Mismatched forward and reverse sequence files in Dada2 step

[tangmaomao16]

I have the sequencing sample names like “H01” and “H01_1”. And I have problem when using
qiime dada2 denoise-paired --i-demultiplexed-seqs demux.qza --p-trunc-len-f 290 --p-trunc-len-r 256 --p-trim-left-f 26 --p-trim-left-r 26 --o-representative-se quences rep-seqs-dada2.qza --o-table table-dada2.qza --p-n-threads 0 --o-denoising-stats stats-dada2.qza --verbose

The error information is
DADA2 R package version: 1.6.0

1. Filtering Error in filterAndTrim(unfiltsF, filtsF, unfiltsR, filtsR, truncLen = c(truncLenF, :
   These are the errors (up to 5) encountered in individual cores…
   Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
   Mismatched forward and reverse sequence files: 41704， 46618.
   Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
   Mismatched forward and reverse sequence files: 46618， 41704.

I unzip the demux.qza file. And I see the files names :
H01_0_L001_R1_001.fastq.gz
H01_1_2_L001_R1_001.fastq.gz
H01_1_3_L001_R2_001.fastq.gz
H01_1_L001_R2_001.fastq.gz

How can I fix the problem? I cannot change my samples’ name because the author want to give such names.

[jwdebelius (Justine Debelius)]

Hi @tangmaomao16,

You could try using a - instead of an _ when you import the names with the manifest. However, if the author isnt going to see the analysis IDs, my suggestion would be to rename with a working ID and then return to the original name.

Best,
Justine