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kundajelab / atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline
BSD 3-Clause "New" or "Revised" License
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error in loading caTools #122

Closed timydaley closed 6 years ago

timydaley commented 6 years ago

Sorry for bothering you again. I'm getting mapped files but the pipeline isn't finishing. The error is Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/users/tdaley/R/x86_64-pc-linux-gnu-library/3.2/bitops/libs/bitops.so': libimf.so: cannot open shared object file: No such file or directory Error: package ‘caTools’ could not be loaded

My conda environment is as follows

[tdaley@sh-08-12 /scratch/PI/whwong/tdaley/scATACseq]$ uname -a Linux sh-08-12.int 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7 19:03:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux [tdaley@sh-08-12 /scratch/PI/whwong/tdaley/scATACseq]$ conda env list

conda environments:

# base * /home/users/tdaley/miniconda3 bds_atac /home/users/tdaley/miniconda3/envs/bds_atac bds_atac_py3 /home/users/tdaley/miniconda3/envs/bds_atac_py3

[tdaley@sh-08-12 /scratch/PI/whwong/tdaley/scATACseq]$ source activate bds_atac (bds_atac) [tdaley@sh-08-12 /scratch/PI/whwong/tdaley/scATACseq]$ which conda ~/miniconda3/bin/conda (bds_atac) [tdaley@sh-08-12 /scratch/PI/whwong/tdaley/scATACseq]$ conda list

packages in environment at /home/users/tdaley/miniconda3/envs/bds_atac:

#

Name Version Build Channel

argcomplete 1.9.4 py27_0
argh 0.26.1 py27_0 bioconda bedtools 2.26.0 0 bioconda bioconductor-biocgenerics 0.18.0 r3.2.2_0 bioconda bioconductor-biocparallel 1.4.3 r3.2.2_0 bioconda bioconductor-biostrings 2.38.4 0 bioconda bioconductor-genomeinfodb 1.6.3 0 bioconda bioconductor-genomicranges 1.22.4 0 bioconda bioconductor-iranges 2.4.8 0 bioconda bioconductor-rsamtools 1.22.0 r3.2.2_1 bioconda bioconductor-s4vectors 0.8.11 0 bioconda bioconductor-xvector 0.10.0 1 bioconda bioconductor-zlibbioc 1.16.0 r3.2.2_1 bioconda biopython 1.71 py27h637b7d7_0
boost 1.57.0 4
bowtie2 2.2.6 py27_0 bioconda bx-python 0.7.3 py27_0 bioconda bzip2 1.0.6 h14c3975_5
ca-certificates 2018.03.07 0 anaconda cairo 1.14.8 0
certifi 2018.4.16 py27_0 anaconda curl 7.60.0 h84994c4_0
cutadapt 1.9.1 py27_0 bioconda cycler 0.10.0 py27hc7354d3_0
cython 0.28.2 py27h14c3975_0
expat 2.2.5 he0dffb1_0
fastqc 0.11.5 1 bioconda fisher 0.1.4 py27_0 bioconda fontconfig 2.12.1 3
freetype 2.5.5 2
gffutils 0.9 py27_0 bioconda ghostscript 9.18 1 bioconda glib 2.56.1 h000015b_0
gnuplot 4.6.0 1 bioconda graphviz 2.38.0 5 anaconda gsl 1.16 1 asmeurer harfbuzz 0.9.39 2
htslib 1.4 0 bioconda icu 58.2 h9c2bf20_1
intel-openmp 2018.0.0 8
java-jdk 8.0.92 1 bioconda jinja2 2.10 py27h4114e70_0
jpeg 9b h024ee3a_2
libcurl 7.60.0 h1ad7b7a_0
libedit 3.1.20170329 h6b74fdf_2
libffi 3.2.1 hd88cf55_4
libgcc 7.2.0 h69d50b8_2
libgcc-ng 7.2.0 hdf63c60_3
libgfortran 3.0.0 1
libgfortran-ng 7.2.0 hdf63c60_3
libiconv 1.14 0
libopenblas 0.2.20 h9ac9557_4
libpng 1.6.34 hb9fc6fc_0
libssh2 1.8.0 h9cfc8f7_4
libstdcxx-ng 7.2.0 hdf63c60_3
libtiff 4.0.9 he85c1e1_1
libtool 2.4.6 h544aabb_3
libuuid 1.0.3 h1bed415_2
libxml2 2.9.8 h26e45fe_1
macs2 2.1.1.20160309 r3.2.2_0 bioconda markupsafe 1.0 py27h97b2822_1
matplotlib 1.5.1 np111py27_0
metaseq 0.5.6 py27_0 bioconda mkl 2018.0.2 1
mysql-connector-c 6.1.11 hf4847fb_0
ncurses 6.1 hf484d3e_0
nomkl 2.0 0
nose 1.3.7 py27heec2199_2
numpy 1.11.3 py27_nomkl_0 [nomkl] openblas 0.2.19 0
openssl 1.0.2o h20670df_0 anaconda pandas 0.23.0 py27h637b7d7_0
pango 1.36.8 3 asmeurer pcre 8.42 h439df22_0
perl-threaded 5.22.0 10 bioconda picard 1.126 4 bioconda pigz 2.3 0
pip 10.0.1 py27_0
pixman 0.34.0 hceecf20_3
preseq 2.0.2 gsl1.16_0 bioconda pybedtools 0.6.9 py27_1 bioconda pycairo 1.13.3 py27hea6d626_0
pyfaidx 0.4.7.1 py27_0 bioconda pyparsing 2.2.0 py27hf1513f8_1
pyqt 4.10.4 py27_0 asmeurer pysam 0.8.2.1 py27_0 bcbio python 2.7.15 h1571d57_0
python-dateutil 2.6.1 py27h4ca5741_1
python-levenshtein 0.12.0 py27_1 bioconda pytz 2018.4 py27_0
pyyaml 3.12 py27h2d70dd7_1
qt 4.8.7 4
r 3.2.2 0
r-base 3.2.2 0 asmeurer r-bitops 1.0_6 r3.2.2_1a
r-boot 1.3_17 r3.2.2_0a
r-catools 1.17.1 r3.2.2_2a
r-class 7.3_14 r3.2.2_0a
r-cluster 2.0.3 r3.2.2_0a
r-codetools 0.2_14 r3.2.2_0a
r-foreign 0.8_66 r3.2.2_0a
r-futile.logger 1.4.1 r3.2.2_0 bioconda r-futile.options 1.0.0 r3.2.2_0 bioconda r-kernsmooth 2.23_15 r3.2.2_0a
r-lambda.r 1.1.7 r3.2.2_0 bioconda r-lattice 0.20_33 r3.2.2_0a
r-mass 7.3_45 r3.2.2_0a
r-matrix 1.2_2 r3.2.2_0a
r-mgcv 1.8_9 r3.2.2_0a
r-nlme 3.1_122 r3.2.2_0a
r-nnet 7.3_11 r3.2.2_0a
r-recommended 3.2.2 r3.2.2_0
r-rpart 4.1_10 r3.2.2_0a
r-snow 0.4_1 r3.2.2_0 bioconda r-snowfall 1.84_6.1 r3.2.2_0 bioconda r-spatial 7.3_11 r3.2.2_0a
r-spp 1.13 r3.2.2_0 bioconda r-survival 2.38_3 r3.2.2_0a
readline 7.0 ha6073c6_4
sambamba 0.6.6 1 bioconda samtools 1.2 2 bioconda scikit-learn 0.19.1 py27_nomklh6479e79_0 [nomkl] scipy 1.1.0 py27_nomklh9d22d0a_0 [nomkl] setuptools 39.1.0 py27_0
simplejson 3.15.0 py27h14c3975_0
sip 4.19.8 py27hf484d3e_0
six 1.10.0 py27hdcd7534_1
sqlite 3.23.1 he433501_0
system 5.8 2
tk 8.6.7 hc745277_3
trim-galore 0.4.1 0 bioconda ucsc-bedclip 357 1 bioconda ucsc-bedgraphtobigwig 357 1 bioconda ucsc-bedtobigbed 357 1 bioconda ucsc-bigwigaverageoverbed 357 1 bioconda ucsc-bigwiginfo 357 1 bioconda ucsc-fetchchromsizes 357 1 bioconda ucsc-twobittofa 357 1 bioconda ucsc-wigtobigwig 357 1 bioconda wheel 0.31.1 py27_0
xz 5.2.4 h14c3975_4
yaml 0.1.7 had09818_2
zlib 1.2.11 ha838bed_2

I would assume that there is an issue with my LD_LIBRARY_PATH, which is below echo $LD_LIBRARY_PATH /share/software/user/open/java/1.8.0_131/jre/lib/amd64/server:/share/software/user/open/java/1.8.0_131/jre/lib/amd64:/share/software/user/open/java/1.8.0_131/lib/amd64

Thank you again for your help.

leepc12 commented 6 years ago

This looks like a conflicting dependencies problem.

Please remove any R, Python related things (export $PATH=...) from your ~/.bashrc and try again.

Pipeline needs to use R installed in the conda environment but it used your local installation for R (/home/users/tdaley/R).

Thanks,

Jin

On Tue, Jun 5, 2018 at 6:48 PM, Timothy Daley notifications@github.com wrote:

Sorry for bothering you again. I'm getting mapped files but the pipeline isn't finishing. The error is Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/users/tdaley/R/x86_64- pc-linux-gnu-library/3.2/bitops/libs/bitops.so': libimf.so: cannot open shared object file: No such file or directory Error: package ‘caTools’ could not be loaded

My conda environment is as follows

[tdaley@sh-08-12 /scratch/PI/whwong/tdaley/scATACseq]$ uname -a Linux sh-08-12.int 3.10.0-693.21.1.el7.x86_64 #1 https://github.com/kundajelab/atac_dnase_pipelines/issues/1 SMP Wed Mar 7 19:03:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux [tdaley@sh-08-12 /scratch/PI/whwong/tdaley/scATACseq]$ conda env list conda environments:

base * /home/users/tdaley/miniconda3 bds_atac /home/users/tdaley/miniconda3/envs/bds_atac bds_atac_py3 /home/users/tdaley/miniconda3/envs/bds_atac_py3

[tdaley@sh-08-12 /scratch/PI/whwong/tdaley/scATACseq]$ source activate bds_atac (bds_atac) [tdaley@sh-08-12 /scratch/PI/whwong/tdaley/scATACseq]$ which conda ~/miniconda3/bin/conda (bds_atac) [tdaley@sh-08-12 /scratch/PI/whwong/tdaley/scATACseq]$ conda list packages in environment at /home/users/tdaley/miniconda3/envs/bds_atac: Name Version Build Channel

argcomplete 1.9.4 py27_0 argh 0.26.1 py27_0 bioconda bedtools 2.26.0 0 bioconda bioconductor-biocgenerics 0.18.0 r3.2.2_0 bioconda bioconductor-biocparallel 1.4.3 r3.2.2_0 bioconda bioconductor-biostrings 2.38.4 0 bioconda bioconductor-genomeinfodb 1.6.3 0 bioconda bioconductor-genomicranges 1.22.4 0 bioconda bioconductor-iranges 2.4.8 0 bioconda bioconductor-rsamtools 1.22.0 r3.2.2_1 bioconda bioconductor-s4vectors 0.8.11 0 bioconda bioconductor-xvector 0.10.0 1 bioconda bioconductor-zlibbioc 1.16.0 r3.2.2_1 bioconda biopython 1.71 py27h637b7d7_0 boost 1.57.0 4 bowtie2 2.2.6 py27_0 bioconda bx-python 0.7.3 py27_0 bioconda bzip2 1.0.6 h14c3975_5 ca-certificates 2018.03.07 0 anaconda cairo 1.14.8 0 certifi 2018.4.16 py27_0 anaconda curl 7.60.0 h84994c4_0 cutadapt 1.9.1 py27_0 bioconda cycler 0.10.0 py27hc7354d3_0 cython 0.28.2 py27h14c3975_0 expat 2.2.5 he0dffb1_0 fastqc 0.11.5 1 bioconda fisher 0.1.4 py27_0 bioconda fontconfig 2.12.1 3 freetype 2.5.5 2 gffutils 0.9 py27_0 bioconda ghostscript 9.18 1 bioconda glib 2.56.1 h000015b_0 gnuplot 4.6.0 1 bioconda graphviz 2.38.0 5 anaconda gsl 1.16 1 asmeurer harfbuzz 0.9.39 2 htslib 1.4 0 bioconda icu 58.2 h9c2bf20_1 intel-openmp 2018.0.0 8 java-jdk 8.0.92 1 bioconda jinja2 2.10 py27h4114e70_0 jpeg 9b h024ee3a_2 libcurl 7.60.0 h1ad7b7a_0 libedit 3.1.20170329 h6b74fdf_2 libffi 3.2.1 hd88cf55_4 libgcc 7.2.0 h69d50b8_2 libgcc-ng 7.2.0 hdf63c60_3 libgfortran 3.0.0 1 libgfortran-ng 7.2.0 hdf63c60_3 libiconv 1.14 0 libopenblas 0.2.20 h9ac9557_4 libpng 1.6.34 hb9fc6fc_0 libssh2 1.8.0 h9cfc8f7_4 libstdcxx-ng 7.2.0 hdf63c60_3 libtiff 4.0.9 he85c1e1_1 libtool 2.4.6 h544aabb_3 libuuid 1.0.3 h1bed415_2 libxml2 2.9.8 h26e45fe_1 macs2 2.1.1.20160309 r3.2.2_0 bioconda markupsafe 1.0 py27h97b2822_1 matplotlib 1.5.1 np111py27_0 metaseq 0.5.6 py27_0 bioconda mkl 2018.0.2 1 mysql-connector-c 6.1.11 hf4847fb_0 ncurses 6.1 hf484d3e_0 nomkl 2.0 0 nose 1.3.7 py27heec2199_2 numpy 1.11.3 py27_nomkl_0 [nomkl] openblas 0.2.19 0 openssl 1.0.2o h20670df_0 anaconda pandas 0.23.0 py27h637b7d7_0 pango 1.36.8 3 asmeurer pcre 8.42 h439df22_0 perl-threaded 5.22.0 10 bioconda picard 1.126 4 bioconda pigz 2.3 0 pip 10.0.1 py27_0 pixman 0.34.0 hceecf20_3 preseq 2.0.2 gsl1.16_0 bioconda pybedtools 0.6.9 py27_1 bioconda pycairo 1.13.3 py27hea6d626_0 pyfaidx 0.4.7.1 py27_0 bioconda pyparsing 2.2.0 py27hf1513f8_1 pyqt 4.10.4 py27_0 asmeurer pysam 0.8.2.1 py27_0 bcbio python 2.7.15 h1571d57_0 python-dateutil 2.6.1 py27h4ca5741_1 python-levenshtein 0.12.0 py27_1 bioconda pytz 2018.4 py27_0 pyyaml 3.12 py27h2d70dd7_1 qt 4.8.7 4 r 3.2.2 0 r-base 3.2.2 0 asmeurer r-bitops 1.0_6 r3.2.2_1a r-boot 1.3_17 r3.2.2_0a r-catools 1.17.1 r3.2.2_2a r-class 7.3_14 r3.2.2_0a r-cluster 2.0.3 r3.2.2_0a r-codetools 0.2_14 r3.2.2_0a r-foreign 0.8_66 r3.2.2_0a r-futile.logger 1.4.1 r3.2.2_0 bioconda r-futile.options 1.0.0 r3.2.2_0 bioconda r-kernsmooth 2.23_15 r3.2.2_0a r-lambda.r 1.1.7 r3.2.2_0 bioconda r-lattice 0.20_33 r3.2.2_0a r-mass 7.3_45 r3.2.2_0a r-matrix 1.2_2 r3.2.2_0a r-mgcv 1.8_9 r3.2.2_0a r-nlme 3.1_122 r3.2.2_0a r-nnet 7.3_11 r3.2.2_0a r-recommended 3.2.2 r3.2.2_0 r-rpart 4.1_10 r3.2.2_0a r-snow 0.4_1 r3.2.2_0 bioconda r-snowfall 1.84_6.1 r3.2.2_0 bioconda r-spatial 7.3_11 r3.2.2_0a r-spp 1.13 r3.2.2_0 bioconda r-survival 2.38_3 r3.2.2_0a readline 7.0 ha6073c6_4 sambamba 0.6.6 1 bioconda samtools 1.2 2 bioconda scikit-learn 0.19.1 py27_nomklh6479e79_0 [nomkl] scipy 1.1.0 py27_nomklh9d22d0a_0 [nomkl] setuptools 39.1.0 py27_0 simplejson 3.15.0 py27h14c3975_0 sip 4.19.8 py27hf484d3e_0 six 1.10.0 py27hdcd7534_1 sqlite 3.23.1 he433501_0 system 5.8 2 tk 8.6.7 hc745277_3 trim-galore 0.4.1 0 bioconda ucsc-bedclip 357 1 bioconda ucsc-bedgraphtobigwig 357 1 bioconda ucsc-bedtobigbed 357 1 bioconda ucsc-bigwigaverageoverbed 357 1 bioconda ucsc-bigwiginfo 357 1 bioconda ucsc-fetchchromsizes 357 1 bioconda ucsc-twobittofa 357 1 bioconda ucsc-wigtobigwig 357 1 bioconda wheel 0.31.1 py27_0 xz 5.2.4 h14c3975_4 yaml 0.1.7 had09818_2 zlib 1.2.11 ha838bed_2

I would assume that there is an issue with my LD_LIBRARY_PATH, which is below echo $LD_LIBRARY_PATH /share/software/user/open/java/1.8.0_131/jre/lib/amd64/ server:/share/software/user/open/java/1.8.0_131/jre/lib/ amd64:/share/software/user/open/java/1.8.0_131/lib/amd64

Thank you again for your help.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/kundajelab/atac_dnase_pipelines/issues/122, or mute the thread https://github.com/notifications/unsubscribe-auth/AIOd_FVzczfSHy8CGn35W2lQgtp31mVbks5t5zT6gaJpZM4Ub2ug .

timydaley commented 6 years ago

I commented out lines in my .bashrc file that have to do with Python and R, and I'm still running into the same error. Below is the contents of my .bashrc file.

.bashrc

Source global definitions

if [ -f /etc/bashrc ]; then

. /etc/bashrc

fi

User specific aliases and functions

export HISTCONTROL=ignoreboth:erasedups # no duplicate entries

export BT2_HOME=/scratch/PI/whwong/tdaley/programs/aligners/bowtie2/bowtie2-2.2.7/

export PYTHONPATH=$PYTHONPATH:/home/tdaley/

export R_LIBS=/home/tdaley/R/

export PATH=$PATH:$HOME/.bds

export R_HOME=/scratch/users/leepc12/bds_pipeline_software/miniconda3/envs/aquas_chipseq/lib/R

aliases

alias jobs='squeue | grep tdaley'

alias node='sdev -p whwong -m 8GB -q normal -t 48:00:00'

alias bignode='sdev -p whwong -m 32GB -q normal -t 48:00:00'

added for MACS

export PATH=$PATH:/home/tdaley/scratch/programs/MACS/bin/

export CRISPY_CODE=/oak/stanford/groups/slqi/cstill/spacer_mix_CDS/spacer_mix/

alias crispy_aligner='function crispy_alignerfunc(){ time python "$CRISPY_CODE"crispy_aligner.py $@; };crispy_alignerfunc'

alias crispy_collapser='function crispy_collapserfunc(){ time python "$CRISPRY_CODE"crispy_collapser.py $@; };crispy_collapserfunc'

export PATH=${PATH}:/scratch/PI/whwong/tdaley/programs/sra/edirect/

export PATH=${PATH}:~/man/

export PATH=${PATH}:/home/users/zduren/software/samtools/bin/

export PATH=${PATH}:/scratch/PI/whwong/tdaley/programs/aligners/bowtie2/bowtie2-2.2.7/

export PATH=${PATH}:/home/users/zduren/bin/bowtie-1.2.2-linux-x86_64/

added by Miniconda3 installer

export PATH="/home/users/tdaley/miniconda3/bin:$PATH"

export PATH=$PATH:$HOME/.bds

export _JAVA_OPTIONS="-Xms256M -Xmx728M -XX:ParallelGCThreads=1"

export PICARDROOT=/scratch/PI/whwong/tdaley/programs/broadinstitute-picard-6aed7e7/

export TMPDIR=/scratch/PI/whwong/tdaley/tmp/

Timothy Daley

Stanford University, Departments of Statistics and Bioengineering.

From: Jin Lee notifications@github.com Sent: Wednesday, June 6, 2018 12:38:18 PM To: kundajelab/atac_dnase_pipelines Cc: Timothy Patrick Daley; Author Subject: Re: [kundajelab/atac_dnase_pipelines] error in loading caTools (#122)

This looks like a conflicting dependencies problem.

Please remove any R, Python related things (export $PATH=...) from your ~/.bashrc and try again.

Pipeline needs to use R installed in the conda environment but it used your local installation for R (/home/users/tdaley/R).

Thanks,

Jin

On Tue, Jun 5, 2018 at 6:48 PM, Timothy Daley notifications@github.com wrote:

Sorry for bothering you again. I'm getting mapped files but the pipeline isn't finishing. The error is Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/users/tdaley/R/x86_64- pc-linux-gnu-library/3.2/bitops/libs/bitops.so': libimf.so: cannot open shared object file: No such file or directory Error: package ‘caTools’ could not be loaded

My conda environment is as follows

[tdaley@sh-08-12 /scratch/PI/whwong/tdaley/scATACseq]$ uname -a Linux sh-08-12.int 3.10.0-693.21.1.el7.x86_64 #1 https://github.com/kundajelab/atac_dnase_pipelines/issues/1 SMP Wed Mar 7 19:03:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux [tdaley@sh-08-12 /scratch/PI/whwong/tdaley/scATACseq]$ conda env list conda environments:

base * /home/users/tdaley/miniconda3 bds_atac /home/users/tdaley/miniconda3/envs/bds_atac bds_atac_py3 /home/users/tdaley/miniconda3/envs/bds_atac_py3

[tdaley@sh-08-12 /scratch/PI/whwong/tdaley/scATACseq]$ source activate bds_atac (bds_atac) [tdaley@sh-08-12 /scratch/PI/whwong/tdaley/scATACseq]$ which conda ~/miniconda3/bin/conda (bds_atac) [tdaley@sh-08-12 /scratch/PI/whwong/tdaley/scATACseq]$ conda list packages in environment at /home/users/tdaley/miniconda3/envs/bds_atac: Name Version Build Channel

argcomplete 1.9.4 py27_0 argh 0.26.1 py27_0 bioconda bedtools 2.26.0 0 bioconda bioconductor-biocgenerics 0.18.0 r3.2.2_0 bioconda bioconductor-biocparallel 1.4.3 r3.2.2_0 bioconda bioconductor-biostrings 2.38.4 0 bioconda bioconductor-genomeinfodb 1.6.3 0 bioconda bioconductor-genomicranges 1.22.4 0 bioconda bioconductor-iranges 2.4.8 0 bioconda bioconductor-rsamtools 1.22.0 r3.2.2_1 bioconda bioconductor-s4vectors 0.8.11 0 bioconda bioconductor-xvector 0.10.0 1 bioconda bioconductor-zlibbioc 1.16.0 r3.2.2_1 bioconda biopython 1.71 py27h637b7d7_0 boost 1.57.0 4 bowtie2 2.2.6 py27_0 bioconda bx-python 0.7.3 py27_0 bioconda bzip2 1.0.6 h14c3975_5 ca-certificates 2018.03.07 0 anaconda cairo 1.14.8 0 certifi 2018.4.16 py27_0 anaconda curl 7.60.0 h84994c4_0 cutadapt 1.9.1 py27_0 bioconda cycler 0.10.0 py27hc7354d3_0 cython 0.28.2 py27h14c3975_0 expat 2.2.5 he0dffb1_0 fastqc 0.11.5 1 bioconda fisher 0.1.4 py27_0 bioconda fontconfig 2.12.1 3 freetype 2.5.5 2 gffutils 0.9 py27_0 bioconda ghostscript 9.18 1 bioconda glib 2.56.1 h000015b_0 gnuplot 4.6.0 1 bioconda graphviz 2.38.0 5 anaconda gsl 1.16 1 asmeurer harfbuzz 0.9.39 2 htslib 1.4 0 bioconda icu 58.2 h9c2bf20_1 intel-openmp 2018.0.0 8 java-jdk 8.0.92 1 bioconda jinja2 2.10 py27h4114e70_0 jpeg 9b h024ee3a_2 libcurl 7.60.0 h1ad7b7a_0 libedit 3.1.20170329 h6b74fdf_2 libffi 3.2.1 hd88cf55_4 libgcc 7.2.0 h69d50b8_2 libgcc-ng 7.2.0 hdf63c60_3 libgfortran 3.0.0 1 libgfortran-ng 7.2.0 hdf63c60_3 libiconv 1.14 0 libopenblas 0.2.20 h9ac9557_4 libpng 1.6.34 hb9fc6fc_0 libssh2 1.8.0 h9cfc8f7_4 libstdcxx-ng 7.2.0 hdf63c60_3 libtiff 4.0.9 he85c1e1_1 libtool 2.4.6 h544aabb_3 libuuid 1.0.3 h1bed415_2 libxml2 2.9.8 h26e45fe_1 macs2 2.1.1.20160309 r3.2.2_0 bioconda markupsafe 1.0 py27h97b2822_1 matplotlib 1.5.1 np111py27_0 metaseq 0.5.6 py27_0 bioconda mkl 2018.0.2 1 mysql-connector-c 6.1.11 hf4847fb_0 ncurses 6.1 hf484d3e_0 nomkl 2.0 0 nose 1.3.7 py27heec2199_2 numpy 1.11.3 py27_nomkl_0 [nomkl] openblas 0.2.19 0 openssl 1.0.2o h20670df_0 anaconda pandas 0.23.0 py27h637b7d7_0 pango 1.36.8 3 asmeurer pcre 8.42 h439df22_0 perl-threaded 5.22.0 10 bioconda picard 1.126 4 bioconda pigz 2.3 0 pip 10.0.1 py27_0 pixman 0.34.0 hceecf20_3 preseq 2.0.2 gsl1.16_0 bioconda pybedtools 0.6.9 py27_1 bioconda pycairo 1.13.3 py27hea6d626_0 pyfaidx 0.4.7.1 py27_0 bioconda pyparsing 2.2.0 py27hf1513f8_1 pyqt 4.10.4 py27_0 asmeurer pysam 0.8.2.1 py27_0 bcbio python 2.7.15 h1571d57_0 python-dateutil 2.6.1 py27h4ca5741_1 python-levenshtein 0.12.0 py27_1 bioconda pytz 2018.4 py27_0 pyyaml 3.12 py27h2d70dd7_1 qt 4.8.7 4 r 3.2.2 0 r-base 3.2.2 0 asmeurer r-bitops 1.0_6 r3.2.2_1a r-boot 1.3_17 r3.2.2_0a r-catools 1.17.1 r3.2.2_2a r-class 7.3_14 r3.2.2_0a r-cluster 2.0.3 r3.2.2_0a r-codetools 0.2_14 r3.2.2_0a r-foreign 0.8_66 r3.2.2_0a r-futile.logger 1.4.1 r3.2.2_0 bioconda r-futile.options 1.0.0 r3.2.2_0 bioconda r-kernsmooth 2.23_15 r3.2.2_0a r-lambda.r 1.1.7 r3.2.2_0 bioconda r-lattice 0.20_33 r3.2.2_0a r-mass 7.3_45 r3.2.2_0a r-matrix 1.2_2 r3.2.2_0a r-mgcv 1.8_9 r3.2.2_0a r-nlme 3.1_122 r3.2.2_0a r-nnet 7.3_11 r3.2.2_0a r-recommended 3.2.2 r3.2.2_0 r-rpart 4.1_10 r3.2.2_0a r-snow 0.4_1 r3.2.2_0 bioconda r-snowfall 1.84_6.1 r3.2.2_0 bioconda r-spatial 7.3_11 r3.2.2_0a r-spp 1.13 r3.2.2_0 bioconda r-survival 2.38_3 r3.2.2_0a readline 7.0 ha6073c6_4 sambamba 0.6.6 1 bioconda samtools 1.2 2 bioconda scikit-learn 0.19.1 py27_nomklh6479e79_0 [nomkl] scipy 1.1.0 py27_nomklh9d22d0a_0 [nomkl] setuptools 39.1.0 py27_0 simplejson 3.15.0 py27h14c3975_0 sip 4.19.8 py27hf484d3e_0 six 1.10.0 py27hdcd7534_1 sqlite 3.23.1 he433501_0 system 5.8 2 tk 8.6.7 hc745277_3 trim-galore 0.4.1 0 bioconda ucsc-bedclip 357 1 bioconda ucsc-bedgraphtobigwig 357 1 bioconda ucsc-bedtobigbed 357 1 bioconda ucsc-bigwigaverageoverbed 357 1 bioconda ucsc-bigwiginfo 357 1 bioconda ucsc-fetchchromsizes 357 1 bioconda ucsc-twobittofa 357 1 bioconda ucsc-wigtobigwig 357 1 bioconda wheel 0.31.1 py27_0 xz 5.2.4 h14c3975_4 yaml 0.1.7 had09818_2 zlib 1.2.11 ha838bed_2

I would assume that there is an issue with my LD_LIBRARY_PATH, which is below echo $LD_LIBRARY_PATH /share/software/user/open/java/1.8.0_131/jre/lib/amd64/ server:/share/software/user/open/java/1.8.0_131/jre/lib/ amd64:/share/software/user/open/java/1.8.0_131/lib/amd64

Thank you again for your help.

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leepc12 commented 6 years ago

Can you temporarily remove your local R (by renaming it or moving it to somewhere) and see if that works? /home/tdaley/R

timydaley commented 6 years ago

That worked. Interesting issue. Thank you so much for your help. I owe you a beer. Cheers.