[BUG] Samtools shared library libcrypto.so.1.0.0 not found

[NVOostende]

Short description of the problem

After updating conda and Anvio to the latest version, samtools had an issue with not finding a shared library libcrypto.so.1.0.0

anvi'o version

anvi-self-test --version

Anvi'o version ...............................: esther (v6.2)
Profile DB version ...........................: 31
Contigs DB version ...........................: 14
Pan DB version ...............................: 13
Genome data storage version ..................: 6
Auxiliary data storage version ...............: 2
Structure DB version .........................: 1

System info

Using Anvio on a cluster (Linux Redhat) and installed Anvio as follows:

conda update conda
conda create -y --name anvio-6.2 python=3.6
conda activate anvio-6.2
conda install -y -c conda-forge -c bioconda anvio==6.2
conda remove -y --force anvio-minimal
conda install -y -c bioconda -c conda-forge anvio-minimal==6.2=py_1
anvi-setup-ncbi-cogs

Detailed description of the issue

Expected samtools to convert .sam files to .bam files, however samtools was not happy:

samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory

(anvio-6.2) [oostende@della5 ~]$ ldd $(which samtools)
	linux-vdso.so.1 =>  (0x00007ffd303b6000)
	libz.so.1 => /tigress/oostende/software/anaconda2/envs/anvio-6.2/bin/../lib/libz.so.1 (0x00002b628067e000)
	libm.so.6 => /lib64/libm.so.6 (0x00002b628087f000)
	libbz2.so.1.0 => /tigress/oostende/software/anaconda2/envs/anvio-6.2/bin/../lib/libbz2.so.1.0 (0x00002b62806cf000)
	liblzma.so.5 => /tigress/oostende/software/anaconda2/envs/anvio-6.2/bin/../lib/liblzma.so.5 (0x00002b62806e3000)
	libcurl.so.4 => /tigress/oostende/software/anaconda2/envs/anvio-6.2/bin/../lib/libcurl.so.4 (0x00002b628070d000)
	libcrypto.so.1.0.0 => not found
	libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b6280b81000)
	libc.so.6 => /lib64/libc.so.6 (0x00002b6280d9d000)
	/lib64/ld-linux-x86-64.so.2 (0x00002b628065b000)
	librt.so.1 => /lib64/librt.so.1 (0x00002b628116b000)
	libnghttp2.so.14 => /tigress/oostende/software/anaconda2/envs/anvio-6.2/bin/../lib/./libnghttp2.so.14 (0x00002b628079e000)
	libssh2.so.1 => /tigress/oostende/software/anaconda2/envs/anvio-6.2/bin/../lib/./libssh2.so.1 (0x00002b62807c6000)
	libssl.so.1.1 => /tigress/oostende/software/anaconda2/envs/anvio-6.2/bin/../lib/./libssl.so.1.1 (0x00002b6281373000)
	libcrypto.so.1.1 => /tigress/oostende/software/anaconda2/envs/anvio-6.2/bin/../lib/./libcrypto.so.1.1 (0x00002b6281403000)
	libgssapi_krb5.so.2 => /tigress/oostende/software/anaconda2/envs/anvio-6.2/bin/../lib/./libgssapi_krb5.so.2 (0x00002b628080b000)
	libkrb5.so.3 => /tigress/oostende/software/anaconda2/envs/anvio-6.2/bin/../lib/./libkrb5.so.3 (0x00002b62816cf000)
	libk5crypto.so.3 => /tigress/oostende/software/anaconda2/envs/anvio-6.2/bin/../lib/./libk5crypto.so.3 (0x00002b628085b000)
	libcom_err.so.3 => /tigress/oostende/software/anaconda2/envs/anvio-6.2/bin/../lib/./libcom_err.so.3 (0x00002b62817a8000)
	libdl.so.2 => /lib64/libdl.so.2 (0x00002b62817ae000)
	libkrb5support.so.0 => /tigress/oostende/software/anaconda2/envs/anvio-6.2/bin/../lib/././libkrb5support.so.0 (0x00002b62819b2000)
	libresolv.so.2 => /lib64/libresolv.so.2 (0x00002b62819c1000)

I tried the following to no avail:

conda install -c bioconda samtools
or
conda install -c bioconda samtools openssl=1.0

[meren]

Unfortunately this is a conda issue, and there is nothing we can do to solve it from here. But there may be some solutions / ideas here:

bioconda/bioconda-recipes#13958

If you solve it please let us know about your solution, @NVOostende. Sorry for the inconvenience.

[NVOostende]

Thank you @meren for the link to bioconda recipes!
Ran
conda install -c bioconda samtools=1.9 --force-reinstall
to update samtools to latest build, and it did the trick.

> samtools --version
samtools 1.9
Using htslib 1.9
Copyright (C) 2018 Genome Research Ltd.

samtools was happy when queried this time around.

[Chris-lad]

Thanks buddy !
I just solved my bug with this !

[BI202020]

thanks @NVOostende. it worked!

[GenomicaMicrob]

After many struggles, this worked for me:
conda config --add channels bioconda
conda config --add channels conda-forge
conda install samtools==1.11

[xiachenrui]

@NVOostende great metheds!!!

[tiagobrc]

Thank you @meren for the link to bioconda recipes!
Ran
conda install -c bioconda samtools=1.9 --force-reinstall
to update samtools to latest build, and it did the trick.

> samtools --version
samtools 1.9
Using htslib 1.9
Copyright (C) 2018 Genome Research Ltd.

samtools was happy when queried this time around.

This worked for me.

[schlogl2017]

This worked for me to install the required lib.
sudo nano /etc/apt/sources.list
add deb http://security.ubuntu.com/ubuntu bionic-security main
sudo apt update && apt-cache policy libssl1.0-dev
sudo apt-get install libssl1.0-dev

[ekiefl]

When following the developer installation instructions, I ran into this same error.

The command supplied in the instructions is:

conda install -y -c bioconda samtools

To solve I ran

conda uninstall -c bioconda samtools

And then

conda install -c bioconda samtools=1.9

This fixed things. I have updated the install instructions.

[Xuelei-Dai]

About this bug, I have found the best way to solve it without installing something, it's very easy as follows:

cd annaconda/envs/samtools/lib
ln -s libcrypto.so.1.1 libcrypto.so.1.0.0

It's OK:)

[hagen-wende]

This worked for me to install the required lib. sudo nano /etc/apt/sources.list add deb http://security.ubuntu.com/ubuntu bionic-security main sudo apt update && apt-cache policy libssl1.0-dev sudo apt-get install libssl1.0-dev

Thank you! this also solved the issue for me! It still was an issue with samtools 1.16.1

[cpplyqz]

About this bug, I have found the best way to solve it without installing something, it's very easy as follows:

cd annaconda/envs/samtools/lib
ln -s libcrypto.so.1.1 libcrypto.so.1.0.0

It's OK:)

Thank you it worked！！！

[genecell]

Great answers! I am using the snakemake workflow, so I add a local env for the samtools commands via vi envs/samtools.yaml:

name: samtools
channels:
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - samtools==1.11

and in the snakemake file:

rule sortBam:
        input: "mapped/bams/{sample}.mapped.bam" 
        output: "mapped/bams/{sample}.bam"
        params:
            tempDir = TEMPDIR
        wildcard_constraints:
            sample="|".join(SAMPLES)
        conda: 'envs/samtools.yaml'
        shell: """
            samtools sort -m 10G -@ 10 {input} -T {params.tempDir} -o {output}
            """