Question

atacseqQC error while splittin the bamfile

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Theo ▴ 10

@theodoregeorgomanolis-7993

Last seen 4 months ago

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

ATACseqQC ATAC-seq error split bam file • 2.2k views

ADD COMMENT • link updated 5.5 years ago by contact • 0 • written 5.5 years ago by Theo ▴ 10

score 0 · Answer 1 · 2019-05-06

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Ou, Jianhong ★ 1.3k

@ou-jianhong-4539

Last seen 3 days ago

United States

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=

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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 COMMENT • link 5.5 years ago Ou, Jianhong ★ 1.3k

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

ADD REPLY • link 5.5 years ago Theo ▴ 10

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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
LCCOLLATE=enUS.UTF-8 [5] LCMONETARY=deDE.UTF-8
LCMESSAGES=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
GenomicScores1.8.0 [3] BSgenome.Hsapiens.UCSC.hg191.4.0 BSgenome1.52.0
[5] ATACseqQC1.8.0
TxDb.Hsapiens.UCSC.hg19.knownGene3.2.2 [7] rGREAT1.16.0
ChIPpeakAnno3.18.0 [9] VennDiagram1.6.20
futile.logger1.4.3 [11] Biostrings2.52.0
XVector0.24.0 [13] RMariaDB1.0.6
org.Hs.eg.db3.8.2 [15] GenomicFeatures1.36.0
AnnotationDbi1.46.0 [17] Biobase2.44.0
rtracklayer1.44.0 [19] ChIPseeker1.20.0
GenomicRanges1.36.0 [21] GenomeInfoDb1.20.0
IRanges2.18.0 [23] S4Vectors0.22.0
BiocGenerics0.30.0

ADD REPLY • link 5.5 years ago Theo ▴ 10

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

Jianhong.

ADD REPLY • link 5.5 years ago Ou, Jianhong ★ 1.3k

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Hi, I am getting the same error with mm10 with v1.8.5 downloaded 8/2/19. Is there any resolution or recommendation for this? Thanks!

Edit - it is giving the same error with 'splitBam' function in v1.9.7 downloaded from github. However, this error has disappeared when using shiftGAlignmentsList in v1.9.7. With v1.8.5 from Bioconductor, both functions gave the error.

ADD REPLY • link 5.3 years ago ian.beddows • 0

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you can update to the development version. Or set flag=scanBamFlag(isSecondaryAlignment = FALSE, isUnmappedQuery=FALSE, isNotPassingQualityControls = FALSE, isSupplementaryAlignment = FALSE) for readBamFile in released version to overcome the issue of all(elementNROWS(gal) < 3) is not TRUE

see https://support.bioconductor.org/p/122819/#123135

From: "ian.beddows [bioc]" noreply@bioconductor.org Reply-To: "reply+9ee280d2+code@bioconductor.org" <reply+9ee280d2+code@bioconductor.org> Date: Friday, August 2, 2019 at 9:40 AM To: "Jianhong Ou, Ph.D." jianhong.ou@duke.edu Subject: [bioc] C: 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=VtppQj4W1krIwaMiKKEZyV4S7oN-rHihMqROuu_fRio&s=QV61Y4n6aFg1XovygloDRAUEr9nemJtoQd7Pbin2nyw&e=

User ian.beddowshttps://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_u_21527_&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=VtppQj4W1krIwaMiKKEZyV4S7oN-rHihMqROuu_fRio&s=h2KjbO0EffKD6uFncnz6W2MFhn9u-6oR34jtnO97CWQ&e= wrote Comment: atacseqQC error while splittin the bamfilehttps://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_120707_-23123438&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=VtppQj4W1krIwaMiKKEZyV4S7oN-rHihMqROuu_fRio&s=C1XzjEp81u7RUI9Y8ODcLb3409zIpBPkXXD3gQZLGJg&e=:

Hi, I am getting the same error with mm10 with v1.8.5 downloaded 8/2/19. Is there any resolution or recommendation for this? Thanks!

ADD REPLY • link 5.3 years ago Ou, Jianhong ★ 1.3k