Plug in error from demux

[serenejiang]

I received the following error when running qiime demux:

Plugin error from demux:

Compressed file ended before the end-of-stream marker was reached

What does this error mean?

[thermokarst]

Hi @serenejiang, we need a bit more information before we can assist you. Can you please provide the following information:

1. What version of QIIME 2 are you using?
2. What is the exact command or commands that you are trying to run?
3. What is the full error produced when running this/these command(s)? Please provide either the output when running your command with the --verbose flag, or alternatively, please attach the log file that is referenced at the bottom of the error message (when run with --verbose).

Thanks!

[serenejiang]

1. I used q2cli version 2017.4.0
2. I ran

  qiime demux emp-paired \
  --i-seqs paired-end-sequences.qza \
  --m-barcodes-file mapping_MrOS.txt \
  --m-barcodes-category BarcodeSequence \
  --verbose \
  --o-per-sample-sequences demux.qza

3. the full error is:

Traceback (most recent call last):
  File "/home/lij014/miniconda3/envs/qiime2/lib/python3.5/site-packages/q2cli/commands.py", line 218, in __call__
    results = action(**arguments)
  File "<decorator-gen-129>", line 2, in emp_paired
  File "/home/lij014/miniconda3/envs/qiime2/lib/python3.5/site-packages/qiime2/sdk/action.py", line 171, in callable_wrapper
    output_types, provenance)
  File "/home/lij014/miniconda3/envs/qiime2/lib/python3.5/site-packages/qiime2/sdk/action.py", line 248, in _callable_executor_
    output_views = callable(**view_args)
  File "/home/lij014/miniconda3/envs/qiime2/lib/python3.5/site-packages/q2_demux/_demux.py", line 331, in emp_paired
    for barcode_record, forward_record, reverse_record in seqs:
  File "/home/lij014/miniconda3/envs/qiime2/lib/python3.5/site-packages/q2_demux/_demux.py", line 161, in __iter__
    self.reverse_generator):
  File "/home/lij014/miniconda3/envs/qiime2/lib/python3.5/site-packages/q2_demux/_demux.py", line 34, in _read_fastq_seqs
    for seq_header, seq, qual_header, qual in itertools.zip_longest(*[fh] * 4):
  File "/home/lij014/miniconda3/envs/qiime2/lib/python3.5/gzip.py", line 287, in read1
    return self._buffer.read1(size)
  File "/home/lij014/miniconda3/envs/qiime2/lib/python3.5/_compression.py", line 68, in readinto
    data = self.read(len(byte_view))
  File "/home/lij014/miniconda3/envs/qiime2/lib/python3.5/gzip.py", line 480, in read
    raise EOFError("Compressed file ended before the "
EOFError: Compressed file ended before the end-of-stream marker was reached

Plugin error from demux:

  Compressed file ended before the end-of-stream marker was reached

Thanks!

[thermokarst]

Hi @serenejiang — QIIME 2 development has been progressing at a rapid pace the last few months - can you please try rerunning this using the latest version of QIIME 2, 2017.7? We are only able to provide support for the most recent version of QIIME 2 (for now - in the future we plan to have a few levels of supported versions of QIIME 2 available to users). Thanks!