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parklab / PaSDqc

A python library for single cell whole-genome sequencing quality evaluation
MIT License
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ValueError: Domain error in arguments #10

Open tamaraprieto opened 5 years ago

tamaraprieto commented 5 years ago

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 libxml2/2.9.7-icu-63.1 loaded 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 libxslt/1.1.32 loaded 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 12.p arm 12.q arm 12.q arm 13.p arm 13.q arm 13.p arm 13.q arm 14.p arm 14.q arm 14.p arm 14.q arm 15.p arm 15.q arm 15.p arm 15.q arm 16.p arm 16.p arm 16.q arm 16.q arm 17.p arm 17.q arm 17.p arm 17.q arm 18.p arm 18.q arm 18.p arm 19.p arm 18.q arm 19.q arm 19.p arm 2.p arm 19.q arm 2.p arm 2.q arm 2.q arm 20.p arm 20.q arm 21.p arm 20.p arm 21.q arm 20.q arm 22.p arm 22.q arm 21.p arm 21.q arm 3.p arm 22.p arm 22.q arm 3.p arm 3.q arm 3.q arm 4.p arm 4.q arm 4.p arm 4.q arm 5.p arm 5.q arm 5.p arm 5.q arm 6.p arm 6.q arm 6.p arm 7.p arm 6.q arm 7.q arm 7.p arm 8.p arm 7.q arm 8.q arm 8.p arm 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

maxwellsh commented 5 years ago

Hi Tamara, I've not seen this before, but my guess is that when the algorithm tries to find a best fit line for the individual chromosome analysis, it ends up making the variance term negative. I suggest plotting the spectrograms for your samples to see if they have the same shape as the ones in the NAR paper.

Best, Max