Closed jolespin closed 6 years ago
Hi Josh,
It looks like the issue is with the precompiled samtools (v1.4) and/or bowtie2 (v2.3.2) binaries included with the software. To fix this, I would suggest downloading and compiling these programs on your own system. Once complete, copy them to MIDAS/bin/Linux
. You can see the binaries MIDAS needs here: https://github.com/snayfach/MIDAS/tree/master/bin/Linux. Let me know if this works for you. I will probably come up with a better solution in the future.
Best, Stephen
So far it's working with the exception of one error (I believe when calling snps
). I replaced the binaries with symbolic links to the samtools and bowtie2 already installed on the machine:
cd /usr/local/devel/ANNOTATION/jespinoz/anaconda/envs/python2/lib/python2.7/site-packages/MIDAS/bin/Linux
ln -s /usr/local/bin/samtools samtools
ln -s /usr/local/bin/bowtie2 bowtie2
ln -s /usr/local/bin/bowtie2-align-l bowtie2-align-l
ln -s /usr/local/bin/bowtie2-align-s bowtie2-align-s
ln -s /usr/local/bin/bowtie2-build bowtie2-build
ln -s /usr/local/bin/bowtie2-build-s bowtie2-build-s
ln -s /usr/local/bin/bowtie2-build-l bowtie2-build-l
This is the error:
Error: Encountered internal Bowtie 2 exception (#1)
Command: bowtie2-build --wrapper basic-0 --threads 2 /usr/local/projdata/0497/projects/CariesBiome/jespinoz/pt_II/metagenome/midas_output/2028.2_midas/snps/temp/genomes.fa /usr/local/projdata/0497/projects/CariesBiome/jespinoz/pt_II/metagenome/midas_output/2028.2_midas/snps/temp/genomes
Glad to hear it! Just double check that they are the correct versions if you haven't already.
On Thu, Sep 14, 2017 at 12:53 PM, Josh L. Espinoza <notifications@github.com
wrote:
So far it's working. I replaced the binaries with symbolic links to the samtools and bowtie2 already installed on the machine:
cd /usr/local/devel/ANNOTATION/jespinoz/anaconda/envs/python2/lib/python2.7/site-packages/MIDAS/bin/Linux ln -s /usr/local/bin/samtools samtools ln -s /usr/local/bin/bowtie2 bowtie2 ln -s /usr/local/bin/bowtie2-align-l bowtie2-align-l ln -s /usr/local/bin/bowtie2-align-s bowtie2-align-s ln -s /usr/local/bin/bowtie2-build bowtie2-build ln -s /usr/local/bin/bowtie2-build-s bowtie2-build-s ln -s /usr/local/bin/bowtie2-build-l bowtie2-build-l
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/snayfach/MIDAS/issues/69#issuecomment-329590790, or mute the thread https://github.com/notifications/unsubscribe-auth/ACAbrXGAqQ7wHKGcggOmLoVXvOYzg0sfks5siYRBgaJpZM4PX4Is .
bowtie2
I'm using is an older 2.2.5
version b/c I was getting the following error when I tried using the newest version:
/usr/local/devel/ANNOTATION/jespinoz/anaconda/envs/python2/lib/python2.7/site-packages/MIDAS/bin/compile_binaries/bowtie2-2.3.2/bowtie2-align-s: error while loading shared libraries: libtbbmalloc_proxy.so.2: cannot open shared object file: No such file or directory
(ERR): Description of arguments failed!
If you run the test script you will find out if your binaries will work or not with MIDAS
On Thu, Sep 14, 2017 at 1:10 PM, Josh L. Espinoza notifications@github.com wrote:
bowtie2 is an older 2.2.5 version b/c I was getting the following error when I tried using the newest version:
/usr/local/devel/ANNOTATION/jespinoz/anaconda/envs/python2/lib/python2.7/site-packages/MIDAS/bin/compile_binaries/bowtie2-2.3.2/bowtie2-align-s: error while loading shared libraries: libtbbmalloc_proxy.so.2: cannot open shared object file: No such file or directory (ERR): Description of arguments failed!
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/snayfach/MIDAS/issues/69#issuecomment-329595020, or mute the thread https://github.com/notifications/unsubscribe-auth/ACAbrVT9mCHcalMFo9lzCNkJ7vTx9wQqks5siYgzgaJpZM4PX4Is .
Ended up installing bowtie2 v2.3.0
and samtools v1.5
with conda
and it worked:
conda install bowtie2 --yes
conda install samtools --yes
Updated my symbolic links and it works.
cd /usr/local/devel/ANNOTATION/jespinoz/anaconda/envs/python2/lib/python2.7/site-packages/MIDAS/bin/Linux
ln -s /usr/local/devel/ANNOTATION/jespinoz/anaconda/envs/python2/bin/samtools samtools
ln -s /usr/local/devel/ANNOTATION/jespinoz/anaconda/envs/python2/bin/bowtie2 bowtie2
ln -s /usr/local/devel/ANNOTATION/jespinoz/anaconda/envs/python2/bin/bowtie2-align-l bowtie2-align-l
ln -s /usr/local/devel/ANNOTATION/jespinoz/anaconda/envs/python2/bin/bowtie2-align-s bowtie2-align-s
ln -s /usr/local/devel/ANNOTATION/jespinoz/anaconda/envs/python2/bin/bowtie2-build bowtie2-build
ln -s /usr/local/devel/ANNOTATION/jespinoz/anaconda/envs/python2/bin/bowtie2-build-s bowtie2-build-s
ln -s /usr/local/devel/ANNOTATION/jespinoz/anaconda/envs/python2/bin/bowtie2-build-l bowtie2-build-l
I use Python 3.6.2 for my main environment and created a new conda environment for Python 2.7.13 in which I installed MIDAS. I am trying to run MIDAS but I am encountering the following errors regarding
libbz2.so.1.0
,gzopen64
andbowtie2-align
.Do any of these look familiar?
Added this to my bash profile:
I ran this command after activating my python2 environment:
Encountered this error: