unoise3 clustering

[nicolereynolds1]

I am trying to cluster my data using unoise3 with the following command: amptk unoise3 -i out_lr22.demux.fq.gz -o out_lr22 -p 98 -e 2.0 --usearch usearch10

I know usearch is no longer included with amptk, but I downloaded it and put it in my path by following the instructions from the amptk documents. However, I keep getting the error: Traceback (most recent call last): File "/opt/miniconda3/envs/amptk/bin/amptk", line 10, in sys.exit(main()) File "/opt/miniconda3/envs/amptk/lib/python3.9/site-packages/amptk/amptk.py", line 784, in main mod.main(arguments) File "/opt/miniconda3/envs/amptk/lib/python3.9/site-packages/amptk/unoise3.py", line 111, in main total = amptklib.countfasta(derep_out) File "/opt/miniconda3/envs/amptk/lib/python3.9/site-packages/amptk/amptklib.py", line 445, in countfasta with open(input, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: 'out_lr22_tmp/out_lr22.EE2.0.derep.fa'

and in the log file the error says: Fatal error: FASTQ input is only allowed with the fastx_uniques command

I tried changing the command from derep_fulllength to fastx_uniques in the unoise3 script, but that also did not work and returned the same error. I cannot figure out why the dereplication continues to fail.