Sample files need to have underscores to be imported but Sample IDs cannot have underscores for deblur


I am importing sequence files of the input-format CasavaOneEightSingleLanePerSampleDirFmt (see below). These are required to be named in the following format for import:

# Import
qiime tools import \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-path seq_files \
  --input-format CasavaOneEightSingleLanePerSampleDirFmt \
  --output-path demux-paired-end.qza

This is not in itself an issue, except that when I try to run deblur on the processed imported sequences, it gives me an error due to the sample IDs having underscores:


# Denoise
qiime quality-filter q-score \
 --i-demux demux-paired-end.qza \
 --o-filtered-sequences demux-filtered.qza \
 --o-filter-stats demux-filter-stats.qza

qiime deblur denoise-16S \
  --i-demultiplexed-seqs demux-filtered.qza \
  --p-trim-length 145 \
  --o-representative-sequences rep-seqs-deblur.qza \
  --o-table table-deblur.qza \
  --p-sample-stats \
  --o-stats deblur-stats.qza


Plugin error from deblur:
  Deblur cannot operate on sample IDs that contain underscores. The following ID(s) contain one or more underscores: J_Hubb_s_12C, J_Hubb_s_25C, J_Hubb_s_ambient, J_Kaplin_8C, J_Kaplin_Ambient, J_Pier_Seawater_R2, J_Pier_Unfiltered_R1.

I have tried to change the sample file names, but then the import doesn't work. I know how to set up the metadata file, but that only comes into play later, not at this stage.

Maybe I am missing something obvious, but I don't know how to resolve this. Please advise!

Other information

  • Version of QIIME 2 you are running, and how it is installed (e.g. Virtualbox, conda, etc.)
    I am running qiime2-2022.8 on a server, where I installed it using conda.

Thank you!

Apologies, this turns out to be a simple fix. I just needed to change the first part of the file name and this solves the proplem, being accepted by both the import and the Deblur.

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