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BoevaLab / HMCan

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HMCan: Segmentation fault (core dumped) #1

Closed nitinnarwade closed 1 year ago

nitinnarwade commented 4 years ago

I am trying to run HMCan v1.43 (GitHub version) by following the instructions given in the readme file and I have ended up with this generalized error Segmentation fault (core dumped). I don’t know why I am getting this error.

Here is the configuration file that I am using for running HMCan:

format bam GCIndex /program/hmcan/data/GC_profile_25KbWindow_Mapp76_hg19.cnp genomePath hg19-chrs minLength 100 medLength 250 maxLength 400 smallBinLength 50 largeBinLength 25000 calculateEmpiricalPvalue True pvalueThreshold 0.05 mergeDistance 200 iterationThreshold 2 finalThreshold 0.1 maxIter 20 PosteriorProb 0.99 PrintWig False PrintPosterior True blackListFile hg19-blacklist.bed PrintBedGraph False CallPeaks True pairedEnds False RemoveDuplicates False

Could you please help me out what's wrong with this.

Thank you. Nitin

AshoorH commented 4 years ago

Hi Nitin,

Could you please also share with me the log file (HMCan output) and the command you used to be able to to troubleshoot the issue better?

Thanks Haitham

nitinnarwade commented 4 years ago

Hi Haitham,

Thank you for your reply.

The output folder has not yet generated. Here is the log, perhaps it would help you to track the step.

HMCan v1.43 : detection of histone modifications in normal and cancer ChIP-seq datasets Reading chip.... Kept 35465400 reads Reading control.... Kept 35264849 reads Segmentation fault (core dumped)

Thank you. Nitin

AshoorH commented 4 years ago

Hi Nitin,

Could you provide me with an example small dataset that produce the segmentation fault so I can try to trace the error?

Thanks Haitham