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marbl / parsnp

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
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error : CRITICAL - Profile not in system path! #86

Closed aliciacb closed 3 years ago

aliciacb commented 3 years ago

Hello,

I have installed version 1.5.0 (but this error also occurs with 1.5.3), following instructions.

I run this command: ./parsnp_linux/parsnp -r reference.fasta -d ../../assemblies/ -c

I get this output: |--Parsnp v1.5--| For detailed documentation please see --> http://harvest.readthedocs.org/en/latest 16:38:15 - CRITICAL - Profile not in system path!

Any ideas what I am doing wrong? Thank you for your help! Alicia

bkille commented 3 years ago

Hi Alicia,

Thanks for using Parsnp! Parsnp has a number of dependencies required for use. Those dependencies must be added to your system path if you are installing from source. Alternatively, if you are installing from conda (recommended), the dependencies will be installed and added to the system path automatically.

aliciacb commented 3 years ago

Thank you for such a quick response. I have tried installing parsnp both from source and from conda. When running conda: conda install -c bioconda parsnp. Only version 1.2 is installed (not the latest 1.5.3). I have tried updating the package but it says 1.2 is the latest on conda. I've also tried with harvesttools but no success either.

bkille commented 3 years ago

This will happen bioconda doesn't have the proper channels set up.

Please see https://bioconda.github.io/user/install.html#set-up-channels

Let me know if this doesn't solve your issue and thanks again for using parsnp!