No option to use ANI?
Closed this issue · 4 comments
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.use_ani". 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!
Hi,
What is the version of parsnp you installed from conda?
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:
- feature:/linux-64::__glibc==2.17=0
- python=3.7 -> libgcc-ng[version='>=11.2.0'] -> __glibc[version='>=2.17']
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:
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!