Hi,

I am trying to get unassigned reads out of my split_libraries.py command. Here is the command:

split_libraries.py \
  -f /home/vicar66/Raw_data/Nov27/fastaconvertionNov28/fasta_converted_Nov27j100.fna \
  -q /home/vicar66/Raw_data/Nov27/fastaconvertionNov28/fasta_converted_Nov27j100.qual \
  -o /home/vicar66/Raw_data/ \
  -m /home/vicar66/mapfile_vincent.txt \
  -w 50 \
  -s 30 \
  -M 2 \
  --reverse_primer_mismatches 2 \
  -H 8 \
  -l 400 \
  -L 500 \
  -a 0 \
  -b variable_length \
  -d \
  -n 1 \
  -z truncate_only \
  --retain_unassigned_reads

Even if I enable --retain_unassigned_reads, and it is mentioned in the log file that retaining unassigned reads is enabled, I only get .txt files and .fna and .qual file of my assigned reads. Anyone could help me?

Thanks!