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LANL-Bioinformatics / PhaME

Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (genes under positive selection) using CDS SNPs.
GNU General Public License v3.0
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samtools issue #11

Open civanovich-senck opened 3 years ago

civanovich-senck commented 3 years ago

Dear devs, Ive run into an small issue, but have no clue how to solve it. So when I start a run I get this message:

Need samtools --version >= 1.3 but you have 0 - please upgrade it.

Ive installed PhaMe through conda, and samtools not only comes with it, but is part of the modules I have available. Also it is on my $PATH. So what gives?

Cristóbal

leannefaulks commented 3 years ago

I am having a similar issue. When I run 'conda list' it tells me I have samtools 1.4.1, so it is there but not being recognized?

mshakya commented 3 years ago

Thank you all and apologies. I am aware of the issue, which has to do with how the version number is parsed. I had fixed this issue in the latest phame, but I haven't pushed to changes to conda. The easiest way right now is to get the latest repo from here and use phame in src/phame instead of the one that is automatically installed by conda. Let me know if this works. I will also update the conda with latest phame in the mean time.

gpmoran commented 3 years ago

samtools is still a problem with the conda version of phame....

aliceseaborn commented 3 years ago

I have also been experiencing the same issue. Has anyone found a work around? Thank you!

mshakya commented 3 years ago

if you use the installation instruction #2 from the README of this repo that involves installing dependencies separately, you should not have the issue. Let me know if this solution works. Also, I have not had a chance to update the conda package yet.

gpmoran commented 3 years ago

Thank you for coming back to us. I have installed Phame using the method to install the dependencies separately. This has created a new PhaME directory with many subdirectories. Is there an example of how to run phame using a .ctl file in this installation?

zzeigler commented 3 years ago

I had success using #2 but I had to use the following python/conda versions for it to work.

Give it a try. The issue seems to be with newer conda versions limiting samtools to an older version that won't work.

[17:14] zzeigler@n400.linode:~
$ python --version
Python 3.6.13
[17:15] zzeigler@n400.linode:~
$ conda --version
conda 4.1.6
mshakya commented 3 years ago

HI @gpmoran , you will have to call the phame script directly. It wont be in your path. For example, if you are running phame from the github directory that you downloaded then you can just do:

src/phame control_file.ctl
drish91 commented 3 years ago

This worked for me too. To summarize, I created a new phame environment and installed the dependencies separately as described in #2. Cloned in the git repo in the same directory. Activated this new environment and ran the phame from the github source.

Though, it would be great if the conda package could be updated asap!

Ajalapond commented 2 years ago

I also have this problem. How can I solve this problem? thank you