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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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No option to use ANI? #125

Closed nicolettacommins closed 1 year ago

nicolettacommins commented 1 year ago

I installed parsnp with conda and I want to use the --use-ani and --min-ani flags. I notice that these options aren't displayed in the help page, but I see them in the source code. When I try to use them I get the error "option --use-ani not recognized." I also noticed that the arg parser takes the flag "--use-ani" but later the code references "args.useani". I wanted to test if there was an issue arising from the "" v. "-" so I tried to install from source. Now I'm running into an issue at this step:

make LDADD=-lMUSCLE-3.7

Where I get: g++ -fopenmp -O2 -m64 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -g -O2 -fopenmp -lstdc++ -lpthread -std=gnu++0x -L/broad/hptmp/nikki/parsnp_source/lib -lMUSCLE-3.7 -o parsnp_core parsnp_core-MuscleInterface.o parsnp_core-parsnp.o parsnp_core-LCB.o parsnp_core-LCR.o parsnp_core-TMum.o parsnp_core-Converter.o parsnp_core-iniFile.o -lMUSCLE-3.7 /bin/ld: cannot find -lMUSCLE-3.7 /bin/ld: cannot find -lMUSCLE-3.7 collect2: error: ld returned 1 exit status make[1]: [parsnp_core] Error 1 make[1]: Leaving directory `/gsap/archive-bacterial/Users/Nikki/sw/parsnp-1.7.4/src' make: [all-recursive] Error 1

I see others have had similar issues but I'm a bit stuck. In any case would appreciate any help in getting the ANI genome recruitment option to work. Thanks!

bkille commented 1 year ago

Hi,

What is the version of parsnp you installed from conda?

nicolettacommins commented 1 year ago

Now that I look it does seem like conda installed an earlier version of parsnp (1.2). When I try to specify the current version I have incompatibility issues with my system:

The following specifications were found to be incompatible with your system:

bkille commented 1 year ago

Ahhh yes. Looks like you are using Python 2. You can create a new environment with parsnp via 

conda create --name parsnp-env "parsnp>=1.7"

Make sure you have the bioconda channel set up, though:

https://bioconda.github.io/#usage

nicolettacommins commented 1 year ago

I set up my environment with Python 3.7 but you're right that I had messed up my conda channel configuration and I was able to fix it. Thanks for your quick reply and helping me find my problem!