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another problem: Error: protect(): protection stack overflow #3
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any idea on this error? |
Not sure. Haven't come across this ever before. Have you tried our
automated pipeline https://github.com/kundajelab/chipseq_pipeline
Anshul
…On Mar 24, 2017 9:10 AM, "Ming Tang" ***@***.***> wrote:
Hi,
another problem with phantompeakqual or with R
Decompressing ChIP file
Decompressing control file
Loading required package: caTools
Reading ChIP tagAlign/BAM file Hs_940_temp//M940_Crep2.tagAlign.gz
opened Hs_940_temp/M940_Crep2_spp_tmp//M940_Crep2.tagAlign144c7b15c3b9
done. read 42273553 fragments
ChIP data read length 37
[1] TRUE
Reading Control tagAlign/BAM file Hs_940_.temp/control.tagAlign.gz
opened Hs_940_.temp/M940_Crep2_spp_tmp//control.tagAlign144c62adab27
done. read 2922304 fragments
Error: protect(): protection stack overflow
Execution halted
Error: protect(): protection stack overflow
Execution halted
I googled and found http://stackoverflow.com/
questions/28728774/how-to-set-max-ppsize-in-r
after adding one line
options("experssion" = 500000)
on top of the run_spp.R script, same error.
Thanks for looking into this.
Tommy
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I actually wrote a snakemake version of the pipeline to accommodate our own usage. I know the bolts and nuts of my own pipeline so I can easily extend it. I will continue to debug...thanks though. Tommy |
http://stackoverflow.com/questions/28728774/how-to-set-max-ppsize-in-r
Can you try with higher max stack size "Rscript --max-ppsize=500000
[RFILE]"? It's 5000 by default and should be between 5000 and 5000000.
Thanks,
Jin
…On Mon, Mar 27, 2017 at 8:30 PM, Ming Tang ***@***.***> wrote:
I actually wrote a snakemake version of the pipeline to accommodate our
own usage. I know the bolts and nuts of my own pipeline so I can easily
extend it.
I will continue to debug...thanks though.
Tommy
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@leepc12 I added |
Hi, |
@leepc12 @andreakcl89 , @crazyhottommy Does this fit with your issue? Has anyone found a fix? |
I have the exact same issue using ATAC_seq workflow provided by the Kundaje lab. I ran it for Xenopus laevis version 9.2, which contains 18 chromosomes and 108015 scaffolds. In terms of proportions, non-mitochondrial chromosomes cover 92% of the genome, a very small percentage is mitochondrial DNA, and 7.7% of the genome is scaffolds. If, as @seenstevo mentioned, the issue is the massive number of scaffolds that the analysis has to run through, maybe it is not too bad to remove 7.7% of the genome to get the analysis done |
The cross correlation analysis is not necessary for ATAC seq data. So you
should simply disable that.
Jin - is there a parameter to disable CC analysis for ATAC/DNase
…On Dec 6, 2017 12:23 AM, "oshomroni" ***@***.***> wrote:
I have the exact same issue using ATAC_seq workflow provided by the
Kundaje lab. I ran it for Xenopus laevis version 9.2, which contains 18
chromosomes and 108015 scaffolds. In terms of proportions,
non-mitochondrial chromosomes cover 92% of the genome, a very small
percentage is mitochondrial DNA, and 7.7% of the genome is scaffolds. If,
as @seenstevo <https://github.com/seenstevo> mentioned, the issue is the
massive number of scaffolds that the analysis has to run through, maybe it
is not too bad to remove 7.7% of the genome to get the analysis done
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@seenstevo no, I am processing the same human data. somehow in a different computing cluster, the error disappeared. |
I added "Rscript --max-ppsize=500000" inside the postalign_xcor.bds script before ${RUN_SPP}, and it worked. Guess you need a good server with tons of memory for this to work. |
You can disable cross correlation analysis by activating pipeline's flag
`-no_xcor`.
Jin
|
Hi,
another problem with phantompeakqual or with R
I googled and found http://stackoverflow.com/questions/28728774/how-to-set-max-ppsize-in-r
after adding one line
options("experssion" = 500000)
on top of the run_spp.R script, same error.
Thanks for looking into this.
Tommy
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