Hello! I have read several helpful tutorial posts on the dada2 error, however after trying to re-run with single reads only, I still get this error:
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
The command I used for single-reads was: qiime dada2 denoise-single --i-demultiplexed-seqs demux-single-end.qza --p-trim-left 0 --p-trunc-len 250 --o-representative-sequences rep-seqs-single-dada2.qza --o-table table-single-dada2.qza --o-denoising-stats stats-single-dada2.qza --p-n-threads 0 --verbose
This was the warning output:
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.
Command: run_dada_single.R /tmp/qiime2-archive-_9d58djz/12dde99a-8e91-47f5-85b9-732ecd23c254/data /tmp/tmpqedh3p0i/output.tsv.biom /tmp/tmpqedh3p0i/track.tsv /tmp/tmpqedh3p0i 250 0 2.0 2 Inf consensus 1.0 0 1000000 NULL 16
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.2 / RcppParallel: 4.4.4
- Filtering
*** caught segfault ***
address (nil), cause 'unknown'
Traceback:
1: is(object, "classRepresentation")
2: isClassDef(Class)
3: isVirtualClass(class)
4: initialize(value, ...)
5: initialize(value, ...)
6: methods::new(def, ...)
7: g$new(con = path, path = descr, ...)
8: .ShortReadFile(.FastqStreamer_g, con, reader = .binReader, readerBlockSize = as.integer(readerBlockSize), skips = 0L, adds = n, ith = 0L, recycle = TRUE, sampler = streamer, verbose = verbose)
9: .ShortReadFile(.FastqStreamer_g, con, reader = .binReader, readerBlockSize = as.integer(readerBlockSize), skips = 0L, adds = n, ith = 0L, recycle = TRUE, sampler = streamer, verbose = verbose)
10: FastqStreamer(fn, n = n)
11: FastqStreamer(fn, n = n)
12: (function (fn, fout, truncQ = 2, truncLen = 0, maxLen = Inf, minLen = 20, trimLeft = 0, trimRight = 0, maxN = 0, minQ = 0, maxEE = Inf, rm.phix = TRUE, orient.fwd = NULL, n = 1e+06, OMP = TRUE, compress = TRUE, verbose = FALSE, ...) { if (!OMP) { ompthreads <- .Call(ShortRead:::.set_omp_threads, 1L) on.exit(.Call(ShortRead:::.set_omp_threads, ompthreads)) } start <- max(1, trimLeft + 1, na.rm = TRUE) end <- truncLen if (end < start) { end = NA } end <- end - start + 1 if (fn == fout) { stop("The output and input files must be different.") } f <- FastqStreamer(fn, n = n) on.exit(close(f)) if (file.exists(fout)) { if (file.remove(fout)) { if (verbose) message("Overwriting file:", fout) } else { stop("Failed to overwrite file:", fout) } } first = TRUE inseqs = 0 outseqs = 0 while (length(suppressWarnings(fq <- yield(f)))) { inseqs <- inseqs + length(fq) if (!is.null(orient.fwd)) { if (!C_isACGT(orient.fwd)) stop("Non-ACGT characters detected in orient.fwd") barlen <- nchar(orient.fwd) fq.rc <- reverseComplement(fq) keepF <- narrow(sread(fq), 1, barlen) == orient.fwd keepR <- narrow(sread(fq.rc), 1, barlen) == orient.fwd & !keepF fq <- ShortReadQ(sread = c(sread(fq[keepF]), sread(fq.rc[keepR])), quality = c(quality(quality(fq[keepF])), quality(quality(fq.rc[keepR]))), id = c(id(fq[keepF]), id(fq.rc[keepR]))) } if (is.finite(maxLen)) { fq <- fq[width(fq) <= maxLen] } fq <- fq[width(fq) >= start] fq <- narrow(fq, start = start, end = NA) if (trimRight > 0) { fq <- fq[width(fq) > trimRight] fq <- narrow(fq, start = NA, end = width(fq) - trimRight) } enc <- encoding(quality(fq)) if (is.numeric(truncQ)) { ind <- which(enc == truncQ) if (length(ind) != 1) stop("Encoding for this truncQ value not found.") truncQ <- names(enc)[[ind]] } if (length(fq) > 0) fq <- trimTails(fq, 1, truncQ) truncQ <- enc[truncQ] if (!is.na(end)) { fq <- fq[width(fq) >= end] } fq <- narrow(fq, start = 1, end = end) fq <- fq[width(fq) >= minLen] fq <- fq[nFilter(maxN)(fq)] keep <- rep(TRUE, length(fq)) qq <- as(quality(fq), "matrix") if (minQ > truncQ) keep <- keep & (apply(qq, 1, min, na.rm = TRUE) > minQ) if (maxEE < Inf) { keep <- keep & C_matrixEE(qq) <= maxEE } fq <- fq[keep] if (rm.phix) { is.phi <- isPhiX(as(sread(fq), "character"), ...) fq <- fq[!is.phi] } outseqs <- outseqs + length(fq) if (first) { writeFastq(fq, fout, "w", compress = compress) first = FALSE } else { writeFastq(fq, fout, "a", compress = compress) } } if (verbose) { outperc <- round(outseqs * 100/inseqs, 1) outperc <- paste(" (", outperc, "%)", sep = "") message("Read in ", inseqs, ", output ", outseqs, outperc, " filtered sequences.", sep = "") } if (outseqs == 0) { message(paste("The filter removed all reads:", fout, "not written.")) file.remove(fout) } return(invisible(c(reads.in = inseqs, reads.out = outseqs)))})(dots[[1L]][[1L]], dots[[2L]][[1L]], truncQ = 2L, truncLen = 250L, trimLeft = 0L, trimRight = 0, maxLen = Inf, minLen = 20, maxN = 0, minQ = 0, maxEE = 2, rm.phix = TRUE, orient.fwd = NULL, n = 1e+05, OMP = FALSE, compress = TRUE, verbose = FALSE)
13: .mapply(FUN, dots, MoreArgs)
14: FUN(X[[i]], ...)
15: lapply(X = S, FUN = FUN, ...)
16: doTryCatch(return(expr), name, parentenv, handler)
17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
18: tryCatchList(expr, classes, parentenv, handlers)
19: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
20: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
21: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
22: FUN(X[[i]], ...)
23: lapply(seq_len(cores), inner.do)
24: mclapply(seq_len(n), do_one, mc.preschedule = mc.preschedule, mc.set.seed = mc.set.seed, mc.silent = mc.silent, mc.cores = mc.cores, mc.cleanup = mc.cleanup, affinity.list = affinity.list)
25: mcmapply(fastqFilter, fwd, filt, MoreArgs = list(truncQ = truncQ, truncLen = truncLen, trimLeft = trimLeft, trimRight = trimRight, maxLen = maxLen, minLen = minLen, maxN = maxN, minQ = minQ, maxEE = maxEE, rm.phix = rm.phix, orient.fwd = orient.fwd, n = n, OMP = OMP, compress = compress, verbose = verbose), mc.cores = ncores, mc.silent = TRUE)
26: filterAndTrim(unfilts, filts, truncLen = truncLen, trimLeft = trimLeft, maxEE = maxEE, truncQ = truncQ, rm.phix = TRUE, multithread = multithread, maxLen = maxLen)
27: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
28: suppressWarnings(filterAndTrim(unfilts, filts, truncLen = truncLen, trimLeft = trimLeft, maxEE = maxEE, truncQ = truncQ, rm.phix = TRUE, multithread = multithread, maxLen = maxLen))
An irrecoverable exception occurred. R is aborting now ...
*** caught bus error ***
address 0x2ae1b4527604, cause 'non-existent physical address'
Traceback:
1: readBin(con, raw(), n)
2: reader(con, readerBlockSize)
3: x$yield(...)
4: yield(f)
5: yield(f)
6: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
7: suppressWarnings(fq <- yield(f))
8: (function (fn, fout, truncQ = 2, truncLen = 0, maxLen = Inf, minLen = 20, trimLeft = 0, trimRight = 0, maxN = 0, minQ = 0, maxEE = Inf, rm.phix = TRUE, orient.fwd = NULL, n = 1e+06, OMP = TRUE, compress = TRUE, verbose = FALSE, ...) { if (!OMP) { ompthreads <- .Call(ShortRead:::.set_omp_threads, 1L) on.exit(.Call(ShortRead:::.set_omp_threads, ompthreads)) } start <- max(1, trimLeft + 1, na.rm = TRUE) end <- truncLen if (end < start) { end = NA } end <- end - start + 1 if (fn == fout) { stop("The output and input files must be different.") } f <- FastqStreamer(fn, n = n) on.exit(close(f)) if (file.exists(fout)) { if (file.remove(fout)) { if (verbose) message("Overwriting file:", fout) } else { stop("Failed to overwrite file:", fout) } } first = TRUE inseqs = 0 outseqs = 0 while (length(suppressWarnings(fq <- yield(f)))) { inseqs <- inseqs + length(fq) if (!is.null(orient.fwd)) { if (!C_isACGT(orient.fwd)) stop("Non-ACGT characters detected in orient.fwd") barlen <- nchar(orient.fwd) fq.rc <- reverseComplement(fq) keepF <- narrow(sread(fq), 1, barlen) == orient.fwd keepR <- narrow(sread(fq.rc), 1, barlen) == orient.fwd & !keepF fq <- ShortReadQ(sread = c(sread(fq[keepF]), sread(fq.rc[keepR])), quality = c(quality(quality(fq[keepF])), quality(quality(fq.rc[keepR]))), id = c(id(fq[keepF]), id(fq.rc[keepR]))) } if (is.finite(maxLen)) { fq <- fq[width(fq) <= maxLen] } fq <- fq[width(fq) >= start] fq <- narrow(fq, start = start, end = NA) if (trimRight > 0) { fq <- fq[width(fq) > trimRight] fq <- narrow(fq, start = NA, end = width(fq) - trimRight) } enc <- encoding(quality(fq)) if (is.numeric(truncQ)) { ind <- which(enc == truncQ) if (length(ind) != 1) stop("Encoding for this truncQ value not found.") truncQ <- names(enc)[[ind]] } if (length(fq) > 0) fq <- trimTails(fq, 1, truncQ) truncQ <- enc[truncQ] if (!is.na(end)) { fq <- fq[width(fq) >= end] } fq <- narrow(fq, start = 1, end = end) fq <- fq[width(fq) >= minLen] fq <- fq[nFilter(maxN)(fq)] keep <- rep(TRUE, length(fq)) qq <- as(quality(fq), "matrix") if (minQ > truncQ) keep <- keep & (apply(qq, 1, min, na.rm = TRUE) > minQ) if (maxEE < Inf) { keep <- keep & C_matrixEE(qq) <= maxEE } fq <- fq[keep] if (rm.phix) { is.phi <- isPhiX(as(sread(fq), "character"), ...) fq <- fq[!is.phi] } outseqs <- outseqs + length(fq) if (first) { writeFastq(fq, fout, "w", compress = compress) first = FALSE } else { writeFastq(fq, fout, "a", compress = compress) } } if (verbose) { outperc <- round(outseqs * 100/inseqs, 1) outperc <- paste(" (", outperc, "%)", sep = "") message("Read in ", inseqs, ", output ", outseqs, outperc, " filtered sequences.", sep = "") } if (outseqs == 0) { message(paste("The filter removed all reads:", fout, "not written.")) file.remove(fout) } return(invisible(c(reads.in = inseqs, reads.out = outseqs)))})(dots[[1L]][[1L]], dots[[2L]][[1L]], truncQ = 2L, truncLen = 250L, trimLeft = 0L, trimRight = 0, maxLen = Inf, minLen = 20, maxN = 0, minQ = 0, maxEE = 2, rm.phix = TRUE, orient.fwd = NULL, n = 1e+05, OMP = FALSE, compress = TRUE, verbose = FALSE)
9: .mapply(FUN, dots, MoreArgs)
10: FUN(X[[i]], ...)
11: lapply(X = S, FUN = FUN, ...)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
16: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
17: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
18: FUN(X[[i]], ...)
19: lapply(seq_len(cores), inner.do)
20: mclapply(seq_len(n), do_one, mc.preschedule = mc.preschedule, mc.set.seed = mc.set.seed, mc.silent = mc.silent, mc.cores = mc.cores, mc.cleanup = mc.cleanup, affinity.list = affinity.list)
21: mcmapply(fastqFilter, fwd, filt, MoreArgs = list(truncQ = truncQ, truncLen = truncLen, trimLeft = trimLeft, trimRight = trimRight, maxLen = maxLen, minLen = minLen, maxN = maxN, minQ = minQ, maxEE = maxEE, rm.phix = rm.phix, orient.fwd = orient.fwd, n = n, OMP = OMP, compress = compress, verbose = verbose), mc.cores = ncores, mc.silent = TRUE)
22: filterAndTrim(unfilts, filts, truncLen = truncLen, trimLeft = trimLeft, maxEE = maxEE, truncQ = truncQ, rm.phix = TRUE, multithread = multithread, maxLen = maxLen)
23: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
24: suppressWarnings(filterAndTrim(unfilts, filts, truncLen = truncLen, trimLeft = trimLeft, maxEE = maxEE, truncQ = truncQ, rm.phix = TRUE, multithread = multithread, maxLen = maxLen))
An irrecoverable exception occurred. R is aborting now ...
Bus error
I have attached my demux qzv for both single and paired to view as well. demux-paired-end.qzv (294.5 KB) demux-single-end.qzv (289.4 KB)
Perhaps I need to re-download and import my fastq.gz files from the IlluminaBase Space again?
Thank you for your help!
Hannah
