A R package and executable for the preprocessing, statistical analysis, and downstream testing and visualization of differentially methylated regions (DMRs) from CpG count matrices (Bismark cytosine reports)
I am running 80 RRBS samples, with 3 covariates: Age, Gender and Batch.
this is my running code: run.txt
I tried with 2 samples but without Batch as a covariate and it worked.
The error that I get is the following:
Rscript --vanilla /ibex/scratch/covid19/dnam/dmrsrich/DM.R --genome hg38 --coverage 1 --perGroup '0.75' --minCpGs 5 --maxPerms 10 --maxBlockPerms 10 --cutoff '0.05' --testCovariate Group --adjustCovariate 'Sex;Age;Batch' --sexCheck TRUE --GOfuncR TRUE --EnsDb FALSE --cores 20
[DMRichR] Initializing 15-11-2023 09:08:58 PM
[DMRichR] Processing arguments from script 15-11-2023 09:09:30 PM
genome = hg38
coverage = 1
perGroup = 0.75
minCpGs = 5
maxPerms = 10
maxBlockPerms = 10
cutoff = 0.05
testCovariate = Group
adjustCovariate = Sex
adjustCovariate = Age
adjustCovariate = Batch
cores = 20
sexCheck = TRUE
EnsDb = FALSE
GOfuncR = TRUE
[DMRichR] Selecting annotation databases 15-11-2023 09:09:31 PM
Loading BSgenome.Hsapiens.UCSC.hg38.masked
Loading TxDb.Hsapiens.UCSC.hg38.knownGene
Loading org.Hs.eg.db
Saving Rdata...
[DMRichR] Processing Bismark cytosine reports 15-11-2023 09:09:36 PM
Selecting files...
Reading cytosine reports...
[read.bismark] Parsing files and constructing valid loci ...
Done in 117 secs
[read.bismark] Parsing files and constructing 'M' and 'Cov' matrices ...
Done in 75.1 secs
[read.bismark] Constructing BSseq object ...
Assigning sample metadata with Group as factor of interest...
DataFrame with 80 rows and 4 columns
Group Age Sex Batch
<factor> <numeric> <factor> <factor>
ICU01 ICU_ABS 72 Male Batch12
ICU02 ICU_ABS 51 Female Batch12
ICU03 ICU_ABS 64 Male Batch1
ICU04 ICU_ABS 71 Male Batch1
ICU05 ICU_ABS 50 Female Batch1
... ... ... ... ...
NON36 NONICU 63 Female Batch10
NON37 NONICU 84 Female Batch10
NON38 NONICU 33 Male Batch10
NON39 NONICU 77 Male Batch10
NON40 NONICU 84 Female Batch11
Checking sex of samples...
Sex of all samples matched correctly. Sex choromosomes will now be dropped
Filtering CpGs for Group...
Assuming adjustment covariate Sex is discrete and including it for filtering...
Assuming adjustment covariate Age is continuous and excluding it from filtering...
Assuming adjustment covariate Batch is discrete and including it for filtering...
slurmstepd: error: poll(): Bad address
Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) :
cannot coerce class '"try-error"' to a data.frame
Calls: <Anonymous> ... <Anonymous> -> as.data.frame -> as.data.frame.default
In addition: Warning messages:
1: In dir.create("RData") : 'RData' already exists
2: In parallel::mclapply(., FUN = as.matrix, mc.cores = cores) :
scheduled cores 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20 did not deliver results, all values of the jobs will be affected
3: In parallel::mclapply(., FUN = DelayedMatrixStats::colSums2, mc.cores = cores) :
scheduled cores 19, 18, 17, 16, 15, 12, 11, 10, 9, 8, 7, 6, 5, 4, 2, 20 encountered errors in user code, all values of the jobs will be affected
Execution halted
10502
I will run two samples with the Batch as a covariate. Before I also tried to run with different number of cpu-per-task (1, 10 and 20) as well as ntask (1, 20, 20) in my SBATCH params.
Hi!
I am running 80 RRBS samples, with 3 covariates: Age, Gender and Batch. this is my running code: run.txt I tried with 2 samples but without Batch as a covariate and it worked. The error that I get is the following:
I will run two samples with the Batch as a covariate. Before I also tried to run with different number of cpu-per-task (1, 10 and 20) as well as ntask (1, 20, 20) in my SBATCH params.