Thanks, my manifest file is working now by creating a csv file (manifest) in window and save it as csv (MS DOS) or creating the manifest file using R code.
With the following syntax:
qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path csv2
--output-path paired30.qza
--source-format PairedEndFastqManifestPhred33
I have imported my raw paired sequencing data with the output file "paired30.qza"
Then, with the following syntax:
qiime demux summarize
--i-data paired30.qza
--o-visualization demux30.qzv
I have the following error:
Plugin error from demux:
Compressed file ended before the end-of-stream marker was reached
Debug info has been saved to /tmp/qiime2-q2cli-err-qper0vdr.log
The following is the texts from the log file:
Traceback (most recent call last):
File "/home/213002h/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/q2cli/commands.py", line 274, in call
results = action(**arguments)
File "", line 2, in summarize
File "/home/213002h/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/home/213002h/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/sdk/action.py", line 428, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File "/home/213002h/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/q2_demux/_summarize/_visualizer.py", line 117, in summarize
for seq in _read_fastq_seqs(file):
File "/home/213002h/miniconda3/envs/qiime2-2018.4/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/213002h/miniconda3/envs/qiime2-2018.4/lib/python3.5/gzip.py", line 287, in read1
return self._buffer.read1(size)
File "/home/213002h/miniconda3/envs/qiime2-2018.4/lib/python3.5/_compression.py", line 68, in readinto
data = self.read(len(byte_view))
File "/home/213002h/miniconda3/envs/qiime2-2018.4/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
I thought that the error may come from my raw data. So I imported raw sequencing data divided by groups (such as first 10 sample, then 11 to 20 ...). Re-run "qiime demux summarize" for each group. The error message appeared for some groups. However after further dividing the raw data group to identify the raw sequencing data with problem I cannot find any raw sequencing data with the problem. I am confused. Thanks, Brad