I'm attempting to use filter_fasta.py in macqiime to remove sequences from a fastq based on a .txt file of read IDs.
filter_fasta.py -f my_reads.fastq -o filtered_reads.fq -s read_ids.txt -n
The input file has 366000 reads. The output file is 366000 reads. Nothing is being removed. I ensured the read IDs are actually represented in the fastq with grep. My read ID .txt file has only one ID per line. Any ideas what could be wrong?