bowtie2-align-s: error while loading shared libraries: libtbb.so.2

rpetit3 commented 3 years ago

Hi everyone!

Posting this incase others get this issue, I'll submit a PR. Just installed bowtie2 and am getting the following:

(bactopia-test) rpetit@staphopia:~$ bowtie2 --version
/local/home/rpetit/miniconda3/envs/bowtie2-latest/bin/bowtie2-align-s: error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory
(ERR): Description of arguments failed!
Exiting now ...

In this fresh environment the version of tbb installed is: conda-forge/linux-64::tbb-2021.1.1-h4bd325d_0

Downgrade `tbb` fixes isssue

Good news is downgrading the tbb version solves the problem.

(bowtie2-latest) rpetit@staphopia:~$ conda install -c conda-forge 'tbb=2020.2'
(bowtie2-latest) rpetit@staphopia:~$ bowtie2 --version
/local/home/rpetit/miniconda3/envs/bowtie2-latest/bin/bowtie2-align-s version 2.4.2
64-bit
Built on default-bf91a638-95fa-4b77-97c5-abccd9855c3e
Mon Nov  2 17:36:36 UTC 2020
Compiler: gcc version 7.5.0 (crosstool-NG 1.24.0.131_87df0e6_dirty)
Options: -O3 -msse2 -funroll-loops -g3 -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /local/home/rpetit/miniconda3/envs/bowtie2-latest/include -fdebug-prefix-map=/opt/conda/conda-bld/bowtie2_1604337828546/work=/usr/local/src/conda/bowtie2-2.4.2 -fdebug-prefix-map=/local/home/rpetit/miniconda3/envs/bowtie2-latest=/usr/local/src/conda-prefix -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

Details about fresh Bowtie2 environment

(bactopia-test) rpetit@staphopia:~$ conda create -n bowtie2-latest -y -c conda-forge -c bioconda bowtie2
Collecting package metadata (current_repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.9.2

Please update conda by running

    $ conda update -n base -c defaults conda

## Package Plan ##

  environment location: /local/home/rpetit/miniconda3/envs/bowtie2-latest

  added / updated specs:
    - bowtie2

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    bowtie2-2.4.2              |   py38h1c8e9b9_1        12.7 MB  bioconda
    ------------------------------------------------------------
                                           Total:        12.7 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-4.5-1_gnu
  bowtie2            bioconda/linux-64::bowtie2-2.4.2-py38h1c8e9b9_1
  ca-certificates    conda-forge/linux-64::ca-certificates-2020.12.5-ha878542_0
  certifi            conda-forge/linux-64::certifi-2020.12.5-py38h578d9bd_1
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.35.1-hea4e1c9_2
  libffi             conda-forge/linux-64::libffi-3.3-h58526e2_2
  libgcc-ng          conda-forge/linux-64::libgcc-ng-9.3.0-h2828fa1_18
  libgomp            conda-forge/linux-64::libgomp-9.3.0-h2828fa1_18
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-9.3.0-h6de172a_18
  ncurses            conda-forge/linux-64::ncurses-6.2-h58526e2_4
  openssl            conda-forge/linux-64::openssl-1.1.1j-h7f98852_0
  perl               conda-forge/linux-64::perl-5.32.0-h36c2ea0_0
  pip                conda-forge/noarch::pip-21.0.1-pyhd8ed1ab_0
  python             conda-forge/linux-64::python-3.8.8-hffdb5ce_0_cpython
  python_abi         conda-forge/linux-64::python_abi-3.8-1_cp38
  readline           conda-forge/linux-64::readline-8.0-he28a2e2_2
  setuptools         conda-forge/linux-64::setuptools-49.6.0-py38h578d9bd_3
  sqlite             conda-forge/linux-64::sqlite-3.34.0-h74cdb3f_0
  tbb                conda-forge/linux-64::tbb-2021.1.1-h4bd325d_0
  tk                 conda-forge/linux-64::tk-8.6.10-h21135ba_1
  wheel              conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_1
  zlib               conda-forge/linux-64::zlib-1.2.11-h516909a_1010

Downloading and Extracting Packages
bowtie2-2.4.2        | 12.7 MB   |                                                                                                                                                                                                                                                                                       |   0% bowtie2-2.4.2        | 12.7 MB   | 3                                                                                                                                                                                                                                                                                     |   0% bowtie2-2.4.2        | 12.7 MB   | #################################################                                                                                                                                                                                                                                     |  18% bowtie2-2.4.2        | 12.7 MB   | ########################################################################################################2                                                                                                                                                                             |  38% bowtie2-2.4.2        | 12.7 MB   | ##################################################################################################################################################################################################################################################################################### | 100%

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate bowtie2-latest
#
# To deactivate an active environment, use
#
#     $ conda deactivate

(bactopia-test) rpetit@staphopia:~$ conda activate bowtie2-latest
(bowtie2-latest) rpetit@staphopia:~$ bowtie2 --version
/local/home/rpetit/miniconda3/envs/bowtie2-latest/bin/bowtie2-align-s: error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory
(ERR): Description of arguments failed!
Exiting now ...

guillaumecharbonnier commented 3 years ago

Hi, there is the same issue with salmon.

mattgalbraith commented 3 years ago

Same issue with 2.4.2 and 2.4.1 in environments with both Python 3.8 and 3.7. Thanks for the tip about downgrading tbb!

bernt-matthias commented 3 years ago

should be fixed https://github.com/bioconda/bioconda-recipes/pull/27174 ?

scholtalbers commented 2 years ago

I just now encountered this issue when installing the latest bismark in Galaxy.

bowtie2 --version database/dependencies/_conda/envs/mulled-v1-9f2317dbfb405ed6926c55752e5c11678eee3256a6ea680d1c0f912251153030/bin/bowtie2-align-s: error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory

Fixed it by installing tbb 2020.2

conda install tbb=2020.2
bowtie2 --version database/dependencies/_conda/envs/mulled-v1-9f2317dbfb405ed6926c55752e5c11678eee3256a6ea680d1c0f912251153030/bin/bowtie2-align-s version 2.3.5.1

Reading through the other comments/PRs this tbb dependency issue should have been fixed globally, but it doesn't seem to work for me anymore.

bioconda / bioconda-recipes