qiime quality-control exclude-seqs message

Technical Support
1

Hi,

I am running the following commands to remove the host seqs from rep-seqs:

qiime quality-control exclude-seqs \
  --i-query-sequences rep-seqs.qza \
  --i-reference-sequences hg38.sequences.qza \
  --p-method blast \
  --p-threads 12 \
  --p-perc-identity 0.97 \
  --p-perc-query-aligned 0.97 \
  --o-sequence-hits hits.qza \
  --o-sequence-misses misses.qza\
  --verbose

qiime feature-table tabulate-seqs \
  --i-data hits.qza \
  --o-visualization hits.qzv \
  --verbose

qiime feature-table tabulate-seqs \
  --i-data misses.qza \
  --o-visualization misses.qzv

misses.qzv/.qza is produced, but not hits.qzv/.qza and misses.qza includes the same number of seqs with rep-seqs.qza.

QIIME2 produces this message:

Warning: [blastn] Examining 5 or more matches is recommended
/home/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/skbio/io/registry.py:548: FormatIdentificationWarning: <_io.BufferedReader name='/t
mp/qiime2-archive-q0ul0x0v/ad0f9080-2fde-4162-b59a-f06be14c7794/data/dna-sequences.fasta'> does not look like a fasta file
  % (file, fmt), FormatIdentificationWarning)
Traceback (most recent call last):
  File "/home/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/commands.py", line 329, in __call__
    results = action(**arguments)
  File "<decorator-gen-346>", line 2, in tabulate_seqs
  File "/home/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
    output_types, provenance)
  File "/home/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/action.py", line 452, in _callable_executor_
    ret_val = self._callable(output_dir=temp_dir, **view_args)
  File "/home/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2_feature_table/_summarize/_visualizer.py", line 46, in tabulate_seqs
    seq_len_stats = _compute_descriptive_stats(seq_lengths)
  File "/home/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2_feature_table/_summarize/_visualizer.py", line 206, in _compute_descript
ive_stats
    raise ValueError('No values provided.')
ValueError: No values provided.

Plugin error from feature-table:

  No values provided.

What could be the problem here?

Thank you very much for your help!

2

The error message you posted above is a little confusing, it looks to me like its multiple messages concatenated together, can you confirm that? The first line (or two?) are from the exclude-seqs output, while the rest appear to be from the first call to tabulate-seqs - the error is telling you that the hits.qza file, while present, is completely empty.

3

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.