Cannot use MIDAS with python2 conda environment

[snayfach]

Cannot use MIDAS with python2 conda environment

[snayfach]

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

[jolespin]

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

[jolespin]

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

[snayfach]

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 ***@***.*** > 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 <#69 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACAbrXGAqQ7wHKGcggOmLoVXvOYzg0sfks5siYRBgaJpZM4PX4Is> .

[jolespin]

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!

[snayfach]

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 ***@***.***> 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 <#69 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACAbrVT9mCHcalMFo9lzCNkJ7vTx9wQqks5siYgzgaJpZM4PX4Is> .