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Commit 5add902e authored by Thamer Alsulaiman's avatar Thamer Alsulaiman
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reversing memory change in map_reads.py

parent 45521260
1 merge request!3Containerized version of chip-seq analysis
Pipeline #15176 failed with stages
......@@ -179,8 +179,10 @@ def align_pe(fastq, sai, reference, fastq_basename):
# Determine the available memory on the host system (kB).
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)
mem_per_thread = math.floor( avail_sys_mem * 0.7)
mem_per_thread = math.floor((avail_sys_mem // cpu_count()) * 0.85)
#mem_per_thread = math.floor( avail_sys_mem * 0.7)
mem_per_thread = mem_per_thread * 4
steps = [
"cat %s" % (sam_filename),
"grep -v -F -f %s" % (badcigar_filename),
......
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