non-existent physical address', caught bus error.

Hi,

I ran dada2 with the command below and got the error:
Given error: address 0x2ac83afde87c, cause ‘non-existent physical address’, caught bus error.

I noticed from previous topics that this error would apparently be hardware, but I tested it running on both our cluster bridge machine and SLURM job and got the same error message. I also tested with test data (mockrobiota paired-end) and see the same error.

Could the error not be related to QIIME2 installation? Any suggestion?

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_paired.R /home/luiz.nunes/qiime2-tmp/tmpsd3k4xue/forward /home/luiz.nunes/qiime2-tmp/tmpsd3k4xue/reverse /home/luiz.nunes/qiime2-tmp/tmpsd3k4xue/output.tsv.biom /home/luiz.nunes/qiime2-tmp/tmpsd3k4xue/track.tsv /home/luiz.nunes/qiime2-tmp/tmpsd3k4xue/filt_f /home/luiz.nunes/qiime2-tmp/tmpsd3k4xue/filt_r 0 0 0 0 2.0 2.0 2 consensus 1.0 1 1000000

R version 3.5.1 (2018-07-02) 
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.2 / RcppParallel: 4.4.3 
1) Filtering 
 *** caught bus error ***
address 0x7ffffff7a210, cause 'non-existent physical address'

Traceback:
 1: isNamespace(ns)
 2: findHomeNS(name, frame, cntxt)
 3: nsName(findHomeNS(name, frame, cntxt))
 4: getInlineInfo(name, cntxt, guardOK = TRUE)
 5: tryInline(call, cb, cntxt)
 6: cmpCall(e, cb, cntxt)
 7: cmp(value, cb, ncntxt)
 8: cmpComplexAssign(symbol, lhs, value, superAssign, cb, cntxt)
 9: h(e, cb, cntxt)
10: tryInline(call, cb, cntxt)
11: cmpCall(e, cb, cntxt)
12: cmp(body, cb, lcntxt)
13: cmpForBody(callidx, body, ci, cb, cntxt)
14: h(e, cb, cntxt)
15: tryInline(call, cb, cntxt)
16: cmpCall(e, cb, cntxt)
17: cmp(subexp, cb, ncntxt, setloc = FALSE)
18: h(e, cb, cntxt)
19: tryInline(call, cb, cntxt)
20: cmpCall(e, cb, cntxt)
21: cmp(value, cb, ncntxt)
22: cmpSymbolAssign(symbol, value, superAssign, cb, cntxt)
23: h(e, cb, cntxt)
24: tryInline(call, cb, cntxt)
25: cmpCall(e, cb, cntxt)
26: cmp(subexp, cb, ncntxt, setloc = FALSE)
27: h(e, cb, cntxt)
28: tryInline(call, cb, cntxt)
29: cmpCall(e, cb, cntxt)
30: cmp(then.expr, cb, cntxt)
31: h(e, cb, cntxt)
32: tryInline(call, cb, cntxt)
33: cmpCall(e, cb, cntxt)
34: cmp(e, cb, cntxt, setloc = FALSE)
35: genCode(body(f), ncntxt, loc = loc)
36: cmpfun(f)
37: doTryCatch(return(expr), name, parentenv, handler)
38: tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: tryCatchList(expr, classes, parentenv, handlers)
40: tryCatch(cmpfun(f), error = function(e) {    notifyCompilerError(paste(e$message, "at", deparse(e$call)))    f})
41: compiler:::tryCmpfun(new("MethodDefinition", .Data = function (from,     to = "Vector", strict = TRUE) if (strict) {    from <- {        value <- new("IRanges")        for (what in c("start", "width", "NAMES", "elementType",         "elementMetadata", "metadata")) slot(value, what) <- slot(from,             what)        value    }    from} else from, target = new("signature", .Data = c("GroupedIRanges", "Vector"), names = c("from", "to"), package = c("XVector", "S4Vectors")), defined = new("signature", .Data = c("GroupedIRanges", "Vector"), names = c("from", "to"), package = c("XVector", "S4Vectors")), generic = "coerce"))
42: asMethod(object)
43: as(object, superClass)
44: .valid.Vector.length(x)
45: valid.func(object)
46: validityMethod(as(object, superClass))
47: isTRUE(x)
48: anyStrings(validityMethod(as(object, superClass)))
49: validObject(ans)
50: bindROWS(x_slot, slot_list)
51: bindROWS(x_slot, slot_list)
52: FUN(X[[i]], ...)
53: lapply(setNames(pslotnames, pslotnames), function(slotname) {    x_slot <- slot(x, slotname)    if (is.null(x_slot))         return(NULL)    slot_list <- lapply(objects, slot, slotname)    bindROWS(x_slot, slot_list)})
54: lapply(setNames(pslotnames, pslotnames), function(slotname) {    x_slot <- slot(x, slotname)    if (is.null(x_slot))         return(NULL)    slot_list <- lapply(objects, slot, slotname)    bindROWS(x_slot, slot_list)})
55: .nextMethod(x, objects, use.names = use.names, ignore.mcols = ignore.mcols,     check = FALSE)
56: eval(call, callEnv)
57: eval(call, callEnv)
58: callNextMethod(x, objects, use.names = use.names, ignore.mcols = ignore.mcols,     check = FALSE)
59: bindROWS(x, list(...), ignore.mcols = ignore.mcols)
60: bindROWS(x, list(...), ignore.mcols = ignore.mcols)
61: .local(x, ...)
62: .Primitive("c")(new("DNAStringSet", pool = new("SharedRaw_Pool",     xp_list = list(<pointer: (nil)>), .link_to_cached_object_list = list(        <environment>)), ranges = new("GroupedIRanges", group = 1L,     start = 1L, width = 5386L, NAMES = "phix", elementType = "ANY",     elementMetadata = NULL, metadata = list()), elementType = "DNAString",     elementMetadata = NULL, metadata = list()))
63: .Primitive("c")(new("DNAStringSet", pool = new("SharedRaw_Pool",     xp_list = list(<pointer: (nil)>), .link_to_cached_object_list = list(        <environment>)), ranges = new("GroupedIRanges", group = 1L,     start = 1L, width = 5386L, NAMES = "phix", elementType = "ANY",     elementMetadata = NULL, metadata = list()), elementType = "DNAString",     elementMetadata = NULL, metadata = list()))
64: do.call(c, FASTAlist)
65: do.call(c, FASTAlist)
66: readFasta(system.file("extdata", "phix_genome.fa", package = "dada2"))
67: readFasta(system.file("extdata", "phix_genome.fa", package = "dada2"))
68: sread(readFasta(system.file("extdata", "phix_genome.fa", package = "dada2")))
69: .class1(object)
70: as(sread(readFasta(system.file("extdata", "phix_genome.fa", package = "dada2"))),     "character")
71: isPhiX(as(sread(fqR), "character"), ...)
72: (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0,     0), maxLen = c(Inf, Inf), minLen = c(20, 20), trimLeft = c(0,     0), trimRight = c(0, 0), minQ = c(0, 0), maxEE = c(Inf, Inf),     rm.phix = c(TRUE, TRUE), matchIDs = FALSE, orient.fwd = NULL,     id.sep = "\\s", id.field = 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))    }    if (!is.character(fn) || length(fn) != 2)         stop("Two paired input file names required.")    if (!is.character(fout) || length(fout) != 2)         stop("Two paired output file names required.")    if (any(duplicated(c(fn, fout)))) {        stop("The output and input file names must be different.")    }    for (var in c("maxN", "truncQ", "truncLen", "maxLen", "minLen",         "trimLeft", "trimRight", "minQ", "maxEE", "rm.phix")) {        if (length(get(var)) == 1) {            assign(var, c(get(var), get(var)))        }        if (length(get(var)) != 2) {            stop(paste("Input variable", var, "must be length 1 or 2 (Forward, Reverse)."))        }    }    startF <- max(1, trimLeft[[1]] + 1, na.rm = TRUE)    startR <- max(1, trimLeft[[2]] + 1, na.rm = TRUE)    endF <- truncLen[[1]]    if (endF < startF) {        endF = NA    }    endF <- endF - startF + 1    endR <- truncLen[[2]]    if (endR < startR) {        endR = NA    }    endR <- endR - startR + 1    fF <- FastqStreamer(fn[[1]], n = n)    on.exit(close(fF))    fR <- FastqStreamer(fn[[2]], n = n)    on.exit(close(fR), add = TRUE)    if (file.exists(fout[[1]])) {        if (file.remove(fout[[1]])) {            if (verbose)                 message("Overwriting file:", fout[[1]])        }        else {            stop("Failed to overwrite file:", fout[[1]])        }    }    if (file.exists(fout[[2]])) {        if (file.remove(fout[[2]])) {            if (verbose)                 message("Overwriting file:", fout[[2]])        }        else {            stop("Failed to overwrite file:", fout[[2]])        }    }    first = TRUE    remainderF <- ShortReadQ()    remainderR <- ShortReadQ()    casava <- "Undetermined"    inseqs = 0    outseqs = 0    while (TRUE) {        suppressWarnings(fqF <- yield(fF))        suppressWarnings(fqR <- yield(fR))        if (length(fqF) == 0 && length(fqR) == 0) {            break        }        inseqs <- inseqs + length(fqF)        if (matchIDs) {            if (first) {                if (is.null(id.field)) {                  id1 <- as.character(id(fqF)[[1]])                  id.fields <- strsplit(id1, id.sep)[[1]]                  ncolon <- sapply(gregexpr(":", id.fields),                     length)                  ncoltab <- table(ncolon)                  if (max(ncolon) == 6 && ncoltab["6"] == 1) {                    casava <- "Current"                    id.field <- which(ncolon == 6)                  }                  else if (max(ncolon) == 4 && ncoltab["4"] ==                     1) {                    casava <- "Old"                    id.field <- which(ncolon == 4)                  }                  else {                    stop("Couldn't automatically detect the sequence identifier field in the fastq id string.")                  }                }            }            else {                fqF <- append(remainderF, fqF)                fqR <- append(remainderR, fqR)            }        }        else {            if (length(fqF) != length(fqR))                 stop("Mismatched forward and reverse sequence files: ",                   length(fqF), ", ", length(fqR), ".")        }        if (matchIDs) {            idsF <- sapply(strsplit(as.character(id(fqF)), id.sep),                 `[`, id.field)            idsR <- sapply(strsplit(as.character(id(fqR)), id.sep),                 `[`, id.field)            if (casava == "Old") {                idsF <- sapply(strsplit(idsF, "#"), `[`, 1)            }            lastF <- max(c(0, which(idsF %in% idsR)))            lastR <- max(c(0, which(idsR %in% idsF)))            if (lastF < length(fqF)) {                remainderF <- fqF[(lastF + 1):length(fqF)]            }            else {                remainderF <- ShortReadQ()            }            if (lastR < length(fqR)) {                remainderR <- fqR[(lastR + 1):length(fqR)]            }            else {                remainderR <- ShortReadQ()            }            fqF <- fqF[idsF %in% idsR]            fqR <- fqR[idsR %in% idsF]        }        if (!is.null(orient.fwd)) {            if (!C_isACGT(orient.fwd))                 stop("Non-ACGT characters detected in orient.fwd")            barlen <- nchar(orient.fwd)            keepF <- narrow(sread(fqF), 1, barlen) == orient.fwd            keepR <- (narrow(sread(fqR), 1, barlen) == orient.fwd) &                 !keepF            fq <- ShortReadQ(sread = c(sread(fqF[keepF]), sread(fqR[keepR])),                 quality = c(quality(quality(fqF[keepF])), quality(quality(fqR[keepR]))),                 id = c(id(fqF[keepF]), id(fqR[keepR])))            fqR <- ShortReadQ(sread = c(sread(fqR[keepF]), sread(fqF[keepR])),                 quality = c(quality(quality(fqR[keepF])), quality(quality(fqF[keepR]))),                 id = c(id(fqR[keepF]), id(fqF[keepR])))            fqF <- fq            rm(fq)        }        if (is.finite(maxLen[[1]]) || is.finite(maxLen[[2]])) {            keep <- width(fqF) <= maxLen[[1]] & width(fqR) <=                 maxLen[[2]]            fqF <- fqF[keep]            fqR <- fqR[keep]        }        keep <- (width(fqF) >= startF & width(fqR) >= startR)        fqF <- fqF[keep]        fqF <- narrow(fqF, start = startF, end = NA)        fqR <- fqR[keep]        fqR <- narrow(fqR, start = startR, end = NA)        if (trimRight[[1]] > 0) {            keep <- width(fqF) > trimRight[[1]]            fqF <- fqF[keep]            fqR <- fqR[keep]            fqF <- narrow(fqF, start = NA, end = width(fqF) -                 trimRight[[1]])        }        if (trimRight[[2]] > 0) {            keep <- width(fqR) > trimRight[[2]]            fqF <- fqF[keep]            fqR <- fqR[keep]            fqR <- narrow(fqR, start = NA, end = width(fqR) -                 trimRight[[2]])        }        encF <- encoding(quality(fqF))        encR <- encoding(quality(fqR))        if (is.numeric(truncQ)) {            indF <- which(encF == truncQ[[1]])            indR <- which(encR == truncQ[[2]])            if (!(length(indF) == 1 && length(indR) == 1))                 stop("Encoding for this truncQ value not found.")            truncQ <- c(names(encF)[[indF]], names(encR)[[indR]])        }        if (length(fqF) > 0) {            rngF <- trimTails(fqF, 1, truncQ[[1]], ranges = TRUE)            fqF <- narrow(fqF, 1, end(rngF))        }        if (length(fqR) > 0) {            rngR <- trimTails(fqR, 1, truncQ[[2]], ranges = TRUE)            fqR <- narrow(fqR, 1, end(rngR))        }        truncQ <- c(encF[truncQ[1]], encR[truncQ[2]])        keep <- (width(fqF) > 0 & width(fqR) > 0)        fqF <- fqF[keep]        fqR <- fqR[keep]        keep <- rep(TRUE, length(fqF))        if (!is.na(endF)) {            keep <- keep & (width(fqF) >= endF)        }        if (!is.na(endR)) {            keep <- keep & (width(fqR) >= endR)        }        fqF <- fqF[keep]        fqR <- fqR[keep]        fqF <- narrow(fqF, start = 1, end = endF)        fqR <- narrow(fqR, start = 1, end = endR)        keep <- width(fqF) >= minLen[[1]] & width(fqR) >= minLen[[2]]        fqF <- fqF[keep]        fqR <- fqR[keep]        suppressWarnings(keep <- nFilter(maxN[[1]])(fqF) & nFilter(maxN[[2]])(fqR))        fqF <- fqF[keep]        fqR <- fqR[keep]        keep <- rep(TRUE, length(fqF))        qmat <- as(quality(fqF), "matrix")        if (minQ[[1]] > truncQ[[1]])             suppressWarnings(keep <- keep & (apply(qmat, 1, min,                 na.rm = TRUE) > minQ[[1]]))        if (maxEE[[1]] < Inf)             keep <- keep & C_matrixEE(qmat) <= maxEE[[1]]        qmat <- as(quality(fqR), "matrix")        if (minQ[[2]] > truncQ[[2]])             suppressWarnings(keep <- keep & (apply(qmat, 1, min,                 na.rm = TRUE) > minQ[[2]]))        if (maxEE[[2]] < Inf)             keep <- keep & C_matrixEE(qmat) <= maxEE[[2]]        fqF <- fqF[keep]        fqR <- fqR[keep]        rm(qmat)        if (length(fqF) != length(fqR))             stop("Filtering caused mismatch between forward and reverse sequence lists: ",                 length(fqF), ", ", length(fqR), ".")        if (rm.phix[[1]] && rm.phix[[2]]) {            is.phi <- isPhiX(as(sread(fqF), "character"), ...)            is.phi <- is.phi | isPhiX(as(sread(fqR), "character"),                 ...)        }        else if (rm.phix[[1]] && !rm.phix[[2]]) {            is.phi <- isPhiX(as(sread(fqF), "character"), ...)        }        else if (!rm.phix[[1]] && rm.phix[[2]]) {            is.phi <- isPhiX(as(sread(fqR), "character"), ...)        }        if (any(rm.phix)) {            fqF <- fqF[!is.phi]            fqR <- fqR[!is.phi]        }        outseqs <- outseqs + length(fqF)        if (first) {            writeFastq(fqF, fout[[1]], "w", compress = compress)            writeFastq(fqR, fout[[2]], "w", compress = compress)            first = FALSE        }        else {            writeFastq(fqF, fout[[1]], "a", compress = compress)            writeFastq(fqR, fout[[2]], "a", compress = compress)        }    }    if (outseqs == 0) {    }    if (verbose) {        outperc <- round(outseqs * 100/inseqs, 1)        outperc <- paste(" (", outperc, "%)", sep = "")        message("Read in ", inseqs, " paired-sequences, output ",             outseqs, outperc, " filtered paired-sequences.",             sep = "")    }    if (outseqs == 0) {        message(paste("The filter removed all reads:", fout[[1]],             "and", fout[[2]], "not written."))        file.remove(fout[[1]])        file.remove(fout[[2]])    }    return(invisible(c(reads.in = inseqs, reads.out = outseqs)))})(dots[[1L]][[1L]], dots[[2L]][[1L]], truncQ = 2L, truncLen = c(0L, 0L), trimLeft = c(0L, 0L), trimRight = 0, maxLen = Inf, minLen = 20,     maxN = 0, minQ = 0, maxEE = c(2, 2), rm.phix = TRUE, orient.fwd = NULL,     matchIDs = FALSE, id.sep = "\\s", id.field = NULL, n = 1e+05,     OMP = TRUE, compress = TRUE, verbose = FALSE)
73: .mapply(FUN, dots, MoreArgs)
74: FUN(X[[i]], ...)
75: lapply(X = X, FUN = FUN, ...)
76: 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)
77: mcmapply(fastqPairedFilter, mapply(c, fwd, rev, SIMPLIFY = FALSE),     mapply(c, filt, filt.rev, SIMPLIFY = FALSE), 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,         matchIDs = matchIDs, id.sep = id.sep, id.field = id.field,         n = n, OMP = OMP, compress = compress, verbose = verbose),     mc.cores = ncores, mc.silent = TRUE)
78: filterAndTrim(unfiltsF, filtsF, unfiltsR, filtsR, truncLen = c(truncLenF,     truncLenR), trimLeft = c(trimLeftF, trimLeftR), maxEE = c(maxEEF,     maxEER), truncQ = truncQ, rm.phix = TRUE, multithread = multithread)
79: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
80: suppressWarnings(filterAndTrim(unfiltsF, filtsF, unfiltsR, filtsR,     truncLen = c(truncLenF, truncLenR), trimLeft = c(trimLeftF,         trimLeftR), maxEE = c(maxEEF, maxEER), truncQ = truncQ,     rm.phix = TRUE, multithread = multithread))
An irrecoverable exception occurred. R is aborting now ...
Traceback (most recent call last):
  File "/home/luiz.nunes/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 234, in denoise_paired
    run_commands([cmd])
  File "/home/luiz.nunes/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
    subprocess.run(cmd, check=True)
  File "/home/luiz.nunes/miniconda3/envs/qiime2-2019.7/lib/python3.6/subprocess.py", line 418, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/home/luiz.nunes/qiime2-tmp/tmpsd3k4xue/forward', '/home/luiz.nunes/qiime2-tmp/tmpsd3k4xue/reverse', '/home/luiz.nunes/qiime2-tmp/tmpsd3k4xue/output.tsv.biom', '/home/luiz.nunes/qiime2-tmp/tmpsd3k4xue/track.tsv', '/home/luiz.nunes/qiime2-tmp/tmpsd3k4xue/filt_f', '/home/luiz.nunes/qiime2-tmp/tmpsd3k4xue/filt_r', '0', '0', '0', '0', '2.0', '2.0', '2', 'consensus', '1.0', '1', '1000000']' died with <Signals.SIGBUS: 7>.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/luiz.nunes/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py", line 327, in __call__
    results = action(**arguments)
  File "</home/luiz.nunes/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-465>", line 2, in denoise_paired
  File "/home/luiz.nunes/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
    output_types, provenance)
  File "/home/luiz.nunes/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/home/luiz.nunes/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 249, in denoise_paired
    " and stderr to learn more." % e.returncode)
Exception: An error was encountered while running DADA2 in R (return code -7), please inspect stdout and stderr to learn more.

I am seeing the error caught bus error ***
address 0x7ffffff7a210, cause ‘non-existent physical address’ in denoise step. I found that the error only occurs when I perform this step by paired-end, not seeing the error in single-end:

(qiime2-2019.7) menegidio @ Cthulhu: $ qiime dada2 denoise-paired --i-demultiplexed-seqs demux-trimmed.qza --p-trunc-len-f 160 --p-trunc-len-r 160 --o -representative-sequences dada2-paired-end-rep-seqs.qza --o-table dada2-paired-end-table.qza --o-denoising-stats dada2-paired-end-stats.qza
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.

*(qiime2-2019.7) menegidio @ Cthulhu: $ qiime dada2 denoise-single *
*> --i-demultiplexed-seqs demux-trimmed.qza *
*> --p-trim-left 13 *
*> --p-trunc-len 160 *
*> --o-representative-sequences dada2-single-end-rep-seqs.qza *
*> --o-table dada2-single-end-table.qza *
> --o-denoising-stats dada2-single-end-stats.qza
Saved FeatureTable [Frequency] to: dada2-single-end-table.qza
Saved FeatureData [Sequence] to: dada2-single-end-rep-seqs.qza
Saved SampleData [DADA2Stats] to: dada2-single-end-stats.qza

Hello @fabianomenegidio,

Welcome to the Qiime 2, forums! :qiime2:

I'm glad that denoise-single is working well. I've not see the 'non-existent physical address' error before, but I think Evan has some advice in this thread:

Does that help? Have you tried rerunning that command and see if it just happens to work the second time?

Colin

I checked the topics that say the problem could be hardware related. The problem is that the same is true of the HPC, the HPC proxy machine, and my notebook, which would be very coincidental.

R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-conda_cos6-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> .libPaths()
[1] "/home/luiz.nunes/miniconda3/envs/qiime2-2019.7/lib/R/library"
> 
>

I agree!

I wonder if this strange error is simply your system running out of RAM. How large (in gigabytes) are your compressed fastq input files? How much RAM/Memory does your system have?

Colin

Notebook: 16GB
Proxy Server: 32GB
HPC: 120Gb allocate

Data in qza: ~ 4GB

16 GB of ram for 4 GB in input data seems OK.

I wonder if the HPC disk drive allocation might be running low. What happens if you use up your full 120 GB?

Have you tried running it again and seeing how well it works?

Colin

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.