diff --git a/assembly_workflow.py b/assembly_workflow.py
index d9f44b8..6152e74 100644
--- a/assembly_workflow.py
+++ b/assembly_workflow.py
@@ -571,7 +571,7 @@ def abundance_sample(name, paired):
 	if paired == "paired":
 		if input_extension in ["fastq.gz", "fq.gz"]:
 			if pair_identifier == "kneaddata_default":
-				command = '''{a} && {b} && {c} && {d} && {e} && {f} && {g} && {h} && {i}'''.format(
+				command = '''{a} && {b} && {c} && {d}; {e} && {f} && {g} && {h} && {i}'''.format(
 					a = "if [ ! -s " + contigs + " ]; then echo -e \"Sequence Id\tBin Id\tSequence length (bp)\tBam Id\tCoverage\tMapped reads\" > [targets[0]] && echo -e \"Bin Id\tBin size (Mbp)\t" + name.split("/")[-1] + ".sorted: mapped reads\t" + name.split("/")[-1] + ".sorted: % mapped reads\t" + name.split("/")[-1] + ".sorted: % binned populations\t" + name.split("/")[-1] + ".sorted: % community\" > [targets[1]] && echo 0 > [targets[2]]; else samtools index " + bam_sorted + " -@ " + str(cores) + " " + bam_index,
 					b = "python " + assembly_tasks_folder + "checkm.py coverage " + bin + " [targets[0]] " + bam_sorted + " -x fa -t " + str(cores) + " -r " + args.checkm_coverage_options,
 					c = "python " + assembly_tasks_folder + "checkm.py profile [targets[0]] --tab_table -f [targets[1]]",
@@ -583,7 +583,7 @@ def abundance_sample(name, paired):
 					i = "echo $((paired1+paired2+unpaired1+unpaired2)) &>> [targets[2]]"
 					)
 			else:
-				command = '''{a} && {b} && {c} && {d} && {e} && {f} && {i}'''.format(
+				command = '''{a} && {b} && {c} && {d}; {e} && {f} && {i}'''.format(
 					a = "if [ ! -s " + contigs + " ]; then echo -e \"Sequence Id\tBin Id\tSequence length (bp)\tBam Id\tCoverage\tMapped reads\" > [targets[0]] && echo -e \"Bin Id\tBin size (Mbp)\t" + name.split("/")[-1] + ".sorted: mapped reads\t" + name.split("/")[-1] + ".sorted: % mapped reads\t" + name.split("/")[-1] + ".sorted: % binned populations\t" + name.split("/")[-1] + ".sorted: % community\" > [targets[1]] && echo 0 > [targets[2]]; else samtools index " + bam_sorted + " -@ " + str(cores) + " " + bam_index,
 					b = "python " + assembly_tasks_folder + "checkm.py coverage " + bin + " [targets[0]] " + bam_sorted + " -x fa -t " + str(cores) + " -r " + args.checkm_coverage_options,
 					c = "python " + assembly_tasks_folder + "checkm.py profile [targets[0]] --tab_table -f [targets[1]]",
@@ -594,7 +594,7 @@ def abundance_sample(name, paired):
 					)
 		elif input_extension in ["fastq", "fq"]:
 			if pair_identifier == "kneaddata_default":
-				command = '''{a} && {b} && {c} && {d} && {e} && {f} && {g} && {h} && {i}'''.format(
+				command = '''{a} && {b} && {c} && {d}; {e} && {f} && {g} && {h} && {i}'''.format(
 					a = "if [ ! -s " + contigs + " ]; then echo -e \"Sequence Id\tBin Id\tSequence length (bp)\tBam Id\tCoverage\tMapped reads\" > [targets[0]] && echo -e \"Bin Id\tBin size (Mbp)\t" + name.split("/")[-1] + ".sorted: mapped reads\t" + name.split("/")[-1] + ".sorted: % mapped reads\t" + name.split("/")[-1] + ".sorted: % binned populations\t" + name.split("/")[-1] + ".sorted: % community\" > [targets[1]] && echo 0 > [targets[2]]; else samtools index " + bam_sorted + " -@ " + str(cores) + " " + bam_index,
 					b = "python " + assembly_tasks_folder + "checkm.py coverage " + bin + " [targets[0]] " + bam_sorted + " -x fa -t " + str(cores) + " -r " + args.checkm_coverage_options,
 					c = "python " + assembly_tasks_folder + "checkm.py profile [targets[0]] --tab_table -f [targets[1]]",
@@ -606,7 +606,7 @@ def abundance_sample(name, paired):
 					i = "echo $((paired1+paired2+unpaired1+unpaired2)) &>> [targets[2]]"
 					)
 			else:
-				command = '''{a} && {b} && {c} && {d} && {e} && {f} && {i}'''.format(
+				command = '''{a} && {b} && {c} && {d}; {e} && {f} && {i}'''.format(
 					a = "if [ ! -s " + contigs + " ]; then echo -e \"Sequence Id\tBin Id\tSequence length (bp)\tBam Id\tCoverage\tMapped reads\" > [targets[0]] && echo -e \"Bin Id\tBin size (Mbp)\t" + name.split("/")[-1] + ".sorted: mapped reads\t" + name.split("/")[-1] + ".sorted: % mapped reads\t" + name.split("/")[-1] + ".sorted: % binned populations\t" + name.split("/")[-1] + ".sorted: % community\" > [targets[1]] && echo 0 > [targets[2]]; else samtools index " + bam_sorted + " -@ " + str(cores) + " " + bam_index,
 					b = "python " + assembly_tasks_folder + "checkm.py coverage " + bin + " [targets[0]] " + bam_sorted + " -x fa -t " + str(cores) + " -r " + args.checkm_coverage_options,
 					c = "python " + assembly_tasks_folder + "checkm.py profile [targets[0]] --tab_table -f [targets[1]]",
@@ -617,7 +617,7 @@ def abundance_sample(name, paired):
 					)
 	elif paired in ["unpaired", "concatenated"]:
 		if input_extension in ["fastq.gz", "fq.gz"]:
-			command = '''{a} && {b} && {c} && {d} && {e} '''.format(
+			command = '''{a} && {b} && {c} && {d}; {e} '''.format(
 				a = "if [ ! -s " + contigs + " ]; then echo -e \"Sequence Id\tBin Id\tSequence length (bp)\tBam Id\tCoverage\tMapped reads\" > [targets[0]] && echo -e \"Bin Id\tBin size (Mbp)\t" + name.split("/")[-1] + ".sorted: mapped reads\t" + name.split("/")[-1] + ".sorted: % mapped reads\t" + name.split("/")[-1] + ".sorted: % binned populations\t" + name.split("/")[-1] + ".sorted: % community\" > [targets[1]] && echo 0 > [targets[2]]; else samtools index " + bam_sorted + " -@ " + str(cores) + " " + bam_index,
 				b = "python " + assembly_tasks_folder + "checkm.py coverage " + bin + " [targets[0]] " + bam_sorted + " -x fa -t " + str(cores) + " -r " + args.checkm_coverage_options,
 				c = "python " + assembly_tasks_folder + "checkm.py profile [targets[0]] --tab_table -f [targets[1]]",
@@ -625,7 +625,7 @@ def abundance_sample(name, paired):
 				e = "echo $(zcat " + name + "." + input_extension + "|wc -l)/4|bc &>> [targets[2]]"
 				)
 		elif input_extension in ["fastq", "fq"]:
-			command = '''{a} && {b} && {c} && {d} && {e} '''.format(
+			command = '''{a} && {b} && {c} && {d}; {e} '''.format(
 				a = "if [ ! -s " + contigs + " ]; then echo -e \"Sequence Id\tBin Id\tSequence length (bp)\tBam Id\tCoverage\tMapped reads\" > [targets[0]] && echo -e \"Bin Id\tBin size (Mbp)\t" + name.split("/")[-1] + ".sorted: mapped reads\t" + name.split("/")[-1] + ".sorted: % mapped reads\t" + name.split("/")[-1] + ".sorted: % binned populations\t" + name.split("/")[-1] + ".sorted: % community\" > [targets[1]] && echo 0 > [targets[2]]; else samtools index " + bam_sorted + " -@ " + str(cores) + " " + bam_index,
 				b = "python " + assembly_tasks_folder + "checkm.py coverage " + bin + " [targets[0]] " + bam_sorted + " -x fa -t " + str(cores) + " -r " + args.checkm_coverage_options,
 				c = "python " + assembly_tasks_folder + "checkm.py profile [targets[0]] --tab_table -f [targets[1]]",