Question: ChIPQC failed on chrM
0
gravatar for seasky002002
2.4 years ago by
seasky0020020 wrote:

Hi,

I encountered an error while using ChIPQC. It reported an error after calculation shift for chrM. I pasted the error message below. It looks like happened on chrM, so i change the parameter chromosomes to exclude chrM, and the ChIPQC program run successfully. 

But i still curious why the error happened on chrM. Would someone can give me an answer?

Thank you!

 

 

The error message:

Calculating shift for chrM

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Error in names(res) <- nms :
  'names' attribute [18] must be the same length as the vector [1]
Calls: ChIPQC -> bplapply -> bplapply -> bplapply -> bplapply

 

chipqc • 800 views
ADD COMMENTlink modified 2.4 years ago by Thomas Carroll400 • written 2.4 years ago by seasky0020020

Hello

I get this same error at the start of my run. Was there a solution to this? My sessionInfo is attached below but also I get a message when I load the library, not sure if this has anything to do with it: No methods found in "RSQLite" for requests: dbGetQuery

Bam file has 93 contigs
Error in names(res) <- nms : 
  'names' attribute [28] must be the same length as the vector [4]
Calls: ChIPQC -> bplapply -> bplapply -> bplapply -> bplapply

 

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.8 (Final)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] ChIPQC_1.10.3              DiffBind_2.2.12           
 [3] SummarizedExperiment_1.4.0 Biobase_2.34.0            
 [5] GenomicRanges_1.26.4       GenomeInfoDb_1.10.3       
 [7] IRanges_2.8.2              S4Vectors_0.12.2          
 [9] BiocGenerics_0.20.0        ggplot2_2.2.1             

ADD REPLYlink written 2.3 years ago by meeta.mistry20

 

 

 

hi,

The original error looks to do with the way ChIPQC calculates cross coverage. The ChrM may cause some problems here because it is circular.

I believe there is a way to check for circular chromosomes so I will look to remove any circular chromosomes while providing a warning for the user.

For now the solution is to remove the mitochondrial chromosome.

I usually provide ChIPQC with a vector of the main chromosomes omitting ChrM and the contigs which haven't been fully assembled into main chromosomes.

Something like

> chromosomesToTest <- c(paste0("chr",c(1:22,"X","Y")))

> chromosomesToTest
 [1] "chr1"  "chr2"  "chr3"  "chr4"  "chr5"  "chr6"  "chr7"  "chr8"  "chr9"  "chr10" "chr11" "chr12"
[13] "chr13" "chr14" "chr15" "chr16" "chr17" "chr18" "chr19" "chr20" "chr21" "chr22" "chrX"  "chrY"

> my_experiment = ChIPQC(experiment="CellLine_Experiment_Sheet.csv", annotation="hg19",chromosomes=chromosomesToTest)

I will look to update ChIPQC to remove the ChrM internally in the next version.

best,

tom

ADD REPLYlink written 2.2 years ago by Thomas Carroll400
Answer: ChIPQC failed on chrM
0
gravatar for Thomas Carroll
2.4 years ago by
United States/New York/The Rockefeller University
Thomas Carroll400 wrote:

hi,

Could you let me know what version of ChIPQC you are using? The result from a call to sessionInfo() should be good.

best,

tom

 

 

ADD COMMENTlink written 2.4 years ago by Thomas Carroll400
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