Error in mash sketch
Opened this issue · 2 comments
I use Mash as one of the dependencies of PanACoTA. I got the following error while sketching:
error: mash sketch -o Acetobacter_orleanensis/mash_files/all-genomes-Acetobacter_orleanensis -p 1 -l Acetobacter_orleanensis/mash_files/list-to-sketch-Acetobacter_orleanensis.txt -s 1e4 does not exist
I used the following command:
PanACoTA prepare -t 104099 -s "Acetobacter orleanensis"
But file 'list-to-sketch-Acetobacter_orleanensis.txt' exists and located in the right directory.
Hey, did you find any solution for this issue? I am having the same problem right now.
I had the same problem, this is what worked for me (macOS):
Try: mash --version to see if your mash is accessible, in my case it wasn't, I was getting an error related to no command found
Ensure that your mash is downloaded in the correct environment and accessible when you run PanACoTA.
Once I had the downloading in the correct environment sorted I was getting an error code related to '/usr/lib/libgsl.25.dylib' (no such file, not in dyld cache) when running mash --version
I then listed my gsl brew list gsl in which I noted that all gsl version were 2.7.1, and mash is trying to access 2.5
Then I ran conda install -c conda-forge gsl=2.5
Once this was finished I ran mash --version again, this time getting the version number rather than an error.
Following this I was able to execute PanACoTA with no issues.
Hopefully this is helpful, my first time trying to provide a solution, so please let know if I could format something better.