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a-h-b / dadasnake

Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake
GNU General Public License v3.0
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Initializing dada2_env.yml failed #30

Closed Pawelco2 closed 1 year ago

Pawelco2 commented 1 year ago

Hello! I came across your algorithm and wanted to check the possibilities it offers. The idea seems wonderful!

I'm a beginner at bioinformatics, so I'm not able to resolve such complex issues, that I've encountered here. I'm not also an experienced linux user but finally I managed to follow your manual. However, I'm stuck at "Initialize conda environments: " - it seems dada2_env.yml. might be broken. I've reinstalled conda and started from scratch several times, but I keep getting exactly the same issue at dada2_env.yml.

I attach the error code below.

(env) pawel@HP:~/dadasnake$ ./dadasnake -i config/config.init.yaml
Initializing conda environments.

Final resource settings:
maxCores: 1
Building DAG of jobs...
Creating conda environment ../workflow/envs/add_R_env.yml...
Downloading and installing remote packages.
Environment for ../workflow/envs/add_R_env.yml created (location: ../conda/082bc6d2876235cd5a86d65fec4a6b48)
Creating conda environment ../workflow/envs/blast_env.yml...
Downloading and installing remote packages.
Environment for ../workflow/envs/blast_env.yml created (location: ../conda/534f9f6712e1af6533276dc176024136)
Creating conda environment ../workflow/envs/dadasnake_env.yml...
Downloading and installing remote packages.
Environment for ../workflow/envs/dadasnake_env.yml created (location: ../conda/dea9e5a1f589b5df38f3d8647e300592)
Creating conda environment ../workflow/envs/fastqc.yml...
Downloading and installing remote packages.
Environment for ../workflow/envs/fastqc.yml created (location: ../conda/83107ed4a9dc38962bf38b6777f27edc)
Creating conda environment ../workflow/envs/tax4fun2_env.yml...
Downloading and installing remote packages.
Environment for ../workflow/envs/tax4fun2_env.yml created (location: ../conda/6b9d58a1b41bedc2390b748ad3db6406)
Creating conda environment ../workflow/envs/dada2_env.yml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /home/pawel/dadasnake/workflow/envs/dada2_env.yml:
  Package                                   Version  Build                Channel                    Size
───────────────────────────────────────────────────────────────────────────────────────────────────────────
  Install:
───────────────────────────────────────────────────────────────────────────────────────────────────────────

  + _libgcc_mutex                               0.1  conda_forge          conda-forge/linux-64     Cached
  + _openmp_mutex                               4.5  1_gnu                conda-forge/linux-64     Cached
  + _r-mutex                                  1.0.1  anacondar_1          conda-forge/noarch       Cached
  + binutils_impl_linux-64                     2.35  h18a2f87_9           conda-forge/linux-64     Cached
  + binutils_linux-64                          2.35  heab0d09_28          conda-forge/linux-64     Cached
  + bioconductor-biobase                     2.48.0  r40h037d062_0        bioconda/linux-64           2MB
  + bioconductor-biocgenerics                0.34.0  r40_0                bioconda/noarch           707kB
  + bioconductor-biocparallel                1.22.0  r40h5f743cb_0        bioconda/linux-64           1MB
  + bioconductor-biostrings                  2.56.0  r40h037d062_0        bioconda/linux-64          15MB
  + bioconductor-dada2                       1.16.0  r40h5f743cb_0        bioconda/linux-64           3MB
  + bioconductor-decipher                    2.16.0  r40h037d062_0        bioconda/linux-64          12MB
  + bioconductor-delayedarray                0.14.0  r40h037d062_0        bioconda/linux-64           2MB
  + bioconductor-genomeinfodb                1.24.0  r40_0                bioconda/noarch             4MB
  + bioconductor-genomeinfodbdata             1.2.3  r40_0                bioconda/noarch             7kB
  + bioconductor-genomicalignments           1.24.0  r40h037d062_0        bioconda/linux-64           2MB
  + bioconductor-genomicranges               1.40.0  r40h037d062_0        bioconda/linux-64           2MB
  + bioconductor-iranges                     2.22.1  r40h037d062_0        bioconda/linux-64           3MB
  + bioconductor-rhtslib                     1.20.0  r40h037d062_0        bioconda/linux-64           2MB
  + bioconductor-rsamtools                    2.4.0  r40h5f743cb_0        bioconda/linux-64           4MB
  + bioconductor-s4vectors                   0.26.0  r40h037d062_0        bioconda/linux-64           2MB
  + bioconductor-shortread                   1.46.0  r40h5f743cb_0        bioconda/linux-64           5MB
  + bioconductor-summarizedexperiment        1.18.1  r40_0                bioconda/noarch             3MB
  + bioconductor-xvector                     0.28.0  r40h037d062_0        bioconda/linux-64         755kB
  + bioconductor-zlibbioc                    1.34.0  r40h037d062_0        bioconda/linux-64         116kB
  + bwidget                                  1.9.14  0                    conda-forge/linux-64     Cached
  + bzip2                                     1.0.8  h516909a_3           conda-forge/linux-64     Cached
  + c-ares                                   1.11.0  h470a237_1           bioconda/linux-64          89kB
  + ca-certificates                       2020.6.20  hecda079_0           conda-forge/linux-64     Cached
  + cairo                                    1.16.0  h3fc0475_1005        conda-forge/linux-64        2MB
  + certifi                               2020.6.20  py38h32f6830_0       conda-forge/linux-64      155kB
  + curl                                     7.71.1  he644dc0_6           conda-forge/linux-64      142kB
  + fontconfig                               2.13.1  h1056068_1002        conda-forge/linux-64      374kB
  + freetype                                 2.10.2  he06d7ca_0           conda-forge/linux-64     Cached
  + fribidi                                  1.0.10  h516909a_0           conda-forge/linux-64      115kB
  + gcc_impl_linux-64                         7.5.0  hdb87b24_16          conda-forge/linux-64       40MB
  + gcc_linux-64                              7.5.0  hf34d7eb_28          conda-forge/linux-64     Cached
  + gettext                                0.19.8.1  hc5be6a0_1002        conda-forge/linux-64     Cached
  + gfortran_impl_linux-64                    7.5.0  h1104b78_16          conda-forge/linux-64        9MB
  + gfortran_linux-64                         7.5.0  ha781d05_28          conda-forge/linux-64     Cached
  + glib                                     2.66.0  h0dae87d_0           conda-forge/linux-64        4MB
  + graphite2                                1.3.13  he1b5a44_1001        conda-forge/linux-64     Cached
  + gsl                                         2.6  h294904e_0           conda-forge/linux-64        3MB
  + gxx_impl_linux-64                         7.5.0  h1104b78_16          conda-forge/linux-64       10MB
  + gxx_linux-64                              7.5.0  ha781d05_28          conda-forge/linux-64     Cached
  + harfbuzz                                  2.7.2  hee91db6_0           conda-forge/linux-64        2MB
  + icu                                        67.1  he1b5a44_0           conda-forge/linux-64       13MB
  + jpeg                                         9d  h516909a_0           conda-forge/linux-64     Cached
  + kernel-headers_linux-64                  2.6.32  h77966d4_13          conda-forge/noarch       Cached
  + krb5                                     1.17.1  hfafb76e_3           conda-forge/linux-64        2MB
  + ld_impl_linux-64                           2.35  h769bd43_9           conda-forge/linux-64     Cached
  + libblas                                   3.8.0  17_openblas          conda-forge/linux-64     Cached
  + libcblas                                  3.8.0  17_openblas          conda-forge/linux-64       11kB
  + libcurl                                  7.71.1  hcdd3856_6           conda-forge/linux-64      320kB
  + libedit                            3.1.20191231  he28a2e2_2           conda-forge/linux-64     Cached
  + libev                                      4.33  h516909a_1           conda-forge/linux-64     Cached
  + libffi                                    3.2.1  he1b5a44_1007        conda-forge/linux-64     Cached
  + libgcc-devel_linux-64                     7.5.0  h42c25f5_16          conda-forge/linux-64        4MB
  + libgcc-ng                                 9.3.0  h24d8f2e_16          conda-forge/linux-64        8MB
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  + libgomp                                   9.3.0  h24d8f2e_16          conda-forge/linux-64      387kB
  + libiconv                                   1.16  h516909a_0           conda-forge/linux-64     Cached
  + liblapack                                 3.8.0  17_openblas          conda-forge/linux-64     Cached
  + libnghttp2                               1.41.0  hab1572f_1           conda-forge/linux-64      726kB
  + libopenblas                              0.3.10  pthreads_hb3c22a3_4  conda-forge/linux-64     Cached
  + libpng                                   1.6.37  hed695b0_2           conda-forge/linux-64     Cached
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  + libtiff                                   4.1.0  hc7e4089_6           conda-forge/linux-64     Cached
  + libuuid                                  2.32.1  h14c3975_1000        conda-forge/linux-64     Cached
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  + libxcb                                     1.13  h14c3975_1002        conda-forge/linux-64     Cached
  + libxml2                                  2.9.10  h68273f3_2           conda-forge/linux-64        1MB
  + lz4-c                                     1.9.2  he1b5a44_3           conda-forge/linux-64     Cached
  + make                                        4.3  h516909a_0           conda-forge/linux-64     Cached
  + ncurses                                     6.2  he1b5a44_1           conda-forge/linux-64     Cached
  + openssl                                  1.1.1h  h516909a_0           conda-forge/linux-64        2MB
  + pango                                    1.42.4  h7062337_4           conda-forge/linux-64      533kB
  + pcre                                       8.44  he1b5a44_0           conda-forge/linux-64     Cached
  + pcre2                                     10.35  h2f06484_0           conda-forge/linux-64      701kB
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  + pthread-stubs                               0.4  h14c3975_1001        conda-forge/linux-64     Cached
  + python                                    3.8.5  h1103e12_8_cpython   conda-forge/linux-64       23MB
  + python_abi                                  3.8  1_cp38               conda-forge/linux-64        4kB
  + r-assertthat                              0.2.1  r40h6115d3f_2        conda-forge/noarch       Cached
  + r-backports                              1.1.10  r40hcdcec82_0        conda-forge/linux-64       93kB
  + r-base                                    4.0.2  he766273_1           conda-forge/linux-64       25MB
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  + r-ellipsis                                0.3.1  r40hcdcec82_0        conda-forge/linux-64     Cached
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  + r-jpeg                                  0.1_8.1  r40hcdcec82_1        conda-forge/linux-64       52kB
  + r-labeling                                  0.3  r40h6115d3f_1003     conda-forge/noarch         68kB
  + r-lambda.r                                1.2.4  r40h6115d3f_1        conda-forge/noarch        122kB
  + r-lattice                               0.20_41  r40hcdcec82_2        conda-forge/linux-64        1MB
  + r-latticeextra                           0.6_29  r40h6115d3f_1        conda-forge/noarch          2MB
  + r-lifecycle                               0.2.0  r40h6115d3f_1        conda-forge/noarch        114kB
  + r-magrittr                                  1.5  r40h6115d3f_1003     conda-forge/noarch        171kB
  + r-mass                                   7.3_53  r40hcdcec82_0        conda-forge/linux-64        1MB
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  + r-nlme                                  3.1_149  r40h9bbef5b_0        conda-forge/linux-64        2MB
  + r-permute                                 0.9_5  r40h6115d3f_3        conda-forge/noarch        519kB
  + r-pillar                                  1.4.6  r40h6115d3f_0        conda-forge/noarch        199kB
  + r-pkgbuild                                1.1.0  r40h6115d3f_0        conda-forge/noarch        160kB
  + r-pkgconfig                               2.0.3  r40h6115d3f_1        conda-forge/noarch       Cached
  + r-pkgload                                 1.1.0  r40h0357c0b_0        conda-forge/linux-64      171kB
  + r-plogr                                   0.2.0  r40h6115d3f_1003     conda-forge/noarch         20kB
  + r-plyr                                    1.8.6  r40h0357c0b_1        conda-forge/linux-64      850kB
  + r-png                                     0.1_7  r40hcdcec82_1004     conda-forge/linux-64       59kB
  + r-praise                                  1.0.0  r40h6115d3f_1004     conda-forge/noarch         24kB
  + r-prettyunits                             1.1.1  r40h6115d3f_1        conda-forge/noarch       Cached
  + r-processx                                3.4.4  r40hcdcec82_0        conda-forge/linux-64      302kB
  + r-ps                                      1.3.4  r40hcdcec82_0        conda-forge/linux-64      239kB
  + r-r6                                      2.4.1  r40h6115d3f_1        conda-forge/noarch         65kB
  + r-rcolorbrewer                            1.1_2  r40h6115d3f_1003     conda-forge/noarch         60kB
  + r-rcpp                                  1.0.4.6  r40h0357c0b_1        conda-forge/linux-64        2MB
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  + r-rcurl                                1.98_1.2  r40hcdcec82_1        conda-forge/linux-64      984kB
  + r-reshape2                                1.4.4  r40h0357c0b_1        conda-forge/linux-64      138kB
  + r-rlang                                   0.4.7  r40hcdcec82_0        conda-forge/linux-64        1MB
  + r-rprojroot                               1.3_2  r40h6115d3f_1003     conda-forge/noarch         96kB
  + r-rsqlite                                 2.2.0  r40h0357c0b_2        conda-forge/linux-64        1MB
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  + r-scales                                  1.1.1  r40h6115d3f_0        conda-forge/noarch        569kB
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  + r-withr                                   2.2.0  r40h6115d3f_1        conda-forge/noarch        232kB
  + r-zeallot                                 0.1.0  r40h6115d3f_1002     conda-forge/noarch       Cached
  + readline                                    8.0  he28a2e2_2           conda-forge/linux-64     Cached
  + sed                                         4.8  hbfbb72e_0           conda-forge/linux-64      269kB
  + seqtk                                       1.3  hed695b0_2           bioconda/linux-64          40kB
  + setuptools                               49.6.0  py38h32f6830_1       conda-forge/linux-64      963kB
  + sqlite                                   3.33.0  h4cf870e_0           conda-forge/linux-64        1MB
  + sysroot_linux-64                           2.12  h77966d4_13          conda-forge/noarch       Cached
  + tk                                       8.6.10  hed695b0_0           conda-forge/linux-64     Cached
  + tktable                                    2.10  h555a92e_3           conda-forge/linux-64     Cached
  + wheel                                    0.35.1  pyh9f0ad1d_0         conda-forge/noarch         30kB
  + xorg-kbproto                              1.0.7  h14c3975_1002        conda-forge/linux-64     Cached
  + xorg-libice                              1.0.10  h516909a_0           conda-forge/linux-64     Cached
  + xorg-libsm                                1.2.3  h84519dc_1000        conda-forge/linux-64     Cached
  + xorg-libx11                              1.6.12  h516909a_0           conda-forge/linux-64     Cached
  + xorg-libxau                               1.0.9  h14c3975_0           conda-forge/linux-64     Cached
  + xorg-libxdmcp                             1.1.3  h516909a_0           conda-forge/linux-64     Cached
  + xorg-libxext                              1.3.4  h516909a_0           conda-forge/linux-64     Cached
  + xorg-libxrender                          0.9.10  h516909a_1002        conda-forge/linux-64     Cached
  + xorg-renderproto                         0.11.1  h14c3975_1002        conda-forge/linux-64     Cached
  + xorg-xextproto                            7.3.0  h14c3975_1002        conda-forge/linux-64     Cached
  + xorg-xproto                              7.0.31  h14c3975_1007        conda-forge/linux-64     Cached
  + xz                                        5.2.5  h516909a_1           conda-forge/linux-64     Cached
  + zlib                                     1.2.11  h516909a_1009        conda-forge/linux-64     Cached
  + zstd                                      1.4.5  h6597ccf_2           conda-forge/linux-64     Cached

  Summary:

  Install: 185 packages

  Total download: 299MB

───────────────────────────────────────────────────────────────────────────────────────────────────────────

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
ERROR conda.core.link:_execute(733): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.3-r40_0'.
Rolling back transaction: ...working... done
class: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.3-r40_0
location of failed script: /home/pawel/dadasnake/conda/e113b36d0031c615c2a05b811c538959/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout: /home/pawel/dadasnake/conda/e113b36d0031c615c2a05b811c538959/share/bioconductor-genomeinfodbdata-1.2.3-0/GenomeInfoDbData_1.2.3.tar.gz: FAILED
/home/pawel/dadasnake/conda/e113b36d0031c615c2a05b811c538959/share/bioconductor-genomeinfodbdata-1.2.3-0/GenomeInfoDbData_1.2.3.tar.gz: FAILED
/home/pawel/dadasnake/conda/e113b36d0031c615c2a05b811c538959/share/bioconductor-genomeinfodbdata-1.2.3-0/GenomeInfoDbData_1.2.3.tar.gz: FAILED
ERROR: post-link.sh was unable to download any of the following URLs with the md5sum 720784da6bddbd4e18ab0bccef6b0a95:
https://bioconductor.org/packages/3.11/data/annotation/src/contrib/GenomeInfoDbData_1.2.3.tar.gz
https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.3.tar.gz
https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.3_src_all.tar.gz

stderr:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   416  100   416    0     0   1320      0 --:--:-- --:--:-- --:--:--  1324
md5sum: WARNING: 1 computed checksum did NOT match
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   153  100   153    0     0    193      0 --:--:-- --:--:-- --:--:--   192
md5sum: WARNING: 1 computed checksum did NOT match
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   153  100   153    0     0    194      0 --:--:-- --:--:-- --:--:--   194
md5sum: WARNING: 1 computed checksum did NOT match

return code: 1

kwargs:
{}

Traceback (most recent call last):
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/site-packages/conda/exceptions.py", line 1129, in __call__
    return func(*args, **kwargs)
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/site-packages/conda_env/cli/main.py", line 80, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/site-packages/conda/notices/core.py", line 72, in wrapper
    return_value = func(*args, **kwargs)
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/site-packages/conda_env/cli/main_create.py", line 156, in execute
    result[installer_type] = installer.install(prefix, pkg_specs, args, env)
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/site-packages/mamba/mamba_env.py", line 173, in mamba_install
    handle_txn(conda_transaction, prefix, args, True)
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/site-packages/mamba/linking.py", line 44, in handle_txn
    unlink_link_transaction.execute()
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/site-packages/conda/core/link.py", line 284, in execute
    self._execute(tuple(concat(interleave(self.prefix_action_groups.values()))))
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/site-packages/conda/core/link.py", line 747, in _execute
    raise CondaMultiError(tuple(concatv(
conda.CondaMultiErrorclass: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.3-r40_0
location of failed script: /home/pawel/dadasnake/conda/e113b36d0031c615c2a05b811c538959/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout: /home/pawel/dadasnake/conda/e113b36d0031c615c2a05b811c538959/share/bioconductor-genomeinfodbdata-1.2.3-0/GenomeInfoDbData_1.2.3.tar.gz: FAILED
/home/pawel/dadasnake/conda/e113b36d0031c615c2a05b811c538959/share/bioconductor-genomeinfodbdata-1.2.3-0/GenomeInfoDbData_1.2.3.tar.gz: FAILED
/home/pawel/dadasnake/conda/e113b36d0031c615c2a05b811c538959/share/bioconductor-genomeinfodbdata-1.2.3-0/GenomeInfoDbData_1.2.3.tar.gz: FAILED
ERROR: post-link.sh was unable to download any of the following URLs with the md5sum 720784da6bddbd4e18ab0bccef6b0a95:
https://bioconductor.org/packages/3.11/data/annotation/src/contrib/GenomeInfoDbData_1.2.3.tar.gz
https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.3.tar.gz
https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.3_src_all.tar.gz

stderr:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   416  100   416    0     0   1320      0 --:--:-- --:--:-- --:--:--  1324
md5sum: WARNING: 1 computed checksum did NOT match
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   153  100   153    0     0    193      0 --:--:-- --:--:-- --:--:--   192
md5sum: WARNING: 1 computed checksum did NOT match
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   153  100   153    0     0    194      0 --:--:-- --:--:-- --:--:--   194
md5sum: WARNING: 1 computed checksum did NOT match

return code: 1

kwargs:
{}

: <exception str() failed>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/pawel/dadasnake/conda/snakemake_env/bin/mamba", line 11, in <module>
    sys.exit(main())
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/site-packages/mamba/mamba.py", line 923, in main
    return mamba_env.main()
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/site-packages/mamba/mamba_env.py", line 196, in main
    return conda_env_main()
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/site-packages/conda_env/cli/main.py", line 91, in main
    return conda_exception_handler(do_call, args, parser)
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/site-packages/conda/exceptions.py", line 1429, in conda_exception_handler
    return_value = exception_handler(func, *args, **kwargs)
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/site-packages/conda/exceptions.py", line 1132, in __call__
    return self.handle_exception(exc_val, exc_tb)
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/site-packages/conda/exceptions.py", line 1161, in handle_exception
    return self.handle_application_exception(exc_val, exc_tb)
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/site-packages/conda/exceptions.py", line 1175, in handle_application_exception
    self._print_conda_exception(exc_val, exc_tb)
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/site-packages/conda/exceptions.py", line 1179, in _print_conda_exception
    print_conda_exception(exc_val, exc_tb)
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/site-packages/conda/exceptions.py", line 1106, in print_conda_exception
    stderrlog.error("\n%r\n", exc_val)
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/logging/__init__.py", line 1506, in error
    self._log(ERROR, msg, args, **kwargs)
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/logging/__init__.py", line 1624, in _log
    self.handle(record)
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/logging/__init__.py", line 1633, in handle
    if (not self.disabled) and self.filter(record):
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/logging/__init__.py", line 821, in filter
    result = f.filter(record)
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/site-packages/conda/gateways/logging.py", line 50, in filter
    record.msg = record.msg % new_args
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/site-packages/conda/__init__.py", line 107, in __repr__
    errs.append(e.__repr__())
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/site-packages/conda/__init__.py", line 64, in __repr__
    return '%s: %s' % (self.__class__.__name__, str(self))
  File "/home/pawel/dadasnake/conda/snakemake_env/lib/python3.10/site-packages/conda/__init__.py", line 68, in __str__
    return str(self.message % self._kwargs)
ValueError: unsupported format character 'T' (0x54) at index 1132
a-h-b commented 1 year ago

Hi there- thanks for reaching out. It took some time for me to test this. Looks like the genominfodbdata package doesn't want to install. The good news is that it does not seem to be needed anymore. You can comment it out in line 23 of workflow/envs/dada2_env.yaml. I will also make a new release in a moment. Best wishes - A