Common mistake & gotchas

Python OSError

If python throws an error like

OSError: [Errno 2] No such file or directory: '/path/to/your_tmp_directory/tmpXXXXX.sh'

then double-check to make sure the directory /path/to/your_tmp_directory actually exists!

Python ImportError

If python throws an error like

Traceback (most recent call last):
  File "path/to/SmileTrain/otu_caller.py", line 12, in <module>
    import check_fastq_format
  File "/path/to/SmileTrain/check_fastq_format.py", line 11, in <module>
    from Bio import SeqIO
ImportError: No module named Bio

it means you, as a user, need to have biopython available. For coyote users, you might need module add biopython.

usearch errors

If usearch throws an error like

---Fatal error---
Phred score 45 out of range 0..41

this means that your fastq file is in the wrong format. It is probably is Illumina 1.3. Running convert_fastq_format.py or otu_caller.py --convert might fix it.