Hi,
I am importing sequence files of the input-format CasavaOneEightSingleLanePerSampleDirFmt (see below). These are required to be named in the following format for import:
'.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz'
# 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:
Code:
# 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
Error:
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!