Question: atacseqQC error while splittin the bamfile
0
gravatar for theodore.georgomanolis
7 weeks ago by
Germany

Hi all, anyone can help with the following from the ATACseqQC package:

objs <- splitBam(bamfile, tags=tags, outPath=outPath,
+                  txs=txs, genome=genome,
+                  conservation=phastCons100way.UCSC.hg19)

ERROR as follows:

[E::sam_parse1] unrecognized type N

[W::sam_read1] Parse error at line 26

[E::sam_parse1] unrecognized type N

[W::sam_read1] Parse error at line 26

Error in shiftGAlignmentsList(chunk0, positive = positive,negative = negative) : all(elementNROWS(gal) < 3) is not TRUE

this happens while I am trying to split the bam file into nucleosomefree, mono/di/trinucleosome areas

thank you beforehand

ADD COMMENTlink modified 6 weeks ago by contact0 • written 7 weeks ago by theodore.georgomanolis0
Answer: atacseqQC error while splittin the bamfile
0
gravatar for Ou, Jianhong
7 weeks ago by
Ou, Jianhong1.1k
United States
Ou, Jianhong1.1k wrote:

Hi,

Could you share me the bamfile which can repeat the error?

Jianhong.

From: "theodore.georgomanolis [bioc]" noreply@bioconductor.org Reply-To: "reply+316c39ef+code@bioconductor.org" <reply+316c39ef+code@bioconductor.org> Date: Sunday, May 5, 2019 at 10:22 AM To: "Jianhong Ou, Ph.D." jianhong.ou@duke.edu Subject: [bioc] atacseqQC error while splittin the bamfile

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=mjeKwwdmBi7GscOXZ286PlRB-INjIVKONsDUc7gNBxg&s=At4vkeLtZXEDjKUiw9QI6KxWogokoMCvxR-i56_Uv1o&e=

User theodore.georgomanolishttps://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_u_7993_&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=mjeKwwdmBi7GscOXZ286PlRB-INjIVKONsDUc7gNBxg&s=41tnwQPRGp33poa-p_H_nax962uRWWJsGfLFfoPMcfQ&e= wrote Question: atacseqQC error while splittin the bamfilehttps://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_120707_&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=mjeKwwdmBi7GscOXZ286PlRB-INjIVKONsDUc7gNBxg&s=ch79-dHbzeEhQfPpR42yt0ytiKSaEIb4EH84lwBnzp0&e=:

Hi all, anyone can help with the following from the ATACseqQC package:

objs <- splitBam(bamfile, tags=tags, outPath=outPath,

  • txs=txs, genome=genome,

  • conservation=phastCons100way.UCSC.hg19)

ERROR as follows:

[E::samparse1] unrecognized type N [W::samread1] Parse error at line 26 [E::samparse1] unrecognized type N [W::samread1] Parse error at line 26 Error in shiftGAlignmentsList(chunk0, positive = positive, negative = negative) : all(elementNROWS(gal) < 3) is not TRUE

this happens while I am trying to split the bam file into nucleosomefree, mono/di/trinucleosome areas

thank you beforehand

ADD COMMENTlink written 7 weeks ago by Ou, Jianhong1.1k

sorry for replying after so long I am sending you an email with the bam file

ADD REPLYlink written 6 weeks ago by theodore.georgomanolis0

by the way the script I used was the one provided I changed nothing in order to see if it works in my case. Session info:

> sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Linux Mint 18.3

Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding locale: [1] LCCTYPE=enUS.UTF-8
LCNUMERIC=C LCTIME=enUS.UTF-8
LC
COLLATE=enUS.UTF-8 [5] LCMONETARY=deDE.UTF-8
LC
MESSAGES=enUS.UTF-8 LCPAPER=deDE.UTF-8 LCNAME=C
[9] LCADDRESS=C LCTELEPHONE=C
LCMEASUREMENT=deDE.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] grid parallel stats4 stats
graphics grDevices utils datasets methods base

other attached packages: [1] phastCons100way.UCSC.hg193.7.2
GenomicScores
1.8.0 [3] BSgenome.Hsapiens.UCSC.hg191.4.0 BSgenome1.52.0
[5] ATACseqQC1.8.0
TxDb.Hsapiens.UCSC.hg19.knownGene
3.2.2 [7] rGREAT1.16.0
ChIPpeakAnno
3.18.0 [9] VennDiagram1.6.20
futile.logger
1.4.3 [11] Biostrings2.52.0
XVector
0.24.0 [13] RMariaDB1.0.6
org.Hs.eg.db
3.8.2 [15] GenomicFeatures1.36.0
AnnotationDbi
1.46.0 [17] Biobase2.44.0
rtracklayer
1.44.0 [19] ChIPseeker1.20.0
GenomicRanges
1.36.0 [21] GenomeInfoDb1.20.0
IRanges
2.18.0 [23] S4Vectors0.22.0
BiocGenerics
0.30.0

ADD REPLYlink written 6 weeks ago by theodore.georgomanolis0

Hi, Have a try with newest version of ATACseqQC. The error should be handled by the program.

Jianhong.

ADD REPLYlink written 4 weeks ago by Ou, Jianhong1.1k
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