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Error: package ‘DiffBind’ could not be loaded
Hi there,
I've tried installing your patched version, but I keep getting this error.
The standard ChIPQC can be installed with no errors.
✓ checking for file ‘/tmp/RtmpeVdiP2/remotes1c7059b5a299/shengqh-ChIPQC-a120b45/DESCRIPTION’ (1.7s)
─ preparing ‘ChIPQC’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘ChIPQC_1.21.0.tar.gz’
* installing *source* package ‘ChIPQC’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘DiffBind’ in .recacheSubclasses(def@className, def, env):
(converted from warning) undefined subclass "UnstitchedGPos" of class "GRanges_OR_NULL"; definition not updated
Error: package ‘DiffBind’ could not be loaded
Execution halted
ERROR: lazy loading failed for package ‘ChIPQC’
* removing ‘/home/r.vd.weide/R/x86_64-pc-linux-gnu-library/3.6/ChIPQC’
* restoring previous ‘/home/r.vd.weide/R/x86_64-pc-linux-gnu-library/3.6/ChIPQC’
Error: Failed to install 'ChIPQC' from GitHub:
(converted from warning) installation of package ‘/tmp/RtmpeVdiP2/file1c7029fd9f38/ChIPQC_1.21.0.tar.gz’ had non-zero exit status
version()
_
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 3
minor 6.3
year 2020
month 02
day 29
svn rev 77875
language R
version.string R version 3.6.3 (2020-02-29)
nickname Holding the Windsock
Can you help me figuring this out?
Many thanks,
Robin
Error in reading Bam file
Hello,
I am trying to read sample file in chipQC and getting an error for reading bam file into object.
here is the head of my sample file.
## Load libraries
library(BiocManager)
library(ChIPQC)
library("BiocParallel")
register(DoparParam())
registered()
bpparam("SerialParam")
## Load sample data
samples <- read.csv('../meta/Brg1_metadatasheet_MP.csv')
head(samples)
## Create ChIPQC object
chipObj <- ChIPQC(samples, annotation="hg19")
head(samples)
SampleID,Factor,Replicate,bamReads,Peaks,PeakCaller,Condition,Phenotype
S7,H460,1,S7_H460_WT-ready.bam,S7_H460_WT-NF_peaks.narrowPeak,narrow,BRG1-WT,WT
S8,H460,1,S8_H460_KO-ready.bam,S8_H460_KO-NF_peaks.narrowPeak,narrow,BRG1-NULL,KO
Error
Error in h(simpleError(msg, call)) : error in evaluating the argument 'table' in selecting a method for function '%in%': invalid class "PhredQuality" object: undefined class for slot "elementMetadata" ("DataTable_OR_NULL")
Can you please suggest the solution?
Thank you,
Preeti
question about the chipqc on single-end sequencing data
I have seen your ChIPQCsample-class.R code in /R dir, and I realize that the way you handle the error: length of names [9] doesn't equal to the length of ref [7] is just judge the exist of fragmentlength and relativecrosscoverage value and set to 0 if doesn't exists. Is what I understand is right?
And the problem is that single-end sequencing data doesn't support the calculation of fragment-length, which is caused by the out range of the readlength(object) in crosscoverage(object) and return NA values, so any calculation about the fragmentlength doesn't support. Is what I understand is right?
Error in if (!bpschedule(BPPARAM) || length(X) == 1L || bpnworkers(BPPARAM) == : missing value where TRUE/FALSE needed
Hello
Can you please let me know the reason of this error:
samples = read.csv("QCexperiment.csv")
BRD4 = ChIPQC(samples, consensus=TRUE, bCount=TRUE, summits=250,
annotation="hg19",
blacklist = blacklist.hg19)
'BiocParallel' did not register default BiocParallelParam:
comparison of these types is not implemented
Error in if (!bpschedule(BPPARAM) || length(X) == 1L || bpnworkers(BPPARAM) == :
missing value where TRUE/FALSE needed
Calls: ChIPQC -> bplapply -> bplapply -> bplapply -> bplapply
Execution halted
Thanks
Error in ChIPQC(samples) : Unable to process. Each bam file must be associated with at most one peakset.
Hi,
I get this error when I run the ChIPQC package on my data (single sample). The commands are mentioned below:
## Load sample data
samples <- read.csv('meta/samplesheet.csv')
View(samples)
## Create ChIPQC object
chipObj <- ChIPQC(samples, annotation="hg19")
The samplesheet.csv:
SampleID,Tissue,Factor,Replicate,bamReads,Peaks
SRR,PCa,AR,1,data/bams/SRR.sambamba.sorted.uniquemapped.bam,data/peakcalls/LNCaP_AR_macs2_peaks.narrowPeak
I am not sure what exactly am I doing wrong.
Any help will be much appreciated. Thanks!
"NAs produced by integer overflow" warnings
I tried to run experiment=ChIPQC("samples.csv", annotation="hg38", consensus = TRUE, bCount=TRUE). It does not give errors, but gives me many warnings of "NAs produced by integer overflow" and the result object does not contain anything for "Reads, Map%, Filt%, Dup%, ReadL, FragL, RelCC, SSD, RiP%, RiBL%".
When I try to see the object by typing experiment
It gives an incomplete dataframe
Samples: 18 : HIF2A_M1A_1 HIF2A_M1A_2 ... PAX8_M1Ac PAX8_LM1Bc
Tissue Factor Condition Treatment Replicate Peaks
HIF2A_M1A_1 M1A HIF2A a a 1 32684
HIF2A_M1A_2 M1A HIF2A a a 2 32684
HIF2A_M1A_3 M1A HIF2A a a 3 32684
HIF2A_M1A_4 M1A HIF2A a a 4 32684
HIF2A_LM1B_1 LM1B HIF2A a a 1 32684
HIF2A_LM1B_2 LM1B HIF2A a a 2 32684
HIF2A_LM1B_3 LM1B HIF2A a a 3 32684
HIF2A_LM1B_4 LM1B HIF2A a a 4 32684
PAX8_M1A_1 M1A PAX8 a a 1 32684
PAX8_M1A_2 M1A PAX8 a a 2 32684
PAX8_M1A_3 M1A PAX8 a a 3 32684
PAX8_LM1B_1 LM1B PAX8 a a 1 32684
PAX8_LM1B_2 LM1B PAX8 a a 2 32684
PAX8_LM1B_3 LM1B PAX8 a a 3 32684
HIF2A_M1Ac M1A Control a a c1 32684
HIF2A_LM1Bc LM1B Control a a c2 32684
PAX8_M1Ac M1A Control a a c3 32684
PAX8_LM1Bc LM1B Control a a c4 32684
followed by error message
Error in names(res) <- c("Reads", "Map%", "Filt%", "Dup%", "ReadL", "FragL", :
'names' attribute [9] must be the same length as the vector [7]
The same problem possibly is discussed here (https://support.bioconductor.org/p/122763/).
Could you have a look into this?
Thank you very much for your help.
'browser' must be a non-empty character string
I first installed ChIPQC from Conda or Docker. Both gave me the error
"names' attribute [9] must be the same length as the vector [7]"
for ChIPQCreport.
Then I installed it from this git but got the following error and warning:
> ChIPQCreport(exampleExp)
Saving 7 x 7 in image
Saving 7 x 7 in image
Saving 7 x 7 in image
Using Sample as id variables
Saving 7 x 7 in image
Saving 7 x 7 in image
Error in browseURL(paste0("file://", normalizePath(file.path(reportFolder, :
'browser' must be a non-empty character string
In addition: Warning message:
Removed 1200 row(s) containing missing values (geom_path).
By the way, my data is on hg38. Is the warning related to this? It seems only hg19 is supported.
Custom annotation
Hi, I wonder if there is a way to use custom annotation in ChIPQC? Do I need to load a txdb file and how to use it?
ChIPQC makes a neverending loop while using all chromosomes
Hi,
thank you for fixing the error
"names' attribute [9] must be the same length as the vector [7]"
I have installed your fork project and while running ChIPQC on all chromosomes it seems to enter a loop, since it finishes the computation on chromosome Y and begins again from chromosome 1.
I do not know if this should be reported directly to the ChIPQC's author. If so, I apologize.
Thanks
Laura
Generating a QC report for a ChIP-seq sample
Hi,
Thanks for developing this user-friendly tool. When i intends to generate a QC report for a ATAC-seq bam files. The error occured:
Error in names(res) <- c("Reads", "Map%", "Filt%", "Dup%", "ReadL", "FragL", :
'names' attribute [9] must be the same length as the vector [7]
The code is
sample = ChIPQCsample("/home/vip1/atac/align/4612.raw.bam",annotation = "mm10")
sample
ChIPQCreport(sample)
I sincerely hope to get your kind reply.
option to remove X11 calls?
I would like to use this tool inside a pipeline that I run on the cluster. However, it seems that there is no option to bypass calls to X11 (which I assume are issued for some diagnostic figures) and thus in a cluster environment I get an error. Could you please add an option to turn off interactive plotting.
Thanks!
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