Can someone please help me knowing what is the problem with my manifest file? I have installed qiime2-2018.8, on ubuntu. my reads are paired-end fastq.gz I run this command; "qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path manifest --output-path paired-end-…

Hi @farhad63 , Are you positive it's encoded with Phred64 and not Phred33? Here's one post that helps figuring that out. My guess is you might just have an input format that is PairedEndFastqManifestPhred33. Couldn't hurt to try and see if the error goes away...

Hi Devon Thanks for the reply. I think I should not use manifest to import my data (I should use casava related command) as it it is fastq.gz and not fast q?

Hi @farhad63 , I think you're combining two separate ideas here: The file may be compressed (.fastq.gz) or uncompressed file (.fastq). The file may be imported with one of several import types, including either the Casava flavor or via the Manifest file method. There are many ways to get data into…

Hi Devon Thanks for the help I have paired-end read of 18S got demultiplexed by sequencing company as fastq.gz file (one forward & one reverse file for each sample)

Thanks for the tips, @devonorourke ! @farhad63 , first off, if you update to the latest release of QIIME 2 you will receive a much more detailed error message telling you exactly what is wrong with your manifest file. I just took a quick glance and noticed a typo in the first line: [image] farhad…

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Manifest is not a(n) PairedEndFastqManifestPhred64 file

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