Error in importing data using manifest

Technical Support
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1

Hi!
I am trying to import a data base using manifest. But everytime I try to run the code, the following message appears:
There was a problem importing /Users/giulianapazmino/Desktop/manifestgz.txt: /Users/giulianapazmino/Desktop/manifestgz.txt is not a(n) PairedEndFastqManifestPhred33 file:**
Found header on line 1 with the following labels: ['sample-id\tforward-absolute-filepath\treverse-absolute-filepath'], expected: ['sample-id', 'absolute-filepath', 'direction']

I am using the following manifest archive
sample-id forward-absolute-filepath reverse-absolute-filepath
sample-1 /Users/giulianapazmino/Desktop/lung/SRR15242156_1.fastq /Users/giulianapazmino/Desktop/lung/SRR15242156_2.fastq
sample-2 /Users/giulianapazmino/Desktop/lung/SRR15242164_1.fastq /Users/giulianapazmino/Desktop/lung/SRR15242164_2.fastq
sample-3 /Users/giulianapazmino/Desktop/lung/SRR15242165_1.fastq /Users/giulianapazmino/Desktop/lung/SRR15242165_2.fastq
sample-4 /Users/giulianapazmino/Desktop/lung/SRR15242158_1.fastq /Users/giulianapazmino/Desktop/lung/SRR15242158_2.fastq

What should I do?
manifest.txt (545 Bytes)

2

Hi @gspazmino,

You need to provide the qiime command that you used. Your manifest file looks okay... Based on this error message I am assuming that you are mixing-up the import commands for single-end vs paired-end data.

That is, this error message:

Tells me that you are running this command:

qiime tools import \
  --type 'SampleData[SequencesWithQuality]' \
  --input-format SingleEndFastqManifestPhred33V2
  --input-path se-33-manifest \
  --output-path single-end-demux.qza \

when you should in fact be running:

qiime tools import \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-format PairedEndFastqManifestPhred33V2
  --input-path pe-33-manifest \
  --output-path paired-end-demux.qza \

Note the --type and input-format flags. See the documentation about using the manifest format

-Mike

3

Thank you so much!
I used the code:
(qiime2-2023.2) giulianapazmino@Giulianas-MacBook-Air seqs % qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path manifest.txt
--output-path demux-paired-end-sequences.qza
--input-format PairedEndFastqManifestPhred33V2

and it worked. But right now i have this problem:
qiime demux summarize \

--i-data demux-paired-end-sequences.qza \

--o-visualization demux-paired-end-sequences.qzv

Plugin error from demux:

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

Debug info has been saved to /var/folders/66/pqztp5t15rj016ym8qhg93sh0000gn/T/qiime2-q2cli-err-1hbetql7.log

1 Like
5

This tells me that the demux-paired-end-sequences.qza file is corrupted. Perhaps the file failed to completely write, or was an incomplete download to a local computer?

8

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