Manifest file not working, other solutions on forum do not fix

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Hello,

Sorry if this is too simple a problem, but my colleagues and I have not been able to figure out the issue. My manifest file follows the required format and is the exact same format I've used for other imports, however when I try to import my files using :

qiime tools import
--type 'SampleData[SequencesWithQuality]'
--input-path sparrow_2sparrow_2-pe-33-manifest.csv (6.8 KB)
sparrow_2-se-33-manifest.csv (3.2 KB)
-pe-33-manifest.csv
--output-path paired-end-demux.qza
--source-format PairedEndFastqManifestPhred33

I get the following error :

An unexpected error has occurred:
No transformation from <class 'q2_types.per_sample_sequences._format.PairedEndFastqManifestPhred33'> to <class 'q2_types.per_sample_sequences._format.SingleLanePerSampleSingleEndFastqDirFmt'>

When I try single end, passing :

qiime tools import
--type 'SampleData[SequencesWithQuality]'
--input-path sparrow_2-se-33-manifest.csv
--output-path single-end-demux.qza
--source-format SingleEndFastqManifestPhred33

I get this error :

There was a problem importing sparrow_2-se-33-manifest.csv:
sparrow_2-se-33-manifest.csv is not a(n) SingleEndFastqManifestPhred33 file

Troubleshooting steps I've tried :

  • using different filepaths, eg $PWD/file, the absolute filepath from root, file name only while working in directory with files
  • saving as different types of CSV from excel
  • saving as CSV from textwrangler, viewing invisibles to be sure there aren't any extra line brakes etc
  • Importing as .fastq.gz, and unzipping then trying as .fastq

I sent my colleague a subset of my sequences and my manifest file, and after re-saving as a CSV he was able to get it to work, but on my computer it will not! Am I missing something obvious? I have uploaded both SE and PE manifest files to this post. Thank you in advance for any tips!

2

@mberlow thank you for extensively troubleshooting and documenting your trials and tribulations!

I think I've spotted the problem:

SampleData[SequencesWithQuality] is a single-end read format. I believe you want SampleData[PairedEndSequencesWithQuality]

Try:

qiime tools import \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-path sparrow_2-pe-33-manifest.csv \
  --output-path paired-end-demux.qza \
  --source-format PairedEndFastqManifestPhred64

Let me know if that helps!

1 Like
3

THIS WORKED :sob::sob::sob: Thank you so much it was rough to be stuck on the first step for two weeks! I appreciate you!

3 Likes
4

yikes! should have gotten in touch sooner! glad we were able to put you on the right track :smile:

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