Question: TarSeqQC TargetExperiment() Error- failed to stop SOCKcluster cluster-error writing to connection
gravatar for bioinf
18 months ago by
bioinf10 wrote:


TarSeqQC seems to be a wonderful package for TS. I ran it successfully on extdata (test data) on Windows 8.1 64-bit PC as well as Rstudio server, but getting following error while running on my data on Rstudio server (bam=1.2GB, fasta file=1.4GB, bed file=25MB):

org_panel <- TargetExperiment(org_bed, org_bam, org_fasta, attribute="coverage", feature="cds", pileupP=PileupParam(max_depth=100))

Error: failed to stop ‘SOCKcluster’ cluster: error writing to connection

I think the issue may be related to BiocParallel. I am using BiocParallel 1.8.2

​Kindly guide.


ADD COMMENTlink modified 18 months ago by Martin Morgan ♦♦ 22k • written 18 months ago by bioinf10
gravatar for Martin Morgan
18 months ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

This may indicate an error trying to move too much data from the worker back to the master; you could try BiocParallel::register(BiocParallel::SerialParam()) before the call to TargetExperiment() to run in serial mode.

ADD COMMENTlink written 18 months ago by Martin Morgan ♦♦ 22k

Thanks. I ran it again with the option you mentioned, but TargetExperiment() is taking a lot of time. Do you have an idea how much time it should take to process 1GB bam and 1GB fasta for TargetExperiment()? I am trying to run it from last few days, sometimes it ran for full day too.


ADD REPLYlink written 18 months ago by bioinf10

Its running since yesterday and got the following error now:

Error in `[.data.frame`(info, , "chr") : undefined columns selected

In addition: Warning messages:
1: In .local(.Object, ...) :
  Your bed file have duplicated features. Removing 
            duplicated ...
2: In (function (..., deparse.level = 1)  :
  number of columns of result is not a multiple of vector length (arg 2)
ADD REPLYlink written 18 months ago by bioinf10
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