I seem to be having trouble importing my data.
All my files are named with the same format
and keep receiving this error message
"There was a problem importing /dataset/FACE_soil_microbiome/itmp/MS211111-1408:
Unrecognized file (/dataset/FACE_soil_microbiome/itmp/MS211111-1408/LDK8547_6B2_L001_R2_098.fastq.gz) for CasavaOneEightSingleLanePerSampleDirFmt."
Although I can't seem to find any difference in file type or name format.
I have tried removing this particular file and the same error appears for another file.
I have 108 samples (216 files R1 and R2) and so I'm not sure how many other files will have this error
Can you post the entire command that you are using to try to import?
qiime tools import
--output-path VL_16S_PE.qza \
I believe you are running into this because your CASAVA file numbers are not 001, which is not a problem, do not go through and rename them It is just so strong a convention that we use it to validate the file names. You should be able to use a "manifest" import.
Your import command would look something like this:
qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path FACE_soil_manifest \
--output-path paired-end-demux.qza \
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