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bwa-mem2 index module is tagged with 'process_single'; and is allocated only 6GB of memory as a result. If you run nf-raredisease on iGenomes (e.g. with --genome GRCh38), it tries to index the genome and the pipeline will crash due to this step running out of memory.
@lfearnley the default configurations used in raredisease are written keeping the test profile(&dataset, which is tiny) in mind. You should override these values like @fa2k has done in his configs here to get it to work on larger datasets.
Description of the bug
bwa-mem2 index module is tagged with 'process_single'; and is allocated only 6GB of memory as a result. If you run nf-raredisease on iGenomes (e.g. with
--genome GRCh38
), it tries to index the genome and the pipeline will crash due to this step running out of memory.BWA MEM2 requires ~84GB for indexing of GRCh38 - https://github.com/bwa-mem2/bwa-mem2/blob/master/README.md describes it as "# Indexing the reference sequence (Requires 28N GB memory where N is the size of the reference sequence)."
Command used and terminal output
No response
Relevant files
No response
System information
No response
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