install with docker produces error -- executables not in path

[Josh Lefler]

I follow the installation instructions for installation via docker and it doesn’t report any issues when running. However, I attempt to run metabat via the runMetabat.sh script and it says metabat2 is not in my PATH.

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I notice in the logging output for the docker build command that it installs every executable file (runmetabat.sh, aggregatebindepths.pl,etc.) to usr/local/bin except for metabat and metabat2. I can try and put these executables somewhere in my path (either in usr/local/bin or somewhere else) and it still gives me the PATH error.

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I should add I have successfully installed metabat/metabat2 without using docker but I get malloc memory errors during runtime (after it generates the depth.txt file) which is why I decided to switch to trying out the docker version.

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Any help would be appreciated!

[Rob Egan]

Thanks for this bug report. Indeed we neglected to set the install rules for those two important binaries. The patch is up on the master branch and is the latest image on docker hub, which works for me now.

[Rob Egan]

The malloc errors you report indicate that your machine does not have sufficient memory to run on your dataset. You may need to run on a larger machine or trim down the size of your data (say but choosing a longer minimum length for contigs).

[Josh Lefler]

Thanks for your help and the timely response! The docker version successfully installed but I could never get the runMetaBat.sh to run on my samples – it didn’t seem to recognize my inputs and kept printing the help message.

It’s weird that I would get a memory overflow error because it was only 3 samples, one of which was rather meager in size. I went back, reinstalled metabat from source like I did previously, ran it again and it worked! (might have been all the other scripts I had running concurrently when I first attempted to bin…not sure). No troubles when installing from source now (so far), but I just wanted to report back!