About “Fastq manifest” formats:import paired-end data error

User Support
#1

Hello, I’m having some problems when use qiime2-2019.10 import paired end data:
error:

There was a problem importing mainfest.txt:

  mainfest.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']

This is my Fastq manifest,like this manifest file,:

sample-id	forward-absolute-filepath	reverse-absolute-filepath
H1	/home/Project/16S/data/A01_1.fastq.gz	/home/Project/16S/data/A01_2.fastq.gz
H2	/home/Project/16S/data/A04_1.fastq.gz	/home/Project/16S/data/A04_2.fastq.gz
H3	/home/Project/16S/data/A021_1.fastq.gz	/home/Project/16S/data/A021_2.fastq.gz
H4	/home/Project/16S/data/A08_1.fastq.gz	/home/Project/16S/data/A08_2.fastq.gz
H5	/home/Project/16S/data/A084_1.fastq.gz	/home/Project/16S/data/A084_2.fastq.gz

My command:

qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' \
                             --input-path mainfest.txt \
                             --input-format PairedEndFastqManifestPhred33 \
                             --output-path demux.qza

Thanks!

#2

Hello @wfgui, can you try changing the --input-format from PairedEndFastqManifestPhred33 to PairedEndFastqManifestPhred33V2? Thank you.

#4

I’m not sure if this changes something but you can try taking sample-id, forward-absolute-filepath, reverse-absolute-filepath in quote like “sample-id”.

#5

The problem has been solved.Thanks.

#6

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