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Murali-group / Beeline

BEELINE: evaluation of algorithms for gene regulatory network inference
GNU General Public License v3.0
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Not able to run SCRIBE #45

Closed Zengggg closed 3 years ago

Zengggg commented 3 years ago

Hi, I reinstalled BEELINE, and it seems that BEELINE has been installed successfully. The command line output is as below:

zengyp@ubuntu:~/Single_cell/1/Beeline-master$ . setupAnacondaVENV.sh 
Setting up Anaconda Python virtual environment...
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/zengyp/anaconda3/envs/BEELINE

  added / updated specs:
    - matplotlib==3.0.2
    - networkx==2.2
    - numpy==1.15.4
    - pandas==0.23.4
    - python=3.7.1
    - pyyaml==5.1.1
    - r=3.5.0
    - rpy2==2.9.1
    - scikit-learn==0.21.2
    - seaborn==0.9.0
    - tqdm==4.28.1

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  _r-mutex           pkgs/r/linux-64::_r-mutex-1.0.0-anacondar_1
  binutils_impl_lin~ pkgs/main/linux-64::binutils_impl_linux-64-2.33.1-he6710b0_7
  binutils_linux-64  pkgs/main/linux-64::binutils_linux-64-2.33.1-h9595d00_15
  blas               pkgs/main/linux-64::blas-1.0-mkl
  bwidget            pkgs/main/linux-64::bwidget-1.9.11-1
  bzip2              pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0
  ca-certificates    pkgs/main/linux-64::ca-certificates-2021.1.19-h06a4308_0
  cairo              pkgs/main/linux-64::cairo-1.14.12-h8948797_3
  certifi            pkgs/main/linux-64::certifi-2020.12.5-py37h06a4308_0
  curl               pkgs/main/linux-64::curl-7.67.0-hbc83047_0
  cycler             pkgs/main/linux-64::cycler-0.10.0-py37_0
  dbus               pkgs/main/linux-64::dbus-1.13.18-hb2f20db_0
  decorator          pkgs/main/noarch::decorator-4.4.2-pyhd3eb1b0_0
  expat              pkgs/main/linux-64::expat-2.2.10-he6710b0_2
  fontconfig         pkgs/main/linux-64::fontconfig-2.13.1-h6c09931_0
  freetype           pkgs/main/linux-64::freetype-2.10.4-h5ab3b9f_0
  fribidi            pkgs/main/linux-64::fribidi-1.0.10-h7b6447c_0
  gcc_impl_linux-64  pkgs/main/linux-64::gcc_impl_linux-64-7.3.0-habb00fd_1
  gcc_linux-64       pkgs/main/linux-64::gcc_linux-64-7.3.0-h553295d_15
  gfortran_impl_lin~ pkgs/main/linux-64::gfortran_impl_linux-64-7.3.0-hdf63c60_1
  gfortran_linux-64  pkgs/main/linux-64::gfortran_linux-64-7.3.0-h553295d_15
  glib               pkgs/main/linux-64::glib-2.63.1-h5a9c865_0
  graphite2          pkgs/main/linux-64::graphite2-1.3.14-h23475e2_0
  gsl                pkgs/main/linux-64::gsl-2.4-h14c3975_4
  gst-plugins-base   pkgs/main/linux-64::gst-plugins-base-1.14.0-hbbd80ab_1
  gstreamer          pkgs/main/linux-64::gstreamer-1.14.0-hb453b48_1
  gxx_impl_linux-64  pkgs/main/linux-64::gxx_impl_linux-64-7.3.0-hdf63c60_1
  gxx_linux-64       pkgs/main/linux-64::gxx_linux-64-7.3.0-h553295d_15
  harfbuzz           pkgs/main/linux-64::harfbuzz-1.8.8-hffaf4a1_0
  icu                pkgs/main/linux-64::icu-58.2-he6710b0_3
  intel-openmp       pkgs/main/linux-64::intel-openmp-2020.2-254
  jinja2             pkgs/main/noarch::jinja2-2.11.3-pyhd3eb1b0_0
  joblib             pkgs/main/noarch::joblib-1.0.0-pyhd3eb1b0_0
  jpeg               pkgs/main/linux-64::jpeg-9b-h024ee3a_2
  kiwisolver         pkgs/main/linux-64::kiwisolver-1.3.1-py37h2531618_0
  krb5               pkgs/main/linux-64::krb5-1.16.4-h173b8e3_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7
  libcurl            pkgs/main/linux-64::libcurl-7.67.0-h20c2e04_0
  libedit            pkgs/main/linux-64::libedit-3.1.20191231-h14c3975_1
  libffi             pkgs/main/linux-64::libffi-3.2.1-hf484d3e_1007
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libgfortran-ng     pkgs/main/linux-64::libgfortran-ng-7.3.0-hdf63c60_0
  libpng             pkgs/main/linux-64::libpng-1.6.37-hbc83047_0
  libssh2            pkgs/main/linux-64::libssh2-1.9.0-h1ba5d50_1
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  libtiff            pkgs/main/linux-64::libtiff-4.1.0-h2733197_1
  libuuid            pkgs/main/linux-64::libuuid-1.0.3-h1bed415_2
  libxcb             pkgs/main/linux-64::libxcb-1.14-h7b6447c_0
  libxml2            pkgs/main/linux-64::libxml2-2.9.10-hb55368b_3
  lz4-c              pkgs/main/linux-64::lz4-c-1.9.3-h2531618_0
  make               pkgs/main/linux-64::make-4.2.1-h1bed415_1
  markupsafe         pkgs/main/linux-64::markupsafe-1.1.1-py37h14c3975_1
  matplotlib         pkgs/main/linux-64::matplotlib-3.0.2-py37h5429711_0
  mkl                pkgs/main/linux-64::mkl-2020.2-256
  mkl-service        pkgs/main/linux-64::mkl-service-2.3.0-py37he8ac12f_0
  mkl_fft            pkgs/main/linux-64::mkl_fft-1.2.0-py37h23d657b_0
  mkl_random         pkgs/main/linux-64::mkl_random-1.1.1-py37h0573a6f_0
  ncurses            pkgs/main/linux-64::ncurses-6.2-he6710b0_1
  networkx           pkgs/main/linux-64::networkx-2.2-py37_1
  numpy              pkgs/main/linux-64::numpy-1.15.4-py37h7e9f1db_0
  numpy-base         pkgs/main/linux-64::numpy-base-1.15.4-py37hde5b4d6_0
  openssl            pkgs/main/linux-64::openssl-1.1.1i-h27cfd23_0
  pandas             pkgs/main/linux-64::pandas-0.23.4-py37h04863e7_0
  pango              pkgs/main/linux-64::pango-1.42.4-h049681c_0
  patsy              pkgs/main/linux-64::patsy-0.5.1-py37_0
  pcre               pkgs/main/linux-64::pcre-8.44-he6710b0_0
  pip                pkgs/main/linux-64::pip-20.3.3-py37h06a4308_0
  pixman             pkgs/main/linux-64::pixman-0.40.0-h7b6447c_0
  pyparsing          pkgs/main/noarch::pyparsing-2.4.7-pyhd3eb1b0_0
  pyqt               pkgs/main/linux-64::pyqt-5.9.2-py37h05f1152_2
  python             pkgs/main/linux-64::python-3.7.1-h0371630_7
  python-dateutil    pkgs/main/noarch::python-dateutil-2.8.1-pyhd3eb1b0_0
  pytz               pkgs/main/noarch::pytz-2021.1-pyhd3eb1b0_0
  pyyaml             pkgs/main/linux-64::pyyaml-5.1.1-py37h7b6447c_0
  qt                 pkgs/main/linux-64::qt-5.9.7-h5867ecd_1
  r                  pkgs/r/linux-64::r-3.5.0-r350_0
  r-assertthat       pkgs/r/linux-64::r-assertthat-0.2.0-r350h912f1d8_0
  r-base             pkgs/r/linux-64::r-base-3.5.0-h1e0a451_1
  r-bh               pkgs/r/linux-64::r-bh-1.66.0_1-r350h912f1d8_0
  r-bindr            pkgs/r/linux-64::r-bindr-0.1.1-r350h912f1d8_0
  r-bindrcpp         pkgs/r/linux-64::r-bindrcpp-0.2.2-r350hebe7666_0
  r-bit              pkgs/r/linux-64::r-bit-1.1_12-r350hb353451_0
  r-bit64            pkgs/r/linux-64::r-bit64-0.9_7-r350hb353451_0
  r-blob             pkgs/r/linux-64::r-blob-1.1.1-r350h912f1d8_0
  r-boot             pkgs/r/linux-64::r-boot-1.3_20-r350h912f1d8_0
  r-class            pkgs/r/linux-64::r-class-7.3_14-r350hb353451_4
  r-cli              pkgs/r/linux-64::r-cli-1.0.0-r350h912f1d8_0
  r-cluster          pkgs/r/linux-64::r-cluster-2.0.7_1-r350h6ecb4d7_0
  r-codetools        pkgs/r/linux-64::r-codetools-0.2_15-r350h912f1d8_0
  r-crayon           pkgs/r/linux-64::r-crayon-1.3.4-r350h912f1d8_0
  r-dbi              pkgs/r/linux-64::r-dbi-0.8-r350h912f1d8_0
  r-dbplyr           pkgs/r/linux-64::r-dbplyr-1.2.1-r350h912f1d8_0
  r-digest           pkgs/r/linux-64::r-digest-0.6.15-r350hb353451_0
  r-dplyr            pkgs/r/linux-64::r-dplyr-0.7.4-r350hebe7666_0
  r-foreign          pkgs/r/linux-64::r-foreign-0.8_70-r350hb353451_0
  r-glue             pkgs/r/linux-64::r-glue-1.2.0-r350hb353451_0
  r-kernsmooth       pkgs/r/linux-64::r-kernsmooth-2.23_15-r350h6ecb4d7_4
  r-lattice          pkgs/r/linux-64::r-lattice-0.20_35-r350hb353451_0
  r-magrittr         pkgs/r/linux-64::r-magrittr-1.5-r350h912f1d8_4
  r-mass             pkgs/r/linux-64::r-mass-7.3_49-r350hb353451_0
  r-matrix           pkgs/r/linux-64::r-matrix-1.2_14-r350hb353451_0
  r-memoise          pkgs/r/linux-64::r-memoise-1.1.0-r350h912f1d8_0
  r-mgcv             pkgs/r/linux-64::r-mgcv-1.8_23-r350hb353451_0
  r-nlme             pkgs/r/linux-64::r-nlme-3.1_137-r350h6ecb4d7_0
  r-nnet             pkgs/r/linux-64::r-nnet-7.3_12-r350hb353451_0
  r-pillar           pkgs/r/linux-64::r-pillar-1.2.1-r350h912f1d8_0
  r-pkgconfig        pkgs/r/linux-64::r-pkgconfig-2.0.1-r350h912f1d8_0
  r-plogr            pkgs/r/linux-64::r-plogr-0.2.0-r350h912f1d8_0
  r-prettyunits      pkgs/r/linux-64::r-prettyunits-1.0.2-r350h912f1d8_0
  r-purrr            pkgs/r/linux-64::r-purrr-0.2.4-r350hb353451_0
  r-r6               pkgs/r/linux-64::r-r6-2.2.2-r350h912f1d8_0
  r-rcpp             pkgs/r/linux-64::r-rcpp-0.12.16-r350hebe7666_0
  r-recommended      pkgs/r/linux-64::r-recommended-3.5.0-r350_0
  r-rlang            pkgs/r/linux-64::r-rlang-0.2.0-r350hb353451_0
  r-rpart            pkgs/r/linux-64::r-rpart-4.1_13-r350hb353451_0
  r-rsqlite          pkgs/r/linux-64::r-rsqlite-2.1.0-r350hebe7666_0
  r-spatial          pkgs/r/linux-64::r-spatial-7.3_11-r350hb353451_4
  r-survival         pkgs/r/linux-64::r-survival-2.42_3-r350hb353451_0
  r-tibble           pkgs/r/linux-64::r-tibble-1.4.2-r350hb353451_0
  r-tidyselect       pkgs/r/linux-64::r-tidyselect-0.2.4-r350hebe7666_0
  r-utf8             pkgs/r/linux-64::r-utf8-1.1.3-r350hb353451_0
  readline           pkgs/main/linux-64::readline-7.0-h7b6447c_5
  rpy2               pkgs/r/linux-64::rpy2-2.9.1-py37r350h035aef0_0
  scikit-learn       pkgs/main/linux-64::scikit-learn-0.21.2-py37hd81dba3_0
  scipy              pkgs/main/linux-64::scipy-1.5.2-py37h0b6359f_0
  seaborn            pkgs/main/noarch::seaborn-0.9.0-pyh91ea838_1
  setuptools         pkgs/main/linux-64::setuptools-52.0.0-py37h06a4308_0
  sip                pkgs/main/linux-64::sip-4.19.8-py37hf484d3e_0
  six                pkgs/main/linux-64::six-1.15.0-py37h06a4308_0
  sqlite             pkgs/main/linux-64::sqlite-3.33.0-h62c20be_0
  statsmodels        pkgs/main/linux-64::statsmodels-0.11.1-py37h7b6447c_0
  tk                 pkgs/main/linux-64::tk-8.6.10-hbc83047_0
  tktable            pkgs/main/linux-64::tktable-2.10-h14c3975_0
  tornado            pkgs/main/linux-64::tornado-6.1-py37h27cfd23_0
  tqdm               pkgs/main/linux-64::tqdm-4.28.1-py37h28b3542_0
  wheel              pkgs/main/noarch::wheel-0.36.2-pyhd3eb1b0_0
  xz                 pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
  yaml               pkgs/main/linux-64::yaml-0.1.7-had09818_2
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3
  zstd               pkgs/main/linux-64::zstd-1.4.5-h9ceee32_0

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate BEELINE
#
# To deactivate an active environment, use
#
#     $ conda deactivate

R version 3.5.0 (2018-04-23) -- "Joy in Playing"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-conda_cos6-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages('https://cran.r-project.org/src/contrib/PRROC_1.3.1.tar.gz', type = 'source')
inferring 'repos = NULL' from 'pkgs'
trying URL 'https://cran.r-project.org/src/contrib/PRROC_1.3.1.tar.gz'
Content type 'application/x-gzip' length 335708 bytes (327 KB)
==================================================
downloaded 327 KB

* installing *source* package ‘PRROC’ ...
** package ‘PRROC’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PRROC)
> 
>

when I try to run 'python BLRunner.py --config config-files/config.yaml' for SCRIBE, it output an error, the command line output is as below:

(BEELINE) zengyp@ubuntu:~/Single_cell/1/Beeline-master$ python BLRunner.py --config config-files/config.yaml
Skipping PIDC
Skipping GRNVBEM
Skipping GENIE3
Skipping GRNBOOST2
Skipping PPCOR
Skipping SCODE
Skipping SCNS
Skipping SINCERITIES
Skipping LEAP
Skipping GRISLI
Skipping SINGE
<BLRun.BLRun object at 0x7fc6bb52c208>
Evaluation started
docker run --rm -v /home/zengyp/Single_cell/1/Beeline-master:/data/ scribe:base /bin/sh -c "time -v -o data/outputs/example/GSD/SCRIBE/time0.txt Rscript runScribe.R -e data/inputs/example/GSD/SCRIBE/ExpressionData0.csv -c data/inputs/example/GSD/SCRIBE/CellData0.csv -g data/inputs/example/GSD/SCRIBE/GeneData.csv -o data/outputs/example/GSD/SCRIBE/ -d 5 -l 0 -m ucRDI -x uninormal --outFile outFile0.csv -i"
Error in library(monocle, warn.conflicts = FALSE, quietly = TRUE) : 
  there is no package called ‘monocle’
Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
Execution halted
docker run --rm -v /home/zengyp/Single_cell/1/Beeline-master:/data/ scribe:base /bin/sh -c "time -v -o data/outputs/example/GSD/SCRIBE/time1.txt Rscript runScribe.R -e data/inputs/example/GSD/SCRIBE/ExpressionData1.csv -c data/inputs/example/GSD/SCRIBE/CellData1.csv -g data/inputs/example/GSD/SCRIBE/GeneData.csv -o data/outputs/example/GSD/SCRIBE/ -d 5 -l 0 -m ucRDI -x uninormal --outFile outFile1.csv -i"
Error in library(monocle, warn.conflicts = FALSE, quietly = TRUE) : 
  there is no package called ‘monocle’
Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
Execution halted
outputs/example/GSD/SCRIBE/outFile0.csv does not exist, skipping...
Evaluation complete
adyprat commented 3 years ago

Looks like it is an issue with monocle installation in the Docker with bioconductor, which seems to have been updated recently. I'll push an update that sets it up to use an older version of monocle as in the original paper.

adyprat commented 3 years ago

Hi,

So looks like the BiocManager no longer points to the older version of monocle. That said, I have always had trouble setting up Dockerfile to point to appropriate R libraries (it should be using monocle 2 instead of 3, which is the default now).

Fortunately, a work around to this issue is to use an existing docker image instead of building one from Dockerfile, which is now available on Docker hub.

Please run the following commands: docker pull grnbeeline/scribe:base docker tag grnbeeline/scribe:base scribe:base

Re-run your script to run Scribe and let me know if this works.

Best, Aditya

adyprat commented 3 years ago

Hey @Zengggg , I updated all the scripts under BLRun/ to pre-built Docker images. Please use the updated version and let me know if you still have any trouble running the algorithms. You don't have to run . initialize.sh to build docker images locally anymore either. Best, -Aditya

Zengggg commented 3 years ago

Thank you very much! I can run it successfully now.