Error in if (cj == upper) next : missing value where TRUE/FALSE needed Calls: chicagoPipeline -> normaliseOtherEnds -> .addTLB -> cut2

[Anupam Bhattacharya]

Hi,

Chicago program runs successfully on the GM_rep1.chinput,GM_rep2.chinput and GM_rep3.chinput.

But while running  GM12878 datasets, it is showing the following error.

‌

Filtering out 79 other ends with top 0.01% number of trans-interactions

Binning...

Error in if (cj == upper) next : missing value where TRUE/FALSE needed

Calls: chicagoPipeline -> normaliseOtherEnds -> .addTLB -> cut2

In addition: Warning message:

In (1:g) * nnm : NAs produced by integer overflow

Execution halted

‌

Would you please guide me on how to resolve the issue or what parameter I need to change?

I am attaching the settings file for your reference.

Thank you for your time.

Regards;

Anupam

[曹唱唱]

Same errors also happened on my computer running Chicago.

Waiting for help

[曹唱唱]

Adding the following command: cd <- modifySettings(cd, settings=list(tlb.minProxOEPerBin=50000, tlb.minProxB2BPerBin=2500)) could solve this issue.

This error was also mentioned in the release note for chicago v1.15 (as shown in the file ‘NEW’).

However, the following command still installed v1.13 by default. (at least on my computer)

install.packages("devtools")
library(devtools)
install_bitbucket("chicagoTeam/Chicago", subdir="Chicago")

Hope this helps.