Reconstruct fragment rep seqs problem with sidle

Library Plugin Support
1

Hi jwdebelius,

I am a newbie of qiime 2 and q2-sidle also. Unfortunately I have some problem with q2-sidle reconstruct fragment rep seqs command. I follow the q2-sidle tutorial and everything went ok except when I try to reconstruct the phylogenetic tree. For all q2-sidle procedure I used greengens 13_8 database and its rep-set-aligned tree at 99% .

this is the command line that I used:
qiime sidle reconstruct-fragment-rep-seqs --i-reconstruction-map sample_map.qza --i-reconstruction-summary sample_summary.qza --i-aligned-sequences 13_8_aligned-sequences.qza --o-representative-fragments sample_rep-seq-fragments.qza

I paste the --verbose output that I obtain:

Traceback (most recent call last):

  • File "/home/christian/miniconda2/envs/qiime2/lib/python3.8/site-packages/q2cli/commands.py", line 520, in call*
  • results = self._execute_action(*
  • File "/home/christian/miniconda2/envs/qiime2/lib/python3.8/site-packages/q2cli/commands.py", line 581, in _execute_action*
  • results = action(*arguments)
  • File "", line 2, in reconstruct_fragment_rep_seqs*
  • File "/home/christian/miniconda2/envs/qiime2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable*
  • outputs = self.callable_executor(*
  • File "/home/christian/miniconda2/envs/qiime2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 583, in callable_executor*
  • self.signature.coerce_given_outputs(output_views, output_types,*
  • File "/home/christian/miniconda2/envs/qiime2/lib/python3.8/site-packages/qiime2/core/type/signature.py", line 492, in coerce_given_outputs*
  • output = self._create_output_artifact(*
  • File "/home/christian/miniconda2/envs/qiime2/lib/python3.8/site-packages/qiime2/core/type/signature.py", line 516, in _create_output_artifact*
  • artifact = qiime2.sdk.Artifact._from_view(*
  • File "/home/christian/miniconda2/envs/qiime2/lib/python3.8/site-packages/qiime2/sdk/result.py", line 360, in _from_view*
  • result = transformation(view, validate_level)*
  • File "/home/christian/miniconda2/envs/qiime2/lib/python3.8/site-packages/qiime2/core/transform.py", line 70, in transformation*
  • new_view = transformer(view)*
  • File "/home/christian/miniconda2/envs/qiime2/lib/python3.8/site-packages/qiime2/core/transform.py", line 221, in wrapped*
  • file_view = transformer(view)*
  • File "/home/christian/miniconda2/envs/qiime2/lib/python3.8/site-packages/q2_types/feature_data/_transformer.py", line 385, in _16*
  • _series_to_fasta_format(ff, data)*
  • File "/home/christian/miniconda2/envs/qiime2/lib/python3.8/site-packages/q2_types/feature_data/_transformer.py", line 272, in _series_to_fasta_format*
  • skbio.io.write(sequence, format='fasta', into=f)*
  • File "/home/christian/miniconda2/envs/qiime2/lib/python3.8/site-packages/skbio/io/registry.py", line 1166, in write*
  • return io_registry.write(obj, format, into, *kwargs)
  • File "/home/christian/miniconda2/envs/qiime2/lib/python3.8/site-packages/skbio/io/registry.py", line 619, in write*
  • writer(obj, into, *kwargs)
  • File "/home/christian/miniconda2/envs/qiime2/lib/python3.8/site-packages/skbio/io/registry.py", line 1082, in wrapped_writer*
  • writer_function(obj, fhs[-1], *kwargs)
  • File "/home/christian/miniconda2/envs/qiime2/lib/python3.8/site-packages/skbio/io/format/fasta.py", line 800, in _dna_to_fasta*
  • _sequences_to_fasta([obj], fh, qual, id_whitespace_replacement,*
  • File "/home/christian/miniconda2/envs/qiime2/lib/python3.8/site-packages/skbio/io/format/fasta.py", line 907, in _sequences_to_fasta*
  • _generator_to_fasta(*
  • File "/home/christian/miniconda2/envs/qiime2/lib/python3.8/site-packages/skbio/io/registry.py", line 1082, in wrapped_writer*
  • writer_function(obj, fhs[-1], *kwargs)
  • File "/home/christian/miniconda2/envs/qiime2/lib/python3.8/site-packages/skbio/io/format/fasta.py", line 774, in _generator_to_fasta*
  • for header, seq_str, qual_scores in formatted_records:*
  • File "/home/christian/miniconda2/envs/qiime2/lib/python3.8/site-packages/skbio/io/format/_base.py", line 150, in _format_fasta_like_records*
  • raise ValueError(*
    ValueError: 1st sequence does not contain any characters (i.e., it is an empty/blank sequence). Writing empty sequences is not supported.

Plugin error from sidle:

  • 1st sequence does not contain any characters (i.e., it is an empty/blank sequence). Writing empty sequences is not supported.*

I repeat all procedures several times with this result. Can you help me, I don't understand what went wrong?

Thank you so much for your help

Regards,

Andrea

3

Hi @andrea_petrucca,

I made this public so that others can find it and benefit.

The error is a convoluted way of saying your reconstruction doesn't have any sequences that need to be written.

I would recommend going back and checking your database reconstruction as well as your tables to see if this makes sense.

Best,
Justine

2 Likes