DADA2 Error (return code 1)

[Nicholas_Bokulich]

Hi @cjweiss,

Thanks for posting!

@cjweiss

Mismatched forward and reverse sequence files: 17737, 17732.

Apparently you have an unequal number of sequences in your forward and reverse sequence files. See this thread for a similar error and some suggestions for diagnosing the error (including, near the bottom of the thread, a way to find the problem sequences):

Error in filtering using DADA2

Hello, all I am using qiime2 to analyze ITS2 amplicon sequencing data, and now saw immediate errors when using the following command, qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux-ITS-paired-end.qza --p-trunc-len-f 265 --p-trim-left-f 19 --p-trunc-len-r 250 --p-trim-left-r 20 --p-n-threads 16 --p-max-ee 4 --o-table ITS-table-both_forward_reverse_max_ee_4 --o-representative-sequences ITS-seqs_both_forward_reverse_max_ee_4 --verbose Errors are Running external command line…

@cjweiss

I have tried re-importing. I have double checked and even re-created the manifest file. I have also validated the demux file.

Thanks for trying these, but alas that's not the issue — you either imported the wrong files, or these files just have unequal seq numbers for some other reason (e.g., something was trimmed or corrupted). So these files are fine and will validate — they just don't match in the way that they need to (i.e., the forward read is missing its reverse pair )

I hope that helps! Let us know if you are able to identify the problem!