Question

TarSeqQC TargetExperiment() Error- failed to stop SOCKcluster cluster-error writing to connection

1

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bioinf ▴ 10

@bioinf-12080

Last seen 6 months ago

United States

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!

TarSeqQC R ngs biocparallel • 1.9k views

ADD COMMENT • link updated 7.5 years ago by Martin Morgan 25k • written 7.5 years ago by bioinf ▴ 10

score 0 · Answer 1 · 2017-06-15

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Martin Morgan 25k

@martin-morgan-1513

Last seen 4 months ago

United States

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 COMMENT • link 7.5 years ago Martin Morgan 25k

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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 REPLY • link 7.5 years ago bioinf ▴ 10

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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 REPLY • link 7.5 years ago bioinf ▴ 10

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Hi,

have you found a solution for your error 2 ?

2: In (function (..., deparse.level = 1) : number of columns of result is not a multiple of vector length (arg 2)

I have quite the same error :

myPanel = TargetExperiment(bedfile, bamfile, fastafile, feature="amplicon", BPPARAM=BPPARAM, attribute="coverage") 
Error in `[.data.frame`(info, , "chr") : undefined columns selected 
In addition: Warning message: 
In (function (..., deparse.level = 1)  :  
  number of columns of result is not a multiple of vector length (arg 2)

Thank you in advance

ADD REPLY • link 4.6 years ago marc.deloger.gr • 0