Hi,
When I am trying to import my file in Qiime2, it is displaying the following error "Duplicate samples in forward reads: {'MOLWAT2', 'MOLWAT1'}". But, those two are independent and are not duplicates. I used the following command for importing
qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path /scratch/vv00010/DW_All
--input-format CasavaOneEightSingleLanePerSampleDirFmt
--output-path DW-sequences.qza
DW_All file is present in my directory and it contains a lot of fastq.gz types and each one of them is independent and does not duplicate. These are MOLWAT reads
MOLWAT1_S107_L001_R1_001.fastq.gz
MOLWAT1_S107_L001_R2_001.fastq.gz
MOLWAT1_S42_L001_R1_001.fastq.gz
MOLWAT1_S42_L001_R2_001.fastq.gz
MOLWAT2_S108_L001_R1_001.fastq.gz
MOLWAT2_S108_L001_R2_001.fastq.gz
MOLWAT2_S95_L001_R1_001.fastq.gz
MOLWAT2_S95_L001_R2_001.fastq.gz
MOLWAT3_S109_L001_R1_001.fastq.gz
MOLWAT3_S109_L001_R2_001.fastq.gz
Please help me solve this error.
In the Casava naming convention, the first(in reality, it is whatever comes before the fourth underscore to the left from the end of the filename) part of the file name is inferred to be the sample name. You state that 'MOLWAT2', 'MOLWAT1' are both independent samples, which makes sense, but your error message seems to be saying that there are duplicates of both of those samples, that is that it found multiple samples called MOLWAT1 and multiple called MOLWAT2. Could you tell us more about how the study was structured? What is the difference between MOLWAT1_S107 and MOLWAT1_S42, are they from the same sample but sequenced with a different primer? If they really are part of the same sample, it might be that you will need to use a manifest import rather than the Casava import. As a matter of personal interest, what does MOLWAT mean?
Thank you @Keegan-Evans for your response. Yeah, I renamed the samples MOLWAT4 and MOLWAT5. So MOLWAT is molecular-grade water. Those are all PCR blanks, for identification I gave that name. Now it worked after I renamed them.
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