"KeyError: 'chr1'" on MacOS

[frankyan]

Run iMARGI-Docker on MacOS Mojave, get the "KeyError: 'chr1'" in the parsing step.

OS: MacOS Mojave
Locale: en_US.UTF-8

[frankyan]

It's caused by BWA and the Docker memory limit on Windows and Mac system. Linux system is OK because it can use all the memory on your machine without any limitation.

The memory required by BWA depends on the size of the reference genome. For the human genome, it needs about 5GB for building or loading index files. If the memory is not enough, BWA will generate an empty BAM file without any warning or error information. Then in the following steps of the pipeline will throw a lot of error information containing "KeyError 'chr1'".

The default memory limit of Docker on Windows and Mac is 2GB. So you must to set it to at least 6GB. It means that your computer has at least 8GB memory. As your system and other software also need memory, so there might be less than 6GB memory left for Docker. So we listed the required memory as 16GB On the GitHub page. If you have only 8GB, please try it and let me know whether it works and how much time it cost (bwa is very slow with limited memory).