountered in median for 3221 results

16.q arm
/home/uvi/be/.local/lib/python3.5/site-packages/numpy/lib/function_base.py:4035: RuntimeWarning:

Invalid value encountered in median for 5056 results

17.p arm
/home/uvi/be/.local/lib/python3.5/site-packages/numpy/lib/function_base.py:4035: RuntimeWarning:

Invalid value encountered in median for 6323 results

17.q arm
/home/uvi/be/.local/lib/python3.5/site-packages/numpy/lib/function_base.py:4035: RuntimeWarning:

Invalid value encountered in median for 7648 results

18.p arm
18.q arm
19.p arm
19.q arm
2.p arm
/home/uvi/be/.local/lib/python3.5/site-packages/numpy/lib/function_base.py:4035: RuntimeWarning:

Invalid value encountered in median for 8000 results

2.q arm
/home/uvi/be/.local/lib/python3.5/site-packages/numpy/lib/function_base.py:4035: RuntimeWarning:

Invalid value encountered in median for 7759 results

20.p arm
20.q arm
21.p arm
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/PaSDqc/lib/python3.5/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/PaSDqc/bin/PaSDqc", line 102, in _build_and_save
psd = PaSDqc.PSDTools.SamplePSD.build_from_dir(str(dir_in), sample=sample, clean=clean)
File "/PaSDqc/lib/python3.5/site-packages/PaSDqc/PSDTools.py", line 268, in build_from_dir
df = cls._build_dataframe(file_list, build)
File "/PaSDqc/lib/python3.5/site-packages/PaSDqc/PSDTools.py", line 318, in _build_dataframe
[psd.PSD_LS_chrom(f_cent, freq=freq) for psd in psd_list]
File "/PaSDqc/lib/python3.5/site-packages/PaSDqc/PSDTools.py", line 318, in
[psd.PSD_LS_chrom(f_cent, freq=freq) for psd in psd_list]
File "/PaSDqc/lib/python3.5/site-packages/PaSDqc/PSDTools.py", line 207, in PSD_LS_chrom
pwr_p, count_p = self.PSD_LS_manual(df_p, freq, l_seg, p_overlap, verbose=verbose)
File "/PaSDqc/lib/python3.5/site-packages/PaSDqc/PSDTools.py", line 164, in PSD_LS_manual
starts, ends = ChromPSD._welch_seg_bounds(df.pos, l_seg, p_overlap)
File "/PaSDqc/lib/python3.5/site-packages/PaSDqc/PSDTools.py", line 59, in _welch_seg_bounds
ends[-1] = pos.iloc[-1]
IndexError: index -1 is out of bounds for axis 0 with size 0
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/PaSDqc/bin/PaSDqc", line 265, in
args.func(args)
File "/PaSDqc/bin/PaSDqc", line 210, in QC
PSD(args)
File "/PaSDqc/bin/PaSDqc", line 95, in PSD
[p.get() for p in res]
File "/PaSDqc/bin/PaSDqc", line 95, in
[p.get() for p in res]
File "/PaSDqc/lib/python3.5/multiprocessing/pool.py", line 644, in get
raise self._value
IndexError: index -1 is out of bounds for axis 0 with size 0`

Do you have any idea about what can be happening here?
I just find this error for some of the single-cells, not all of them.
Thanks in advance