You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
The BEDTOOLS_GENOMECOV step can require a lot of memory when working on merged replicates.
In my case (GRCh38), this takes 80-120Gb in total.
The module runs bedtools genomecov, followed by sorting. This sorting step doesn't actually change anything for me, as the bedtools genomecov output is already sorted. I suspect this is always the case, as the input for genomecov must be sorted.
We could also potentially change the tag here, but the tool is not multithreaded so additional cpus are not helpful, and process_high_memory defaults to excessively large amounts of memory.
The text was updated successfully, but these errors were encountered:
Scratch that, I've just tested and hit the following error on a different sample: CDX18_I_REP3.mLb.clN.bedGraph is not case-sensitive sorted at line 23978872. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again.
So sorting is required.
Suggest that we just increase the memory allocation for this process, at least when replicates are being merged.
Description of feature
The
BEDTOOLS_GENOMECOV
step can require a lot of memory when working on merged replicates.In my case (GRCh38), this takes 80-120Gb in total.
The module runs
bedtools genomecov
, followed by sorting. This sorting step doesn't actually change anything for me, as thebedtools genomecov
output is already sorted. I suspect this is always the case, as the input for genomecov must be sorted.We could also potentially change the tag here, but the tool is not multithreaded so additional cpus are not helpful, and process_high_memory defaults to excessively large amounts of memory.
The text was updated successfully, but these errors were encountered: