New to Qiime2 Mismatched sequence ids:

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Thanks @megladds! I cracked open your files, and found the following first three ids in each file:

barcodes:

@M01522:85:000000000-AU4UD:1:1101:19131:1345 2:N:0:2
@M01522:85:000000000-AU4UD:1:1101:16978:1376 1:N:0:2
@M01522:85:000000000-AU4UD:1:1101:18361:1378 2:N:0:2

forward:

@M01522:85:000000000-AU4UD:1:1101:19131:1345 1:N:0:2
@M01522:85:000000000-AU4UD:1:1101:18045:1364 1:N:0:2
@M01522:85:000000000-AU4UD:1:1101:16978:1376 1:N:0:2

reverse:

@M01522:85:000000000-AU4UD:1:1101:19131:1345 2:N:0:2
@M01522:85:000000000-AU4UD:1:1101:18045:1364 2:N:0:2
@M01522:85:000000000-AU4UD:1:1101:16978:1376 2:N:0:2

Those should all match up, but you can see here, you are missing the second record (@M01522:85:000000000-AU4UD:1:1101:18045:1364 1:N:0:2) in your barcode file.

I then went ahead and checked the line count in each file (they should all be the same):

$ wc -l barcodes.fastq
 17047564 barcodes.fastq
$ wc -l forward.fastq
 17611740 forward.fastq
$ wc -l reverse.fastq
 17611740 reverse.fastq

Looks like you are missing some records in your barcodes file! I would suggest contacting your sequencing facility (or whoever prepared these files for you) and see if they have any thoughts.

Good luck and keep us posted! :t_rex:

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