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XPRESSyourself / XPRESSpipe

An alignment and analysis pipeline for Ribosome Profiling and RNA-seq data
https://xpresspipe.readthedocs.io/en/latest/
GNU General Public License v3.0
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Metagene OOM error #37

Closed j-berg closed 4 years ago

j-berg commented 4 years ago

Describe the bug Looks like memory load is too high with current throttling for metagene

To Reproduce Steps to reproduce the behavior:

  1. Run metagene with high file load

Screenshots

Evaluating the metagene profile for...
Processing of batch 1 of 2 complete...
Processing of batch 2 of 2 complete...

Converting positions to metapositions...
Resetting parallelization specs based on max file size to be processed:
Max number of workers: 20
Number of threads per worker (where available): 1
slurmstepd: error: _is_a_lwp: open() /proc/#####/status failed: No such file or directory
slurmstepd: error: Detected 7 oom-kill event(s) in step #######.batch cgroup. Some of your processes may have been killed by the cgroup out-of-memory handler.
(END)

Desktop (please complete the following information): HPC

j-berg commented 4 years ago

Modified BAM file thresholding for parallelization. Fixed by 27eaaed and updated in v0.4.3