Samtools Faidx Error Message

Question

[florian.grosmaire]

Hello everybody,

I try to use the folowing samtools command :"samtools faidx myseq.fasta" but it gives me this error message :

dyld: Library not loaded: @rpath/libcrypto.1.0.0.dylib
  Referenced from: /Users/macbook/opt/anaconda3/envs/myenv/bin/samtools
  Reason: image not found
Abort trap: 6

I dont really uderstand. Could someone help me ? It would be really nice ! Thanks in advance !

[Alex Reynolds]

Perhaps some of the advice here might help for getting OpenSSL libraries installed and linked:

[John Marshall]

That's working around the effect, rather than working around the cause. If the OP fixes this libcrypto problem they'll have a working samtools executable, but it'll still be a massively out-of-date version of samtools!

(For when you do want to reproduce an old analysis with an old samtools, the way to do it is to ask for the corresponding versions of openssl etc that the old samtools was built with: conda create -n myoldenv samtools=1.4.1 openssl=1.0.2u or similar. Then no hacking symlinks within system directories will be necessary.)

[Alex Reynolds]

Great point. I don't track what versions of dynamic libraries that tools use. One more argument in favor of static binaries.

[florian.grosmaire]

Thanks for your help

Answer 1

[John Marshall]

This is a currently-existing limitation in conda: conda has given you an out of date version of samtools. See also this Twitter thread.

At the moment, you should work around this by creating your Conda environment and specifying the current version of samtools desired explicitly:

conda create -n myenv 'samtools>=1.11'

[John Marshall]

This is (for now) fixed; plain conda create -n myenv samtools will give you an up-to-date version of samtools.

[florian.grosmaire]

Thanks a lots! this solution worked