libcrypto.so.1.0.0 error in cnv_facets.

[wangxlab]

Hi,

I installed cnv_facets through bioconda and was testing it. I think installation was okay, but I get error while running cnv_facets. Please see the error message below. It says "snp-pileup: error while loading shared libraries: libcrypto.so.1.0.0"

I installed cnv_facets on supercomputer (Pittsburgh Supercomputing center, PSC). A PSC staff said that "libcrypto.so.1.0.0" is an old library and it was replaced by 'libcrypto.so.1.0.2k' during system upgrade. And, he said that "libcrypto.so.1.0.0" is not installable any more. I pasted his email at the bottom, after error message

I wonder if you can change cnv_facets to use the new library, libcrypto.so.1.0.2k. Or, do you have any advice for me to solve this problem?

########################################################## snp-pileup: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory Error in checkForRemoteErrors(val) : one node produced an error: Error in computing snp pileup. Exit code 127 from execution of ./6713_3_2.csv.gz_191108-122923_6b7acb9f5bc/snp_pileup.1.sh Calls: exec_snp_pileup_parallel ... clusterApply -> staticClusterApply -> checkForRemoteErrors Execution halted

#################################################

taking the nodes to CentOS 7.6, which may have cause some older libraries to get dropped (and which may not be possible to install). In fact, if you look in /usr/lib64/ there it is the newer version:

[gomez@r005 lib64]$ pwd /usr/lib64 [gomez@r005 lib64]$ ls -l libcrypto* lrwxrwxrwx 1 root root 19 Oct 23 12:27 libcrypto.so -> libcrypto.so.1.0.2k lrwxrwxrwx 1 root root 19 Oct 23 12:23 libcrypto.so.10 -> libcrypto.so.1.0.2k -rwxr-xr-x 1 root root 2516624 Mar 12 2019 libcrypto.so.1.0.2k [gomez@r005 lib64]$

[dariober]

Hi- I'm not sure why this is happening. Can you try to install cnv_facets in its own environment? Like:

conda create -n env_cnv_facets
conda activate env_cnv_facets
conda install cnv_facets

# Run cnv_facets.R as required:
cnv_facets.R ...

If this works, try reinstalling samtools, bcftools and snp-pileup in your working environment (or just use the new env_cnv_facets)

I'm not sure it matters, but make sure your conda channels are in the right order (see https://bioconda.github.io/user/install.html#set-up-channels) and you use the latest version of conda.

Let me know how you get on...

[wangxlab]

Hi,

Thank you for your advice. I removed cnv_facets and reinstalled. I made sure the conda channels are in the right order and also I installed snp-pileup in the working environment. (I can't install samtools as it was already installed as a module in the supercomputer). But, I got the same error message while running cnv_facets.

I tried to install cnv_facets to another supercomputer in my university. Strangely, this cnv_facets is working well without any error, although the new version of "libcrypto.so.1.0.2k" is installed like the Pittsburgh Supercomputing center (PSC). So, I am using cnv_facets in the supercomputer in my university.

Thank you for your help, though! Sanghoon

[dariober]

I removed cnv_facets and reinstalled

Rather than removing and reinstalling, I would try creating a new conda environment as suggested in my previous post. In this way, you get a fresh installation of all the dependencies. By the way, I don't know how you are using conda, but in general is better to create a dedicated environment for each project you have and install there the dependencies.

[dariober]

Sorry about that and thanks for reporting the issue. The latest conda recipe should have this problem fixed. See https://github.com/bioconda/bioconda-recipes/pull/19969 for some explanation.