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

[Paige M.]

Hello, I followed the 2 suggestions made in another post about this same problem.  The post was started by valer...@gmail.com 2017 with a followup in 2020 for another person.

I am still getting this error.  My install is with miniconda3, not miniconda2 like the previous persons. Does that make any difference?  If so, what can I do?  If not, please let me know the options.  Oh, I did check my personal install of samtools and it is 1.11 which I updated to 1.13.

miniconda3/envs/ddocent_env/bin/dDocent: line 32: [: : integer expression expected

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

[Paige M.]

Hello,

I gave up on this for a long time and just used another type of software to call SNPs.  Now - with a bit more experience and a new dataset I really wanted to try on dDocent pipeline- I solved the problem.  I did try the conda  update and new install of dDocent suggested again but that still didn't work.  Instead inside the ddocent conda environment I had created I simply had to run: conda install -c bioconda 'samtools>=1.16.1' 

Note that I definitely need to point to the version of samtools I wanted to get this to work.  Just an update or generic call to install samtools did not work.

Just adding this in case anyone else has a similar problem.  It is a simple fix, but I am someone who only uses computers for bioinformatics so simple problems can throw me easily!

[Jon Puritz]

Also, see note here: https://github.com/jpuritz/dDocent#if-you-are-getting-samtools-errors

--
You received this message because you are subscribed to the Google Groups "dDocent User Help Forum" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ddocent+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/ddocent/61a0cabd-399d-42b4-b2ee-2d2987e9c2fdn%40googlegroups.com.

--

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