Converting fastq files to qza


I am new QIIME2 user. I have fastq files in the form of paired end reads. I am using QIIME 2 via virtual box. I have downloaded the files and created a manifest file. I am now trying to convert these files to a qza so that i can start the trimming/cutadapt process.

I am using the following command, however i continue to get an error.

qiime tools import \

--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path manifest.txt
--output-path paired-end-demux.qza
--input-format PairedEndFastqManifestPhred33V2
There was a problem importing manifest.txt:

/tmp/q2-SingleLanePerSamplePairedEndFastqDirFmt-x08c60m0/R5614_74_L001_R2_001.fastq.gz is not a(n) FastqGzFormat file:

Header on line 5 is not FASTQ, records may be misaligned

I would appreciate some assistance.

Many thanks,


Hello @Veral,

Welcome to the forum!

There was a problem importing manifest.txt:

It is better to post the "manifest.txt" file since the problem is with it.

Best wishes,


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Hi @the_dummy and @Veral,

The error message tells you the problem:

I would recommend checking the file format. Make sure the file is gzipped (I usually do this by first trying to open it and second trying to gunzip) and then check it. If the file has a problem, you will need to go back to the original source.


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Hi Guys,

Thank you for the prompt response.

I was able to sort out the problem by going to the original source.

Thanks for helping,


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