Common errors
Below are common errors encountered when executing mgatk.
There are two common sources of this. 1) the argument of the --input flag was incompatible with the mode or 2) the mitochondria genome is incorrectly specified.
ERROR: Could not import any samples from the user specification
ERROR: check flags, logs, and input configuration (including reference mitochondrial genome)
For bcall mode, the input should be one .bam file. For call, the input should be a folder of .bam files. Otherwise, verify that the correct mitochondrial genome was specified with the --mito-genome flag.
For certain operations, particularly in bcall mode, mgatk will attempt to have many
files open. This can cause errors like the following:
OSError: [Errno 24] could not open alignment file `xxxxxxxxx.bam`: Too many open files.
In OSX and most unix-based operating systems, the max number of file descriptors
that you can have open is fixed (for my Mac, it was 256), which can mess up the parallel
processing performed in mgatk. To change this, add ulimit -n 1024 or some
other large number to your ~/.bash_profile as this is an environment variable that
needs to be set in each shell session. This number should be greater than the number
of samples nominated.
In very large data settings, it may not be possible to open as many files as there
are cells/samples (some file systems have hard upper bounds. In the bcall mode,
we can get around this using the --nsamples X flag, where X is the number of
samples to be porcessed in a given setting. As long as X is less than the max
allowed by your OS, things should work without error.
The best work-around is to try using the tenx mode (assuming that your data
can be reformatted in this way) with ~ 12 cores (mgatk produces the same # of intermediate
files as there are cores available).
