Question: ChIPQC: Error in names(res) <- nms
0
gravatar for nbkingsley
16 months ago by
nbkingsley0
nbkingsley0 wrote:

I am trying to use ChIPQC to evaluate some horse ChIP-seq data. I am using the following lines of code in a script on a cluster:

 

samples = read.csv("Equine_ChIPQC_Samplesheet.csv")

my_experiment = ChIPQC(samples, chromosomes=NULL)

save(my_experiment, file="Equine_ChIPQC_metrics.Rdata")

 

And after running for some time (30-40 minutes on a high memory node), the run fails. When I look at the end of the output, I see the following lines:

...

Calculating coverage histogram for Un0051

 

Calculating SSD for Un0051

 

Calculating unique positions per strand for Un0051

 

Calculating shift for Un0051

 

300 / 300

Counting reads in features for Un0051

 

Signal over peaks for Un0051

 

done

Calculating coverage

Calculating coverage histogram for Un0097

 

Calculating SSD for Un0097

 

Calculating unique positions per strand for Un0097

 

Calculating shift for Un0097

 

300 / 300

Counting reads in features for Un0097

 

Signal over peaks for Un0097

 

done

Calculating coverage

Calculating Summits on  Un0097  ..

Error in names(res) <- nms :

 'names' attribute [20] must be the same length as the vector [1]

Calls: ChIPQC -> bplapply -> bplapply -> bplapply -> bplapply

In addition: Warning messages:

1: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :

 number of items read is not a multiple of the number of columns

2: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :

 number of items read is not a multiple of the number of columns

3: stop worker failed:

 'clear_cluster' receive data failed:

 reached elapsed time limit

Execution halted

 

Any suggestions about how to trouble-shoot this issue would be very helpful! (Please note that the horse genome has a fictitious chromosome called "chromosome unknown" which accounts for the "Un" part of the chromosome name.)

chipqc chip-seq • 322 views
ADD COMMENTlink written 16 months ago by nbkingsley0
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