Issue with pon.binsize about dryclean HOT 6 CLOSED

please try with this pon: https://mskilab-pipeline.s3.amazonaws.com/dryclean/pon/hg19/fixed.detergent.rds

from dryclean.

Thank you very much! It looks like I am getting past this check now, however I am now getting the below error:

Loading PON...
PON loaded
Loading coverage
Loading PON a.k.a detergent
Let's begin, this is whole exome/genome
Median-centering the sample
Initializing wash cycle
Using the detergent provided to start washing
lambdas calculated
calculating A and B
calculating v and s
Error in if (e < 1e-06 || k > maxiter) { :
missing value where TRUE/FALSE needed
Calls: -> wash_cycle -> apg_project
4: (function ()
traceback(2))()
3: apg_project(m.vec, U, lambda1, lambda2)
2: wash_cycle(m.vec = m.vec, L.burnin = L.burnin, S.burnin = S.burnin,
r = r, U.hat = U.hat, V.hat = V.hat, sigma.hat = sigma.hat)
1: dryclean_object$clean(cov = opt$input, center = opt$center, cbs = opt$cbs,
cnsignif = opt$cnsignif, mc.cores = opt$cores, verbose = TRUE,
use.blacklist = opt$blacklist, blacklist_path = opt$blacklist_path,
germline.filter = opt$germline.filter, field = opt$field,
testing = opt$testing)

Is this also related to the PON, or is it more likely an issue with my coverage input?

from dryclean.

It is most likely the coverage input issue, are you using a mask?

from dryclean.

I am not, I am using the direct "cov.rds" output from FragCounter. Also, one thing to note is that this is whole-exome data rather than whole-genome. Would that be a potential cause of the issue?

from dryclean.

yes, that is probably the cause, can you try setting 'wgs' parameter to FALSE when you initialize the PON object?

from dryclean.

I just tried this out, and it is working on my personal computer but not on our cluster, so I believe it's like an issue outside of Dryclean itself. Thank you very much for your help!

from dryclean.