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
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1. Bug description
I'm using echolocator via Docker. I would like to run the function
finemap_lociusing UKB as LD_reference. The function gets stucked trying to install the conda env echoR_mini. WithLD_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
Console output
Data
I am using the docker image In got using docker pull bschilder/echolocator
3. Session info