runChicago.R errors during "Reading NBaitsPerBin file" step

Issue #47 new
Former user created an issue

Hi,

I have been trying to get Chicago working, but I keep getting this output:

Starting chicagoPipeline...


*** Running normaliseBaits...

Normalising baits...
Reading NPerBin file...
Computing binwise means...

*** Running normaliseOtherEnds...

Preprocessing input...
Computing trans-counts...
Filtering out 178 other ends with top 0.01% number of trans-interactions
Binning...
Computing total bait counts...
Reading NBaitsPerBin file...
/var/spool/slurm/slurmd/job34277626/slurm_script: line 11: 52938 Killed

I am using version 1.13.0 installed using biocLite, I also tried installing using bitbucket, but it keeps defaulting to an earlier version (1.1.8) for some reason. A co-worker was able to run this file using version 1.6.0 so not sure if it is a bug in the new version or something with my installation or some other package that is being used at this step that is missing. I am using R 3.6.0

I was hoping you could advise why I might be getting this error. Let me know if you need more information about the error or my input files.

Thanks!

Comments (1)

  1. XianglongTan

    I have the same issue as well, it seems like something happened during the .Nbpb file reading.

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