Closed muffato closed 9 months ago
I've started both commands. Will report on the runtime and memory usage when they complete.
First snag: [ERROR] --cs or --MD doesn't work with --split-prefix
. --cs=short
was required by HiMut for somatic variant calling.
-I
mode5h 50 min runtime, 45 GB RAM
--split-prefix
mode19h 30 min runtime, 29 GB RAM.
I can see in the log file how the target genome was virtually split into three chunks, each under 4 Gbp, and reads were aligned to each chunk. That's why it was about 3 times as slow as the -I
mode.
For this pipeline, I would go with the -I
option as i) the extra memory requirement isn't hard to fulfil and is worth the speed increase, ii) --split-prefix
clashes with -cs
Description of the bug
By default, minimap2 can only deal with genomes up to 4 Gbp. For larger genomes, it needs either the
--split-prefix
option or the-I
option. See more information at https://github.com/lh3/minimap2/blob/master/FAQ.md#3-the-output-sam-doesnt-have-a-headerWithout that, samtools complain and the process crashes.
Command used and terminal output
Relevant files
No response
System information
No response