# Workflow conda install: bowtie 2 issue ("/bowtie2-align-s: error while loading shared libraries: libtbb.so.2)

**URL:** <https://forum.biobakery.org/t/workflow-conda-install-bowtie-2-issue-bowtie2-align-s-error-while-loading-shared-libraries-libtbb-so-2/1831>\
**Category:** bioBakery workflows\
**Created:** [March 22, 2021, 5:34pm UTC](https://forum.biobakery.org/t/workflow-conda-install-bowtie-2-issue-bowtie2-align-s-error-while-loading-shared-libraries-libtbb-so-2/1831 "2021-03-22T17:34:32Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![ewissel](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/ewissel/32/568_2.png) [@ewissel](https://forum.biobakery.org/u/ewissel)\
**Post date:** [March 22, 2021, 5:34pm UTC](https://forum.biobakery.org/t/workflow-conda-install-bowtie-2-issue-bowtie2-align-s-error-while-loading-shared-libraries-libtbb-so-2/1831/1 "2021-03-22T17:34:32Z")

</div>

I have created a conda install of the workflow using the following commands:

```auto
conda create -n env_name -c bioconda python=3.7
conda activate env_name
conda install -c biobakery biobakery_workflows
pip install leveldb

```

I try to run the `wmgx` workflow on demo data using the follow (each flag seems to be required for my install of the workflow to attempt a run):

```auto
biobakery_workflows wmgx --input fastq/ --output demo_out/ --bypass-strain-profiling --local-jobs 6 --threads 2 --qc-options="--trimmomatic=/data/Microbiome/RefData/Metagenomics/biobakery_workflows_databases/Trimmomatic-0.39/" --functional-profiling-options="--nucleotide-database /data/Microbiome/RefData/Metagenomics/biobakery_workflows_databases/humann/humann_database/chocophlan/ --protein-database /data/Microbiome/RefData/Metagenomics/biobakery_workflows_databases/humann/uni_db/uniref"

```

I get the following error:

```auto
Task 7 failed
 Name: kneaddata ____ LD96R2_subsample
 Original error:
 Error executing action 0. Original Exception:
 Traceback (most recent call last):
   File "/home/emilyw/.conda/envs/shotgun_134/lib/python3.7/site-packages/anadama2/runners.py", line 201, in _run_task_locally
     action_func(task)
   File "/home/emilyw/.conda/envs/shotgun_134/lib/python3.7/site-packages/anadama2/helpers.py", line 89, in actually_sh
     ret = _sh(s, **kwargs)
   File "/home/emilyw/.conda/envs/shotgun_134/lib/python3.7/site-packages/anadama2/util/ __init__.py", line 320, in sh
     raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1]))
 anadama2.util.ShellException: [Errno 1] Command `kneaddata --input /home/emilyw/biobakery_demo/fastq/LD96R2_subsample.fastq.gz --output /home/emilyw/biobakery_demo/demo_out/kneaddata/main --threads 2 --output-prefix LD96R2_subsample --reference-db /software/biobakery/biobakery_workflows_databases/kneaddata_db_human_genome --trimmomatic=/data/Microbiome/RefData/Metagenomics/biobakery_workflows_databases/Trimmomatic-0.39/ --serial --run-trf && mv /home/emilyw/biobakery_demo/demo_out/kneaddata/main/LD96R2_subsample.repeats.removed.fastq /home/emilyw/biobakery_demo/demo_out/kneaddata/main/LD96R2_subsample.fastq' failed.
 Out: b'Decompressing gzipped file ...\n\nInitial number of reads ( /home/emilyw/biobakery_demo/demo_out/kneaddata/main/decompressed_2jyhcrre_LD96R2_subsample.fastq ): 108134.0\nRunning Trimmomatic ... \nTotal reads after trimming ( /home/emilyw/biobakery_demo/demo_out/kneaddata/main/LD96R2_subsample.trimmed.fastq ): 108119.0\nDecontaminating ...\nRunning bowtie2 ... \nError executing: /home/emilyw/.conda/envs/shotgun_134/bin/bowtie2 --threads 2 --very-sensitive --phred33 -x /software/biobakery/biobakery_workflows_databases/kneaddata_db_human_genome/Homo_sapiens_demo -U /home/emilyw/biobakery_demo/demo_out/kneaddata/main/LD96R2_subsample.trimmed.fastq --un /home/emilyw/biobakery_demo/demo_out/kneaddata/main/LD96R2_subsample_Homo_sapiens_demo_bowtie2_clean.fastq --al /home/emilyw/biobakery_demo/demo_out/kneaddata/main/LD96R2_subsample_Homo_sapiens_demo_bowtie2_contam.fastq -S /dev/null\n\nError message returned from bowtie2 :\n/home/emilyw/.conda/envs/shotgun_134/bin/bowtie2-align-s: error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory\n(ERR): Description of arguments failed!\nExiting now ...\n\nSubprocess reported error. Please see log file for more details.\n'
 Err: b''

```

When I run `bowtie2 -h`, I get:

```auto
/home/emilyw/.conda/envs/shotgun_134/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 ...

```

Based on [this post I found online](http://www.metagenomics.wiki/tools/bowtie2/install/libtbb-so-2), I had a server administrator sudo install the TBB library, but this did not solve the issue. I then tried to uninstall the bowtie2 that came with the workflow/kneaddata (`conda remove bowtie2`), but I would have to delete all the workflow software for conda to successfully remove bowtie2.

I decided to try to manually delete bowtie2 from my conda directories by deleting the executable from `./conda/pkgs/bowtie2*` then reinstall bowtie2 with conda, but this also did not solve the problem.

I’m not sure else how I can troubleshoot this problem. It seems to be an issue with the conda install of bowtie2 as part of the workflow. Note that two weeks ago, I didn’t have this problem, but since trying to recreate the conda env. using the steps above, this problem has arisen. Was there by chance a new update in that time?

---

<div class="post-metadata">

**Author:** ![ewissel](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/ewissel/32/568_2.png) [@ewissel](https://forum.biobakery.org/u/ewissel)\
**Post date:** [March 23, 2021, 9:47pm UTC](https://forum.biobakery.org/t/workflow-conda-install-bowtie-2-issue-bowtie2-align-s-error-while-loading-shared-libraries-libtbb-so-2/1831/2 "2021-03-23T21:47:43Z")

</div>

update: I was able to get around this by just running the following in a new env:  
`conda install -c biobakery biobakery_workflows`  
`conda install tbb=2020.2`

I’m using humann version 3.0.0.alpha.3 and biobakery\_workflows version 3.0.0-alpha.7. I get an error now where the biobakery\_workflow tries to create the `esc.csv` files at the end using `humann_regroup_table uniref90_level4ec` instead of `uniref90_rxn`, so I’ll keep investigating that at least the workflow runs now!

---

<div class="post-metadata">

**Author:** ![tamburin](https://avatars.discourse-cdn.com/v4/letter/t/3ec8ea/32.png) [@tamburin](https://forum.biobakery.org/u/tamburin)\
**Post date:** [March 26, 2021, 2:38am UTC](https://forum.biobakery.org/t/workflow-conda-install-bowtie-2-issue-bowtie2-align-s-error-while-loading-shared-libraries-libtbb-so-2/1831/3 "2021-03-26T02:38:22Z")

</div>

I had a similar issue while installing panphlan 3.1 with conda:

```
~/miniconda3/envs/bowtie2/bin/bowtie2-align-s: symbol lookup error:
~/miniconda3/envs/bowtie2/bin/bowtie2-align-s: undefined symbol: _ZN3tbb10interface78internal15task_arena_base19internal_initializeEv
(ERR): Description of arguments failed!
Exiting now ...

```

Downgrading tbb as described above worked for me as well. Commenting in case anyone comes across this post while looking for panphlan support.