qiime quality-control exclude-seqs message


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\

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

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
    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!

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.

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