version of Samtools installed in your $PATH is not optimized for dDocent error when doing bioconda installation

[valer...@gmail.com]

Has anyone had the error below when using bioconda to install dDocent 2.2.19?

$ dDocent
dDocent 2.2.19
Contact jpu...@gmail.com with any problems
Checking for required software
miniconda2/envs/ddocent_env/bin/dDocent: line 46: [: : integer expression expected
The version of Samtools installed in your $PATH is not optimized for dDocent.
Please install at least version 1.3.0

I had miniconda2 installed already for another program so I just updated conda to version 4.3.25. My original installation of miniconda2 added miniconda2/bin directory to my $PATH in my .bashrc file. Then, I did the following for the bioconda installation of dDocent:

$ conda config --add channels conda-forge
$ conda config --add channels defaults
Warning: 'defaults' already in 'channels' list, moving to the top
$ conda config --add channels r
$ conda config --add channels bioconda
$ conda create -n ddocent_env ddocent
Fetching package metadata ...............
Solving package specifications: .

Package plan for installation in environment /miniconda2/envs/ddocent_env:

The following NEW packages will be INSTALLED:

bamtools: 2.4.0-3 bioconda
bedtools: 2.26.0-0 bioconda
boost: 1.61.0-py27_0
bwa: 0.7.15-1 bioconda
bzip2: 1.0.6-3
cd-hit: 4.6.8-0 bioconda
certifi: 2016.2.28-py27_0
cmake: 3.6.3-0
curl: 7.54.1-0
ddocent: 2.2.19-0 bioconda
expat: 2.1.0-0
freebayes: 1.1.0.46-htslib1.5_0 bioconda
gawk: 4.1.3-1 bioconda
gmp: 6.1.0-0
gnuplot: 4.6.0-1 bioconda
htslib: 1.5-0 bioconda
icu: 54.1-0
krb5: 1.13.2-0
libgcc: 5.2.0-0
libssh2: 1.8.0-0
mawk: 1.3.4-0 bioconda
mpfr: 3.1.5-0
ncurses: 5.9-10
openjdk: 8.0.121-1
openssl: 1.0.2l-0
parallel: 20170422-pl5.22.0_0 bioconda
pear: 0.9.6-2 bioconda
perl: 5.22.0.1-0 conda-forge
perl-threaded: 5.22.0-pl5.22.0_12 bioconda
perl-vcftools-vcf: 0.953-3 bioconda
pip: 9.0.1-py27_1
python: 2.7.13-0
rainbow: 2.0.4-0 bioconda
readline: 6.2-2
samtools: 1.5-1 bioconda
seqtk: 1.2-0 bioconda
setuptools: 36.4.0-py27_0
sparsehash: 2.0.2-0 bioconda
sqlite: 3.13.0-0
stacks: 1.46-boost1.61_1 bioconda
tk: 8.5.18-0
trimmomatic: 0.36-5 bioconda
unzip: 6.0-0 conda-forge
vcflib: 1.0.0_rc1-0 bioconda
vcftools: 0.1.14-5 bioconda
velvet: 1.2.10-1 bioconda
wheel: 0.29.0-py27_0
xz: 5.2.3-0
zlib: 1.2.11-0

Proceed ([y]/n)? y

gmp-6.1.0-0.ta 100% |################################| Time: 0:00:00 22.38 MB/s
gnuplot-4.6.0- 100% |################################| Time: 0:00:01 1.70 MB/s
ncurses-5.9-10 100% |################################| Time: 0:00:00 20.82 MB/s
openjdk-8.0.12 100% |################################| Time: 0:00:02 26.10 MB/s
openssl-1.0.2l 100% |################################| Time: 0:00:00 25.43 MB/s
perl-5.22.0.1- 100% |################################| Time: 0:00:01 9.57 MB/s
readline-6.2-2 100% |################################| Time: 0:00:00 14.22 MB/s
sparsehash-2.0 100% |################################| Time: 0:00:00 13.78 MB/s
tk-8.5.18-0.ta 100% |################################| Time: 0:00:00 22.22 MB/s
unzip-6.0-0.ta 100% |################################| Time: 0:00:00 13.96 MB/s
xz-5.2.3-0.tar 100% |################################| Time: 0:00:00 24.15 MB/s
zlib-1.2.11-0. 100% |################################| Time: 0:00:00 18.96 MB/s
bamtools-2.4.0 100% |################################| Time: 0:00:00 2.12 MB/s
bedtools-2.26. 100% |################################| Time: 0:00:00 5.22 MB/s
bwa-0.7.15-1.t 100% |################################| Time: 0:00:00 6.16 MB/s
cd-hit-4.6.8-0 100% |################################| Time: 0:00:00 3.17 MB/s
mawk-1.3.4-0.t 100% |################################| Time: 0:00:00 2.87 MB/s
mpfr-3.1.5-0.t 100% |################################| Time: 0:00:00 21.54 MB/s
parallel-20170 100% |################################| Time: 0:00:00 3.46 MB/s
pear-0.9.6-2.t 100% |################################| Time: 0:00:00 17.60 MB/s
perl-threaded- 100% |################################| Time: 0:00:00 790.02 kB/s
python-2.7.13- 100% |################################| Time: 0:00:00 25.54 MB/s
seqtk-1.2-0.ta 100% |################################| Time: 0:00:00 548.67 kB/s
trimmomatic-0. 100% |################################| Time: 0:00:00 1.00 MB/s
vcflib-1.0.0_r 100% |################################| Time: 0:00:04 14.17 MB/s
velvet-1.2.10- 100% |################################| Time: 0:00:00 20.66 MB/s
boost-1.61.0-p 100% |################################| Time: 0:00:00 21.62 MB/s
certifi-2016.2 100% |################################| Time: 0:00:00 21.37 MB/s
gawk-4.1.3-1.t 100% |################################| Time: 0:00:00 2.40 MB/s
perl-vcftools- 100% |################################| Time: 0:00:00 7.10 MB/s
rainbow-2.0.4- 100% |################################| Time: 0:00:00 7.61 MB/s
wheel-0.29.0-p 100% |################################| Time: 0:00:00 9.82 MB/s
cmake-3.6.3-0. 100% |################################| Time: 0:00:00 17.79 MB/s
htslib-1.5-0.t 100% |################################| Time: 0:00:00 3.09 MB/s
samtools-1.5-1 100% |################################| Time: 0:00:00 3.43 MB/s
setuptools-36. 100% |################################| Time: 0:00:00 15.73 MB/s
stacks-1.46-bo 100% |################################| Time: 0:00:01 14.42 MB/s
vcftools-0.1.1 100% |################################| Time: 0:00:00 12.83 MB/s
freebayes-1.1. 100% |################################| Time: 0:00:00 14.54 MB/s
pip-9.0.1-py27 100% |################################| Time: 0:00:00 17.08 MB/s
ddocent-2.2.19 100% |################################| Time: 0:00:00 13.46 MB/s
#
# To activate this environment, use:
# > source activate ddocent_env
#
# To deactivate an active environment, use:
# > source deactivate
#

It looks like samtools 1.5 was installed and there is also a samtools 1.4 in my miniconda2/pkgs directory so I have at least version 1.3.0 installed as required.

-Valerie

[Jon Puritz]

Hi Valerie,

BWA recently changed their version numbering and I haven’t changed the bioconda version yet.  If you download the latest version of dDocent from github and place it in your "miniconda2/envs/ddocent_env/bin/dDocent” directory it should work.

Jon

-- 

Jon Puritz, PhD

Assistant Professor
Department of Biological Sciences
University of Rhode Island
120 Flagg Road, Kingston, RI 02881

Webpage: MarineEvoEco.com

Cell: 401-338-8739

"The most valuable of all talents is that of never using two words when one will do.” -Thomas Jefferson

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[valer...@gmail.com]

Thanks, Jon. I downloaded dDocent 2.2.20 from github and replaced the dDocent script in my miniconda2/envs/ddocent_env/bin directory, but I am still getting the same error:

$ dDocent
dDocent 2.2.20

Contact jpu...@gmail.com with any problems
Checking for required software

/miniconda2/envs/ddocent_env/bin/dDocent: line 46: [: : integer expression expected

The version of Samtools installed in your $PATH is not optimized for dDocent.
Please install at least version 1.3.0

I checked samtools to see if it was working properly and got an error about not finding GLIBC, which is required by samtools, see below. I think this could be the issue. Is there an additional package that I should be installing in the dDocent environment?

$ samtools
samtools: /lib64/libm.so.6: version `GLIBC_2.23' not found (required by samtools)
samtools: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by samtools)

Thanks.

-Valerie

[seth musker]

Hi Valerie,

I had exactly this problem and solved it by extracting the bit of code related to samtools from the "install_dDocent_requirements" file which comes with running

curl -L -O https://github.com/jpuritz/dDocent/archive/v2.2.16.tar.gz
tar xvzf v2.2.16.tar.gz

 and copying the samtools file into the miniconda install. Here's what I ran

curl -L -o samtools-1.3.1.tar.bz2 "https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2"

tar xvjf samtools-1.3.1.tar.bz2 

cd samtools-1.3.1/

./configure

make

chmod +x samtools

cp -f samtools /your/directory/miniconda3/envs/ddocent_env/bin

cd .. 

You can then activate the dDocent environment 

source activate ddocent_env

and it should work.

Cheers,

S

[Jon Puritz]

Hi Valerie and Seth,

I traced the route of this problem and it stems from conflicting versions of libraries on various condo channels. Very frustrating!

Seth’s workaround will fix things temporarily, but here’s the fix to help with further bioconda installations. Basically, we are going to change the priority of different conda channels for package installation. These are listed in you ~/.condarc files

If you followed my original instructions, your file may look like this:

cat ~/.condarc

channels:
  - bioconda
  - r
  - defaults
  - conda-forge

And according to new bioconda best practices, we want it to look like this:

channels:
  - bioconda
  - conda-forge
  - defaults
  - r

This file can be changed with a simple text editor such as nano.

After you make that change and you’ve activate your dDocent environment, run these commands:

conda uninstall bzip2 This should uninstall bzip2, samtools, and dDocent

conda install ddocent Then you should be ready to go.

-- 

Jon Puritz, PhD

Assistant Professor
Department of Biological Sciences
University of Rhode Island
120 Flagg Road, Kingston, RI 02881

Webpage: MarineEvoEco.com

Cell: 401-338-8739

"The most valuable of all talents is that of never using two words when one will do.” -Thomas Jefferson

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[Seth Musker]

Thanks Jon!

---

From: Jon Puritz
Sent: ‎2017-‎09-‎14 15:10
To: seth musker; ddo...@googlegroups.com
Subject: Re: [dDocent User Group] version of Samtools installed in your $PATHis not optimized for dDocent error when doing bioconda installation

Hi Valerie and Seth,

I traced the route of this problem and it stems from conflicting versions of libraries on various condo channels. Very frustrating!

Seth’s workaround will fix things temporarily, but here’s the fix to help with further bioconda installations. Basically, we are going to change the priority of different conda channels for package installation. These are listed in you ~/.condarc files

If you followed my original instructions, your file may look like this:

cat ~/.condarc

channels:
  - bioconda
  - r
  - defaults
  - conda-forge

And according to new bioconda best practices, we want it to look like this:

channels:
  - bioconda
  - r
  - conda-forge
  - defaults

To unsubscribe from this group and stop receiving emails from it, send an email to ddocent+u...@googlegroups.com.

[valer...@gmail.com]

Thanks, Seth and Jon, for your help. I followed Jon's new instructions and that worked. dDocent is now running with the bioconda installation for me.

-Valerie

[caroli...@gmail.com]

Hi Jon,

I ran into the same problem:

/.conda/envs/ddocent_env/bin/dDocent: line 6: export: `2.7.8': not a valid identifier

dDocent 2.7.8 

Contact jpu...@uri.edu with any problems 

 

Checking for required software

The version of Samtools installed in your $PATH is not optimized for dDocent.

Please install at least version 1.3.0

I tried your fix (and also Seth's), but still getting the same error message.

Any suggestions?

-Carol

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[Jon Puritz]

Hi Carol,

The newest version (on GitHub) will fix this. The easiest way to get the newest version (and replace your conda version is below):

Note-activate your conda environment before running these commands

update=`which dDocent`

wget https://raw.githubusercontent.com/jpuritz/dDocent/master/dDocent

chmod +x dDocent

mv -f dDocent $update

That should fix it.

Hope that helps,

Jon

-- 

Jon Puritz, PhD

Assistant Professor

Department of Biological Sciences

University of Rhode Island

120 Flagg Road,  Kingston, RI 02881

Webpage: MarineEvoEco.com

Cell: 401-338-8739

Work: 401-874-9020

"The most valuable of all talents is that of never using two words when one will do. ”  -Thomas Jefferson

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[caroli...@gmail.com]

Hi Jon,

Thanks for the reply. 

Updating conda and then dDocent solved the problem!

Cheers,

Carol.

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[Paige M.]

Hello, I started a new conversation about this issue because this is older.  Sorry if that wasn't the proper way to get help.

I am having the same problems and I tried both fixes suggested in this thread.  Neither fixed my problem. I am running miniconda3, not miniconda2 as in the other examples.  I don't know why that would matter, but is there something else I should do?

Thankyou