Unable to import demultiplexed paired end files

Hi all-

I am trying to import concatenated files using qiime2 on a Linux system. I successfully uploaded my manifest, but I keep getting the following error:

(qiime2-2019.10) amundy@daceton:~/Analysis_1$ qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path /home/amundy/Concat_files --input-format CasavaOneEightSingleLanePerSampleDirFmt --output-path Demux/demux-paired-end.qza &
[1] 6193
(qiime2-2019.10) amundy@daceton:~/Analysis_1$ There was a problem importing /home/amundy/Concat_files:

Missing one or more files for CasavaOneEightSingleLanePerSampleDirFmt: ‘.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz’

I did my best to read up on the issue, and most of what I found suggested that my files need to be zipped to import in the Casava format I’m trying to use. But when I went to fix this, it appears that my files are already zipped, if I’m understanding the next error correctly:

(qiime2-2019.10) amundy@daceton:~$ zip -q /home/amundy/Concat_files

zip error: Nothing to do! (/home/amundy/Concat_files.zip)

**of note, my files look like this:

140301.f.fastq.gz
140301.r.fastq.gz
etc.

Please help!

Hi @amundy,
Welcome to the forum!
I believe your problem is that you are trying to use the Casava import method but your fastq files do not follow the expected naming convention. See this section of the import tutorial for the acceptable file names. Your easiest solution is to use the manifest import approach explained there.
Let us know if you run into any other issues!

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