"Missing one or more files" When Importing PE Demultiplexed Files

Hi there,

I have 48 fastq files to import. They are all in the format ED[23][90][0-9][0-9]-cytb_R[12]_001.fastq.gz, and are all paired (e.g. every R1 has an R2 pair). They're PE, and demultiplexed (I believe with Casava 1.8 -- fresh off a NovaSeq.) I'm running the standard importing code from the tutorial, but always getting an error. Is it because of the -cytb_ in the file name?

qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path cytb/ --input-format CasavaOneEightSingleLanePerSampleDirFmt --output-path demux-cytb.qza

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

I'm running qiime2 2021.4 on Ubuntu 16.04 installed with conda.

Thanks for your help,


Here are some screenshots that may help show the problem too. It doesn't seem to be due to the gene being in the file name. Any thoughts?

Hi @alexkrohn - the issue is that your filenames do not match the pattern specified above for the CasavaOneEightSingleLanePerSampleDirFmt. The issue is you don't have a lane number field.

The good news is there is a laneless variant of the import format: CasavaOneEightLanelessPerSampleDirFmt, which matches the following pattern: .+_.+_R[12]_001\.fastq\.gz, and I think this might work for your files.

qiime tools import \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-path cytb/ \
  --input-format CasavaOneEightLanelessPerSampleDirFmt \
  --output-path demux-cytb.qza

If that format doesn't work, simply fall back to the manifest format, that's what its there for.

Keep us posted!


Hi @thermokarst! CasavaOneEightLanelessPerSampleDirFmt gave the same error, so I used the Manifest File. That worked well. Thanks for your help!

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.