Error importing fastq files using “Fastq manifest” formats

Hi QIIME2 team,
I have a persistent error when I try to import single-end using SingleEndFastqManifestPhred3.


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


/software/software/QIIME2/2018.2/lib/python3.5/site-packages/matplotlib/ UserWarning: Duplicate key in file "/home/p277936/.config/matplotlib/matplotlibrc", line #17
(fname, cnt))
There was a problem importing manifest.txt:

/local/1498484/q2-SingleLanePerSampleSingleEndFastqDirFmt-_1v7m77v/CH3E_50_L001_R1_001.fastq.gz is not a(n) FastqGzFormat file:

Missing sequence for record beginning on line 5

Manifest file: NOTE: they dont even are named as in the error appears :confused:


how fastqfile looks like


Could someone help explain what is happening?
If you requiired mor details please et me know
Thanks in advance!!

An off-topic reply has been split into a new topic: How to use/define new source formats?

Please keep replies on-topic in the future.

Hey there @EGA!

I will try!

Let’s break down the error message: in the file for the forwards reads of sample CH3E, the fastq record beginning on line 5 is missing sequence data.

Is there screenshot you provided for sample CH3E? If not, can you send along a screenshot for that sample?

They look right to me - you specified the sample ID is CH3E, and that was is what is reflected in the filename during import (CH3E_50_L001_R1_001.fastq.gz). The first part of the filename is the sample ID. The rest is described here:

The underscore-separated fields in this file name are the sample identifier, the barcode sequence or a barcode identifier, the lane number, the read number, and the set number.

Basically, everything besides the sample ID and the read direction don’t really serve a purpose at this stage (and on) in an analysis.

Hope that helps, looking forward to your reply! :qiime2:

Hi thermokarst,
Thanks for your reply!
Here the screenshot.

I see some empty sequences. For trimming the barcodes and demultiplexing I used the -cutadapt command maybe it is causing the problem?

Looking forward to your reply :slight_smile:

1 Like

Ah ha!


Check out this post for a workaround!

Let us know if you need help with any of that! :qiime2: :t_rex:

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