my file name format is
I ran the below command to import my data
qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path casava-18-paired-end-demultiplexed --input-format CasavaOneEightSingleLanePerSampleDirFmt --output-path demux-paired-end.qza
And error message is:
There was a problem importing casava-18-paired-end-demultiplexed:
Missing one or more files for CasavaOneEightSingleLanePerSampleDirFmt: '.+_.+_L[0-9][0-9][0-9]_R_001\.fastq\.gz’
I have both R1 and R2 file. It is paired end.
I figured it out that it was the format of my file name. After correction I was able to import my data. Fastq manifest takes too long when you have more samples.