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

[alexkrohn]

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?

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

Error:
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,

Alex

[alexkrohn]

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?

[thermokarst]

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!

[alexkrohn]

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