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Question: TarSeqQC TargetExperiment() Error- failed to stop SOCKcluster cluster-error writing to connection
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gravatar for bioinf
5 months ago by
bioinf0
bioinf0 wrote:

Hi,

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):

library(TarSeqQC)
library(BiocParallel)                                                                 
library(cowplot)
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.

Thanks!

ADD COMMENTlink modified 5 months ago by Martin Morgan ♦♦ 20k • written 5 months ago by bioinf0
0
gravatar for Martin Morgan
5 months ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k 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 5 months ago by Martin Morgan ♦♦ 20k

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 5 months ago by bioinf0

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 5 months ago by bioinf0
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