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I started anew and seems multithreading not possible....what does it mean?
frrom the console :
out <- filterAndTrim(fnFs, filtFs, fnRs, filtRs, truncLen=c(200,200), + maxN=0, maxEE=c(2,2), truncQ=2, rm.phix=TRUE, + compress=TRUE, multithread=TRUE) # On Windows set multithread=FALSE Multithreading has been DISABLED, as forking is not supported on .Platform$OS.type 'windows' > head(out) reads.in reads.out TA-2423-Rhizo2Ser205-1-ENDO_S58_L001_R1_001.fastq 80846 79511 TA-2423-Rhizo2Ser205-2-ENDO_S59_L001_R1_001.fastq 88318 86841 TA-2423-Rhizo2Ser205-3-ENDO_S60_L001_R1_001.fastq 74490 72962 TA-2423-Rhizo2Ser211-1-ENDO_S64_L001_R1_001.fastq 89280 87813 TA-2423-Rhizo2Ser211-2-ENDO_S65_L001_R1_001.fastq 74096 72708 TA-2423-Rhizo2Ser211-3-ENDO_S66_L001_R1_001.fastq 84392 82972 >