Removed debugging code and fixed memory_per_thread assignment

workflow/scripts/convert_reads.py

@@ -111,8 +111,6 @@ def convert_mapped_pe(bam, bam_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 ) * 0.7)
-    # DEBUGGING
-    mem_per_thread = mem_per_thread * 4
     samtools_sort_command = \
         "samtools sort -m %d  -n -@%d -o %s %s" \
         % (mem_per_thread, cpu_count(), nmsrt_bam_filename, bam)

workflow/scripts/map_reads.py

@@ -179,9 +179,8 @@ 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)
-    # DEBUGGING
-    mem_per_thread = mem_per_thread * 4
+    #mem_per_thread = math.floor((avail_sys_mem // cpu_count()) * 0.85)
+    mem_per_thread = math.floor( avail_sys_mem * 0.7)
     steps = [
         "cat %s" % (sam_filename),
         "grep -v -F -f %s" % (badcigar_filename),

workflow/scripts/motif_search.py

@@ -15,7 +15,6 @@ import shutil
 import subprocess
 from multiprocessing import Pool
 import pandas as pd
-import utils2 as utils
 
 
 EPILOG = '''