help protection stack overflow

[Riccardo Aiese Cigliano]

Hello,

I have recently started to use idr-code to analyse chip-seq data. I had a problem when I tried to lunch the peak calling on individual replicates after concatenating the controls. In particular I have a "protection stack overflow" message when the program starts to analyze the concatenated replicates. I have also tried to increase the ppsize value by changing the command line as follows:

Rscript --max-ppsize=500000 run_spp.R -p=2 -c=IS2.tagAlign.gz -i=control.tagAlign.gz -npeak=300000 -savr -savp -savn -savd -rf -out="phantomPeakStatsReps_A.tab"

This is the output:

ChIP data: IS2.tagAlign.gz 

Control data: control.tagAlign.gz 

strandshift(min): -500 

strandshift(step): 5 

strandshift(max) 1500 

user-defined peak shift NA 

exclusion(min): 10 

exclusion(max): NaN 

num parallel nodes: 2 

FDR threshold: 0.01 

NumPeaks Threshold: 3e+05 

Output Directory: . 

narrowPeak output file name: ./IS2.tagAlign_VS_control.tagAlign.narrowPeak 

regionPeak output file name: ./IS2.tagAlign_VS_control.tagAlign.regionPeak 

Rdata filename: ./IS2.tagAlign.Rdata 

plot pdf filename: ./IS2.tagAlign.pdf 

result filename: phantomPeakStatsReps_A.tab 

Overwrite files?: TRUE

Decompressing ChIP file

Decompressing control file

Carico il pacchetto richiesto: caTools

Reading ChIP tagAlign/BAM file IS2.tagAlign.gz 

opened /tmp/RtmpAVd07i/IS2.tagAlign2571e56c77f

done. read 7879040 fragments

ChIP data read length 36 

[1] TRUE

Reading Control tagAlign/BAM file control.tagAlign.gz 

opened /tmp/RtmpAVd07i/control.tagAlign25753437268

done. read 318153 fragments

Error: protect(): stuck overflow

Can anybody help me with this?

Thank you in advance,

Riccardo

[Anshul Kundaje]

I've not seen this before. Check that the control tagAlign has no errors in terms of coordinates. strand etc. Also check that you are not running out of memory and maybe also try a different temporary directory using --tmpdir=[TEMPDIRECTORYPATH]

Do you see the same error if you run it on the individual chip/control replicates?

-Anshul.

[Riccardo Aiese Cigliano]

Thank you for your answer. I don't have the same type of error when I use individual replicates separately but only when I concatenate them. I have also tried on a different computer with more memory and I still have the same error. I will try with changing the temporary directory. Do you have any other suggestions?

Thank you in advance,

Riccardo