Long time QIIME1 user, new QIIIME2, trying to understand how to import files. We have 3 files with multiple samples from the Illumina MiSeq sequencer. The Files are R1 - forward, R2 -barcodes, and R3 reverse. Multiple samples are included in these files.
head of forward:
@MISEQ01:230:000000000-BJB48:1:1101:15468:1595 1:N:0:
TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGTCTGTTAAGTCAGCGGTCAAAGCCCGGGGCTCAACCCCGGCCCGCCGTTGAAACTGGCAGTCTCGAGTTGGAGAGAAGTATGCGGAATGCGCGGTG
+
1>111111B1B110A0AE0FEG000AEG1FG11/AFE121A1/B/A//A//>//>/>0FF221BB21@//?//111BBF//<@BCEC1GGCC//BCC?@C?CC..DBGD0/</.<CD0/0.GE0/0//..CC:00CC.??@E0B.C-?E?
@MISEQ01:230:000000000-BJB48:1:1101:15537:1602 1:N:0:
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
AABCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFADFFFFFFAC
@MISEQ01:230:000000000-BJB48:1:1101:18142:1620 1:N:0:
TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTGCGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTGGAAACTACCGAACTAGAGTGTCGGAGAGGTAAGTGGAATTCCTAGT
I have been trying to import these files into QIIME2 and have been using qiime2 import using:
qiime tools import --type EMPPairedEndSequences --input-path ~/QIIME2_2_fastq --output-path ~/QIIME2_2_fastq/emp-paired-end-sequences.qza
qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path ~/QIIME2_2_fastq --source-format CasavaOneEightSingleLanePerSampleDirFmt --output-path ~/QIIME2_2_fastq/emp-paired-end-sequences.qza
Neither one works, both error respectively with:
Missing one or more files for EMPPairedEndDirFmt: 'barcodes.fastq.gz'
Missing one or more files for CasavaOneEightSingleLanePerSampleDirFmt: '.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz'
I'm just wondering what the issue is? Should I demultiplex the samples in each of the runs? Should I create a manifest? Thank you.