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Question: ShortRead error when reading BAM file
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gravatar for Alex Gutteridge
7.1 years ago by
United States
Alex Gutteridge650 wrote:
I'm trying to load a BAM file generated by Mosaik using ShortRead, but I'm getting the following error: > aln.bam = > readAligned("data/ALIGNMENT/A430001.1.samtools.bam",type="BAM") Error: Input/Output 'readAligned' failed to parse files dirPath: 'data/ALIGNMENT/A430001.1.samtools.bam' pattern: '' type: 'BAM' error: INTEGER() can only be applied to a 'integer', not a 'symbol' > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ShortRead_1.8.1 Rsamtools_1.2.3 lattice_0.19-13 [4] Biostrings_2.18.0 GenomicRanges_1.2.1 IRanges_1.8.2 loaded via a namespace (and not attached): [1] Biobase_2.10.0 grid_2.12.0 hwriter_1.2 tools_2.12.0 I ran samtools from the command-line over the original Mosiak BAM file and it completed fine: samtools view -b A430001.1.bam > A430001.1.samtools.bam but I get the above error on both the Mosaik original and samtools processed BAM file. I also tried the debug suggested here: https://stat.ethz.ch/pipermail/bioconductor/2010-October/035745.html but it segfaulted: > param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE, + what = ShortRead:::.readAligned_bamWhat()) > > res = scanBam('data/ALIGNMENT/A430001.1.samtools.bam', param=param) *** caught segfault *** address (nil), cause 'unknown' Traceback: 1: .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...) 2: .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = param) 3: scanBam("data/ALIGNMENT/A430001.1.samtools.bam", param = param) 4: scanBam("data/ALIGNMENT/A430001.1.samtools.bam", param = param) Any suggestions to debug the file would be gratefully accepted. -- Alex Gutteridge
ADD COMMENTlink modified 7.1 years ago by Martin Morgan ♦♦ 22k • written 7.1 years ago by Alex Gutteridge650
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gravatar for Martin Morgan
7.1 years ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:
On 09/15/2011 02:35 AM, Alex Gutteridge wrote: > I'm trying to load a BAM file generated by Mosaik using ShortRead, but > I'm getting the following error: > >> aln.bam = readAligned("data/ALIGNMENT/A430001.1.samtools.bam",type="BAM") > Error: Input/Output > 'readAligned' failed to parse files > dirPath: 'data/ALIGNMENT/A430001.1.samtools.bam' > pattern: '' > type: 'BAM' > error: INTEGER() can only be applied to a 'integer', not a 'symbol' >> sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ShortRead_1.8.1 Rsamtools_1.2.3 lattice_0.19-13 > [4] Biostrings_2.18.0 GenomicRanges_1.2.1 IRanges_1.8.2 > > loaded via a namespace (and not attached): > [1] Biobase_2.10.0 grid_2.12.0 hwriter_1.2 tools_2.12.0 > > I ran samtools from the command-line over the original Mosiak BAM file > and it completed fine: > > samtools view -b A430001.1.bam > A430001.1.samtools.bam > > but I get the above error on both the Mosaik original and samtools > processed BAM file. > > I also tried the debug suggested here: > https://stat.ethz.ch/pipermail/bioconductor/2010-October/035745.html but > it segfaulted: > >> param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE, > + what = ShortRead:::.readAligned_bamWhat()) >> >> res = scanBam('data/ALIGNMENT/A430001.1.samtools.bam', param=param) > > *** caught segfault *** > address (nil), cause 'unknown' > > Traceback: > 1: .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...) > 2: .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = param) > 3: scanBam("data/ALIGNMENT/A430001.1.samtools.bam", param = param) > 4: scanBam("data/ALIGNMENT/A430001.1.samtools.bam", param = param) > > Any suggestions to debug the file would be gratefully accepted. Hi Alex -- I'd stick with param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE, what = ShortRead:::.readAligned_bamWhat()) res = scanBam('data/ALIGNMENT/A430001.1.samtools.bam', param=param) as the starting point for debugging. My first suggestion is to update R to R-2-13.1, install Rsamtools, and try again. The next is more complicated, but not to bad. Start R with the 'gdb' debugger, provoke the error, and then find where the error occurred. It'll look some thing like R -d gdb gdb> run ... > ## now at the R prompt, do what you need to segfault ... gdb> where you'll have to type the 'run' and 'where' commands; 'where' will generate a backtrace, and if you could forward that to me (e.g., copy / paste) that would be great. Martin -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD COMMENTlink written 7.1 years ago by Martin Morgan ♦♦ 22k
On Thu, 15 Sep 2011 06:19:29 -0700, Martin Morgan wrote: > On 09/15/2011 02:35 AM, Alex Gutteridge wrote: >> I'm trying to load a BAM file generated by Mosaik using ShortRead, >> but >> I'm getting the following error: >> >>> aln.bam = >>> readAligned("data/ALIGNMENT/A430001.1.samtools.bam",type="BAM") >> Error: Input/Output >> 'readAligned' failed to parse files >> dirPath: 'data/ALIGNMENT/A430001.1.samtools.bam' >> pattern: '' >> type: 'BAM' >> error: INTEGER() can only be applied to a 'integer', not a 'symbol' >>> sessionInfo() >> R version 2.12.0 (2010-10-15) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] ShortRead_1.8.1 Rsamtools_1.2.3 lattice_0.19-13 >> [4] Biostrings_2.18.0 GenomicRanges_1.2.1 IRanges_1.8.2 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.10.0 grid_2.12.0 hwriter_1.2 tools_2.12.0 >> >> I ran samtools from the command-line over the original Mosiak BAM >> file >> and it completed fine: >> >> samtools view -b A430001.1.bam > A430001.1.samtools.bam >> >> but I get the above error on both the Mosaik original and samtools >> processed BAM file. >> >> I also tried the debug suggested here: >> https://stat.ethz.ch/pipermail/bioconductor/2010-October/035745.html >> but >> it segfaulted: >> >>> param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE, >> + what = ShortRead:::.readAligned_bamWhat()) >>> >>> res = scanBam('data/ALIGNMENT/A430001.1.samtools.bam', param=param) >> >> *** caught segfault *** >> address (nil), cause 'unknown' >> >> Traceback: >> 1: .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...) >> 2: .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = >> param) >> 3: scanBam("data/ALIGNMENT/A430001.1.samtools.bam", param = param) >> 4: scanBam("data/ALIGNMENT/A430001.1.samtools.bam", param = param) >> >> Any suggestions to debug the file would be gratefully accepted. > > Hi Alex -- > > I'd stick with > > param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE, > what = ShortRead:::.readAligned_bamWhat()) > res = scanBam('data/ALIGNMENT/A430001.1.samtools.bam', param=param) > > as the starting point for debugging. > > My first suggestion is to update R to R-2-13.1, install Rsamtools, > and try again. > > The next is more complicated, but not to bad. Start R with the 'gdb' > debugger, provoke the error, and then find where the error occurred. > It'll look some thing like > > R -d gdb > gdb> run > ... > > ## now at the R prompt, do what you need to segfault > ... > gdb> where > > you'll have to type the 'run' and 'where' commands; 'where' will > generate a backtrace, and if you could forward that to me (e.g., copy > / paste) that would be great. > > Martin Hi Martin, Slightly different traceback with latest version, but essentially the same: > library(ShortRead) Loading required package: IRanges Attaching package: 'IRanges' The following object(s) are masked from 'package:base': cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, setdiff, table, union Loading required package: GenomicRanges Loading required package: Biostrings Loading required package: lattice Loading required package: Rsamtools > aln = readAligned("data/ALIGNMENT/A430001.1.bam",type="BAM") Error: Input/Output 'readAligned' failed to parse files dirPath: 'data/ALIGNMENT/A430001.1.bam' pattern: '' type: 'BAM' error: INTEGER() can only be applied to a 'integer', not a 'symbol' file: data/ALIGNMENT/A430001.1.bam > param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE, + what = ShortRead:::.readAligned_bamWhat()) > res = scanBam('data/ALIGNMENT/A430001.1.samtools.bam', param=param) *** caught segfault *** address (nil), cause 'unknown' Traceback: 1: .Call(func, .extptr(file), space, flag, simpleCigar, ...) 2: doTryCatch(return(expr), name, parentenv, handler) 3: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4: tryCatchList(expr, classes, parentenv, handlers) 5: tryCatch({ .Call(func, .extptr(file), space, flag, simpleCigar, ...)}, error = function(err) { stop(conditionMessage(err), "\n file: ", path(file))}) 6: .io_bam(.scan_bamfile, file, param = param, path(file), index(file), "rb", reverseComplement, tmpl) 7: scanBam(bam, param = param) 8: scanBam(bam, param = param) 9: eval(expr, envir, enclos) 10: eval(call, sys.frame(sys.parent())) 11: callGeneric(bam, ..., param = param) 12: scanBam("data/ALIGNMENT/A430001.1.samtools.bam", param = param) 13: scanBam("data/ALIGNMENT/A430001.1.samtools.bam", param = param) ############### > sessionInfo() R version 2.13.1 (2011-07-08) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ShortRead_1.10.4 Rsamtools_1.4.3 lattice_0.19-30 [4] Biostrings_2.20.3 GenomicRanges_1.4.8 IRanges_1.10.6 loaded via a namespace (and not attached): [1] Biobase_2.12.2 grid_2.13.1 hwriter_1.3 ########### Here is the result of segfaulting under gdb: ######### Program received signal SIGSEGV, Segmentation fault. R_gc_internal (size_needed=0) at memory.c:1427 1427 SEXP next = NEXT_NODE(s); (gdb) where #0 R_gc_internal (size_needed=0) at memory.c:1427 #1 0x000000000041e7f3 in Rf_cons (car=0x1bf38af0, cdr=0x163ef338) at memory.c:2083 #2 0x0000000000555780 in Rf_evalList (el=0x1be8f6e0, rho=0x1c31a7a0, call=0x1be8f6a8, n=1) at eval.c:1836 #3 0x0000000000554a17 in Rf_eval (e=0x1be8f6a8, rho=0x1c31a7a0) at eval.c:501 #4 0x0000000000555580 in Rf_evalListKeepMissing (el=0x1c31a2f0, rho=0x1c31a7a0) at eval.c:1900 #5 0x0000000000555ba5 in Rf_DispatchOrEval (call=0x1c31a360, op=0x1640f938, generic=0x616594 "[<-", args=0x1c31a328, rho=0x1c31a7a0, ans=0x7fff256b5858, dropmissing=0, argsevald=0) at eval.c:2381 #6 0x000000000048f300 in do_subassign (call=0x0, op=0x8d1d78, args=0x5443474741544747, rho=0x1c31a7a0) at subassign.c:1313 #7 0x0000000000554981 in Rf_eval (e=0x1c31a360, rho=0x1c31a7a0) at eval.c:482 #8 0x0000000000557324 in do_set (call=0x1c31a408, op=0x1640e788, args=0x1c31a3d0, rho=0x1c31a7a0) at eval.c:1722 #9 0x0000000000554981 in Rf_eval (e=0x1c31a408, rho=0x1c31a7a0) at eval.c:482 #10 0x0000000000556c84 in applydefine (call=<value optimized="" out="">, op=0x1640e788, args=<value optimized="" out="">, rho=0x1c31a7a0) at eval.c:1678 #11 0x0000000000554981 in Rf_eval (e=0x1be8f590, rho=0x1c31a7a0) at eval.c:482 #12 0x00000000005560ee in do_begin (call=0x1be8f360, op=0x1640e590, args=0x5443474741544747, rho=0x1c31a7a0) at eval.c:1420 #13 0x0000000000554981 in Rf_eval (e=0x1be8f360, rho=0x1c31a7a0) at eval.c:482 -- Alex Gutteridge
ADD REPLYlink written 7.1 years ago by Alex Gutteridge650
Hi Alex -- Unfortunately, not informative; it looks like the call has completed but corrupted memory in the process. Any chance of a small data set, e.g., using samtools to select a portion of the file? Along the lines of samtools view -b A430001.1.bam chr1:1-1000000 > A430001.1.subset.bam Or is there a reference MOSAIK output file somewhere that I can access? Also, does specifying 'which' help, e.g., param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE, what = ShortRead:::.readAligned_bamWhat(), which=GRanges("chr1", IRanges(1, 100000))) And if you're being indulgent and none of the above point to the problem / are doable, create a file ~/.R/Makevars with CFLAGS += -g O0 -Dinline="" (that's the letter O and the number zero) and reinstalling Rsamtools (this'll compile without any C optimizations) then R -d valgrind -f test.R looking for output that says 'invalid read' or 'invalid write'. Thanks for working with me on this. Martin On 09/16/2011 03:36 AM, Alex Gutteridge wrote: > On Thu, 15 Sep 2011 06:19:29 -0700, Martin Morgan wrote: >> On 09/15/2011 02:35 AM, Alex Gutteridge wrote: >>> I'm trying to load a BAM file generated by Mosaik using ShortRead, but >>> I'm getting the following error: >>> >>>> aln.bam = >>>> readAligned("data/ALIGNMENT/A430001.1.samtools.bam",type="BAM") >>> Error: Input/Output >>> 'readAligned' failed to parse files >>> dirPath: 'data/ALIGNMENT/A430001.1.samtools.bam' >>> pattern: '' >>> type: 'BAM' >>> error: INTEGER() can only be applied to a 'integer', not a 'symbol' >>>> sessionInfo() >>> R version 2.12.0 (2010-10-15) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] ShortRead_1.8.1 Rsamtools_1.2.3 lattice_0.19-13 >>> [4] Biostrings_2.18.0 GenomicRanges_1.2.1 IRanges_1.8.2 >>> >>> loaded via a namespace (and not attached): >>> [1] Biobase_2.10.0 grid_2.12.0 hwriter_1.2 tools_2.12.0 >>> >>> I ran samtools from the command-line over the original Mosiak BAM file >>> and it completed fine: >>> >>> samtools view -b A430001.1.bam > A430001.1.samtools.bam >>> >>> but I get the above error on both the Mosaik original and samtools >>> processed BAM file. >>> >>> I also tried the debug suggested here: >>> https://stat.ethz.ch/pipermail/bioconductor/2010-October/035745.html but >>> it segfaulted: >>> >>>> param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE, >>> + what = ShortRead:::.readAligned_bamWhat()) >>>> >>>> res = scanBam('data/ALIGNMENT/A430001.1.samtools.bam', param=param) >>> >>> *** caught segfault *** >>> address (nil), cause 'unknown' >>> >>> Traceback: >>> 1: .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...) >>> 2: .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = >>> param) >>> 3: scanBam("data/ALIGNMENT/A430001.1.samtools.bam", param = param) >>> 4: scanBam("data/ALIGNMENT/A430001.1.samtools.bam", param = param) >>> >>> Any suggestions to debug the file would be gratefully accepted. >> >> Hi Alex -- >> >> I'd stick with >> >> param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE, >> what = ShortRead:::.readAligned_bamWhat()) >> res = scanBam('data/ALIGNMENT/A430001.1.samtools.bam', param=param) >> >> as the starting point for debugging. >> >> My first suggestion is to update R to R-2-13.1, install Rsamtools, >> and try again. >> >> The next is more complicated, but not to bad. Start R with the 'gdb' >> debugger, provoke the error, and then find where the error occurred. >> It'll look some thing like >> >> R -d gdb >> gdb> run >> ... >> > ## now at the R prompt, do what you need to segfault >> ... >> gdb> where >> >> you'll have to type the 'run' and 'where' commands; 'where' will >> generate a backtrace, and if you could forward that to me (e.g., copy >> / paste) that would be great. >> >> Martin > > Hi Martin, > > Slightly different traceback with latest version, but essentially the same: > >> library(ShortRead) > Loading required package: IRanges > > Attaching package: 'IRanges' > > The following object(s) are masked from 'package:base': > > cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, > pmin, pmin.int, rbind, rep.int, setdiff, table, union > > Loading required package: GenomicRanges > Loading required package: Biostrings > Loading required package: lattice > Loading required package: Rsamtools >> aln = readAligned("data/ALIGNMENT/A430001.1.bam",type="BAM") > Error: Input/Output > 'readAligned' failed to parse files > dirPath: 'data/ALIGNMENT/A430001.1.bam' > pattern: '' > type: 'BAM' > error: INTEGER() can only be applied to a 'integer', not a 'symbol' > file: data/ALIGNMENT/A430001.1.bam >> param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE, > + what = ShortRead:::.readAligned_bamWhat()) >> res = scanBam('data/ALIGNMENT/A430001.1.samtools.bam', param=param) > *** caught segfault *** > address (nil), cause 'unknown' > > Traceback: > 1: .Call(func, .extptr(file), space, flag, simpleCigar, ...) > 2: doTryCatch(return(expr), name, parentenv, handler) > 3: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > 4: tryCatchList(expr, classes, parentenv, handlers) > 5: tryCatch({ .Call(func, .extptr(file), space, flag, simpleCigar, > ...)}, error = function(err) { stop(conditionMessage(err), "\n file: ", > path(file))}) > 6: .io_bam(.scan_bamfile, file, param = param, path(file), index(file), > "rb", reverseComplement, tmpl) > 7: scanBam(bam, param = param) > 8: scanBam(bam, param = param) > 9: eval(expr, envir, enclos) > 10: eval(call, sys.frame(sys.parent())) > 11: callGeneric(bam, ..., param = param) > 12: scanBam("data/ALIGNMENT/A430001.1.samtools.bam", param = param) > 13: scanBam("data/ALIGNMENT/A430001.1.samtools.bam", param = param) > > ############### > >> sessionInfo() > R version 2.13.1 (2011-07-08) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ShortRead_1.10.4 Rsamtools_1.4.3 lattice_0.19-30 > [4] Biostrings_2.20.3 GenomicRanges_1.4.8 IRanges_1.10.6 > > loaded via a namespace (and not attached): > [1] Biobase_2.12.2 grid_2.13.1 hwriter_1.3 > > ########### > > Here is the result of segfaulting under gdb: > > ######### > > Program received signal SIGSEGV, Segmentation fault. > R_gc_internal (size_needed=0) at memory.c:1427 > 1427 SEXP next = NEXT_NODE(s); > (gdb) where > #0 R_gc_internal (size_needed=0) at memory.c:1427 > #1 0x000000000041e7f3 in Rf_cons (car=0x1bf38af0, cdr=0x163ef338) > at memory.c:2083 > #2 0x0000000000555780 in Rf_evalList (el=0x1be8f6e0, rho=0x1c31a7a0, > call=0x1be8f6a8, n=1) at eval.c:1836 > #3 0x0000000000554a17 in Rf_eval (e=0x1be8f6a8, rho=0x1c31a7a0) at > eval.c:501 > #4 0x0000000000555580 in Rf_evalListKeepMissing (el=0x1c31a2f0, > rho=0x1c31a7a0) at eval.c:1900 > #5 0x0000000000555ba5 in Rf_DispatchOrEval (call=0x1c31a360, op=0x1640f938, > generic=0x616594 "[<-", args=0x1c31a328, rho=0x1c31a7a0, > ans=0x7fff256b5858, dropmissing=0, argsevald=0) at eval.c:2381 > #6 0x000000000048f300 in do_subassign (call=0x0, op=0x8d1d78, > args=0x5443474741544747, rho=0x1c31a7a0) at subassign.c:1313 > #7 0x0000000000554981 in Rf_eval (e=0x1c31a360, rho=0x1c31a7a0) at > eval.c:482 > #8 0x0000000000557324 in do_set (call=0x1c31a408, op=0x1640e788, > args=0x1c31a3d0, rho=0x1c31a7a0) at eval.c:1722 > #9 0x0000000000554981 in Rf_eval (e=0x1c31a408, rho=0x1c31a7a0) at > eval.c:482 > #10 0x0000000000556c84 in applydefine (call=<value optimized="" out="">, > op=0x1640e788, args=<value optimized="" out="">, rho=0x1c31a7a0) at eval.c:1678 > #11 0x0000000000554981 in Rf_eval (e=0x1be8f590, rho=0x1c31a7a0) at > eval.c:482 > #12 0x00000000005560ee in do_begin (call=0x1be8f360, op=0x1640e590, > args=0x5443474741544747, rho=0x1c31a7a0) at eval.c:1420 > #13 0x0000000000554981 in Rf_eval (e=0x1be8f360, rho=0x1c31a7a0) at > eval.c:482 > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD REPLYlink written 7.1 years ago by Martin Morgan ♦♦ 22k
Hi Martin, Just to update on this, I tried your first suggestion and lo and behold the smaller BAM file loaded fine. I'm now going through each chromosome of the larger BAM to see if I can narrow down where the issue is. The original BAM is ~2.7GB in size, I assume the error couldn't simply be a function of that? Alex Gutteridge On Fri, 16 Sep 2011 06:43:51 -0700, Martin Morgan wrote: > Hi Alex -- > > Unfortunately, not informative; it looks like the call has completed > but corrupted memory in the process. > > Any chance of a small data set, e.g., using samtools to select a > portion of the file? Along the lines of > > samtools view -b A430001.1.bam chr1:1-1000000 > > A430001.1.subset.bam > > Or is there a reference MOSAIK output file somewhere that I can > access? > > Also, does specifying 'which' help, e.g., > > param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE, > what = ShortRead:::.readAligned_bamWhat(), > which=GRanges("chr1", IRanges(1, 100000))) > > And if you're being indulgent and none of the above point to the > problem / are doable, create a file ~/.R/Makevars with > > CFLAGS += -g O0 -Dinline="" > > (that's the letter O and the number zero) and reinstalling Rsamtools > (this'll compile without any C optimizations) then > > R -d valgrind -f test.R > > looking for output that says 'invalid read' or 'invalid write'. > Thanks for working with me on this. > > Martin > > On 09/16/2011 03:36 AM, Alex Gutteridge wrote: >> On Thu, 15 Sep 2011 06:19:29 -0700, Martin Morgan wrote: >>> On 09/15/2011 02:35 AM, Alex Gutteridge wrote: >>>> I'm trying to load a BAM file generated by Mosaik using ShortRead, >>>> but >>>> I'm getting the following error: >>>> >>>>> aln.bam = >>>>> readAligned("data/ALIGNMENT/A430001.1.samtools.bam",type="BAM") >>>> Error: Input/Output >>>> 'readAligned' failed to parse files >>>> dirPath: 'data/ALIGNMENT/A430001.1.samtools.bam' >>>> pattern: '' >>>> type: 'BAM' >>>> error: INTEGER() can only be applied to a 'integer', not a >>>> 'symbol' >>>>> sessionInfo() >>>> R version 2.12.0 (2010-10-15) >>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>> >>>> locale: >>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] ShortRead_1.8.1 Rsamtools_1.2.3 lattice_0.19-13 >>>> [4] Biostrings_2.18.0 GenomicRanges_1.2.1 IRanges_1.8.2 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] Biobase_2.10.0 grid_2.12.0 hwriter_1.2 tools_2.12.0 >>>> >>>> I ran samtools from the command-line over the original Mosiak BAM >>>> file >>>> and it completed fine: >>>> >>>> samtools view -b A430001.1.bam > A430001.1.samtools.bam >>>> >>>> but I get the above error on both the Mosaik original and samtools >>>> processed BAM file. >>>> >>>> I also tried the debug suggested here: >>>> >>>> https://stat.ethz.ch/pipermail/bioconductor/2010-October/035745.html >>>> but >>>> it segfaulted: >>>> >>>>> param = ScanBamParam(simpleCigar = TRUE, reverseComplement = >>>>> TRUE, >>>> + what = ShortRead:::.readAligned_bamWhat()) >>>>> >>>>> res = scanBam('data/ALIGNMENT/A430001.1.samtools.bam', >>>>> param=param) >>>> >>>> *** caught segfault *** >>>> address (nil), cause 'unknown' >>>> >>>> Traceback: >>>> 1: .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...) >>>> 2: .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param >>>> = >>>> param) >>>> 3: scanBam("data/ALIGNMENT/A430001.1.samtools.bam", param = param) >>>> 4: scanBam("data/ALIGNMENT/A430001.1.samtools.bam", param = param) >>>> >>>> Any suggestions to debug the file would be gratefully accepted. >>> >>> Hi Alex -- >>> >>> I'd stick with >>> >>> param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE, >>> what = ShortRead:::.readAligned_bamWhat()) >>> res = scanBam('data/ALIGNMENT/A430001.1.samtools.bam', param=param) >>> >>> as the starting point for debugging. >>> >>> My first suggestion is to update R to R-2-13.1, install Rsamtools, >>> and try again. >>> >>> The next is more complicated, but not to bad. Start R with the >>> 'gdb' >>> debugger, provoke the error, and then find where the error >>> occurred. >>> It'll look some thing like >>> >>> R -d gdb >>> gdb> run >>> ... >>> > ## now at the R prompt, do what you need to segfault >>> ... >>> gdb> where >>> >>> you'll have to type the 'run' and 'where' commands; 'where' will >>> generate a backtrace, and if you could forward that to me (e.g., >>> copy >>> / paste) that would be great. >>> >>> Martin >> >> Hi Martin, >> >> Slightly different traceback with latest version, but essentially >> the same: >> >>> library(ShortRead) >> Loading required package: IRanges >> >> Attaching package: 'IRanges' >> >> The following object(s) are masked from 'package:base': >> >> cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, >> pmin, pmin.int, rbind, rep.int, setdiff, table, union >> >> Loading required package: GenomicRanges >> Loading required package: Biostrings >> Loading required package: lattice >> Loading required package: Rsamtools >>> aln = readAligned("data/ALIGNMENT/A430001.1.bam",type="BAM") >> Error: Input/Output >> 'readAligned' failed to parse files >> dirPath: 'data/ALIGNMENT/A430001.1.bam' >> pattern: '' >> type: 'BAM' >> error: INTEGER() can only be applied to a 'integer', not a 'symbol' >> file: data/ALIGNMENT/A430001.1.bam >>> param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE, >> + what = ShortRead:::.readAligned_bamWhat()) >>> res = scanBam('data/ALIGNMENT/A430001.1.samtools.bam', param=param) >> *** caught segfault *** >> address (nil), cause 'unknown' >> >> Traceback: >> 1: .Call(func, .extptr(file), space, flag, simpleCigar, ...) >> 2: doTryCatch(return(expr), name, parentenv, handler) >> 3: tryCatchOne(expr, names, parentenv, handlers[[1L]]) >> 4: tryCatchList(expr, classes, parentenv, handlers) >> 5: tryCatch({ .Call(func, .extptr(file), space, flag, simpleCigar, >> ...)}, error = function(err) { stop(conditionMessage(err), "\n file: >> ", >> path(file))}) >> 6: .io_bam(.scan_bamfile, file, param = param, path(file), >> index(file), >> "rb", reverseComplement, tmpl) >> 7: scanBam(bam, param = param) >> 8: scanBam(bam, param = param) >> 9: eval(expr, envir, enclos) >> 10: eval(call, sys.frame(sys.parent())) >> 11: callGeneric(bam, ..., param = param) >> 12: scanBam("data/ALIGNMENT/A430001.1.samtools.bam", param = param) >> 13: scanBam("data/ALIGNMENT/A430001.1.samtools.bam", param = param) >> >> ############### >> >>> sessionInfo() >> R version 2.13.1 (2011-07-08) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] ShortRead_1.10.4 Rsamtools_1.4.3 lattice_0.19-30 >> [4] Biostrings_2.20.3 GenomicRanges_1.4.8 IRanges_1.10.6 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.12.2 grid_2.13.1 hwriter_1.3 >> >> ########### >> >> Here is the result of segfaulting under gdb: >> >> ######### >> >> Program received signal SIGSEGV, Segmentation fault. >> R_gc_internal (size_needed=0) at memory.c:1427 >> 1427 SEXP next = NEXT_NODE(s); >> (gdb) where >> #0 R_gc_internal (size_needed=0) at memory.c:1427 >> #1 0x000000000041e7f3 in Rf_cons (car=0x1bf38af0, cdr=0x163ef338) >> at memory.c:2083 >> #2 0x0000000000555780 in Rf_evalList (el=0x1be8f6e0, rho=0x1c31a7a0, >> call=0x1be8f6a8, n=1) at eval.c:1836 >> #3 0x0000000000554a17 in Rf_eval (e=0x1be8f6a8, rho=0x1c31a7a0) at >> eval.c:501 >> #4 0x0000000000555580 in Rf_evalListKeepMissing (el=0x1c31a2f0, >> rho=0x1c31a7a0) at eval.c:1900 >> #5 0x0000000000555ba5 in Rf_DispatchOrEval (call=0x1c31a360, >> op=0x1640f938, >> generic=0x616594 "[<-", args=0x1c31a328, rho=0x1c31a7a0, >> ans=0x7fff256b5858, dropmissing=0, argsevald=0) at eval.c:2381 >> #6 0x000000000048f300 in do_subassign (call=0x0, op=0x8d1d78, >> args=0x5443474741544747, rho=0x1c31a7a0) at subassign.c:1313 >> #7 0x0000000000554981 in Rf_eval (e=0x1c31a360, rho=0x1c31a7a0) at >> eval.c:482 >> #8 0x0000000000557324 in do_set (call=0x1c31a408, op=0x1640e788, >> args=0x1c31a3d0, rho=0x1c31a7a0) at eval.c:1722 >> #9 0x0000000000554981 in Rf_eval (e=0x1c31a408, rho=0x1c31a7a0) at >> eval.c:482 >> #10 0x0000000000556c84 in applydefine (call=<value optimized="" out="">, >> op=0x1640e788, args=<value optimized="" out="">, rho=0x1c31a7a0) at >> eval.c:1678 >> #11 0x0000000000554981 in Rf_eval (e=0x1be8f590, rho=0x1c31a7a0) at >> eval.c:482 >> #12 0x00000000005560ee in do_begin (call=0x1be8f360, op=0x1640e590, >> args=0x5443474741544747, rho=0x1c31a7a0) at eval.c:1420 >> #13 0x0000000000554981 in Rf_eval (e=0x1be8f360, rho=0x1c31a7a0) at >> eval.c:482 >> -- Alex Gutteridge
ADD REPLYlink written 7.1 years ago by Alex Gutteridge650
On 09/19/2011 05:11 AM, Alex Gutteridge wrote: > Hi Martin, > > Just to update on this, I tried your first suggestion and lo and behold > the smaller BAM file loaded fine. I'm now going through each chromosome > of the larger BAM to see if I can narrow down where the issue is. The > original BAM is ~2.7GB in size, I assume the error couldn't simply be a > function of that? Overall size could be a factor (how much memory do you have?) but the error message is saying that the source code isn't handling this situation (and probably others) appropriately, i.e., a bug. Thanks for continuing to investigate... Martin > > Alex Gutteridge > > On Fri, 16 Sep 2011 06:43:51 -0700, Martin Morgan wrote: >> Hi Alex -- >> >> Unfortunately, not informative; it looks like the call has completed >> but corrupted memory in the process. >> >> Any chance of a small data set, e.g., using samtools to select a >> portion of the file? Along the lines of >> >> samtools view -b A430001.1.bam chr1:1-1000000 > A430001.1.subset.bam >> >> Or is there a reference MOSAIK output file somewhere that I can access? >> >> Also, does specifying 'which' help, e.g., >> >> param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE, >> what = ShortRead:::.readAligned_bamWhat(), >> which=GRanges("chr1", IRanges(1, 100000))) >> >> And if you're being indulgent and none of the above point to the >> problem / are doable, create a file ~/.R/Makevars with >> >> CFLAGS += -g O0 -Dinline="" >> >> (that's the letter O and the number zero) and reinstalling Rsamtools >> (this'll compile without any C optimizations) then >> >> R -d valgrind -f test.R >> >> looking for output that says 'invalid read' or 'invalid write'. >> Thanks for working with me on this. >> >> Martin >> >> On 09/16/2011 03:36 AM, Alex Gutteridge wrote: >>> On Thu, 15 Sep 2011 06:19:29 -0700, Martin Morgan wrote: >>>> On 09/15/2011 02:35 AM, Alex Gutteridge wrote: >>>>> I'm trying to load a BAM file generated by Mosaik using ShortRead, but >>>>> I'm getting the following error: >>>>> >>>>>> aln.bam = >>>>>> readAligned("data/ALIGNMENT/A430001.1.samtools.bam",type="BAM") >>>>> Error: Input/Output >>>>> 'readAligned' failed to parse files >>>>> dirPath: 'data/ALIGNMENT/A430001.1.samtools.bam' >>>>> pattern: '' >>>>> type: 'BAM' >>>>> error: INTEGER() can only be applied to a 'integer', not a 'symbol' >>>>>> sessionInfo() >>>>> R version 2.12.0 (2010-10-15) >>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>> >>>>> locale: >>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices utils datasets methods base >>>>> >>>>> other attached packages: >>>>> [1] ShortRead_1.8.1 Rsamtools_1.2.3 lattice_0.19-13 >>>>> [4] Biostrings_2.18.0 GenomicRanges_1.2.1 IRanges_1.8.2 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] Biobase_2.10.0 grid_2.12.0 hwriter_1.2 tools_2.12.0 >>>>> >>>>> I ran samtools from the command-line over the original Mosiak BAM file >>>>> and it completed fine: >>>>> >>>>> samtools view -b A430001.1.bam > A430001.1.samtools.bam >>>>> >>>>> but I get the above error on both the Mosaik original and samtools >>>>> processed BAM file. >>>>> >>>>> I also tried the debug suggested here: >>>>> >>>>> https://stat.ethz.ch/pipermail/bioconductor/2010-October/035745.html but >>>>> >>>>> it segfaulted: >>>>> >>>>>> param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE, >>>>> + what = ShortRead:::.readAligned_bamWhat()) >>>>>> >>>>>> res = scanBam('data/ALIGNMENT/A430001.1.samtools.bam', param=param) >>>>> >>>>> *** caught segfault *** >>>>> address (nil), cause 'unknown' >>>>> >>>>> Traceback: >>>>> 1: .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...) >>>>> 2: .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = >>>>> param) >>>>> 3: scanBam("data/ALIGNMENT/A430001.1.samtools.bam", param = param) >>>>> 4: scanBam("data/ALIGNMENT/A430001.1.samtools.bam", param = param) >>>>> >>>>> Any suggestions to debug the file would be gratefully accepted. >>>> >>>> Hi Alex -- >>>> >>>> I'd stick with >>>> >>>> param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE, >>>> what = ShortRead:::.readAligned_bamWhat()) >>>> res = scanBam('data/ALIGNMENT/A430001.1.samtools.bam', param=param) >>>> >>>> as the starting point for debugging. >>>> >>>> My first suggestion is to update R to R-2-13.1, install Rsamtools, >>>> and try again. >>>> >>>> The next is more complicated, but not to bad. Start R with the 'gdb' >>>> debugger, provoke the error, and then find where the error occurred. >>>> It'll look some thing like >>>> >>>> R -d gdb >>>> gdb> run >>>> ... >>>> > ## now at the R prompt, do what you need to segfault >>>> ... >>>> gdb> where >>>> >>>> you'll have to type the 'run' and 'where' commands; 'where' will >>>> generate a backtrace, and if you could forward that to me (e.g., copy >>>> / paste) that would be great. >>>> >>>> Martin >>> >>> Hi Martin, >>> >>> Slightly different traceback with latest version, but essentially the >>> same: >>> >>>> library(ShortRead) >>> Loading required package: IRanges >>> >>> Attaching package: 'IRanges' >>> >>> The following object(s) are masked from 'package:base': >>> >>> cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, >>> pmin, pmin.int, rbind, rep.int, setdiff, table, union >>> >>> Loading required package: GenomicRanges >>> Loading required package: Biostrings >>> Loading required package: lattice >>> Loading required package: Rsamtools >>>> aln = readAligned("data/ALIGNMENT/A430001.1.bam",type="BAM") >>> Error: Input/Output >>> 'readAligned' failed to parse files >>> dirPath: 'data/ALIGNMENT/A430001.1.bam' >>> pattern: '' >>> type: 'BAM' >>> error: INTEGER() can only be applied to a 'integer', not a 'symbol' >>> file: data/ALIGNMENT/A430001.1.bam >>>> param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE, >>> + what = ShortRead:::.readAligned_bamWhat()) >>>> res = scanBam('data/ALIGNMENT/A430001.1.samtools.bam', param=param) >>> *** caught segfault *** >>> address (nil), cause 'unknown' >>> >>> Traceback: >>> 1: .Call(func, .extptr(file), space, flag, simpleCigar, ...) >>> 2: doTryCatch(return(expr), name, parentenv, handler) >>> 3: tryCatchOne(expr, names, parentenv, handlers[[1L]]) >>> 4: tryCatchList(expr, classes, parentenv, handlers) >>> 5: tryCatch({ .Call(func, .extptr(file), space, flag, simpleCigar, >>> ...)}, error = function(err) { stop(conditionMessage(err), "\n file: ", >>> path(file))}) >>> 6: .io_bam(.scan_bamfile, file, param = param, path(file), index(file), >>> "rb", reverseComplement, tmpl) >>> 7: scanBam(bam, param = param) >>> 8: scanBam(bam, param = param) >>> 9: eval(expr, envir, enclos) >>> 10: eval(call, sys.frame(sys.parent())) >>> 11: callGeneric(bam, ..., param = param) >>> 12: scanBam("data/ALIGNMENT/A430001.1.samtools.bam", param = param) >>> 13: scanBam("data/ALIGNMENT/A430001.1.samtools.bam", param = param) >>> >>> ############### >>> >>>> sessionInfo() >>> R version 2.13.1 (2011-07-08) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] ShortRead_1.10.4 Rsamtools_1.4.3 lattice_0.19-30 >>> [4] Biostrings_2.20.3 GenomicRanges_1.4.8 IRanges_1.10.6 >>> >>> loaded via a namespace (and not attached): >>> [1] Biobase_2.12.2 grid_2.13.1 hwriter_1.3 >>> >>> ########### >>> >>> Here is the result of segfaulting under gdb: >>> >>> ######### >>> >>> Program received signal SIGSEGV, Segmentation fault. >>> R_gc_internal (size_needed=0) at memory.c:1427 >>> 1427 SEXP next = NEXT_NODE(s); >>> (gdb) where >>> #0 R_gc_internal (size_needed=0) at memory.c:1427 >>> #1 0x000000000041e7f3 in Rf_cons (car=0x1bf38af0, cdr=0x163ef338) >>> at memory.c:2083 >>> #2 0x0000000000555780 in Rf_evalList (el=0x1be8f6e0, rho=0x1c31a7a0, >>> call=0x1be8f6a8, n=1) at eval.c:1836 >>> #3 0x0000000000554a17 in Rf_eval (e=0x1be8f6a8, rho=0x1c31a7a0) at >>> eval.c:501 >>> #4 0x0000000000555580 in Rf_evalListKeepMissing (el=0x1c31a2f0, >>> rho=0x1c31a7a0) at eval.c:1900 >>> #5 0x0000000000555ba5 in Rf_DispatchOrEval (call=0x1c31a360, >>> op=0x1640f938, >>> generic=0x616594 "[<-", args=0x1c31a328, rho=0x1c31a7a0, >>> ans=0x7fff256b5858, dropmissing=0, argsevald=0) at eval.c:2381 >>> #6 0x000000000048f300 in do_subassign (call=0x0, op=0x8d1d78, >>> args=0x5443474741544747, rho=0x1c31a7a0) at subassign.c:1313 >>> #7 0x0000000000554981 in Rf_eval (e=0x1c31a360, rho=0x1c31a7a0) at >>> eval.c:482 >>> #8 0x0000000000557324 in do_set (call=0x1c31a408, op=0x1640e788, >>> args=0x1c31a3d0, rho=0x1c31a7a0) at eval.c:1722 >>> #9 0x0000000000554981 in Rf_eval (e=0x1c31a408, rho=0x1c31a7a0) at >>> eval.c:482 >>> #10 0x0000000000556c84 in applydefine (call=<value optimized="" out="">, >>> op=0x1640e788, args=<value optimized="" out="">, rho=0x1c31a7a0) at >>> eval.c:1678 >>> #11 0x0000000000554981 in Rf_eval (e=0x1be8f590, rho=0x1c31a7a0) at >>> eval.c:482 >>> #12 0x00000000005560ee in do_begin (call=0x1be8f360, op=0x1640e590, >>> args=0x5443474741544747, rho=0x1c31a7a0) at eval.c:1420 >>> #13 0x0000000000554981 in Rf_eval (e=0x1be8f360, rho=0x1c31a7a0) at >>> eval.c:482 >>> > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD REPLYlink written 7.1 years ago by Martin Morgan ♦♦ 22k
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