Error in DADA2

Question

[saiprabhask4]

I want to try DADA2 pipeline for the data analysis, but I got the following error

 "Error in mcmapply(fastqPairedFilter, mapply(c, fwd, rev, SIMPLIFY = FALSE),  : 
  'mc.cores' > 1 is not supported on Windows"

Can anyone please help in resolving this issue. Thanks in advance.

Answer 1

[always_learning]

mc.cores > 1 is not available for windows. You may try as mc.cores = 1 something like below may work.

mcmapply(fastqPairedFilter, mapply(c, fwd, rev, SIMPLIFY = FALSE), mc.cores = 1 )

Can you please try above and let us know.

[saiprabhask4]

Please look at the initial code

 "out <- filterAndTrim(fnFs, filtFs, fnRs, filtRs, truncLen=c(240,160),
              maxN=0, maxEE=c(2,2), truncQ=2, rm.phix=TRUE,
              compress=TRUE, multithread=TRUE)"

When I ran this code, I got the error that I mentioned in the question. I couldnt find mcmapply anywhere in the code so I was intrigued.

[GenoMax]

I have formatted your code correctly. In future use the icon shown below (after highlighting the text you want to format as code) when editing (Screenshot courtsey of @Wouter).

[always_learning]

Can you try this please ?

 out <- filterAndTrim(fnFs, filtFs, fnRs, filtRs, truncLen=c(240,160),
                  maxN=0, maxEE=c(2,2), truncQ=2, rm.phix=TRUE,
                  compress=TRUE, multithread=FALSE)"

[POORNA001]

Ya same here , I also get this error. Can somebody help on this matter. If your suggesting to try as mc.cores = 1 , how to enter this code ? Because in the code there is nothing to set the cores.