Error running DADA2 in 454 data

thermokarst · January 29, 2019, 2:39pm

I found a similar error on the DADA2 error tracker:

Error in err[c(1, 6, 11, 16), ] <- 1 : incorrect number of subscripts on matrix

opened 11:49PM - 16 Nov 18 UTC

closed 02:46AM - 16 Jan 19 UTC

Hi, I am trying to use: errR <- learnErrors(filtRs, multithread=TRUE) t…o generate an error model for my filtered reverse reads. When I run the code on the filtered forward reads it generates the error model just fine. The only issue is with the reverse reads. I have tried more stringent parameters during filtering to increase quality of the reverse reads but the error: Error in err[c(1, 6, 11, 16), ] <- 1 : incorrect number of subscripts on matrix persists. Using R version 3.5.1 and dada2 version 1.10.0 [QIgG_R_filt.fastq.gz](https://github.com/benjjneb/dada2/files/2591263/QIgG_R_filt.fastq.gz)

Maybe you can try some of the checks suggested in that thread? You will already have a copy of DADA2 (and R) on hand in your QIIME 2 env. FWIW, in the linked issue it sounds like the reason this error happened is because all of the reads in the data were unique - no groupings of reads were identified.