Error while loading shared libraries: libcrypto.so.1.0.0

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1

Hello dear IFB team,
I need your help to overcome this problem with libcrypto dependency of samtools.
Although there have been previous reports, the error appears again , and solutions seem to be of Root-rights .
Here is the error:

$ module load samtools/1.9
$ samtools --version
> samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory

but also with newer samtools version:

$  module load samtools/1.13;  module load rsem/1.3.2
$ convert-sam-for-rsem  P10_Aligned.out.bam  converted_P10
>> samtools sort -n -@ 1 -m 1G -o converted_P10.tmp.bam  P10_Aligned.out.bam
>> samtools: error while loading shared libraries: *libcrypto.so.1.0.0*: cannot open shared object file: No such file or directory

I found out from bioconda issues (samtools 1.9 dependency pulls in wrong version of openssl · Issue #12100 · bioconda/bioconda-recipes · GitHub )
of same error that we need to either :

make a sym link of 1.1 --> 1.0.0

cd /shared/ifbstor1/software/miniconda/lib
ln -s libcrypto.so.1.1 libcrypto.so.1.0.0

or downgrade openssl ,from which it depends:

conda install -c bioconda samtools openssl=1.0

which is currently : openssl = 1.1.1k

Otherwise, please instruct me ,if there is something I could do in local environment as user.

Thanks in advance,
Maaria

2

Hello,

We will not link to another version of openssl as it is ugly and may brake other conda environement.

Maybe we can force the openssl version in our samtools conda env, but I think it is a better solution to wait for a fix uptream (ie: the package specification of samtools).

And yes you can resolve it il local environment as user:

module load samtools/1.13;  module load rsem/1.3.2
mkdir lib
cd lib
ln -s /shared/ifbstor1/software/miniconda/envs/samtools-1.13/lib/libcrypto.so libcrypto.so.1.0.0
export LD_LIBRARY_PATH=$(pwd) 
samtools --version
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