Used hardcoded numbers of helper threads for samtools

src/hostile/aligner.py

@@ -131,13 +131,13 @@ def gen_paired_clean_cmd(
             # Count reads in stream before filtering (2048 + 256 = 2304)
             f" | tee >(samtools view -F 2304 -c - > '{count_before_path}')"
             # Discard mapped reads and reads with mapped mates
-            f" | samtools view --threads {int(threads/2)} -f 12 -"
+            f" | samtools view -f 12 -"
             # Count reads in stream after filtering
             f" | tee >(samtools view -F 256 -c - > '{count_after_path}')"
             # Replace paired read headers with integers
             f' | awk \'BEGIN{{FS=OFS="\\t"}} {{$1=int((NR+1)/2)" "; print $0}}\''
             # Stream remaining records into fastq files
-            f" | samtools fastq --threads {int(threads/2)} -c 6 -N -1 '{fastq1_out_path}' -2 '{fastq2_out_path}'"
+            f" | samtools fastq --threads 2 -c 6 -N -1 '{fastq1_out_path}' -2 '{fastq2_out_path}'"
         )
         logging.debug(f"{cmd}")
         return cmd