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
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.
Thank you so much!
I used the code:
(qiime2-2023.2) [email protected] 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
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?