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Commit 8a65eeba authored by Thamer Alsulaiman's avatar Thamer Alsulaiman
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quadruple memory used per thread in alignread step in mapreads.py script

parent d7b5e667
2 merge requests!3Containerized version of chip-seq analysis,!2Added new Docker file for motif search (named meme-5.5.4) installed from...
Pipeline #14466 failed with stages
......@@ -180,7 +180,8 @@ def align_pe(fastq, sai, reference, fastq_basename):
avail_sys_mem = int(subprocess.check_output("grep MemTotal /proc/meminfo | grep -o '[0-9]*'", shell=True).decode("utf-8").strip())
# Divide the total by the number of processors and apply a scaling factor (0.85) to not use all memory.
mem_per_thread = math.floor((avail_sys_mem // cpu_count()) * 0.85)
# DEBUGGING
mem_per_thread = mem_per_thread * 4
steps = [
"cat %s" % (sam_filename),
"grep -v -F -f %s" % (badcigar_filename),
......
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