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

workflow/configs/biohpc.config

@@ -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'

workflow/scripts/convert_reads.py

@@ -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 = \

workflow/scripts/map_reads.py

@@ -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"