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htSeqTools errors

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Juan L. Mateo ▴ 80

@juan-l-mateo-5110

Last seen 10.3 years ago

Hi all, I am trying to use htSeqTools to analyse some ChIP-seq samples and I am getting errors on the methods cmds and giniCoverage. Below I paste the output of a session. Any help will be greatly appreciated. > what=c("rname", "strand", "pos", "qwidth") > param=ScanBamParam(what = what) > > Con_input<-scanBam('Con_input.fastq.bam', param=param)[[1]] > Con_input.reads<-GRanges(seqnames=Rle(Con_input$rname),ranges=IRanges( Con_input$pos, width=Con_input$qwidth)) > samples<-RangedDataList(Con_input=as(Con_input.reads,"RangedData")) > cmds1<-cmds(samples,k=2) Computing coverage... Computing correlations... Error in d[[i]] : subscript out of bounds > ssdCoverage(samples) Con_input 0.2551517 > giniCoverage(samples,mc.cores=1) Simulating uniformily distributed data Error in sample.int(chrLen[i], as.integer(chrReads[i]), replace = T) : invalid 'size' argument In addition: Warning messages: 1: In FUN(X[[1L]], ...) : no non-missing arguments to max; returning -Inf 2: In FUN(X[[1L]], ...) : no non-missing arguments to max; returning -Inf 3: In FUN(X[[1L]], ...) : no non-missing arguments to max; returning -Inf 4: In eval(expr, envir, enclos) : NAs introduced by coercion > sessionInfo() R Under development (unstable) (2012-02-13 r58337) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB LC_NUMERIC=C LC_TIME=en_GB [4] LC_COLLATE=en_GB LC_MONETARY=en_GB LC_MESSAGES=en_GB [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] htSeqTools_1.1.2 BSgenome_1.23.2 MASS_7.3-17 [4] Biobase_2.15.3 Rsamtools_1.7.33 Biostrings_2.23.6 [7] GenomicRanges_1.7.24 IRanges_1.13.24 BiocGenerics_0.1.4 loaded via a namespace (and not attached): [1] bitops_1.0-4.1 zlibbioc_1.1.1 -- ============================= Juan L. Mateo PhD. Centre for Organismal Studies (COS) - University of Heidelberg Im Neuenheimer Feld 230 69120 Heidelberg, Germany Tel: 0049 (0)6221 54 6493 Fax: 0049 (0)6221 54 5639

Coverage htSeqTools Coverage htSeqTools • 2.0k views

ADD COMMENT • link updated 12.8 years ago by Valerie Obenchain ★ 6.8k • written 12.9 years ago by Juan L. Mateo ▴ 80

score 0 · Answer 1 · 2012-02-20

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Valerie Obenchain ★ 6.8k

@valerie-obenchain-4275

Last seen 2.9 years ago

United States

Hi Juan, ccing the author in case he hasn't seen this. Can you provide more information on what 'samples' looks like or the object itself? Valerie On 02/16/12 04:51, Juan L. Mateo wrote: > Hi all, > > I am trying to use htSeqTools to analyse some ChIP-seq samples and I > am getting errors on the methods cmds and giniCoverage. Below I paste > the output of a session. > > Any help will be greatly appreciated. > > > > what=c("rname", "strand", "pos", "qwidth") > > param=ScanBamParam(what = what) > > > > Con_input<-scanBam('Con_input.fastq.bam', param=param)[[1]] > > > Con_input.reads<-GRanges(seqnames=Rle(Con_input$rname),ranges=IRange s(Con_input$pos, > width=Con_input$qwidth)) > > samples<-RangedDataList(Con_input=as(Con_input.reads,"RangedData")) > > cmds1<-cmds(samples,k=2) > Computing coverage... > Computing correlations... > Error in d[[i]] : subscript out of bounds > > ssdCoverage(samples) > Con_input > 0.2551517 > > giniCoverage(samples,mc.cores=1) > Simulating uniformily distributed data > Error in sample.int(chrLen[i], as.integer(chrReads[i]), replace = T) : > invalid 'size' argument > In addition: Warning messages: > 1: In FUN(X[[1L]], ...) : no non-missing arguments to max; returning -Inf > 2: In FUN(X[[1L]], ...) : no non-missing arguments to max; returning -Inf > 3: In FUN(X[[1L]], ...) : no non-missing arguments to max; returning -Inf > 4: In eval(expr, envir, enclos) : NAs introduced by coercion > > > > > > sessionInfo() > R Under development (unstable) (2012-02-13 r58337) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB LC_NUMERIC=C LC_TIME=en_GB > [4] LC_COLLATE=en_GB LC_MONETARY=en_GB LC_MESSAGES=en_GB > [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C > [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] htSeqTools_1.1.2 BSgenome_1.23.2 MASS_7.3-17 > [4] Biobase_2.15.3 Rsamtools_1.7.33 Biostrings_2.23.6 > [7] GenomicRanges_1.7.24 IRanges_1.13.24 BiocGenerics_0.1.4 > > loaded via a namespace (and not attached): > [1] bitops_1.0-4.1 zlibbioc_1.1.1 > >

ADD COMMENT • link 12.8 years ago Valerie Obenchain ★ 6.8k

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Hi Valerie, Thanks for you answer. This object contains 16M reads and I am happy to provide any information that would be useful or even this object which is 206Mb big. > sapply(samples,nrow) Con_input 16513449 Best, Juan On 02/20/2012 08:08 PM, Valerie Obenchain wrote: > Hi Juan, > > ccing the author in case he hasn't seen this. > > Can you provide more information on what 'samples' looks like or the > object itself? > > Valerie > > > > > On 02/16/12 04:51, Juan L. Mateo wrote: >> Hi all, >> >> I am trying to use htSeqTools to analyse some ChIP-seq samples and I >> am getting errors on the methods cmds and giniCoverage. Below I paste >> the output of a session. >> >> Any help will be greatly appreciated. >> >> >> > what=c("rname", "strand", "pos", "qwidth") >> > param=ScanBamParam(what = what) >> > >> > Con_input<-scanBam('Con_input.fastq.bam', param=param)[[1]] >> > >> Con_input.reads<-GRanges(seqnames=Rle(Con_input$rname),ranges=IRang es(Con_input$pos, >> width=Con_input$qwidth)) >> > samples<-RangedDataList(Con_input=as(Con_input.reads,"RangedData")) >> > cmds1<-cmds(samples,k=2) >> Computing coverage... >> Computing correlations... >> Error in d[[i]] : subscript out of bounds >> > ssdCoverage(samples) >> Con_input >> 0.2551517 >> > giniCoverage(samples,mc.cores=1) >> Simulating uniformily distributed data >> Error in sample.int(chrLen[i], as.integer(chrReads[i]), replace = T) : >> invalid 'size' argument >> In addition: Warning messages: >> 1: In FUN(X[[1L]], ...) : no non-missing arguments to max; returning -Inf >> 2: In FUN(X[[1L]], ...) : no non-missing arguments to max; returning -Inf >> 3: In FUN(X[[1L]], ...) : no non-missing arguments to max; returning -Inf >> 4: In eval(expr, envir, enclos) : NAs introduced by coercion >> >> >> >> >> > sessionInfo() >> R Under development (unstable) (2012-02-13 r58337) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_GB LC_NUMERIC=C LC_TIME=en_GB >> [4] LC_COLLATE=en_GB LC_MONETARY=en_GB LC_MESSAGES=en_GB >> [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C >> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] htSeqTools_1.1.2 BSgenome_1.23.2 MASS_7.3-17 >> [4] Biobase_2.15.3 Rsamtools_1.7.33 Biostrings_2.23.6 >> [7] GenomicRanges_1.7.24 IRanges_1.13.24 BiocGenerics_0.1.4 >> >> loaded via a namespace (and not attached): >> [1] bitops_1.0-4.1 zlibbioc_1.1.1 >> >> >

ADD REPLY • link 12.8 years ago Juan L. Mateo ▴ 80

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Hi Juan, we have been working on the giniCoverage function regarding several issues that arised with version 1.0 of the package. They are already available in the development version of the package available from the Bioconductor development repository. Please let me know should you have doubts or experience problems installing that version. As for the cmds function, from your code I assume your data is basically a single sequencing sample, whereas the idea behind the cmds function is to produce a pca-like plot showing separation and relative positioning of several samples to assess their similarities. Nonetheless I'm not sure if the error you are getting is due to that, and would be grateful if you could give me access to your .bam file is possible so I can try to reproduce the error here. Best regards, Oscar On Tue, Feb 21, 2012 at 10:12 AM, Juan L. Mateo < juan.mateo@cos.uni-heidelberg.de> wrote: > Hi Valerie, > > Thanks for you answer. > This object contains 16M reads and I am happy to provide any information > that would be useful or even this object which is 206Mb big. > > > sapply(samples,nrow) > Con_input > 16513449 > > Best, > Juan > > > On 02/20/2012 08:08 PM, Valerie Obenchain wrote: > >> Hi Juan, >> >> ccing the author in case he hasn't seen this. >> >> Can you provide more information on what 'samples' looks like or the >> object itself? >> >> Valerie >> >> >> >> >> On 02/16/12 04:51, Juan L. Mateo wrote: >> >>> Hi all, >>> >>> I am trying to use htSeqTools to analyse some ChIP-seq samples and I >>> am getting errors on the methods cmds and giniCoverage. Below I paste >>> the output of a session. >>> >>> Any help will be greatly appreciated. >>> >>> >>> > what=c("rname", "strand", "pos", "qwidth") >>> > param=ScanBamParam(what = what) >>> > >>> > Con_input<-scanBam('Con_input.**fastq.bam', param=param)[[1]] >>> > >>> Con_input.reads<-GRanges(**seqnames=Rle(Con_input$rname),** >>> ranges=IRanges(Con_input$pos, >>> width=Con_input$qwidth)) >>> > samples<-RangedDataList(Con_**input=as(Con_input.reads,"** >>> RangedData")) >>> > cmds1<-cmds(samples,k=2) >>> Computing coverage... >>> Computing correlations... >>> Error in d[[i]] : subscript out of bounds >>> > ssdCoverage(samples) >>> Con_input >>> 0.2551517 >>> > giniCoverage(samples,mc.cores=**1) >>> Simulating uniformily distributed data >>> Error in sample.int(chrLen[i], as.integer(chrReads[i]), replace = T) : >>> invalid 'size' argument >>> In addition: Warning messages: >>> 1: In FUN(X[[1L]], ...) : no non-missing arguments to max; returning -Inf >>> 2: In FUN(X[[1L]], ...) : no non-missing arguments to max; returning -Inf >>> 3: In FUN(X[[1L]], ...) : no non-missing arguments to max; returning -Inf >>> 4: In eval(expr, envir, enclos) : NAs introduced by coercion >>> >>> >>> >>> >>> > sessionInfo() >>> R Under development (unstable) (2012-02-13 r58337) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_GB LC_NUMERIC=C LC_TIME=en_GB >>> [4] LC_COLLATE=en_GB LC_MONETARY=en_GB LC_MESSAGES=en_GB >>> [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C >>> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] htSeqTools_1.1.2 BSgenome_1.23.2 MASS_7.3-17 >>> [4] Biobase_2.15.3 Rsamtools_1.7.33 Biostrings_2.23.6 >>> [7] GenomicRanges_1.7.24 IRanges_1.13.24 BiocGenerics_0.1.4 >>> >>> loaded via a namespace (and not attached): >>> [1] bitops_1.0-4.1 zlibbioc_1.1.1 >>> >>> >>> >> -- Oscar Reina Research officer, Bioinformatics and Biostatistics unit IRB Barcelona Cluster building, PBC32 Tel (+34) 93 402 0553 Fax (+34) 93 402 0257 oscar.reina@irbbarcelona.org http://www.irbbarcelona.org/bioinformatics [[alternative HTML version deleted]]

ADD REPLY • link 12.8 years ago Oscar Reina ▴ 20

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Hi Oscar, I am aware of the purpose of the cmds function but I got the same error when I have several samples, so, for simplicity, I posted this example with only one sample. I am already using the development version as you can see from the sessionInfo() output at the end of my first email. As I said, I can send you the R objects or bam files, just let me know in which way I should do that since they are too big to be attached in an email Best, Juan On 02/21/2012 10:33 AM, Oscar Reina wrote: > Hi Juan, > > we have been working on the giniCoverage function regarding several > issues that arised with version 1.0 of the package. They are already > available in the development version of the package available from the > Bioconductor development repository. Please let me know should you have > doubts or experience problems installing that version. > > As for the cmds function, from your code I assume your data is basically > a single sequencing sample, whereas the idea behind the cmds function is > to produce a pca-like plot showing separation and relative positioning > of several samples to assess their similarities. Nonetheless I'm not > sure if the error you are getting is due to that, and would be grateful > if you could give me access to your .bam file is possible so I can try > to reproduce the error here. > > Best regards, > > Oscar > > On Tue, Feb 21, 2012 at 10:12 AM, Juan L. Mateo > <juan.mateo at="" cos.uni-heidelberg.de=""> <mailto:juan.mateo at="" cos.uni-heidelberg.de="">> wrote: > > Hi Valerie, > > Thanks for you answer. > This object contains 16M reads and I am happy to provide any > information that would be useful or even this object which is 206Mb big. > > > sapply(samples,nrow) > Con_input > 16513449 > > Best, > Juan > > > On 02/20/2012 08:08 PM, Valerie Obenchain wrote: > > Hi Juan, > > ccing the author in case he hasn't seen this. > > Can you provide more information on what 'samples' looks like or the > object itself? > > Valerie > > > > > On 02/16/12 04:51, Juan L. Mateo wrote: > > Hi all, > > I am trying to use htSeqTools to analyse some ChIP-seq > samples and I > am getting errors on the methods cmds and giniCoverage. > Below I paste > the output of a session. > > Any help will be greatly appreciated. > > > > what=c("rname", "strand", "pos", "qwidth") > > param=ScanBamParam(what = what) > > > > Con_input<-scanBam('Con_input.__fastq.bam', param=param)[[1]] > > > Con_input.reads<-GRanges(__seqnames=Rle(Con_input$rname) ,__ranges=IRanges(Con_input$pos, > width=Con_input$qwidth)) > > > samples<-RangedDataList(Con___input=as(Con_input.reads," __RangedData")) > > cmds1<-cmds(samples,k=2) > Computing coverage... > Computing correlations... > Error in d[[i]] : subscript out of bounds > > ssdCoverage(samples) > Con_input > 0.2551517 > > giniCoverage(samples,mc.cores=__1) > Simulating uniformily distributed data > Error in sample.int <http: sample.int="">(chrLen[i], > as.integer(chrReads[i]), replace = T) : > invalid 'size' argument > In addition: Warning messages: > 1: In FUN(X[[1L]], ...) : no non-missing arguments to max; > returning -Inf > 2: In FUN(X[[1L]], ...) : no non-missing arguments to max; > returning -Inf > 3: In FUN(X[[1L]], ...) : no non-missing arguments to max; > returning -Inf > 4: In eval(expr, envir, enclos) : NAs introduced by coercion > > > > > > sessionInfo() > R Under development (unstable) (2012-02-13 r58337) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB LC_NUMERIC=C LC_TIME=en_GB > [4] LC_COLLATE=en_GB LC_MONETARY=en_GB LC_MESSAGES=en_GB > [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C > [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] htSeqTools_1.1.2 BSgenome_1.23.2 MASS_7.3-17 > [4] Biobase_2.15.3 Rsamtools_1.7.33 Biostrings_2.23.6 > [7] GenomicRanges_1.7.24 IRanges_1.13.24 BiocGenerics_0.1.4 > > loaded via a namespace (and not attached): > [1] bitops_1.0-4.1 zlibbioc_1.1.1 > > > > > > > -- > Oscar Reina > Research officer, Bioinformatics and Biostatistics unit > IRB Barcelona > Cluster building, PBC32 > Tel (+34) 93 402 0553 > Fax (+34) 93 402 0257 > > oscar.reina at irbbarcelona.org <mailto:oscar.reina at="" irbbarcelona.org=""> > http://www.irbbarcelona.org/bioinformatics

ADD REPLY • link 12.8 years ago Juan L. Mateo ▴ 80