Skip to content
Snippets Groups Projects
Commit 1309b519 authored by Thamer Alsulaiman's avatar Thamer Alsulaiman
Browse files

fixed memory assignment per thread to whole memory scaled to 0.7; updated queues for some processes

parent 6f728d3f
Branches
Tags
2 merge requests!3Containerized version of chip-seq analysis,!2Added new Docker file for motif search (named meme-5.5.4) installed from...
Pipeline #14495 failed with stages
......@@ -26,12 +26,10 @@ process {
withName: trimReads {
container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
queue = '256GB,256GBv1'
cpus = 32
}
withName: alignReads{
container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
queue = '256GB,256GBv1'
cpus = 32
}
withName: filterReads{
container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
......@@ -63,27 +61,23 @@ process {
}
withName: plotProfile {
container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
queue = '128GB,256GB,256GBv1'
cpus = 32
queue = 'super'
}
withName: consensusPeaks {
container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
queue = '128GB,256GB,256GBv1'
queue = 'super'
}
withName: peakAnnotation {
container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/r:3.3.2'
queue = '128GB,256GB,256GBv1'
queue = 'super'
}
withName: diffPeaks {
container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/r:3.3.2'
queue = '128GB,256GB,256GBv1'
cpus = 32
}
withName: motifSearch {
executor = 'local'
container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/motif-search:meme-5.5.4'
queue = '128GB,256GB,256GBv1'
//cpus = 32
queue = 'super'
}
withName: multiqcReport {
container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
......
......@@ -110,7 +110,7 @@ def convert_mapped_pe(bam, bam_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)
# DEBUGGING
mem_per_thread = mem_per_thread * 4
samtools_sort_command = \
......
......@@ -138,7 +138,7 @@ def align_se(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)
steps = [
"bwa samse %s %s %s"
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment