diff --git a/CRISPResso2/CRISPRessoPooledCORE.py b/CRISPResso2/CRISPRessoPooledCORE.py
index 738713ff..f1142488 100644
--- a/CRISPResso2/CRISPRessoPooledCORE.py
+++ b/CRISPResso2/CRISPRessoPooledCORE.py
@@ -1173,8 +1173,8 @@ def rreplace(s, old, new):
                                         break
                                     n_reads_at_end = get_n_aligned_bam_region(bam_filename_genome, chr_str, curr_end-5, curr_end+5)
 
-                                sub_chr_command = chr_cmd.replace("__REGION__", ":%d-%d "%(curr_pos, curr_end))
                                 chr_output_filename = _jp('MAPPED_REGIONS/%s_%s_%s.info' % (chr_str, curr_pos, curr_end))
+                                sub_chr_command = chr_cmd.replace("__REGION__", ":%d-%d "%(curr_pos, curr_end)).replace("__DEMUX_CHR_LOGFILENAME__",chr_output_filename)
                                 chr_commands.append(sub_chr_command)
                                 chr_output_filenames.append(chr_output_filename)
                                 curr_pos = curr_end