ATACseqQC splitGAlignmentsByCut: strand values must be in '+' '-' '*'
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mbasam • 0
@mbasam-21086
Last seen 4.5 years ago

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).

ATACseqQC R • 1.5k views
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 4 months ago
United States

Could you please share your session information with us? The most recent release of ATACseqQC is 1.8.1 (https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html). Thanks!

Best regards, Julie

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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] LC
TIME=enUS.UTF-8 LCCOLLATE=enUS.UTF-8
[5] LC
MONETARY=enUS.UTF-8 LCMESSAGES=enUS.UTF-8
[7] LC
PAPER=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] BSgenome
1.52.0
[3] rtracklayer1.44.0
[4] TxDb.Hsapiens.UCSC.hg19.knownGene
3.2.2 [5] GenomicFeatures1.36.1
[6] AnnotationDbi
1.46.0
[7] Biobase2.44.0
[8] phastCons100way.UCSC.hg19
3.7.2
[9] GenomicScores1.8.0
[10] Rsamtools
2.0.0
[11] Biostrings2.52.0
[12] XVector
0.24.0
[13] GenomicRanges1.36.0
[14] GenomeInfoDb
1.20.0
[15] IRanges2.18.1
[16] ATACseqQC
1.8.1
[17] S4Vectors0.22.0
[18] BiocGenerics
0.30.0

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

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Thanks! The main developer Jianhong will work on it and post the solutions here. Best regards, Julie

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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

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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

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Hi, yes the files are in the same directory. That is interesting, so when you tried to test it, it worked for you?

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Entering edit mode

Hi, yes the files are in the same directory. That is interesting, so when you tried to test it, it worked for you?

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