humann 报错，请求瞧一瞧

Question

运行humann代码

time humann --input meta/temp/concat/ADn01.fq  \
  --output meta/temp/humann \
   --threads 6

出现报错

```python

Running metaphlan ........

CRITICAL ERROR: Error executing: /gdata01/user/zhanggh/miniconda3/envs/zshmeta3/bin/metaphlan /gdata01/user/zhanggh/meta/temp/concat/ADn01.fq -t rel_ab -o /gdata01/user/zhanggh/meta/temp/humann/ADn01_humann_temp/ADn01_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out /gdata01/user/zhanggh/meta/temp/humann/ADn01_humann_temp/ADn01_metaphlan_bowtie2.txt --nproc 6

Error message returned from metaphlan :
Traceback (most recent call last):
  File "/gdata01/user/zhanggh/miniconda3/envs/zshmeta3/bin/read_fastx.py", line 8, in <module>
    sys.exit(main())
  File "/gdata01/user/zhanggh/miniconda3/envs/zshmeta3/lib/python3.7/site-packages/metaphlan/utils/read_fastx.py", line 168, in main
    f_nreads, f_avg_read_length = read_and_write_raw(f, opened=False, min_len=min_len, prefix_id=prefix_id)
  File "/gdata01/user/zhanggh/miniconda3/envs/zshmeta3/lib/python3.7/site-packages/metaphlan/utils/read_fastx.py", line 130, in read_and_write_raw
    nreads, avg_read_length = read_and_write_raw_int(inf, min_len=min_len, prefix_id=prefix_id)
  File "/gdata01/user/zhanggh/miniconda3/envs/zshmeta3/lib/python3.7/site-packages/metaphlan/utils/read_fastx.py", line 98, in read_and_write_raw_int
    for idx, record in enumerate(parser(fd), 2):
  File "/gdata01/user/zhanggh/miniconda3/envs/zshmeta3/lib/python3.7/site-packages/Bio/SeqIO/QualityIO.py", line 962, in FastqGeneralIterator
    for line in handle:
  File "/gdata01/user/zhanggh/miniconda3/envs/zshmeta3/lib/python3.7/codecs.py", line 322, in decode
    (result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb5 in position 1407: invalid start byte

Answer 1

由于这个报错是由于处理fastq格式文件时，遇到了无法解码的字节，建议查看文件ADn01.fq，看看是否存在特殊字符、空格等，并根据报错进行调整和替换，以避免无法正确解码。另外，您还可以将文件转换成其他格式后再进行处理，比如使用FASTQDumper 将Fastq格式转换成其他格式，如Fasta或者Fastq GBK格式(genbank)等，这样就可以解决这个问题。