When trying to use ATACseqQC on a larger bamfile, I receive the following error:
Error in .local(x, ...) : strand values must be in '+' '-' '*' Calls: splitGAlignmentsByCut ... normalizestrandreplacement_value -> strand -> strand -> .local
I checked the structure of the bamfile using str(gal) and under strand values I see: Factor w/ 3 levels "+","-","*": 3.
The bamfile is available to be downloaded here: http://s3.amazonaws.com/mudaser/bamfiles/112R-rep1-chr1-bwa.bam
The R script is available to be downloaded here: http://s3.amazonaws.com/mudaser/bamfiles/ATACseq_heatmap.R
The log file that shows the full error is available to be downloaded here: http://s3.amazonaws.com/mudaser/bamfiles/Heatmap.log
Any insight would be much appreciated.
(Ideally, I would like to use the entire bamfile without limiting to chr1, but we received separate errors that I may make another post about at a later time).
Hi Julie,
I have the most recent version of ATACseqQC (1.8.1) installed. Here is the session info:
R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)
Matrix products: default BLAS: /opt/R/3.6.0-Python-3.6.6-foss-2018b/lib64/R/lib/libRblas.so LAPACK: /opt/R/3.6.0-Python-3.6.6-foss-2018b/lib64/R/lib/libRlapack.so
locale: [1] LCCTYPE=enUS.UTF-8 LCNUMERIC=C
[3] LCTIME=enUS.UTF-8 LCCOLLATE=enUS.UTF-8
[5] LCMONETARY=enUS.UTF-8 LCMESSAGES=enUS.UTF-8
[7] LCPAPER=enUS.UTF-8 LCNAME=C
[9] LCADDRESS=C LCTELEPHONE=C
[11] LCMEASUREMENT=enUS.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base
other attached packages: [1] BSgenome.Hsapiens.UCSC.hg191.4.0
[2] BSgenome1.52.0
[3] rtracklayer1.44.0
[4] TxDb.Hsapiens.UCSC.hg19.knownGene3.2.2 [5] GenomicFeatures1.36.1
[6] AnnotationDbi1.46.0
[7] Biobase2.44.0
[8] phastCons100way.UCSC.hg193.7.2
[9] GenomicScores1.8.0
[10] Rsamtools2.0.0
[11] Biostrings2.52.0
[12] XVector0.24.0
[13] GenomicRanges1.36.0
[14] GenomeInfoDb1.20.0
[15] IRanges2.18.1
[16] ATACseqQC1.8.1
[17] S4Vectors0.22.0
[18] BiocGenerics0.30.0
loaded via a namespace (and not attached): [1] ProtGenerics1.16.0 bitops1.0-6
[3] matrixStats0.54.0 bit640.9-7
[5] progress1.2.2 httr1.4.0
[7] tools3.6.0 rGADEM2.32.0
[9] R62.4.0 KernSmooth2.23-15
[11] seqLogo1.50.0 colorspace1.4-1
[13] DBI1.0.0 lazyeval0.2.2
[15] ade41.7-13 motifStack1.28.0
[17] tidyselect0.2.5 prettyunits1.0.2
[19] grImport20.1-5 bit1.1-14
[21] curl3.3 compiler3.6.0
[23] VennDiagram1.6.20 graph1.62.0
[25] formatR1.6 DelayedArray0.10.0
[27] scales1.0.0 randomForest4.6-14
[29] RBGL1.60.0 rappdirs0.3.1
[31] stringr1.4.0 digest0.6.19
[33] jpeg0.1-8 base64enc0.1-3
[35] pkgconfig2.0.2 htmltools0.3.6
[37] dbplyr1.4.1 ensembldb2.8.0
[39] limma3.40.2 regioneR1.16.2
[41] htmlwidgets1.3 rlang0.3.4
[43] RSQLite2.1.1 shiny1.3.2
[45] BiocParallel1.18.0 dplyr0.8.1
[47] RCurl1.95-4.12 magrittr1.5
[49] polynom1.4-0 GO.db3.8.2
[51] GenomeInfoDbData1.2.1 futile.logger1.4.3
[53] Matrix1.2-17 munsell0.5.0
[55] Rcpp1.0.1 stringi1.4.3
[57] yaml2.2.0 edgeR3.26.4
[59] MASS7.3-51.4 SummarizedExperiment1.14.0
[61] zlibbioc1.30.0 BiocFileCache1.8.0
[63] AnnotationHub2.16.0 grid3.6.0
[65] blob1.1.1 promises1.0.1
[67] crayon1.3.4 lattice0.20-38
[69] splines3.6.0 multtest2.40.0
[71] hms0.4.2 locfit1.5-9.1
[73] pillar1.4.1 MotIV1.40.0
[75] seqinr3.4-5 biomaRt2.40.0
[77] futile.options1.0.1 XML3.98-1.20
[79] glue1.3.1 lambda.r1.2.3
[81] BiocManager1.30.4 idr1.2
[83] png0.1-7 httpuv1.5.1
[85] purrr0.3.2 assertthat0.2.1
[87] mime0.6 preseqR4.0.0
[89] xtable1.8-4 AnnotationFilter1.8.0
[91] later0.8.0 survival2.44-1.1
[93] ChIPpeakAnno3.18.1 tibble2.1.3
[95] GenomicAlignments1.20.0 memoise1.1.0
[97] interactiveDisplayBase_1.22.0
Thanks! The main developer Jianhong will work on it and post the solutions here. Best regards, Julie
I am wondering whether you could run the examples at https://bioconductor.org/packages/release/bioc/vignettes/ATACseqQC/inst/doc/ATACseqQC.html, and whether you have the index file 112R-rep1-chr1-bwa.bam.bai in the same directory as 112R-rep1-chr1-bwa.bam file. Best regards, Julie
I made it by myself. I just cannot repeat the error yet. I am looking for the difference of secession info.
Best!
Your sincerely,
Jianhong Ou
On Jul 22, 2019, at 10:18 AM, Julie Zhu [bioc] <noreply@bioconductor.org<a rel="nofollow" href="mailto:noreply@bioconductor.org">noreply@bioconductor.org> wrote:
Activity on a post you are following on support.bioconductor.orghttps://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=ypYXViGpe99gxXOP31b2PHQTpVp93USZzlLqX9HHhf4&s=Qe-NKzG8TfbjMso7g2ZuhEkm-_JqP1UrrdVWbPWFkw4&e=
User Julie Zhuhttps://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_u_3596_&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=ypYXViGpe99gxXOP31b2PHQTpVp93USZzlLqX9HHhf4&s=yAbAo2DHcn9YWRzqOyREA8USelr30NuT7UFC8bnGH5Y&e= wrote Comment: ATACseqQC splitGAlignmentsByCut: strand values must be in '+' '-' '*'https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_122844_-23123059&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=ypYXViGpe99gxXOP31b2PHQTpVp93USZzlLqX9HHhf4&s=4pbH5yGWCb2BNHngqlP7AV0vo8QB3PwxW9MciqvFaQg&e=:
I am wondering whether you could run the examples at https://bioconductor.org/packages/release/bioc/vignettes/ATACseqQC/inst/doc/ATACseqQC.htmlhttps://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_release_bioc_vignettes_ATACseqQC_inst_doc_ATACseqQC.html&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=ypYXViGpe99gxXOP31b2PHQTpVp93USZzlLqX9HHhf4&s=r-0RyxoJMC9hk22Iq1kGacSMYOqXz1zOZL2amOGTMd4&e=, and whether you have the index file 112R-rep1-chr1-bwa.bam.bai in the same directory as 112R-rep1-chr1-bwa.bam file. Best regards, Julie
Hi, yes the files are in the same directory. That is interesting, so when you tried to test it, it worked for you?
Hi, yes the files are in the same directory. That is interesting, so when you tried to test it, it worked for you?