ERROR : pairdist is missing

[snehamurthy21]

Hello,

Im getting this erorr with NAura,

saying pairdist is missing even after its in local bin what to do to solve it?

[afelten-Anses]

Hi Sneha,

It seems that NAuRA cannot find pairdist in your $PATH. Did you add your bin folder in your $PATH with : export PATH=$PATH:/your/bin/path ? Maybe you should rename pairdist.py to pairdist in your bin folder.

The easier way to install NAuRA with dependencies is to use conda with : conda config --add channels afelten conda install naura

Sincerely

[snehamurthy21]

Thank you for your prompt reply, i tried with conda

i get this error of "UnsatisfiableError: The following specifications were found to be incompatible with each other:" and a whole list of them printed below

Package clustalw conflicts for: naura -> clustalw Package sqlite conflicts for: python=2.7 -> sqlite[version='>=3.20.1,<4.0a0|>=3.22.0,<4.0a0|>=3.23.1,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.27.2,<4.0a0|>=3.29.0,<4.0a0|>=3.30.0,<4.0a0|>=3.31.1,<4.0a0'] Package clustalo conflicts for: naura -> clustalo Package ncurses conflicts for: python=2.7 -> ncurses[version='6.0.|>=6.0,<7.0a0|>=6.1,<7.0a0|>=6.2,<7.0a0'] Package biopython conflicts for: naura -> biopython=1.72 Package phylip conflicts for: naura -> phylip Package zlib conflicts for: python=2.7 -> zlib[version='>=1.2.11,<1.3.0a0'] Package openssl conflicts for: python=2.7 -> openssl[version='1.0.|1.0.,>=1.0.2l,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a'] Package pip conflicts for: python=2.7 -> pip Package ca-certificates conflicts for: python=2.7 -> ca-certificates Package libgcc-ng conflicts for: python=2.7 -> libgcc-ng[version='>=7.2.0|>=7.3.0'] Package tk conflicts for: python=2.7 -> tk[version='8.6.|>=8.6.7,<8.7.0a0|>=8.6.8,<8.7.0a0'] Package dendropy conflicts for: naura -> dendropy Package libffi conflicts for: python=2.7 -> libffi[version='3.2.|>=3.2.1,<3.3a0|>=3.3,<3.4.0a0'] Package libstdcxx-ng conflicts for: python=2.7 -> libstdcxx-ng[version='>=7.2.0|>=7.3.0'] Package readline conflicts for: python=2.7 -> readline[version='7.|>=7.0,<8.0a0|>=8.0,<9.0a0'] Package blast conflicts for: naura -> blast Package fastx_toolkit conflicts for: naura -> fastx_toolkit

What would be your solution to tackle this?

[afelten-Anses]

Ok, Did you create a new environment with conda ?

I just tested this, it works for me : conda create --name naura conda activate naura conda config --add channels afelten conda install naura

You can also try to use this yml file to create your environment : conda env create -f environment_naura.yml

[snehamurthy21]

Thank you so much

The installation is complete. But, now im not getting the ouput,

I am giving in two query sequences (lists.txt) and two gbk files (in GENOME folder)

this is my command NAuRA -i GENOME/ -q lists.txt -T 1 --withPhylo --keepBlastAln --nucl

This is my lists.txt /media/cyllene/Sneha/2.IISC/7.Finder/set2/Naura/QueryA.fasta /media/cyllene/Sneha/2.IISC/7.Finder/set2/Naura/QueryB.fasta

my headers of fasta are >QueryA_101 and so on

could you please help i really need to run this tool, its important for my research

[afelten-Anses]

Quite strange, no output or errors ?

[snehamurthy21]

(naura) shivangi@callisto:/media/cyllene/Sneha/2.IISC/7.Finder/set2/Naura$ NAuRA -i genomes -q list_queries.txt -T 5 --withPhylo --keepBlastAln --nucl

This gets printed on my console:

--> Select genbank not already analyzed --> Check externals tools in PATH /home/shivangi/miniconda2/envs/naura/bin/blastn /home/shivangi/miniconda2/envs/naura/bin/blastp /home/shivangi/miniconda2/envs/naura/bin/pairdist.py /home/shivangi/miniconda2/envs/naura/bin/clustalo /home/shivangi/miniconda2/envs/naura/bin/sumtrees.py Nothing to do !