Closed wangxlab closed 4 years ago
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...
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
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.
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.
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]$