I ran it in terminal, I'm sure it'll work now it was the quotation marks.
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but at least we dont get the folder path error anymore.
which qoutation so I remove? as it still did not run qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path /Users/hebahussein/Desktop/manifest --output-path /Users/hebahussein/Desktop/paired-end-demux.qza --input-format PairedEndFastqManifestPhred64V2
Error: Detected invalid character in: ‘SampleData[PairedEndSequencesWithQuality]’
Verify the correct quotes or dashes (ASCII) are being used.
I think it is because the small ' ' marks are being changed to non-ascii marks.
copy the command in this text file.
copy this into terminal.txt (227 Bytes)
And run it.
To avoid this, you can copy the command into a text file that is in "plain text" and then copy it into terminal. OR you can write the whole command in terminal to avoid this. Ben
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I can see you still have single qoutation ’ '. no change but I tried both with and without and still
qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path /Users/hebahussein/Desktop/manifest --output-path /Users/hebahussein/Desktop/paired-end-demux.qza --input-format PairedEndFastqManifestPhred64V2
There was a problem importing /Users/hebahussein/Desktop/manifest:
/Users/hebahussein/Desktop/manifest is not a file.
Ok, change this line in that text file from:
/Users/hebahussein/Desktop/manifest
to:
/Users/hebahussein/Desktop/manifest/6manifest.txt
And re-run the entire command with this new line. Ben
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so I think the problem in the metadata now
or easier; I change the names of columns in the manifest
There was a problem importing /Users/hebahussein/Desktop/manifest/6manifest.txt:
/Users/hebahussein/Desktop/manifest/6manifest.txt is not a(n) PairedEndFastqManifestPhred64V2 file:
’forward-absolute-filepath’ is not a column in the metadata. Available columns: ‘Forward’, 'Reverse’
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rename the column
Forward to forward-absolute-filepath
Reverse to reverse-absolute-filepath
Then rerun! Ben
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wow we both had the same idea
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No this was my fault, I didn’t look up what we needed to name the columns in the manifest. Ben
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at least it started to read files now. That is a progress
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we did it. it started running but there was a bugFile “//miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/skbio/io/registry.py”, line 506, in read
return (x for x in itertools.chain([next(gen)], gen))
File “//miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/skbio/io/registry.py”, line 531, in _read_gen
yield from reader(file, **kwargs)
File “//miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/skbio/io/registry.py”, line 1008, in wrapped_reader
yield from reader_function(fhs[-1], **kwargs)
File “//miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/skbio/io/format/fastq.py”, line 354, in _fastq_to_generator
qual_header)
File “//miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/skbio/io/format/fastq.py”, line 523, in _parse_quality_scores
phred_offset=phred_offset))
File “//miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/skbio/io/format/_base.py”, line 35, in _decode_qual_to_phred
% (phred_range[0], phred_range[1]))
ValueError: Decoded Phred score is out of range [0, 62].
An unexpected error has occurred:
Decoded Phred score is out of range [0, 62].
See above for debug info.
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Change PairedEndFastqManifestPhred64V2 to
PairedEndFastqManifestPhred33V2
Then rerun
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thanks a lot for your help. now how to visualize?
I am excited to see it
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That, you’re going to have to dig around a bit, I have a procedure to do tomorrow AM so I must sleep. Ben
3 Likes
thanks a lot for your help. At least we imported the file. I will do the search
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