finemap_loci with UKB as a LD_reference

[silviettapar]

1. Bug description

I'm using echolocator via Docker. I would like to run the function finemap_loci using UKB as LD_reference. The function gets stucked trying to install the conda env echoR_mini. With LD_reference = "1KGphase3", superpopulation = "EUR", it works.

Expected behaviour

that the function completes

2. Reproducible example

I tried to dubug using get_LD_UKB {echoLD} and the example script in the help

Code

query_dat <- echodata::BST1[seq(1, 50), ] 
locus_dir <- file.path(tempdir(), echodata::locus_dir) 
LD_list <- echoLD:::get_LD_UKB( query_dat = query_dat, locus_dir = locus_dir)

Console output

> query_dat <- echodata::BST1[seq(1, 50), ]
> locus_dir <- file.path(tempdir(), echodata::locus_dir)
> LD_list <- echoLD:::get_LD_UKB( query_dat = query_dat, locus_dir = locus_dir)
Using UK Biobank LD reference panel.
+ UKB LD file name: chr4_14000001_17000001
Downloading full .gz/.npz UKB files and saving to disk.
trying URL 'https://repo.anaconda.com/miniconda/Miniconda3-py38_4.12.0-Linux-x86_64.sh'
Content type 'application/x-sh' length 76120962 bytes (72.6 MB)
==================================================
downloaded 72.6 MB

PREFIX=/home/rstudio/.cache/R/basilisk/1.11.2/0
Unpacking payload ...
Collecting package metadata (current_repodata.json): ...working... done                                        
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/rstudio/.cache/R/basilisk/1.11.2/0

  added / updated specs:
    - _libgcc_mutex==0.1=main
    - _openmp_mutex==4.5=1_gnu
    - brotlipy==0.7.0=py38h27cfd23_1003
    - ca-certificates==2022.3.29=h06a4308_1
    - certifi==2021.10.8=py38h06a4308_2
    - cffi==1.15.0=py38hd667e15_1
    - charset-normalizer==2.0.4=pyhd3eb1b0_0
    - colorama==0.4.4=pyhd3eb1b0_0
    - conda-content-trust==0.1.1=pyhd3eb1b0_0
    - conda-package-handling==1.8.1=py38h7f8727e_0
    - conda==4.12.0=py38h06a4308_0
    - cryptography==36.0.0=py38h9ce1e76_0
    - idna==3.3=pyhd3eb1b0_0
    - ld_impl_linux-64==2.35.1=h7274673_9
    - libffi==3.3=he6710b0_2
    - libgcc-ng==9.3.0=h5101ec6_17
    - libgomp==9.3.0=h5101ec6_17
    - libstdcxx-ng==9.3.0=hd4cf53a_17
    - ncurses==6.3=h7f8727e_2
    - openssl==1.1.1n=h7f8727e_0
    - pip==21.2.4=py38h06a4308_0
    - pycosat==0.6.3=py38h7b6447c_1
    - pycparser==2.21=pyhd3eb1b0_0
    - pyopenssl==22.0.0=pyhd3eb1b0_0
    - pysocks==1.7.1=py38h06a4308_0
    - python==3.8.13=h12debd9_0
    - readline==8.1.2=h7f8727e_1
    - requests==2.27.1=pyhd3eb1b0_0
    - ruamel_yaml==0.15.100=py38h27cfd23_0
    - setuptools==61.2.0=py38h06a4308_0
    - six==1.16.0=pyhd3eb1b0_1
    - sqlite==3.38.2=hc218d9a_0
    - tk==8.6.11=h1ccaba5_0
    - tqdm==4.63.0=pyhd3eb1b0_0
    - urllib3==1.26.8=pyhd3eb1b0_0
    - wheel==0.37.1=pyhd3eb1b0_0
    - xz==5.2.5=h7b6447c_0
    - yaml==0.2.5=h7b6447c_0
    - zlib==1.2.12=h7f8727e_1


The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu
  brotlipy           pkgs/main/linux-64::brotlipy-0.7.0-py38h27cfd23_1003
  ca-certificates    pkgs/main/linux-64::ca-certificates-2022.3.29-h06a4308_1
  certifi            pkgs/main/linux-64::certifi-2021.10.8-py38h06a4308_2
  cffi               pkgs/main/linux-64::cffi-1.15.0-py38hd667e15_1
  charset-normalizer pkgs/main/noarch::charset-normalizer-2.0.4-pyhd3eb1b0_0
  colorama           pkgs/main/noarch::colorama-0.4.4-pyhd3eb1b0_0
  conda              pkgs/main/linux-64::conda-4.12.0-py38h06a4308_0
  conda-content-tru~ pkgs/main/noarch::conda-content-trust-0.1.1-pyhd3eb1b0_0
  conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.8.1-py38h7f8727e_0
  cryptography       pkgs/main/linux-64::cryptography-36.0.0-py38h9ce1e76_0
  idna               pkgs/main/noarch::idna-3.3-pyhd3eb1b0_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.35.1-h7274673_9
  libffi             pkgs/main/linux-64::libffi-3.3-he6710b0_2
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17
  libgomp            pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17
  ncurses            pkgs/main/linux-64::ncurses-6.3-h7f8727e_2
  openssl            pkgs/main/linux-64::openssl-1.1.1n-h7f8727e_0
  pip                pkgs/main/linux-64::pip-21.2.4-py38h06a4308_0
  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py38h7b6447c_1
  pycparser          pkgs/main/noarch::pycparser-2.21-pyhd3eb1b0_0
  pyopenssl          pkgs/main/noarch::pyopenssl-22.0.0-pyhd3eb1b0_0
  pysocks            pkgs/main/linux-64::pysocks-1.7.1-py38h06a4308_0
  python             pkgs/main/linux-64::python-3.8.13-h12debd9_0
  readline           pkgs/main/linux-64::readline-8.1.2-h7f8727e_1
  requests           pkgs/main/noarch::requests-2.27.1-pyhd3eb1b0_0
  ruamel_yaml        pkgs/main/linux-64::ruamel_yaml-0.15.100-py38h27cfd23_0
  setuptools         pkgs/main/linux-64::setuptools-61.2.0-py38h06a4308_0
  six                pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1
  sqlite             pkgs/main/linux-64::sqlite-3.38.2-hc218d9a_0
  tk                 pkgs/main/linux-64::tk-8.6.11-h1ccaba5_0
  tqdm               pkgs/main/noarch::tqdm-4.63.0-pyhd3eb1b0_0
  urllib3            pkgs/main/noarch::urllib3-1.26.8-pyhd3eb1b0_0
  wheel              pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
  xz                 pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
  yaml               pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0
  zlib               pkgs/main/linux-64::zlib-1.2.12-h7f8727e_1


Preparing transaction: ...working... done
Executing transaction: ...working... done
installation finished.
echoconda:: Installing conda via basilisk.
Retrieving conda env name from yaml: echoR_mini
Warning: Could not identify any conda_env matching existing conda environments.
Identified yaml file stored in echoconda.
Retrieving conda env name from yaml: /usr/local/lib/R/site-library/echoconda/conda/echoR_mini.yml
Warning: Could not identify any conda_env matching existing conda environments.
echoconda:: Creating conda environment: echoR_mini
+ '/home/rstudio/.cache/R/basilisk/1.11.2/0/bin/conda' 'create' '--yes' '--prefix' '/home/rstudio/.cache/R/basilisk/1.11.2/echoconda/0.99.8/echoR_mini' 'python=3' '--quiet' '-c' 'conda-forge' '-c' 'bioconda' '-c' 'nodefaults'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/rstudio/.cache/R/basilisk/1.11.2/echoconda/0.99.8/echoR_mini

  added / updated specs:
    - python=3


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _libgcc_mutex-0.1          |      conda_forge           3 KB  conda-forge
    _openmp_mutex-4.5          |            2_gnu          23 KB  conda-forge
    bzip2-1.0.8                |       h4bc722e_7         247 KB  conda-forge
    ca-certificates-2024.8.30  |       hbcca054_0         155 KB  conda-forge
    ld_impl_linux-64-2.43      |       h712a8e2_2         654 KB  conda-forge
    libexpat-2.6.4             |       h5888daf_0          72 KB  conda-forge
    libffi-3.4.2               |       h7f98852_5          57 KB  conda-forge
    libgcc-14.2.0              |       h77fa898_1         829 KB  conda-forge
    libgcc-ng-14.2.0           |       h69a702a_1          53 KB  conda-forge
    libgomp-14.2.0             |       h77fa898_1         450 KB  conda-forge
    liblzma-5.6.3              |       hb9d3cd8_1         109 KB  conda-forge
    libmpdec-4.0.0             |       h4bc722e_0          88 KB  conda-forge
    libsqlite-3.47.2           |       hee588c1_0         853 KB  conda-forge
    libuuid-2.38.1             |       h0b41bf4_0          33 KB  conda-forge
    libzlib-1.3.1              |       hb9d3cd8_2          60 KB  conda-forge
    ncurses-6.5                |       he02047a_1         868 KB  conda-forge
    openssl-3.4.0              |       hb9d3cd8_0         2.8 MB  conda-forge
    pip-24.3.1                 |     pyh145f28c_0         1.2 MB  conda-forge
    python-3.13.1              |ha99a958_102_cp313        31.7 MB  conda-forge
    python_abi-3.13            |          5_cp313           6 KB  conda-forge
    readline-8.2               |       h8228510_1         275 KB  conda-forge
    tk-8.6.13                  |noxft_h4845f30_101         3.2 MB  conda-forge
    tzdata-2024b               |       hc8b5060_0         119 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        43.7 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7
  ca-certificates    conda-forge/linux-64::ca-certificates-2024.8.30-hbcca054_0
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_2
  libexpat           conda-forge/linux-64::libexpat-2.6.4-h5888daf_0
  libffi             conda-forge/linux-64::libffi-3.4.2-h7f98852_5
  libgcc             conda-forge/linux-64::libgcc-14.2.0-h77fa898_1
  libgcc-ng          conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_1
  libgomp            conda-forge/linux-64::libgomp-14.2.0-h77fa898_1
  liblzma            conda-forge/linux-64::liblzma-5.6.3-hb9d3cd8_1
  libmpdec           conda-forge/linux-64::libmpdec-4.0.0-h4bc722e_0
  libsqlite          conda-forge/linux-64::libsqlite-3.47.2-hee588c1_0
  libuuid            conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
  libzlib            conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2
  ncurses            conda-forge/linux-64::ncurses-6.5-he02047a_1
  openssl            conda-forge/linux-64::openssl-3.4.0-hb9d3cd8_0
  pip                conda-forge/noarch::pip-24.3.1-pyh145f28c_0
  python             conda-forge/linux-64::python-3.13.1-ha99a958_102_cp313
  python_abi         conda-forge/linux-64::python_abi-3.13-5_cp313
  readline           conda-forge/linux-64::readline-8.2-h8228510_1
  tk                 conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
  tzdata             conda-forge/noarch::tzdata-2024b-hc8b5060_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ '/home/rstudio/.cache/R/basilisk/1.11.2/0/bin/conda' 'install' '--yes' '--prefix' '/home/rstudio/.cache/R/basilisk/1.11.2/echoconda/0.99.8/echoR_mini' 'python=3'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/rstudio/.cache/R/basilisk/1.11.2/echoconda/0.99.8/echoR_mini

  added / updated specs:
    - python=3


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2024.11.26 |       h06a4308_0         131 KB
    ------------------------------------------------------------
                                           Total:         131 KB

The following packages will be UPDATED:

  ca-certificates    conda-forge::ca-certificates-2024.8.3~ --> pkgs/main::ca-certificates-2024.11.26-h06a4308_0



Downloading and Extracting Packages
ca-certificates-2024 | 131 KB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.11.1

Please update conda by running

    $ conda update -n base -c defaults conda


+ '/home/rstudio/.cache/R/basilisk/1.11.2/0/bin/conda' 'install' '--yes' '--prefix' '/home/rstudio/.cache/R/basilisk/1.11.2/echoconda/0.99.8/echoR_mini' '-c' 'conda-forge' '-c' 'bioconda' '-c' 'nodefaults' 'python=3' 'axel=2' 'bitarray=2' 'fastparquet=0' 'gzip=1' 'htslib=1' 'networkx=2' 'pandas-plink=2' 'pip=22' 'pyarrow=7' 'python=3' 'requests=2' 'rpy2=3' 'scikit-learn=1' 'scipy=1' 'tabix=1' 'tqdm=4' 'wget=1'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... 

Data

I am using the docker image In got using docker pull bschilder/echolocator

3. Session info

<html>
<body>
<!--StartFragment-->
> sessionInfo() R Under development (unstable) (2022-11-07 r83308) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.1 LTS  Matrix products: default BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so  locale:  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8         [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8     [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C         time zone: Etc/UTC tzcode source: system (glibc)  attached base packages: [1] stats     graphics  grDevices utils     datasets  methods   base       other attached packages: [1] snpStats_1.49.0 Matrix_1.5-3    survival_3.4-0  dplyr_1.0.10     loaded via a namespace (and not attached):   [1] splines_4.3.0               BiocIO_1.9.0                bitops_1.0-7                  [4] filelock_1.0.2              tibble_3.1.8                R.oo_1.25.0                   [7] cellranger_1.1.0            basilisk.utils_1.11.0       ggnetwork_0.5.10             [10] graph_1.77.0                rpart_4.1.19                XML_3.99-0.12                [13] lifecycle_1.0.3             mixsqp_0.3-43               pals_1.7                     [16] OrganismDbi_1.41.0          ensembldb_2.23.1            lattice_0.20-45              [19] MASS_7.3-58.1               backports_1.4.1             magrittr_2.0.3               [22] openxlsx_4.2.5.1            Hmisc_4.7-1                 yaml_2.3.6                   [25] zip_2.2.2                   reticulate_1.26             ggbio_1.47.0                 [28] gld_2.6.6                   mapproj_1.2.9               DBI_1.1.3                    [31] RColorBrewer_1.1-3          maps_3.4.1                  zlibbioc_1.45.0              [34] expm_0.999-6                GenomicRanges_1.51.1        purrr_0.3.5                  [37] R.utils_2.12.2              biovizBase_1.47.0           AnnotationFilter_1.23.0      [40] BiocGenerics_0.45.0         RCurl_1.98-1.9              nnet_7.3-18                  [43] VariantAnnotation_1.45.0    rappdirs_0.3.3              GenomeInfoDbData_1.2.9       [46] IRanges_2.33.0              S4Vectors_0.37.0            echofinemap_0.99.4           [49] catalogueR_1.0.0            echoLD_0.99.8               ggrepel_0.9.2                [52] irlba_2.3.5.1               crul_1.3                    echodata_0.99.16             [55] piggyback_0.1.4             codetools_0.2-18            DelayedArray_0.25.0          [58] DT_0.26                     xml2_1.3.3                  tidyselect_1.2.0             [61] farver_2.1.1                httpcode_0.3.0              viridis_0.6.2                [64] matrixStats_0.62.0          stats4_4.3.0                BiocFileCache_2.7.0          [67] base64enc_0.1-3             echotabix_0.99.8            GenomicAlignments_1.35.0     [70] jsonlite_1.8.3              e1071_1.7-12                ellipsis_0.3.2               [73] Formula_1.2-4               tools_4.3.0                 ggnewscale_0.4.8             [76] progress_1.2.2              DescTools_0.99.47           Rcpp_1.0.9                   [79] glue_1.6.2                  gridExtra_2.3               xfun_0.34                    [82] MatrixGenerics_1.11.0       GenomeInfoDb_1.35.3         BiocManager_1.30.19          [85] fastmap_1.1.0               GGally_2.1.2                basilisk_1.11.2              [88] latticeExtra_0.6-30         boot_1.3-28                 fansi_1.0.3                  [91] digest_0.6.30               R6_2.5.1                    colorspace_2.0-3             [94] XGR_1.1.8                   dichromat_2.0-0.1           jpeg_0.1-9                   [97] biomaRt_2.55.0              RSQLite_2.2.18              R.methodsS3_1.8.2           [100] utf8_1.2.2                  tidyr_1.2.1                 generics_0.1.3              [103] hexbin_1.28.2               data.table_1.14.4           rtracklayer_1.59.0          [106] class_7.3-20.1              prettyunits_1.1.1           httr_1.4.4                  [109] htmlwidgets_1.5.4           RCircos_1.2.2               pkgconfig_2.0.3             [112] gtable_0.3.1                Exact_3.2                   blob_1.2.3                  [115] XVector_0.39.0              supraHex_1.37.0             echoconda_0.99.8            [118] htmltools_0.5.3             susieR_0.12.27              RBGL_1.75.0                 [121] ProtGenerics_1.31.0         scales_1.2.1                Biobase_2.59.0              [124] osfr_0.2.9                  lmom_2.9                    png_0.1-7                   [127] knitr_1.40                  rstudioapi_0.14             tzdb_0.3.0                  [130] reshape2_1.4.4              rjson_0.2.21                checkmate_2.1.0             [133] nlme_3.1-160                curl_4.3.3                  proxy_0.4-27                [136] cachem_1.0.6                stringr_1.4.1               rootSolve_1.8.2.3           [139] parallel_4.3.0              foreign_0.8-83              AnnotationDbi_1.61.0        [142] restfulr_0.0.15             pillar_1.8.1                grid_4.3.0                  [145] reshape_0.8.9               vctrs_0.5.0                 dnet_1.1.7                  [148] dbplyr_2.2.1                cluster_2.1.4               htmlTable_2.4.1             [151] Rgraphviz_2.43.0            readr_2.1.3                 GenomicFeatures_1.51.2      [154] mvtnorm_1.1-3               cli_3.4.1                   compiler_4.3.0              [157] Rsamtools_2.15.0            rlang_1.0.6                 crayon_1.5.2                [160] interp_1.1-3                plyr_1.8.8                  fs_1.5.2                    [163] coloc_5.1.0.1               stringi_1.7.8               echoannot_0.99.10           [166] viridisLite_0.4.1           deldir_1.0-6                BiocParallel_1.33.0         [169] assertthat_0.2.1            munsell_0.5.0               Biostrings_2.67.0           [172] lazyeval_0.2.2              downloadR_0.99.5            dir.expiry_1.7.0            [175] echoplot_0.99.6             BSgenome_1.67.1             patchwork_1.1.2             [178] hms_1.1.2                   echolocatoR_2.0.3           bit64_4.0.5                 [181] ggplot2_3.4.0               KEGGREST_1.39.0             SummarizedExperiment_1.29.1 [184] igraph_1.3.5                memoise_2.0.1               bit_4.0.4                   [187] readxl_1.4.1                ape_5.6-2
--
 
  |  
 

<br class="Apple-interchange-newline"><!--EndFragment-->
</body>
</html>